ARTICLE | doi:10.20944/preprints202306.0680.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Prunus dulcis shell extracts; chemical composition; biological activities; GC-MS; HPLC-DAD
Online: 9 June 2023 (07:53:06 CEST)
Prunus dulcis is one of the most widely cultivated species in the world. Its fruit (almond) is rich in various nutritious and bioactive compounds that exert several beneficial effects. The aim of this study was to determine the chemical profile and evaluate the biological potential in vitro of almond shell extracts. The chemical analysis of shell extracts led to the identification of 15 com-pounds by HPLC-DAD of which 11 were first detected in the almond plant. Twenty-six volatile compounds were identified by the GC-MS technique, among them; seven were firstly detected in the studied plant. For the biological activities, the extracts demonstrated moderate inhibition potential against the antioxidant, antidiabetic, and cytotoxic activities. The methanol extract at 50 µg/mL showed the highest antioxidant (45%) and antidiabetic activities (45% against alpha-glucosidase and 31% against alpha-amylase extracts), while the cyclohexane and dichloromethane at 50 µg/mL showed the highest cytotoxic activity towards Hela (32.2% with cyclohexane), and RAW 264-7 (45% with dichloromethane). Overall, these findings demonstrate the potential of almond shell extracts as a source of bioactive compounds that could be applied in the pharmaceutical and medical fields.
ARTICLE | doi:10.20944/preprints202306.0605.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: prostate-specific membrane antigen (PSMA); technetium-99m; single photon emission computed tomography (SPECT); molecular imaging; HYNIC
Online: 8 June 2023 (08:11:15 CEST)
Prostate-specific membrane antigen (PSMA) is a well validated prostate cancer marker, but reported PSMA-targeted tracers derived from the Lys-urea-Glu pharmacophore including the clinically validated [99mTc]Tc-EDDA/HYNIC-iPSMA have high off-target uptake in kidneys, spleen and salivary glands. In this study, we synthesized and evaluated three novel 99mTc-labeled PSMA-targeted tracers and investigated if the tracers derived from the Lys-urea-Aad pharmacophore could have minimized uptake in off-target organs/tissues. In vitro competition binding assays showed that compared with HYNIC-iPSMA, the three novel ligands had slightly weaker PSMA binding affinity (average Ki = 3.11 vs 8.96 - 11.6 nM). Imaging and ex vivo biodistribution studies in LNCaP tumor-bearing mice showed that [99mTc]Tc-EDDA/HYNIC-iPSMA and the three novel tracers successfully visualized LNCaP tumor xenografts in SPECT images and were excreted mainly via the renal pathway. The average tumor uptake at 1 h post-injection varied from 5.40 to 18.8 %ID/g, and the tracers derived from the Lys-urea-Aad pharmacophore had much lower uptake in spleen and salivary glands. Compared with the clinical tracer [99mTc]Tc-EDDA/HYNIC-iPSMA, the Lys-urea-Aad derived [99mTc]Tc-EDDA-KL01127 had lower background uptake and superior tumor-to-background contrast ratios, and is therefore promising for clinical translation to detect prostate cancer lesions with SPECT.
ARTICLE | doi:10.20944/preprints202306.0564.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Green Synthesis; Pectin functionalized silver nanoparticles; Antibacterial activity; Hepatoprotective
Online: 7 June 2023 (14:22:20 CEST)
Present study reports the green synthesis of pectin fabricated silver-based nanocomposite (Pectin-AgNPs) with Carpesiumnepalense leaves extract and evaluated their bactericidal kinetics, in-vivo hepatoprotective and cytotoxic potentials with their possible mechanisms. GC/MS and LC/MS analysis indicated the presence of different new phytochemicals constituents in the plant extract. The physicochemical characterization of Pectin-AgNPs by UV/Vis, SEM, DLS, FTIR and EDX techniques showed the spherical and uniform size range synthesis of nanocomposite i.e. 50-110 nm. The highly significant (P<0.005) antibacterial activity was found against all tested four bacterial strains with the ZIs of 24.8 to 27.2 mm. Significant damage in bacterial cell membrane was also observed in AFM study after treated with Pectin-AgNPs. At the doses of 0.05 mg/kg, nanocomposite showed highly significant (P<0.005)hepatoprotective activity in biochemical and histopathology analysis as compared to CCL4 administered control group. The ameliorative effects of Pectin-AgNPs were observed in PCR analysis on both GAPDH and PPARs genes expression and its potential to restore gene alterations caused by CCl4 intoxication.Pectin-AgNPs produced cytotoxic activity against HeLa cell lines at higher doses with the LC50 of 223.7 µg/mL. The current findings demonstrate positive attributes of pectin fabricated AgNPs as a promising antibacterial, hepatoprotective and cytotoxic agent.
REVIEW | doi:10.20944/preprints202306.0472.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: metallodrugs; medicinal chemistry; chemoproteomics; thermal proteome profiling; pro-metallodrugs; delivery systems; nanoparticles
Online: 7 June 2023 (03:11:30 CEST)
Metals are indispensable in the life of all organisms, in fact, their dysregulation causes various disorders caused by an interruption of their homeostasis. Nowadays different transition metals are incorporated into pharmaceutical products as diagnostic and therapeutic agents because of their electronic structure which gives them versatility in terms of tuning molecule properties, differently from organic molecules. Hence the interest in the study of metal-drug complexes from different points of view was born and many approaches were developed for the characterization, activation, delivery and molecular mechanisms clarification. The integration of these different approaches starting from chemoproteomics passing through nanoparticle systems to different activation strategies allows the understanding of the cellular responses of metallic drugs, which can be the basis for the design of new drugs and/or modification of drugs currently in use. This review aims to briefly summarize the recent advances in this area by describing the technological platforms and their possible applications to identify protein targets for discovering the mechanisms of action of metallodrugs, and to improve their efficiency in terms of administration.
REVIEW | doi:10.20944/preprints202306.0402.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: bioreduction; heterocycles; natural products; NQO1; reductases; synthesis; thioredoxin
Online: 6 June 2023 (07:59:36 CEST)
This review uses the National Cancer Institute (NCI) COMPARE program to establish an extensive list of heterocyclic iminoquinones and quinones with similarities in differential growth inhibition across the 60-cell line panel of the NCI Developmental Therapeutic Program (DTP). Many natural products and synthetic analogues are revealed, as potential NAD(P)H:quinone oxidoreductase 1 (NQO1) substrates through correlations to dipyridoimidazo[5,4-f]benzimidazoleiminoquinone (DPIQ), and as potential thioredoxin reductase (TrxR) inhibitors, through correlations to benzo[1,2,4]triazin-7-ones and pleurotin. The strong correlation to NQO1 infers the enzyme has a major influence on the amount of active compound with benzo[e]perimidines, phenoxazinones, benz[f]pyrido[1,2-a]indole-6,11-quinones, seriniquinones, kalasinamide, indolequinones, and furano[2,3-b]naphthoquinones, hypothesized as prodrugs. Compounds with very strong correlations to known TrxR inhibitors had inverse correlations to the expression of both reductase enzymes, NQO1 and TrxR, including naphtho[2,3-b][1,4]oxazepane-6,11-diones, benzo[a]carbazole-1,4-diones, pyranonaphthoquinones (including kalafungin, nanomycin A, and analogues of griseusin A), and discorhabdin C. Quinoline-5,8-dione scaffolds based on streptonigrin and lavendamycin can correlate to either reductase. Inhibitors of TrxR are not necessarily (imino)quinones, e.g., parthenolides, while oxidizing moieties are essential for correlations to NQO1, as with the mitosenes. Herein, an overview of synthetic methods and biological activity of each family of heterocyclic imino(quinone) is provided.
ARTICLE | doi:10.20944/preprints202306.0385.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: acetaminophen; 1,4-disubstituted 1,2,3-triazoles; molecular hybrids; azide-alkyne cycloaddition; Huisgen reaction; Cu(PPh3)3Br catalyst; click chemistry
Online: 6 June 2023 (05:36:48 CEST)
We hereby describe an efficient method for the preparation of a series of new 1-substituted 1,2,3-triazole-based acetaminophen derivatives through a clean, good-yielding, simple, and expeditious procedure based on the O-propargylation reaction of the acetaminophen (APAP) obtained from expired commercial tablets and the CuBr(PPh3)3-catalyzed Huisgen reaction be-tween O-propargylated APAP and diverse organoazides prepared from commercially available anilines as available starting reagents. An interesting nitric oxide-releasing 1,2,3-triazole hybrid of APAP was also obtained easily using the developed method. The structures of the designed hybrid compounds, which are expected to be pharmacologically active, were fully characterized by FT-IR, 1H- and 13C-NMR and are reported for the first time. According to the in-silico studies performed in this work and literature analysis, these hybrids are interesting models in search of new pharmacological nontoxic agents endowed with anti-inflammatory and anticancer properties.
ARTICLE | doi:10.20944/preprints202306.0205.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: C-scorpionate; anti-cancer drug; anti-proliferation; anti-migration; metabolomics
Online: 2 June 2023 (12:38:19 CEST)
The growing worldwide cancer incidence, coupled to the increasing occurrence of multidrug cancer resistance, requires a continuous effort towards the identification of new leads for cancer management. In this work, two C-scorpionate complexes, [FeCl2(κ3-Tpm)] (1) and [Co(κ3-TpmOH)2] (2), (Tpm = hydrotris(pyrazol-1-yl)methane and TpmOH = 2,2,2-tris(pyrazol-1-yl)ethanol), are studied as potential scaffolds for future anti-cancer drug development. Their cytotoxicity and cell migration inhibitory activity are analyzed, and an untargeted metabolomics approach is em-ployed to elucidate the biological processes significantly affected by these two complexes, using two tumoral cell lines (B16 and HCT116) and a non-tumoral cell line (HaCaT). While [FeCl2(κ3-Tpm)] did not display a significant cytotoxicity, [Co(κ3-TpmOH)2] was particularly cy-totoxic against the B16 cell line. While [Co(κ3-TpmOH)2] significantly inhibited cell migration in all tested cell lines, [FeCl2(κ3-Tpm)] displayed a mixed activity. From a metabolomics perspective, exposure to [FeCl2(κ3-Tpm)] is associated with changes in various metabolic pathways involving tyrosine, where iron-dependent enzymes are particularly relevant. On the other hand, [Co(κ3-TpmOH)2] is associated with dysregulation of cell adhesion and membrane structural pathways, suggesting its antiproliferative and anti-migration properties can be due to changes in the overall cellular adhesion mechanisms.
REVIEW | doi:10.20944/preprints202306.0141.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Mycobacterium tuberculosis; target identification; activity-based probes; affinity-based probes
Online: 2 June 2023 (07:39:37 CEST)
Mycobacterium tuberculosis (Mtb) is the etiological agent of tuberculosis (TB), a disease that alt-hough preventable and curable, remains a global epidemic due to the emergence of resistance and a latent form responsible for a long period of treatment. Drug discovery in TB is a challenging task due to the heterogeneity of the disease, the emergence of resistance and an uncomplete knowledge of the pathophysiology of the disease. The limited permeability of the cell wall and the presence of multiple efflux pumps remain a major barrier to achieve effective intracellular drug accumulation. While the complete genome sequence of Mtb has been determined and several potential protein targets have been validated, the lack of adequate models for in vitro and in vivo studies is a limit-ing factor in TB drug discovery programs. In current therapeutic regimens, less than 0.5% of bac-terial proteins are targeted being the biosynthesis of the cell wall and the energetic metabolism two of the most important processes exploited for TB chemotherapeutics. This review provides an overview on the current challenges in TB drug discovery and emerging Mtb druggable proteins, and how chemical probes for protein profiling enabled the identification of new targets and bi-omarkers, paving the way to disruptive therapeutic regimens and diagnostic tools.
REVIEW | doi:10.20944/preprints202305.1985.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: chitooligosaccharides; biological activities; chitinase; chitosanase; transglycosylation; glycosynthase
Online: 29 May 2023 (07:11:59 CEST)
Chitooligosaccharides (COS) are -1,4-linked homo-oligosaccharides of N-acetylglucosamine (GlcNAc) or glucosamine (GlcN), and also include hetero-oligosaccharides composed of GlcNAc and GlcN. These sugars are of practical importance because of their various biological activities, such as anti-microbial, anti-inflammatory, anti-oxidant and anti-tumor activities, as well as triggering the innate immunity in plants. The reported data on bioactivities of COS used to contain some uncertainties or contradictions, because the experiments were conducted with poorly characterized COS mixtures. Recently, COS have been satisfactorily characterized with respect to their structures, especially the degree of polymerization (DP) and degree of N-acetylation (DA); thus, the structure-bioactivity relationship of COS has become more unambiguous. To date, various green-chemical strategies involving enzymatic synthesis of COS with designed sequences and desired biological activities have been developed. The enzymatic strategies could involve transglycosylation or glycosynthase reactions using reducing end-activated sugars as the donor substrates and chitinase/chitosanase and their mutants as the biocatalysts. Site-specific chitin deacetylases were also proposed to be applicable for this purpose. Furthermore, to improve the yields of the COS products, metabolic engineering techniques could be applied. The above-mentioned approaches will provide the opportunity to produce tailor-made COS, leading to the enhanced utilization of chitin biomass.
ARTICLE | doi:10.20944/preprints202305.1851.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Metabolic syndrome; hypercaloric diet; FFA; Ludwigia; corilagin; ellagic acid; gallic acid
Online: 26 May 2023 (04:40:32 CEST)
Ludwigia octovalvis (Jacq.) P.H. Raven is widely used in traditional medicine for different illnesses included diabetes and hypertension. However, its impact on lipotoxicity and metabolic syndrome in vivo has not been addressed. Therefore, the aim of this study was to evaluate the effects of this plant on the metabolic syndrome parameters in a C57BL6J mouse hypercaloric diet model. L. octovalvis hydroalcoholic extract and its ethyl acetate fraction (25 mg/kg/day) were used for sub-chronic assessment (10 weeks). Also four subfractions (25 mg/kg) were evaluated in the postprandial triglyceridemia test in healthy C57BL6J mice. The hydroalcoholic extract and ethyl acetate fraction significantly decreased body weight gain (-6.9 g and -1.5 g), fasting glycemia (-46.1 and -31.2 mg/dL), systolic (-26.0 and -22.5mmHg) and diastolic (-8.1 and 16.2 mmHg) blood pressure, free fatty acid concentration (-13.8 and -8.0 μg/mL) and insulin-resistance (measured by TyG index, -0.207 and -0.18) compared to the negative control. Postprandial triglyceridemia test showed that the effects in the sub-chronic model are due, at least in part, to improvement in this parameter. L. octovalvis treatments, particularly the hydroalcoholic extract, improve MS alterations and decrease free fatty acid concentration. These effects are possibly due to high contents of corilagin and ellagic acid.
ARTICLE | doi:10.20944/preprints202305.1696.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Soft coral; Klyxum molle; Diterpenoids; Stereochemistry; Antibacterial activity
Online: 24 May 2023 (05:00:56 CEST)
Fifteen new diterpenoids, namely xishaklyanes A-O (1-15), along with three known related ones (16-18), were isolated from the soft coral Klyxum molle collected from Xisha Islands, South China Sea. The stereochemistry of the new compounds were elucidated by a combination of detailed spectroscopic analyses, chemical syntheses, quantum chemical calculations and comparison with the reported data. The absolute configuration of compound 18 was established by the modified Mosher's method for the first time. In bioassay, some of these compounds exhibited considerable antibacterial activities on fish pathogenic bacteria, and compound 4 showed the most effective activity with MIC of 0.225 g/mL against Lactococcus garvieae.
REVIEW | doi:10.20944/preprints202305.1558.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Melanocortin; receptor; peptide; modulator; disease
Online: 23 May 2023 (04:16:14 CEST)
Melanocortins play crucial roles in regulating the stress response, inflammation, and skin pigmentation. In this review, we focus on the melanocortin 1 receptor (MC1R), a G protein-coupled receptor primarily known for regulating skin pigmentation and exhibiting anti-inflammatory effects. First, we provide an overview of the structure, signaling pathways, and related diseases of MC1R. Next, we discuss the potential therapeutic use of synthetic peptides and small molecule modulators of MC1R, highlighting the development of various drugs that enhance stability through amino acid sequence modifications and small molecule drugs to overcome limitations associated with peptide characteristics. Notably, MC1R-targeted drugs have applications beyond skin pigmentation-related diseases, which predominantly affect MC1R in melanocytes. These drugs can also be useful in treating inflammatory diseases with MC1R expression present in various cells. Our review underscores the potential of MC1R-targeted drugs to treat a wide range of diseases and encourages further research in this area.
ARTICLE | doi:10.20944/preprints202305.1321.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Abricó de macaco; antioxidant potential; chemistry characterization; dentistry; microbiology
Online: 18 May 2023 (10:08:10 CEST)
The study of phytotherapy in dentistry is relevant due to the low occurrence of research in the treatment of oral pathologies, such as caries and periodontal disease. Thus, the aim of this research was to characterize the chemical composition of extracts from the leaves of Couroupita guianensis Aubl, including toxicological evaluation and the antioxidant and antimicrobial potential against Staphylococcus aureus, Streptococcus mutans and Candida albicans. Three extracts were prepared using assisted ultrasound, originating the Crude Ultrasound Extract (CUE) and Soxhlet apparatus, originating the Crude Soxhlet Extract (CSE) and the Ethanol Soxhlet Extract (ESE). In the analysis of the chemical composition, the presence of flavonoids, tannins and saponins were detected. LC-DAD analysis revealed the presence of caffeic acid, sinapic acid, rutin, quercetin, luteolin, kaempferol and apigenin in all extracts. In the GC-MS analysis, stigmasterol and β-sitosterol were identified in CUE and CSE. The antioxidant potentials, determined by the DPPH• and ABTS•+ methods, the ESE showed higher antioxidant activity (2.98 ± 0.96 and 4.93 ± 0.90, respectively). In the evaluation of toxicity, the CUE 50µg/mL and the ESE 50 µg/mL presented growth stimulation of Allium cepa roots. At a concentration of 750µg/mL, all extracts inhibited root growth. None of the extracts showed toxicity against Artemia salina. Antibacterial action was detected in all extracts, mainly against the microorganisms S. aureus and S. mutans; however, the antifungal action against C. albicans was not detected. From the results, the extracts of C. guianensis have therapeutic potential for use in the control of microorganisms in the oral microbiota.
ARTICLE | doi:10.20944/preprints202305.1276.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Paeonia suffruticosa; benzofuranones; cytotoxicity; NO production inhibition
Online: 18 May 2023 (05:26:34 CEST)
The Paeonia suffruticosa, called as 'Feng Dan', has been used for thousands of years in traditional Chinese medicine. In our chemical investigation on the root bark of the plant, five new phenolic dimers, namely paeobenzofuranone A‒E (1‒5), have been characterized. Their structures were determined by spectroscopic analysis including 1D and 2D NMR, HRESIMS, UV, and IR, as well as ECD calculations. Compounds 2, 4, and 5 showed cytotoxicity against three human cancer cell lines with IC50 values ranging from 6.7 to 25.1 μM. Compounds 1 and 2 showed certain inhibitory activity on NO production. To the best of our knowledge, the benzofuranone dimers and their cytotoxicity of P. suffruticosa are reported for the first time.
REVIEW | doi:10.20944/preprints202305.1114.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: copper(I); tris(aminomethyl)phosphines; metal complexes; antibacterial activity; antifungal ac-tivity; anticancer activity; plasmid DNA; serum albumin
Online: 16 May 2023 (07:17:54 CEST)
Metal complexes feature a wide range of available geometries, diversified lability, controllable hydrolytic stability, and easily available rich redox activity. These characteristics combined with the specific properties of the coordinated organic molecules result in many different mechanisms of biological action, making each of the myriads of the classes of metal coordination compounds unique. This focused review presents combined and systematized results of the studies of a group of copper(I) (pseudo)halide complexes with aromatic diimines and tris(aminomethyl)phosphines of a general formula [CuX(NN)PR3], where X = I- or NCS-, NN = 2,2’-bipyridyl, 1,10-phenanthroline, 2,9-dimethyl-1,10-phenanthroline or 2,2’-biquinoline, and PR3 = Air-stable tris(aminomethyl)phosphines. The structural and electronic properties of the phosphine ligands and luminescent complexes are discussed. The complexes with 2,9-dimethyl-1,10-phenanthroline, apart from being air- and water-stable, exhibit a very high in vitro antimicriobial activity against the Staphylococcus aureus and Candida albicans. Moreover, some of the complexes also show a strong in vitro antitumor activity against human ovarian carcinoma cell lines: MDAH 2774 and SCOV 3, CT26 (mouse colon carcinoma), and A549 (human lung adenocarcinoma) cell lines. The tested complexes are moderately able to induce DNA lesions through free radical processes, however the trends do not reflect observed differences in biological activity.
ARTICLE | doi:10.20944/preprints202305.0921.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Stenomesson miniatum; Amaryllidaceae alkaloids; Urceolina peruviana; 13C-NMR-based dereplication; A431 human epidermoid carcinoma; skin cancer; Jurkat cells; artefact; Andean traditional medicine
Online: 12 May 2023 (10:12:45 CEST)
The fresh bulbs of Stenomesson miniatum, a plant belonging to Amaryllidaceae family with a poorly investigated phytochemical profile, were traditionally employed by Andean healers to treat tumors and abscesses. The aims of this study were to characterize the alkaloid extract from the bulbs of S. miniatum and test its cytotoxic and antibacterial potential. The alkaloid extract was characterized by dereplication using various techniques (CPC, NMR, UPLC-HRMS) and referring to in-home or online databases for spectroscopic data matching. Cytotoxic activities were evaluated on A431 human epidermoid carcinoma cells through a metabolic assay, and on Jurkat human acute T-leukemia cells through a cell-impermeant fluorescent nuclear probe. Antibacterial assays were carried out against Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus pyogenes by using a standardized microdilution broth method 96-well plate. Eleven known Amaryllidaceae alkaloids were identified together with another compound determined as being an extraction artefact. The alkaloid extract showed good cytotoxic activity against both the tumor cell lines, reaching an IC50 of 3.3 µg/mL against A431 cells and of 10.9 µg/mL against Jurkat cells. The analysis of the fractions allowed the activity to be attributed to the presence of pretazettine and haemathamine. Conversely, no antibacterial activities were recorded for any of the samples.
REVIEW | doi:10.20944/preprints202305.0475.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Nutrigenomics; Antimicrobial resistance; Novel Antibiotics; gut microbiome
Online: 8 May 2023 (08:40:22 CEST)
Nutrigenomics is the study of the interaction of nutrition and genes, focusing on the influence of nutrients on the genome, proteome, and metabolome, and how nutrition affects human health. In the context of nutrigenomics, bioactive components are dietary ingredients that may transmit information from the external environment and alter gene expression in the cell, and hence the overall function of the organism. It is critical to consider food not only as a source of energy and essential nutrients necessary for life and growth, but also as a factor impacting health/disease, biochemical processes, biochemical pathway activation and affecting the diversity of the gut microbiome. Antimicrobial resistance in pathogenic and commensal microorganisms has emerged as a major public health concern due to emerging antimicrobial resistance genes in E. coli isolates from pig, cattle, chicken, and turkey meat, against tetracycline, streptomycin, and sulfonamides. Also, Salmonella spp. and Campylobacter spp. have shown antibiotic resistance at farms and slaughterhouses, and in animal-based food products. A correlation has been proven between a critical nutrient-responsive signaling system and catabolite control of gene expression, and a two-component signaling system that drives antibiotic resistance in E. faecalis, revealing a previously unknown integration between the nutritional status of the cell and intrinsic antibiotic resistance. Moreover, different nutrigenomic approaches can be applied to mitigate possible emergence of antimicrobial resistance against novel antibiotics. However, little progress has been achieved in converting nutrigenomics information into clinical advice, so far.
ARTICLE | doi:10.20944/preprints202305.0276.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: fibroblast activation protein α (FAP-α); cancer-associated fibroblasts (CAFs); FAP inhibitors (FAPIs); PET imaging; gallium-68; (R)-pyrrolidin-2-yl-boronic acid-based radiopharmaceuticals
Online: 5 May 2023 (02:40:01 CEST)
Fibroblast activation protein (FAP) is a membrane-tethered serine protease overexpressed in the reactive stromal fibroblasts of > 90% human carcinomas, which makes it a promising target for developing radiopharmaceuticals for imaging and therapy of carcinomas. Here, we synthesized two novel (R)-pyrrolidin-2-yl-boronic acid-based FAP-targeted ligands; SB02055 (DOTA-conjugated (R)-(1-((6-(3-(piperazin-1-yl)propoxy)quinoline-4-carbonyl)glycyl)pyrrolidin-2-yl)boronic acid) and SB04028 (DOTA-conjugated ((R)-1-((6-(3-(piperazin-1-yl)propoxy)quinoline-4-carbonyl)-D-alanyl)pyrrolidin-2-yl)boronic acid). natGa- and 68Ga-complexes of both ligands were evaluated in preclinical studies and compared to previously reported natGa/68Ga-complexed PNT6555. Enzymatic assays showed that FAP binding affinities (IC50) of natGa-SB02055, natGa-SB04028 and natGa-PNT6555 were 0.41±0.06, 13.9±1.29 and 78.1±4.59 nM, respectively. PET imaging and biodistribution studies in HEK293T:hFAP tumor-bearing mice showed that while [68Ga]Ga-SB02055 presented with a nominal tumor uptake (1.08±0.37 %ID/g), [68Ga]Ga-SB04028 demonstrated clear tumor visualization with ~1.5-fold higher tumor uptake (10.1±0.42 %ID/g) compared to [68Ga]Ga-PNT6555 (6.38±0.45 %ID/g). High accumulation in the bladder indicated renal excretion of all three tracers. [68Ga]Ga-SB04028 displayed low background level uptake in most normal organs, and comparable to [68Ga]Ga-PNT6555. However, since its tumor uptake was considerably higher than [68Ga]Ga-PNT6555, the corresponding tumor-to-organ uptake ratios for [68Ga]Ga-SB04028 were also significantly greater than [68Ga]Ga-PNT6555. Our data demonstrate that (R)-(((quinoline-4-carbonyl)-D-alanyl)pyrrolidin-2-yl)boronic acid is a promising pharmacophore for the design of FAP-targeted radiopharmaceuticals for cancer imaging and radioligand therapy.
ARTICLE | doi:10.20944/preprints202305.0256.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: siRNA prodrug; selective cancer targeting; red light activation; photoreduction; RNAi; azobenzene
Online: 4 May 2023 (10:22:20 CEST)
RNA interference (RNAi) using small interfering RNAs (siRNAs) is a powerful tool to target any protein of interest and is becoming more implementable for in vivo applications due to recent developments in RNA delivery systems. To exploit RNAi for cancer treatment, it is expedient to increase its selectivity by e.g. a prodrug approach to activate the siRNAs upon external triggering, e.g. by using light. Red light is especially well suitable for in vivo applications due to its low toxicity and higher tissue penetration. Known molecular (not nanoparticle based) red light activatable siRNA prodrugs rely on singlet oxygen (1O2) mediated chemistry. 1O2 is highly cytotoxic. Additionally one of the side products in the activation of the known siRNA prodrugs is anthraquinone, which is also toxic. We here report on an improved red light activatable siRNA prodrug, which do not require 1O2 for their activation. The 5’ terminus of its antisense strand is protected with an electron-rich azobenzene promoiety. It gets reduced and cleaved upon red light exposure in the presence of Sn(IV)(pyropheophorbide a)dichloride acting as a catalyst and ascorbate required as a bulk reducing agent producing active siRNAs.
ARTICLE | doi:10.20944/preprints202304.1174.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 7-ethyl-10-hydroxy-camptothecin; valproic acid; biotin; conjugate; synthesis; anticancer
Online: 28 April 2023 (11:09:13 CEST)
Despite the strong anticancer activity of SN38 (7-ethyl-10-hydroxy-camptothecin), some defects prevent its clinical application, such as severe side effects and loss of anticancer activity due to lack of selectivity to cancer cells and hydrolysis of ring E, respectively. To address the issue, herein a multifunctional SN38 derivative (compound 9) containing biotin (tumor-targeting group) and valproic acid (histone deacetylase inhibitor, HDACi) was synthesized via click chemistry and evaluated using MTT assay. The in vitro cytotoxicity study showed that compound 9 exhibited superior cytotoxicity as irinotecan against human cervical cancer HeLa cells, albeit inferior to SN38. More significantly, compound 9 significantly reduced toxicity in mouse embryonic fibroblast NIH3T3 cells, indicating that compound 9 had the capacity to enhance tumor targeting due to its cell selectivity. Further studies demonstrated that compared with irinotecan, compound 9 induced similar apoptosis of cancer cells. Consequently, compound 9 can not only improve its tumor-targeting ability mediated by biotin but also exert the potent anticancer activity through the synergism of SN38 and valproic acid, indicating that the design concept is an effective strategy for structural modification of SN38.
REVIEW | doi:10.20944/preprints202304.1095.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Chemoinformatics; Bioinformatics; Tetracycline; Formulation
Online: 28 April 2023 (03:32:47 CEST)
Chemoinformatics is the combination of physical chemistry theory with computer and information science techniques "in silico techniques" to a variety of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular areas. On the other hand, machine learning has become a vital tool for drug designers to mine chemical information from enormous compound databases in order to build medications with important biological features. In Egypt, chemoinformatics were used recently in different applications. For example; the development of new antimicrobial agents like tetracycline analog B (Iodocycline). Another area of application in bioinformatics included heart disease classification based on hybrid ensemble stacking technique. In the era of COVID-19, hybrid approach for COVID-19 detection from chest radiography was applied. Furthermore, bio/chemoinformatics methods were used to compare antimicrobial medications in order to choose an effective nose-to-brain formulation targeting meningitis infection by using differences in the drugs' primary structural, topological, and electronic characteristics. An example for this included cefotaxime and ceftriaxone that were examined at three levels: at formulation level, by comparing the loading in gelatin and tripalmitin matrices as basis for the production of nanoparticulate systems, at biopharmaceutical level, through interaction with mucin and the P-gp efflux pumps, and at therapeutic level, through studying the interaction with S. pneumoniae bacterial receptors.
REVIEW | doi:10.20944/preprints202304.0933.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Spirocycles; three-dimensional; high-Fsp3; spirocyclizations; cyclodehydration; ketalization; intramolecular Claisen condensation; intramolecular alkylation; approved drugs
Online: 26 April 2023 (03:09:08 CEST)
The use of spirocycles in drug discovery and medicinal chemistry has been booming in the last two decades. This has clearly translated in the landscape of approved drugs. Among two dozen clinically used medicines containing a spirocycle, 50% have been approved in the 21st century. The present review focuses on the notable synthetic routes to such drugs invented in industry and academia and is intended to serve as a useful reference source of synthetic as well as general drug information for researchers engaging in the design of new spirocyclic scaffolds for medicinal use or embarking upon analog syntheses inspired by the existing approved drugs.
ARTICLE | doi:10.20944/preprints202304.0374.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: metallacarboranes; cobalt bis(1,2-dicarbollide), oligofunctionalization; alkylation; stereochemistry
Online: 17 April 2023 (02:56:05 CEST)
The exploitation of the metallacarboranes’ potential in various fields of research and practical ap-plications requires the availability of convenient and versatile methods for their functionalization with various functional moieties and/or linkers of different types and lengths. Herein we report a study on cobalt bis(1,2-dicarbollide) functionalization at 8,8’-boron atoms with different het-ero-bifunctional moieties containing protected hydroxyl function allowing further modification after deprotection. Moreover, an approach to the synthesis of three and four functionalized metallacarboranes, at boron and carbon atoms simultaneously, via additional functionalization at carbon to obtain derivatives carrying three or four rationally oriented and distinct reactive surfaces, is described
ARTICLE | doi:10.20944/preprints202303.0538.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: chicory; sesquiterpene lactones; 11,13-dihydrolactucin; lactucin; plant extraction; semi-synthesis of analytical standards
Online: 3 April 2023 (03:09:48 CEST)
Sesquiterpene lactones (STLs) are a large group of terpenoids most commonly found in plants of the Asteraceae family, e. g. in chicory plants, displaying a wide range of interesting biological activities. However, further studies on the biological potential of chicory derived STLs and analogues are challenging as only four of these molecules are commercially available (as analytical standards), and to date there are no published or patented simple extraction-purification processes capable of large scale STLs isolation. In this work we describe a novel three-step large scale extraction and purification method for the simultaneous purification of 11,13-dihydrolactucin (DHLc) and lactucin (Lc) starting from a chicory genotype rich in these STLs and in the corresponding glycosyl and oxalyl conjugated forms. After a small-scale screening on 100 mg of freeze-dried chicory root powder, the best results were achieved with a 17 h water maceration at 30°C. With these conditions we managed to increase the content of DHLc and Lc, at the same time favouring the hydrolysis of their conjugated forms. On a larger scale, the extraction of 750 g of freeze-dried chicory root powder, followed by a liquid-liquid extraction step and a reversed-phase chromatography, allowed the recovery of 642.3 ± 76.3 mg of DHLc and 175.3 ± 32.9 mg of Lc. The two pure STLs were subsequently used in the context of semi-synthesis to generate analogues for biological evaluation as antibacterial agents. In addition, other described chicory STLs that are not commercially available were also synthesized or extracted to serve as analytical standards for the study. In particular, lactucin-oxalate and 11,13-dihydrolactucin-oxalate were synthesized in two steps starting from Lc and DHLc, respectively. On the other hand, 11β,13-dihydrolactucin-glycoside was obtained after a MeOH/H2O (70/30) extraction, followed by a liquid-liquid extraction step and a reversed-phase chromatography. Together, this work will help facilitate the evaluation of the biological potential of chicory derived STLs and their semisynthetic analogues.
ARTICLE | doi:10.20944/preprints202303.0539.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Antibiotic resistance; metallo-β-lactamases; metal-dependent enzymes; broad-spectrum inhibitors; inhibition assays; enzyme kinetics
Online: 31 March 2023 (03:35:02 CEST)
Metallo-β-lactamases (MBLs) are a group of Zn(II)-dependent enzymes that pose a major threat to global health. They are linked to an increasing number of multi-drug resistant bacterial pathogens, but no clinically useful inhibitor is yet available. Since β-lactam antibiotics, which are inactivated by MBLs, constitute ~65% of all antibiotics used to treat infections, the search for clinically relevant MBL inhibitors is urgent. Here, derivatives of a 2-amino-1-benzyl-4,5-diphenyl-1H-pyrrole-3-carbonitrile (1a) were synthesised and their inhibitory effects assessed against representatives of each of the three subgroups of MBLs (B1, B2, B3). Several compounds are potent inhibitors of each MBL tested, making them excellent candidates for the development of broad-spectrum drug leads. In particular, compound 5f is highly potent across the MBL subfamilies, with Ki values in the low µM range. Furthermore, this compound also dis-plays synergy in combination with antibiotics such as penicillin G, cefuroxime or meropenem. This molecule thus represents one of the most promising compounds developed yet to combat MBLs.
ARTICLE | doi:10.20944/preprints202303.0189.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Antimicrobial peptides; Chitosan; comb-like co-polypeptide; N-carboxyanhydrides; ring-opening polymerization
Online: 10 March 2023 (08:57:12 CET)
The development of antimicrobial resistance to conventional antibiotics is a major global health challenge. Infections caused by multidrug-resistant gram-negative bacteria have been named one of the most urgent global health threats. Considerable efforts are devoted to developing new antibiotic drugs and investigating the mechanism of antibiotic resistance. Recently, Anti-Microbial Peptides (AMPs) have emerged as a new platform for the target and design of novel drug resistant anti-microbial agents promising a new therapeutic strategy. AMPs are rapid, potent, possess an unusually broad spectrum of activity, and have shown efficacy as topical agents. Unlike traditional therapeutics that interfere with essential bacterial enzymes, AMPs interact with microbial membranes through electrostatic interactions and physically damage cell integrity. However, naturally occurring AMPs have limited selectivity and modest efficacy. Therefore, recent efforts have focused on the development of synthetic AMP analogs as suitable drug targets. This work explores the development of novel antimicrobial agents which mimic the structure of graft-copolymers and mirror the mode of action of an AMP. Chitosan-graft-polypeptide side chains are synthesized by the ring-opening polymerization of N-carboxyanhydrides of L-lysine and L-leucine initiated from the functional groups of chitosan. The derivatives with random- and block-copolymer side chains are explored as drug targets. These graft copolymer systems exhibit activity against clinically significant pathogens and disrupt biofilm formation. This work highlights the potential of chitosan-graft-polypeptide structures in biomedical applications.
REVIEW | doi:10.20944/preprints202303.0054.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: natural products; wound healing; phytomolecules; cytotocxic; curcumin
Online: 3 March 2023 (03:37:50 CET)
Wound healing is a process through which skin maintains itself. Once a wound occurs, the inflammatory and proliferative stages are instigated in reaction to injury. It is established that wound restorative comprises four stages including haemostasis, inflammation, proliferation, and remodeling. The amelioration of wound healing is very challenging as tumors can develop at the site of chronic injury. There are numerous plants, plant extracts and plant based natural products were widely used by tribal communities from ancient times for the treatment of cuts, burns, scars, burns and wounds. The therapeutic potential of these plants is recognized due to the presence of phytomolecules such as phenolic compounds, flavonoids, triterpenoids, saponins, tannins, alkaloids and glycosides. The plant used for the treatments of wound healing includes Achillea millefolium, Andrographis paniculata, Boswellia sacra, Calendula officinalis, Crocus sativus, Curcuma longa, Ehretia laevis, Ehretia microphylla, Glycyrrhiza glabra, Malva sylvestris, Rosmarinus officinalis and Salvia officinalis. This assemblage comprises the structures of phytomolecules isolated from the different extracts of these plants, mechanistic insights and important key findings responsible for wound healing. The mechanistic insights involved in wound healing are similar to cytotoxic, anti-inflammatory and antioxidant agents such as ROS generation, DNA fragmentation and western blotting. This review article is an effort to bridge the gaps in the prevailing literature and thus offers gigantic scope for researchers and academicians betrothed in validation of the customary claims and development of safer and efficient and worldwide recognized natural potential candidates as drugs for healing of wounds, burns and cuts.
ARTICLE | doi:10.20944/preprints202302.0456.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Homeopathic; Uric acid; Derivitization
Online: 27 February 2023 (07:46:24 CET)
Uric acid being a diagnostic biomarker of gout and therapeutic agent in homeopathic medicines necessitates to develop simple and specific method for its determination. Therefore, present study describes the development and validation of simple and specific colorimetric method for determination of uric acid in homeopathic tablets. Uric acid upon reaction with acid and reagent mixture produced coloured derivative which was detected at 411 nm. The method was found linear over the whole range investigated with the correlation coefficient (R2) = 0.9975. Beer’s law was obeyed over the concentration ranges from 5.0 µg/mL to 240 µg/mL. The method was found to be reliable (95.7 to 108.2% recovery), repeatable intra-day accuracy (97.01 to 107.4%) and reproducible-inter day accuracy (99.45 to 107.8%) with relative standard deviation less than 5%. The results of the present study indicate the method is easy to perform, specific and suitable to be used for the determination of uric acid in homeopathic Acid Uric Tablet using less expensive derivitization.
ARTICLE | doi:10.20944/preprints202302.0343.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: targeted alpha therapy; alpha-emitter; thorium-226; uranium-230; isotope generator; extraction chromatography
Online: 20 February 2023 (14:17:58 CET)
A unique two-column 230U/226Th generator has been developed. The focus was hold on obtaining 226Th of high purity in a solution amenable to further labeling. The first column of the proposed generator filled with TEVA Resin held 230U, from which 226Th was eluted with 7 M HCl solution. UTEVA Resin pretreated with nitric acid solution was used as a sorbent for the second column for thorium retention. 226Th was extracted with 0.01-0.05 M citric buffer solution. One cycle of generator milking took 5-7 minutes and produced > 90% of 226Th in 1.5 ml of eluate, pH 4.5-5.0. The proposed two-column 230U/226Th generator was tested over two months including a second loading of 230U additionally accumulated from 230Pa. The 230U impurity in 226Th eluate was less than 0.01% allowing to use it directly in synthesis of radiopharmaceutical compounds.
REVIEW | doi:10.20944/preprints202301.0209.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: electrophile signaling; reactive metabolites; crystal structures of protein-electrophile complexes
Online: 20 February 2023 (09:27:32 CET)
Native reactive electrophile species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RES sensing and signaling have begun to bring about improved understanding of localized RES regulatory paradigms. However, studies in purified systems—prerequisites for gaining structure/function insights—prove challenging. We here introduce emerging chemical biology tools available to probe RES signaling, and the new knowledge that these tools have brought to the field. We next discuss existing structural data of RES-sensor proteins complexed with electrophilic metabolites or small molecule drugs (limited to < 300 Da), including challenges faced in acquiring homogenous RES-bound proteins. We further offer considerations that could promote enhanced understanding of RES regulation derived from three-dimensional structures of RES-modified proteins.
ARTICLE | doi:10.20944/preprints202302.0075.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: synthetic methods; 2-nitroperchlorobutadiene; benzoquinolines; cyclization; amines; sulfides; nucleophilic substitution; oxidation; medicinal chemistry
Online: 3 February 2023 (13:49:18 CET)
The reaction of mercaptoacetic acid esters with pentachloro-2-nitro-1,3-butadiene provides appropriate precursors for the synthesis of 2,3,4-trisubstituted benzo[h]quinolines. These heterocycles are easily accessible via a single-step reaction with 1-naphthyl- or 1-anthracenylamine, respectively. Due to steric bulk and high electron density ring closure to benzo[h]quinolines takes place, exclusively. Such highly substituted annelated pyridine systems can be modified in subsequent, selective reactions to build up new N-heterocycles with promising microbiological properties. Antibacterial and antiproliferative assays against four cell mammalian cell lines demonstrate that some of the sulfur-substituted benzo[h]quinolines analogs display potent phenotypic bioactivities in the single-digit micromolar range.
REVIEW | doi:10.20944/preprints202301.0302.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: ferroptosis; senescence; ageing; disease
Online: 17 January 2023 (09:07:35 CET)
Background: Senescence is a cellular ageing process in all multicellular organisms. It is characterized by a decline in cellular functions and proliferation, resulting in increased cellular damage and death. This condition plays an essential role in the ageing process and significantly contributes to the development of age-related complications. On the other hand, ferroptosis is a systemic cell death characterized by excessive iron accumulation followed by the generation of reactive oxygen species (ROS). Oxidative stress is a common trigger of this condition and may be induced by various factors such as toxins, drugs, and inflammation. Ferroptosis is linked to numerous illnesses, including cardiovascular disease, neurodegeneration, and cancer. Relevance of these conditions to ageing and disease: Senescence is believed to contribute to the decline in tissue and organ function that occurs with ageing. It has also been linked to the development of age-related pathologies, such as cardiovascular diseases, diabetes, and cancer. In particular, senescent cells have been shown to produce inflammatory cytokines and other pro-inflammatory molecules that can contribute to these conditions. On the other hand, ferroptosis has been linked to the development of various health disorders, including neurodegeneration, cardiovascular disease, and cancer . It is known to play a role in developing these diseases by promoting the death of damaged or diseased cells and contributing to the inflammation often associated with them. Both senescence and ferroptosis are complex processes that are still not fully understood. Further research is needed to thoroughly understand the role of these processes in ageing and disease, and to identify potential interventions to target these processes to prevent or treat age-related conditions. Objectives: This systematic review aims to assess the potential mechanisms underlying the link connecting senescence, ferroptosis, ageing, and disease.
REVIEW | doi:10.20944/preprints202301.0205.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: antimicrobial peptides; host defense peptides; zinc; metalloAMPs
Online: 12 January 2023 (02:27:32 CET)
Antimicrobial peptides (AMPs) are essential components of innate immunity across all species. AMPs have become the focus of attention in recent years as scientists are addressing antibiotic resistance, a public health crisis that has reached epidemic proportions. This family of peptides are a promising alternative to current antibiotics due to their broad-spectrum antimicrobial activity and tendency to avoid resistance development. A subfamily of AMPs interact with metal ions to potentiate their antimicrobial effectiveness, as such they have been termed metalloAMPs. In this work, we review the scientific literature of metalloAMPs that enhance their antimicrobial efficacy when combined with the essential metal ion, zinc (II). Beyond the role played by Zn(II) as a cofactor in different systems, it is well-known that this metal ion plays an important role in innate immunity. Here, we classify the different types of synergistic interactions between AMPs and Zn(II) into three distinct classes. By better understanding how each class of metalloAMPs uses Zn(II) to potentiate their activity, researchers can begin to exploit these interactions in the development of new antimicrobial agents and accelerate their use as therapeutics.
ARTICLE | doi:10.20944/preprints202301.0076.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; drug repurposing; long COVID; molecular docking; molecular dynamics; SARS-CoV-2
Online: 4 January 2023 (09:38:47 CET)
The novel coronavirus disease 19 (COVID-19) has resulted in an estimated 20 million excess deaths and the recent resurgence of COVID-19 in China is predicted to result in up to 1 million deaths over the next few months. With vaccines unable to halt transmission it is important to continue our quest for safe, effective, affordable drugs that will be available to all countries. Drug repurposing is one of the strategies being explored in this context. Recently, out of 7,817 approved drugs, 214 candidates were systematically down-selected using a combination of 11 filters including approval status, assay data against SARS-CoV-2, pharmacokinetic, pharmacodynamic and toxicity profiles. These drugs were subjected in this study to virtual screening against various targets of SARS-CoV-2 followed by molecular dynamic studies of the best scoring ligands against each target. The chosen molecular targets were Spike receptor binding domain, Nucleocapsid protein RNA binding domain, and key non-structural proteins 3, 5, 12, 13 and 14. Four drugs approved for other indications — alendronate, cromolyn, natamycin and treprostinil — look sufficiently promising from our in silicostudies to warrant further in vitro and in vivo investigations as appropriate to ascertain their extent of anti-viral activities.
SHORT NOTE | doi:10.20944/preprints202212.0230.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: monoamine oxidase; inhibitors; indole; 1,2,4-oxadiazole; drug research; neuroprotective drugs; Parkinson’s disease; MAO
Online: 13 December 2022 (07:12:01 CET)
3-(3,4-Dichlorophenyl)-5-(1H-indol-5-yl)-1,2,4-oxadiazole was synthesized via the condensation of 3,4-dichlorobenzamidoxime and methyl 1H-indole-5-carboxylate using superbasic medium (NaOH/DMSO). The compound was tested as a potential inhibitor of human monoamine oxidase (MAO) A and B. It demonstrated notable inhibition with an IC50 value of 0.036 μM for MAO-B and isoform specificity. The product was characterized by 1H NMR, 13C NMR, and HRMS. In conclusion, the new active MAO-B inhibitor may serve as a candidate for the future discovery of therapeutic agents for neurodegenerative disorders such as Parkinson’s disease.
REVIEW | doi:10.20944/preprints202212.0108.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Dendrimer; biomaterial; cell scaffold; hydrogel; wound repair; adhesion; differentiation; osseointegration.; hydroxyapatite; scaffold
Online: 7 December 2022 (01:57:27 CET)
The capability of radially polymerized bio-dendrimers and hyperbranched polymers for medical applications is well established. Among them, perhaps the most important are those that involve interactions with the regenerative mechanisms of cells. Dendritic polymers due to their distinctive architecture may play a multitude of roles such as protein biomimicry (collagen, elastin, hydroxy apatite production), gene and drug delivery (cell differentiation, antimicrobial protection), surface chemistry and charge modulation (adhesion to cells and tissues), polymer cross-linking (eye, skin and internal organ wound healing). The review highlights all the different categories of hard and soft tissues that may be remediated with their contribution. The reader will be also exposed to the incorporation methods to established biomaterials such as scaffolds, the functionalization strategies, and the synthetic paths for the assembly from biocompatible building blocks and natural metabolites.
ARTICLE | doi:10.20944/preprints202211.0516.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Antivirals; coronavirus; COVID-19; covalent drugs; dynamic light scattering; inhibitors; main protease; natural products
Online: 28 November 2022 (13:40:01 CET)
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the development of direct-acting antiviral drugs due to the coronavirus disease 2019 (COVID-19) pandemic. The main protease of SARS-CoV-2 is a crucial enzyme that breaks down polyproteins synthesized from the viral RNA, making it a validated target for the development of SARS-CoV-2 therapeutics. New chemical phenotypes are frequently discovered in natural goods. In the current study, we used a fluorogenic assay to test a variety of natural products for their ability to inhibit SARS-CoV-2 Mpro. Several compounds were discovered to inhibit the Mpro at low micromolar concentrations. It was possible to crystallize robinetin together with SARS-CoV-2 Mpro, and the X-ray structure revealed covalent interaction with the protease's catalytic Cys145 site. Selected potent molecules also exhibited antiviral properties without cytotoxicity. Some of these powerful inhibitors might be utilized as lead compounds for COVID-19 research.
ARTICLE | doi:10.20944/preprints202211.0509.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: isatin; indolin-2-one; acute myeloid leukemia; apoptosis; ERK1/2; MAPK
Online: 28 November 2022 (09:59:20 CET)
Searching for bioactive compounds within the huge chemical space is like trying to find a needle in a haystack. Isatin is a unique natural compound which is endowed with different biopertinent activities specially in cancer therapy. Herein, we envisaged that adopting a hybrid strategy of isatin and α,β-unsaturated ketone would afford new chemical entities with strong chemotherapeutic potential. Of interest, compounds 5b and 5g demonstrated significant antiproliferative activities against different cancer genotypes according to NCI assay. Concomitantly, their IC50 against HL-60 cells were 0.38 ± 0.08 and 0.57 ± 0.05, respectively, demonstrating remarkable apoptosis and mod-erate cell cycle arrest at G1 phase. Intriguingly, an impressive safety profile for 5b was reflected by a 37.2 times selectivity against HL-60 over PBMC from a healthy donor. This provoked us to further explore their mechanism of action by in vitro and in silico tools. Conclusively, 5b and 5g stand out as strong chemotherapeutic agents that hold a clinical promise against acute myeloid leukemia.
ARTICLE | doi:10.20944/preprints202211.0410.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Leukemia; imidazo[1,2-a]pyridines; selenide; oxidative stress; senescence; chronic myeloid leu-kemia.
Online: 22 November 2022 (07:49:44 CET)
Imidazo[1,2-a]pyridines have been studied regarding drug development. The objective of this work was to evaluate the antileukemic capacity of imidazo[1,2-a]pyridine derivatives by screening its ability as a pro-oxidant. Imidazo[1,2-a]pyridine derivatives were synthesized and oral bioavailability and toxicity were analyzed in silico. Redox screening was performed on human Kasumi, KG-1, K562 and Jurkat leukemia cells. The imidazo[1,2-a]pyridine derivative and the most responsive leukemic cell were selected for cytotoxicity, cell proliferation, cell senescence and oxidative stress assays. The predictive toxicity analysis showed a possible effect on the reproductive system, but without mutagenic, carcinogenic or irritability effects. MRK-107 against K562 cells was the compound that showed the best redox profile. MRK-107 did not induce cell death in K562 and monocyte cells. However, this compound was able to decrease cell proliferation and increase cell senescence after 48 and 72 hours. Furthermore, MRK-107 induced oxidative stress in K562 cells after 72h, increasing lipid peroxidation and decreasing reduced glutathione (GSH) contents. This study demonstrated that MRK-107-induced senescence with the involvement of oxidative stress as a possible mechanism of action, addressing this compound as a potential antitumor drug against chronic myeloid leukemia.
ARTICLE | doi:10.20944/preprints202211.0376.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: synthesis; leishmaniasis; flavonoids; rCPB; molecular modelling.
Online: 21 November 2022 (06:29:51 CET)
Leishmaniasis is a neglected tropical disease and affects more than 350 million people worldwide. However, there are no vaccines for humans, and current treatment is hampered due to its high cost, numerous side effects, and painful administration routes. Ending its epidemics by 2030 has become a United Nations goal, and the multitarget drug strategy emerges as a promising alternative. Flavonoids are an example of multitarget compounds and organic synthesis represents a tool to obtain high yields of these molecules. In our study, we synthesized 17 flavonoid analogs using a scalable, easy-to-reproduce, and inexpensive method. All compounds demonstrated an impressive inhibition capacity against rCPB2.8, rCPB3, and rH84Y, which are highly expressed in the amastigote stage, the target form of the parasite. Compounds 3c, f12a, and f12b stood out as effective against all isoforms and intermolecular interactions were investigated through a molecular modeling study. The compounds were highly potent against the parasite and demonstrated low cytotoxic action against mammalian cells. The results were pioneering, representing an advance in the investigation of the mechanisms behind the antileishmanial action of flavonoid derivatives. Furthermore, compounds have shown to be promising leads for the design of other cysteine protease inhibitors for the treatment of leishmaniasis diseases.
ARTICLE | doi:10.20944/preprints202211.0356.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Focal adhesion kinase; 3D-QSAR; Molecular Dynamics; MM-PB/GBSA; Free energy perturbation
Online: 18 November 2022 (10:13:00 CET)
Precise binding affinity predictions are essential for structure-based drug discovery (SBDD). Focal adhesion kinase (FAK) is a member of the tyrosine kinase protein family and is overexpressed in a variety of human malignancies. Inhibition of FAK using small molecules is a promising therapeutic option for several types of cancer. Here, we conducted computational modeling of FAK targeting inhibitors using 3-dimensional structure-activity relationship (3D-QSAR), molecular dynamics (MD), and hybrid topology-based free energy perturbation (FEP) methods. The structure-activity relationship (SAR) studies between the physicochemical descriptors and inhibitory activities of the chemical compounds were performed with reasonable statistical accuracy using CoMFA and CoMSIA. These are two well-known 3D-QSAR methods based on the principle of supervised machine learning (ML). Essential information regarding residue-specific binding interactions was determined using the MD and MM-PB/GBSA methods. Finally, physics-based relative binding free energy (〖∆∆G〗_RBFE^(A→B)) values of analogous ligands were estimated using the alchemical FEP simulation. An acceptable agreement was observed between the experimental and computed relative binding free energies. The overall results using ML and physics-based hybrid approaches could be useful for the rational optimization of accessible lead compounds with similar scaffolds targeting the FAK receptor.
ARTICLE | doi:10.20944/preprints202211.0296.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: antimicrobial resistance; broad-spectrum antibiotics; antibacterial drug discovery; gram-negative bacteria; pyrrolobenzodiazepines
Online: 16 November 2022 (04:20:55 CET)
It is urgent to find new antibiotic classes to replenish the empty development pipeline of antibiotics. Recently, pyrrolobenzodiazepines (PBDs) with a C8-linked aliphatic-heterocycle have been identified as a new broad spectrum antibiotic class with activity against Gram-negative bacteria. The active imine moiety of the reported lead pyrrolobenzodiazepine compounds was replaced with amide to obtain the non-DNA binding and non-cytotoxic dilactam analogues to further understand the structure activity relationship and improve the safety potential of this class. The synthesized compounds were tested against panels of multidrug resistant Gram-positive and Gram-negative bacteria, including WHO priority pathogens. Minimum inhibitory concentrations for the dilactam analogues ranged from 4 – 32 mg/L for MDR Gram-positive bacteria, compared to 0.03 to 2 mg/L for the corresponding imine analogues while they were found to be inactive against MDR Gram-negative bacteria, with an MIC >32 mg/L, compared to an MIC of 0.5 to 32 mg/L. A molecular modelling study suggests the lack of imine functionality also affects the interaction of PBDs with DNA gyrase. This study suggests the presence of N10-C11 imine moiety is crucial for broad spectrum activity of pyrrolobenzodiazepines.
REVIEW | doi:10.20944/preprints202211.0147.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: topoisomerase; anticancer; cancer; anticancer drugs; enzyme
Online: 8 November 2022 (06:22:07 CET)
Several reviews of inhibitors of topoisomerase II literature have been published covering research before 2018. Therefore, this review is focused primarily on more recent publications with relevant points from the earlier literature. Topoisomerase II is an established target for anticancer drugs, that are further subdivided into poisons and catalytic inhibitors. Whereas most of the topoisomerase II-based drugs in clinical use are mostly topoisomerase II poisons, their mechanism of action has posed severe concern due to DNA damaging potential, including development of multi drug resistance. As a result, we are beginning to see a gradual paradigm shift towards a non-DNA damaging agents, such as the lesser studied topoisomerase II catalytic inhibitors. In addition, this review will describe some novel selective catalytic topoisomerase II inhibitors. The ultimate goal is to bring researchers up to speed by curating and delineating new scaffolds as leads for optimization and development to new potent, safe and selective agents for the treatment of cancer.
ARTICLE | doi:10.20944/preprints202211.0132.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Enterococcus faecalis; natural products; aminoglycosides; aminoglycoside-modifying enzymes; APH(3’)-IIIa; flavone derivative
Online: 8 November 2022 (01:39:19 CET)
Enterococcus faecalis is a bacterium that can develop a multidrug resistance profile associated with the community as well as nosocomial-acquired infections. Among the treatment options for these infections are aminoglycosides combined with bacterial cell wall inhibitors such as beta-lactams, since E. faecalis is intrinsically resistant to aminoglycosides. One of its most representative resistance mechanisms is the expression of aminoglycoside-modifying enzymes, such as the aminoglycoside phosphotransferase type IIIa of E. faecalis (EfAPH(3')-IIIa). This enzyme acts by phosphorylating aminoglycosides in an ATP-dependent reaction, modifying the 3' position of hydroxyl groups of these antibiotics. Considering this scenario, 3,092 natural products obtained from the ZINC22 database were analyzed to select molecules with the highest affinity for the nucleotide-binding pocket of EfAPH(3')-IIIa, which could be potential aminoglycoside adjuvants. The molecules that showed the best-score results obtained from ensemble docking-based virtual screening were ZINC000000952700 (BS-1), ZINC000014793040 (BS-2) and ZINC000015498603 (BS-3). The most promising results were for BS-2, a flavone derivative, due to its improved stability profile in molecular dynamics simulation (average values of RMSD of 0.23 nm, and Rg of 1.94 nm), binding free energy calculations (average ΔG total of -35.3 nm), as well as better toxicological profile (lower probability of hepatotoxicity, carcinogenic, immunotoxicity, mutagenicity, and cytotoxicity effects), compared to BS-1 and BS-3. These results allow us to propose that a flavone derivative may act as an adjuvant to aminoglycosides in the treatment of E. faecalis infections, acting as an inhibitor in the nucleotide-binding pocket of EfAPH(3')-IIIa.
REVIEW | doi:10.20944/preprints202211.0062.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: membrane transporter; SLC; solute carrier; drug design; pharmacokinetics; prodrug; nanoparticle; bile acids
Online: 3 November 2022 (01:09:54 CET)
Transmembrane transport of small organic and inorganic molecules is one of the cornerstones of cellular metabolism. Among transmembrane transporters, solute carrier (SLC) proteins form the largest, albeit very diverse, superfamily with over 400 members. It has been early on recognized that xenobiotics can directly interact with SLCs and that this interaction can fundamentally determine their efficacy, including bioavailability and intertissue distribution. Apart from the well-established prodrug strategy, the chemical ligation of transporter substrates to nanoparticles of various chemical composition has recently been used as a means to enhance their targeting or absorption. In this review, we summarize efforts in drug design exploiting interactions with specific SLC transporters to optimize their therapeutic effects. Furthermore, we describe current and future challenges as well as new directions for the advanced development of therapeutics that target SLC transporters.
ARTICLE | doi:10.20944/preprints202210.0319.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Ochna kibbiensis; antimalarial prophylaxis; in silico; ADMET
Online: 21 October 2022 (03:47:26 CEST)
Ochna kibbiensis (Family: Ochnaceae) has been employed in ethnomedicine for the treatment of malaria, and inflammation among others. The aim of this study was to isolate and characterize prophylactic antimalarial agents from the leaves of O. kibbiensis against Plasmodium berghei, in vivo and in silico. The median lethal dose (LD50) of the methanol extract and its fractions (n-hexane, dichloromethane, ethylacetate and n-butanol) was determined according to Lorke’s method while the antimalarial effect of the extract and its fractions was investigated according to the method described by Peters prophylactic test using Chloroquine-sensitive Plasmodium berghei (NK65). All the extract/fractions exhibited LD50 values ≥ 5000 mg/kg with the exception of the n-butanol fraction (1702.94 mg/kg) which indicate that the plant is non-toxic. Dichloromethane fraction exhibited significant (p<0.05) and dose-dependent prophylactic effect with 47.62, 85.12 and 100.0 % prophylaxis (at 500, 250 & 125 mg/kg) while the least effect was observed by the n-butanol fraction with percentage prophylaxis of 64.29 and 76.19, respectively; the standard drug, pyrimethamine had 95.24 % prophylaxis. Based on the result obtained, dichloromethane fraction of O. kibbiensis was subjected to chromatographic purification which led to the isolation of a mixture of two compounds identified as stigmasterol and β-sitosterol by analysis of the NMR spectral data and comparison with existing literature; the compounds exhibited good binding affinities (- 5.129 and - 4.889 kcal/mol) against pfLDH and favorable ADMET profile. In conclusion, the leaf of O. kibbiensis have demonstrated a significant prophylactic antimalarial activity and the two known steroids (stigmasterol and β-sitosterol) isolated from the dichloromethane fraction for the first time.
COMMUNICATION | doi:10.20944/preprints202210.0053.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Measurement uncertainty; thyroid function tests; quality control; sigma-metric
Online: 7 October 2022 (07:30:21 CEST)
The minimum requirement for uncertainty estimation is to use only intermediate precision (Rw), especially for measurands lacking a reference measurement system such as thyroid functions tests (TFT). In this study, measurement uncertainty (MU) for TSH and FT4 from long-term internal quality control (IQC) data was estimated while reference change values (RCV) were calculated from estimated MU. Furthermore, intermediate precision (Rw) was used to establish appropriate risk-based QC frequency. Twenty fore months of third party IQC data were collected retrospectively, on the Abbott ARCHITECT i1000sr analyzer from INSTITUT PASTEUR OF MSILA laboratory, ALGERIA. The MU, RCV and sigma-metric were estimated simply from the intermediate precision (Rw), while a nomogram relating sigma performance to run size was used to establish QC frequency. The MU for the TSH and FT4 was 12% and 8% respectively. The U one-sided for the TSH and FT4 was 10%, 6.6% respectively. MU and U one-sided of TSH and FT4 met quality requirements for permissible uncertainty (pU %) and allowable total error (ATE %). When monitoring thyroid replacement therapy, an upward minimum change (RCV) of 54% and 22% or a downward of 35% and 18% in serum TSH and FT4 respectively, would be considered significant. Optimal QC strategy for serum TSH was selected to run 4 QC materials every 190 patients sample and to use a multi-rule (13s/22s/R4s/41s). Our results suggest that MU estimation from long-term IQC alone may be acceptable for TFT to assist physician in results interpretation and to establish appropriate QC frequency.
REVIEW | doi:10.20944/preprints202209.0201.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: ligand-based pharmacophores; structure-based pharmacophores; virtual screening; drug design; machine learning; molecular dynamics; de novo design
Online: 14 September 2022 (09:10:58 CEST)
G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. 3D pharmacophore models are powerful computational tools in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and elucidation of ligand-receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning will be highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.
ARTICLE | doi:10.20944/preprints202209.0188.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: MTBC; virtual screening; topological indices; linear discriminant analysis; pharmacological activity distribution diagrams; antimicrobial drugs; drug design
Online: 14 September 2022 (03:32:55 CEST)
A method is developed to identify molecular scaffolds potentially active against the Mycobacterium tuberculosis complex (MTBC). A structurally heterogeneous set of compounds active against MTBC was used to obtain a structural pattern model based on structural invariants. This model was statistically validated through a Leave-n-Out test. It successfully discriminated between active or inactive compounds over 86% in database sets and was also able to select new active chemical structures in external databases. The selection of new substituted pyrimidines, pyrimidones and triazolo[1,5-a]pyrimidines was particularly interesting because these structures could provide new scaffolds in this field. The seven selected candidates were synthesized and six of them showed activity in vitro.
ARTICLE | doi:10.20944/preprints202209.0026.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Bacopa procumbens HPLC characterization; effect of polyphenolic compounds; in vitro and in vivo skin wound; collagen organization
Online: 1 September 2022 (15:44:09 CEST)
Wounds represents a medical problem that contribute importantly to patient morbidity and to the healthcare costs in several pathologies. In Hidalgo, Mexico, Bacopa procumbens plant has been traditionally used for wound healing care for several generations; in vitro and in vivo experiments were design to evaluate the effects of bioactive compounds obtained from B. procumbens aquoethanolic extract and to determine the key pathways involved in wound regeneration. Bioactive compounds were characterized by HPLC- QTOF-MS and proliferation, migration, adhesion, and differentiation studies were done on NIH/3T3 fibroblasts. Polyphenolic compounds from Bacopa procumbens (PB) regulated proliferation and cell adhesion; enhanced migration reducing the artificial scratch area; and modulated cell differentiation. PB compounds were included in a hydrogel for topical administration on rat excision wound model. Histological, histochemical and mechanical analysis showed that PB treatment accelerates wound closure in at least 48 h; reduce inflammation, increasing cell proliferation and deposition and organization of collagen in earlier times. These changes resulted in the formation of a scar with better tensile properties. Immunohistochemistry and RT-PCR molecular analyses demonstrated that treatment induces: i) overexpression of transforming growth factor beta (TGF-β); and ii) the phosphorylation of Smad 2/3 and ERK1/2, suggesting the central role of some PB to enhance wound healing, modulating TGF-β activation.
ARTICLE | doi:10.20944/preprints202208.0352.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Oxidative Stress, Free radical scavenging, Autophagy, Ischemia/reperfusion injury, Hypox-ia/reoxygenation, Mitophagy
Online: 18 August 2022 (14:33:17 CEST)
Ischemia/reperfusion (I/R) injury results in cell death by inducing apoptosis. During I/R, early generation of mitochondrial reactive oxygen species (mtROS) can induce neighboring mitochondria to release additional ROS, a toxic cycle resulting in significant mitochondrial and cellular injury. Oxidative damage in the mitochondria contributes to various pathologies, including I/R injury. Accordingly, preventing mitochondrial oxidative damage should be therapeutically relevant for many disorders, including cardiovascular diseases. We recently discovered an Indole-Peptide-Tempo Conjugate (IPTC) that served as a novel bifunctional agent with both antioxidant and autophagy-modulating capacity. Here, we demonstrate that IPTC can protect H9C2 cardiomyocytes from hypoxia/reoxygenation (H/R) injury that results from mtROS overproduction due to impaired mitophagy and resultant mitochondrial dysfunction. We hypothesize that the mechanism of action of IPTC involves the capacity to decrease mtROS combined with induction of mitophagy.
ARTICLE | doi:10.20944/preprints202208.0103.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Resveratrol; antioxidant metabolism; scavengome; biomimetic oxidation; bioactivity-guided isolation; NMR spectroscopy; xanthine oxidase
Online: 4 August 2022 (05:33:52 CEST)
Resveratrol is a well-known natural polyphenol with a plethora of pharmacological activities. As a potent antioxidant, resveratrol is highly oxidizable, and readily reacts with reactive oxygen species (ROS). Such a reaction not only leads to a decrease in ROS levels in a biological environ-ment but may also generate a wide range of metabolites with altered bioactivities. Inspired by this notion, in the current study, our aim was to take a diversity-oriented chemical approach to study the chemical space of oxidized resveratrol metabolites. Chemical oxidation of resveratrol and a bioactivity-guided isolation strategy using xanthine oxidase (XO) and radical scavenging activities led to the isolation of a diverse group of compounds, including a chlorine-substituted compound (2), two iodine-substituted compounds (3 and 4), two viniferins (5 and 6), an eth-oxy-substituted compound (7) two ethoxy-substituted dimers (8 and 9). Compounds 4, 7, 8 and 9 are reported here for the first time. All compounds without ethoxy-substitution exerted stronger XO inhibition than their parent compound, resveratrol. By enzyme kinetic and in silico docking studies compounds 2, 3 and 4 were identified as potent competitive inhibitors of the enzyme while the viniferins acted as mixed-type inhibitors. Further, compounds 2 and 9 had better DPPH scavenging activity and oxygen radical absorbing capacity than resveratrol. Our results suggest that the antioxidant activity of resveratrol is modulated by the effect of a cascade of chemically stable oxidized metabolites, several of which have significantly altered target specificity as compared to their parent compound.
ARTICLE | doi:10.20944/preprints202208.0074.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: cisplatin; masticadienonic acid; Amphypterygium adstringens; antitumor; xenograft
Online: 3 August 2022 (07:36:50 CEST)
Cisplatin (CDDP) is widely used to treat several types of cancer. However, CDDP induces nephrotoxicity. This toxicity could be avoided, applying a lower cisplatin dose; however, it could induce a lesser therapeutic activity. In this paper, we present the cytotoxic activity against prostate human cancer cell line (PC-3) of the combination of CDDP with masticadienonic acid (MDA), a triterpene isolated from Amphypterygium adstringens.The combinations A (half of the IC50), B (IC50) and C (twice IC50 of the compounds) in a radio 1:1 were evaluated. Our results showed that the B and C combinations presented synergism effect. However, B combination showed almost 100% inhibition of cell proliferative activity and increased apoptosis compared with those presented by each compound apart. A pretreatment of MDA 24 h to cells before the CDDP, AMD or B combination administration result in a resistance to the treatments. A xenograft study using PC-3 cells showed that the combination of 47.5 mM/kg (AMD) plus 4 mM/kg (CDDP) administered weekly for 3 weeks reducing the tumor volume in approximately 47 %. However, the combination of 47.5 mg/kg (AMD) plus 2 mg/kg (CDDP) administered every third day for 21 days reduce, approximately 82% of tumor compared with mice no treated.
ARTICLE | doi:10.20944/preprints202206.0348.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Naltrexone; mu-opioid receptor; MD simulations; MMGBSA; binding free energy
Online: 27 June 2022 (04:09:30 CEST)
Naltrexone (NTX) is a potent opioid antagonist with good blood-brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of NTX and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. NTX and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to Molecular Mechanics Generalized-Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that NTX and its derivatives showed differences in protein-ligand interactions; however, they shared contact with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of NTX compared to its derivatives.
ARTICLE | doi:10.20944/preprints202206.0144.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Molecular docking; molecular dynamics; pharmacophore; molecular modeling; XIAP protein; protein inhibitor; anticancer activity
Online: 9 June 2022 (11:08:29 CEST)
Herein, we are proposing two chalcone molecules, (E)-1-(4-methoxyphenyl)-3-(p-tolyl) prop-2-en-1-one and (E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl) prop-2-en-1-one, based on the anticancer bioactive molecule Xanthohumol, which are suitable for further in vitro and in vivo studies. Their ability to create stable complexes with the antiapoptotic X-linked IAP (XIAP) protein makes them promising anticancer agents. The calculations were based on ligand-based and structure-based virtual screening combined for the pharmacophore built. Additionally, the structures passed Lipinski's rule for drug use, and their reactivity was confirmed using density functional theory studies. The candidates were chosen between 10639400 compounds, and the docking protocols were evaluated using molecular dynamics simulations.
CONCEPT PAPER | doi:10.20944/preprints202205.0388.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: proximity labeling; spatial omics; functional proteomics; interactome mapping; electrophile signaling
Online: 30 May 2022 (06:13:07 CEST)
If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current state-of-the-art and discusses key limitations underlying these emerging approaches, in particular, the limited functional knowledge they provide in understanding local proteomes / interactomes. This limitation is directly linked to the use of non-biologically- or non-pharmaceutically-relevant reactive intermediates in the course of covalently labeling the local proteomes. As such, these methods cannot report on specific functions of localized protein players, nor can they scrutinize whether the specific functions of such proteins/interactomes can be directly manipulated by pharmacologically-relevant small-molecule ligands. The latest data hint that precision localized electrophile delivery concept ushers a means to address this limitation with high spatiotemporal resolution, and ultimately, in relevant live animals.
ARTICLE | doi:10.20944/preprints202205.0097.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: KV1.3; potassium ion channels; antiproliferative activity; apoptosis; anticancer drugs
Online: 9 May 2022 (03:35:09 CEST)
The voltage-gated potassium channel KV1.3 has been recognized as a tumor marker and represents a promising new target for the discovery of new anticancer drugs. We designed a novel structural class of KV1.3 inhibitors through structural optimization of benzamide-based hit compounds and structure-activity relationship studies. The potency, and selectivity of the new KV1.3 inhibitors were investigated using whole-cell patch- and voltage-clamp experiments. 2D and 3D cell models were used to determine antiproliferative activity. Structural optimization resulted in the most potent and selective KV1.3 inhibitor 44 in the series with an IC50 value of 470 nM in oocytes and 950 nM in Ltk cells. Kv1.3 inhibitor 4 induced significant apoptosis in Colo-357 spheroids, while 14, 37, 43, and 44 significantly inhibited Panc-1 proliferation.
REVIEW | doi:10.20944/preprints202204.0151.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Isocyanide-based multicomponent reactions; Antimicrobial Discovery; Antibiotic Resistance; Public Health
Online: 18 April 2022 (03:38:08 CEST)
Multicomponent reactions (MCR) have been used to synthesis a wide range of analogs from several classes of heterocyclic compounds, with multifaceted medicinal uses. The synthesis of highly functionalized molecules in a single pot is a unique property of MCR, allowing researchers to quickly assemble libraries of compounds of biological interest and uncover novel leads as possible therapeutic agents. Isocyanide-based multicomponent reactions have proven to be extremely effective at swiftly specifying members of compound libraries, particularly in discovery of drug . The understanding of structure-activity correlations that drive the development of new goods and technology, requires structural variety in these libraries. In current world, antibiotic resistance is a major ongoing problem which is developing a problematic scenario in public health. The implementation of isocyanide based multicomponent reactions uphold a significant potential in this regard. By utilizing such reactions, new antimicrobial compounds can be discovered and fight against such concerns. This study discusses recent developments in antimicrobial medication discovery using isocyanide-based multicomponent reactions (IMCRs). Furthermore, the article emphasizes the potential of IMCRs in the near future.
REVIEW | doi:10.20944/preprints202204.0065.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; Main protease; Mpro; inhibitors
Online: 8 April 2022 (03:01:37 CEST)
Since the outbreak of COVID-19, one of the strategies used to search for new drugs has been to find inhibitors of the main protease (Mpro) of virus SARS-CoV-2. Initially, previously reported inhibitors of related proteases like the main proteases of SARS-CoV and MERS-CoV were tested. Then a huge effort has been done by the scientific community to design, synthesize and test new small molecules acting as inactivators of SARS-CoV-2 Mpro. From the structure view, these compounds can be classified into two main groups: one corresponds to modified peptides displaying an adequate sequence for high affinity and a reactive warhead, and the second one is a diverse group including chemical compounds which do not have a peptide framework. Although a drug including a SARS-CoV-2 main protease has already been commercialized, denoting the importance of this field, more compounds have been demonstrated to be promising potent inhibitors as potential antiviral drugs.
ARTICLE | doi:10.20944/preprints202204.0063.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: S-allylcysteine; caffeic acid; hybrid compounds; in silico studies; colorectal cancer; cell death; apoptosis
Online: 7 April 2022 (14:16:48 CEST)
Conventional chemotherapy for colorectal cancer (CRC) gives only a small increase in patient survival, since it is often diagnosed in late stages, when tumor has disseminated to other organs. Besides, it is common to observe that malignant cells acquire tumor escape mechanisms which leads to therapy resistance. Considering these facts, the discovery of new molecules with therapeutic potential has become an invaluable tool in chemoprevention. In this context, we previously evaluated two hybrids (SAC-CAFA-MET and SAC-CAFA-PENT) which exhibited selective cytotoxicity against SW480, with better results than the conventional chemotherapeutic agent (5-fluorouracil; 5-FU). Here, we investigated a little deeper in the possible mechanism of these molecules to identify potential therapeutic alternatives for the treatment of CRC. Both compounds induced cell damage and reduced ROS formation. Further evaluations showed that SAC-CAFA-MET induces cell death independent from caspases and p53, but probably mediated by the negative regulation of the proapoptotic Bcl-2. In addition, the lack of activation of caspase 8 and the positive regulation of caspase 3 induced by SAC-CAFA-PENT suggest this compound acts through an apoptotic mechanism, probably initiated by intrinsic pathway. Besides, the down regulation of IL-6 by SAC-CAFA-PENT suggests it also induces a significant anti-inflammatory process. In addition, docking studies would suggest caspase-3 modulation as the primary mechanism by which hybrids elicits apoptosis in human colorectal adenocarcinoma SW480. Meanwhile, DFT calculations suggest that hybrids would produce effects in modulation of ROS in SW480 cells via hydrogen atom transfer pathway (HAT). Finally, both, SAC-CAFA-MET and SAC-CAFA-PENT displayed a favorable pharmacokinetic profile. The current work highlights the potential of the lead compounds SAC-CAFA-MET and SAC-CAFA-PENT as potential agents for colorectal cancer chemoprevention.
ARTICLE | doi:10.20944/preprints202203.0354.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: insecticides; semi-synthetic pesticides; eugenol derivatives; alkoxy alcohols; essential oils; nanoencapsulation biopesticides
Online: 28 March 2022 (06:12:52 CEST)
A new set of alkoxy alcohols were synthesised by reaction of eugenol oxirane with aliphatic and aromatic alcohols. These eugenol derivatives were evaluated against their effect upon the viability of the insect cell line Sf9 (Spodoptera frugiperda).The most promising compounds, 4-(3-(tert-butoxy)-2-hydroxypropyl)-2-methoxyphenol and 4-(2-((4-fluorobenzyl)oxy)-3-hydroxypropyl)-2-methoxyphenol were submitted to in silico assays to predict possible targets. Thought an Inverted Virtual Screening approach, 23 common pesticide targets were screened and the top 2 targets predicted were further evaluated through molecular dynamics simulations and free energy calculations. In addition, these to eugenol derivatives were subjected to encapsulation and release assays using liposome-based nanosystems of egg phosphatidylcholine/cholesterol (7:3), with encapsulation efficiencies higher than 90% and release profiles well described by both Korsmeyer-Peppas and Weibull models.
ARTICLE | doi:10.20944/preprints202203.0157.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Adenosine receptors; methanocarba; bicyclo[3.1.0]hexane; A3 receptors
Online: 10 March 2022 (15:47:10 CET)
In this paper, a series of bicyclo[3.1.0]hexane-based nucleosides were synthesized and evaluated for their P1 receptor affinities in radioligand binding studies. The most potent derivative 30 displayed moderate A3AR affinity (Ki of 0.38 μM) and high A3R selectivity. A subset of compounds varied at 5’-position was further evaluated in functional P2Y1R assays displaying no off-target activity.
REVIEW | doi:10.20944/preprints202203.0032.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: artificial intelligence; machine learning; drug design; covid-19; structure-based drug design; ligand-based drug design
Online: 2 March 2022 (03:00:37 CET)
The recent covid crisis has proven important lessons for academia and industry regarding digital reorganization. Among fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and over. Moreover, drug development is a costly and time-consuming business, and only a minority of approved drugs return the revenue that exceeds the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper will review the most significant research on artificial intelligence in the de novo drug design for COVID-19 pharmaceutical research.
ARTICLE | doi:10.20944/preprints202202.0046.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Cancer; tumor homing peptide; in silico drug discovery; complex network; chemical space network; centrality measure; similarity searching, group fusion; motif discovery; starPep toolbox software
Online: 3 February 2022 (10:14:05 CET)
Peptide-based drugs are promising anticancer candidates due to their biocompatibility, and low toxicity. Particularly, tumor homing peptides (THPs) have the ability to bind specifically to can-cer cells receptors and tumor vasculature. Despite their potential to develop antitumor drugs, there are few available prediction tools to assist the discovery of new THPs. Two webservers based on machine learning models are currently active, the TumorHPD (https://webs.iiitd.edu.in/raghava/tumorhpd) and the THPep (http://codes.bio/thpep), and more recently the SCMTHP (SCMTHP (pmlabstack.pythonanywhere.com), based on scoring card method. Herein, a novel method based on network science and similarity searching implemented in the starPep toolbox (http://mobiosd-hub.com/starpep/) is presented for THPs discovery. The approach leverages from exploring the structural space of THPs with Chemical Space Networks (CSNs) and from applying centrality measures to identify the most relevant and non-redundant THPs sequences within the CSN. Such THPs were considered as queries (Qs) for multi-query similarity searches that applies a group fusion (MAX-SIM rule) model. The resulting multi-query similarity searching models (SSMs) were validated with three benchmarking datasets of THPs/non-THPs. Predictions achieved accuracies ranged from 92.64 to 99.18% and Matthews Correlation Coefficients between 0.894-0.98, outperforming state-of-the-art predictors. The best model was applied to repurpose AMPs from the starPep database as THPs, which were subse-quently optimized for the TH activity. Finally, 54 promising THP leads were discovered, and their sequences were analyzed to encounter novel motifs. These results demonstrate the potential of CSNs and multi-query similarity searching for a rapid and accurate identification of THPs.
ARTICLE | doi:10.20944/preprints202201.0475.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: DAST; semi-synthesis; fluorination; Beckmann-rearrangement; cyclopropane; natural product; ecdysteroid; NMR; structure elucidation; anticancer
Online: 31 January 2022 (21:35:38 CET)
Fluorine represents a privileged building block in pharmaceutical chemistry. Diethylaminosulfur-trifluoride (DAST) is a reagent commonly used for replacement of alcoholic hydroxyl groups with fluorine and is also known to catalyze water elimination and cyclic Beckmann-rearrangement type reactions. In this work we aimed to use DAST for diversity-oriented semisynthetic transformation of natural products bearing multiple hydroxyl groups to prepare new bioactive compounds. Four ecdysteroids, including a new constituent of Cyanotis arachnoidea, were selected as starting materials for DAST-catalyzed transformations. The newly prepared compounds represented combinations of various structural changes DAST was known to catalyze, and a unique cyclopropane ring closure that was found for the first time. Several compounds demonstrated in vitro antitumor properties. A new 17-N-acetylecdysteroid (13) exerted potent antiproliferative activity and no cytotoxicity on drug susceptible and multi-drug resistant mouse T-cell lymphoma cells. Further, compound 13 acted in significant synergism with doxorubicin without detectable direct ABCB1 inhibition. Our results demonstrate that DAST is a versatile tool for diversity-oriented synthesis to expand chemical space towards new bioactive compounds.
ARTICLE | doi:10.20944/preprints202201.0359.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: JAK/STAT3 signaling pathway; Meridianin derivatives; Isothiouronium; Anti-tumor activity
Online: 24 January 2022 (14:06:38 CET)
Hyperactivation of Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) signaling is an attractive therapeutic target for tumor therapy. Herein, forty-eight novel meridianin derivatives were designed and synthesized, and their anti-tumor activity were evaluated in vitro both for activity optimization and structure-activity relationship (SAR) study. The results indicated that most derivatives exhibited significantly improved anti-tumor activity, especially for compound 6e. The compound 6e contains an isothiouronium linked by an alkyl chain consisting of 6 carbon atoms with IC50 ranging from 1.11 to 2.80 μM on various cancer cell lines. Consistently, 6e dose dependently induced the apoptosis of A549 and DU145 cells, in which STAT3 are constitutively active. Western blotting assays indicated that the phosphorylation levels of JAK1, JAK2 and STAT3 were inhibited by 6e at 5 μM without significant change in total STAT3 level. Moreover, 6e also suppressed the expressions of STAT3 downstream genes, including c-Myc, Cyclin D1 and Bcl-XL at 10 μM. An additional in vivo study revealed that 6e at the dose of 10 mg/kg could potently inhibit the DU145 xenograft tumor without obvious body-weight loss. These results clearly indicate that 6e could be a potential anti-tumor agent by targeting JAK/STAT3 signaling pathway.
ARTICLE | doi:10.20944/preprints202201.0063.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Malaria, Plasmodium berghei, Plasmodium falciparum, hepatic stages, blood stages, prophylaxis, tazopsine, dextromethorphan, N-alkylation, hit compounds.
Online: 6 January 2022 (10:11:44 CET)
The alkaloid tazopsine 1 was introduced in the late 2000's as a novel antiplasmodial hit compound active against Plasmodium falciparum hepatic stages, with potential to develop prophylactic drugs based on this novel chemical scaffold. However, the structural determinants of tazopsine 1 bioactivity, together with the exact definition of the pharmacophore, remained elusive, impeding further development. We found that the antitussive drug dextromethorphan (DXM) 3, although lacking the complex pattern of stereospecific functionalization of the natural hit, was harboring significant antiplasmodial activity in vitro despite suboptimal prophylactic activity in a murine model of malaria, which precluded its direct repurposing against malaria. The targeted N-alkylation of nor-DXM 15 delivered a small library of analogues with greatly improved activity over DXM 3 against P. falciparum asexual stages. Amongst these, N-2’-pyrrolylmethyl-nor-DXM 16i showed a 2- to 36-fold superior inhibitory potency compared to tazopsine 1 and DXM 3 against parasite liver and blood stages, with 760 ± 130 nM and 2.1 ± 0.4 µM IC50 values, respectively, as well as liver/blood phase selectivity of 2.8. Furthermore, cpd. 16i showed a 5 to 8-fold increase of activity relatively to DXM 3 against P. falciparum stages I-II and V gametocytes, with 18.5 µM and 13.2 µM IC50 values, respectively. Cpd. 16i can thus be considered a promising novel hit compound against malaria in the ent-morphinan series with putative pan-cycle activity, paving the way for further therapeutic development (e. g., investigation of its prophylactic activity in a mouse model of malaria).
ARTICLE | doi:10.20944/preprints202112.0225.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: RNA targeting; RNA-based interactions; bis-3-chloropiperidines
Online: 14 December 2021 (11:13:29 CET)
After a long limbo, RNA has gained its credibility as a druggable target, fully earning its de-served role in the next-generation area of pharmaceutical R&D. We have recently probed the Trans-Activation Response element (TAR), a RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabiliz-ing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analyti-cal approaches for the study of multicomponent RNA-based interactions.
ARTICLE | doi:10.20944/preprints202112.0090.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: azolo[1,5-a]pyrimidines; benzo[4,5]imidazo[1,2-a][1,2,3]triazolo[4,5-e]pyrimidines; nitrocompounds; anticoagulant; cytokine storm.
Online: 6 December 2021 (15:47:49 CET)
Hypercytokinemia, or cytokine storm, is one of the severe complications of viral and bacterial infections, involving the release of abnormal amounts of cytokines, resulting in a massive inflammatory response. Cytokine storm is associated with COVID-19 and sepsis high mortality rate by developing epithelial dysfunction and coagulopathy, leading to thromboembolism and multiple organ dysfunction syndrome. The anticoagulant therapy is an important tactic to prevent thrombosis in sepsis and COVID-19, but recent data show the incompatibility of modern direct oral anticoagulants and antiviral agents. It seems relevant to develop dual-action drugs with antiviral and anticoagulant properties. At the same time it was shown that azolo[1,5-a]pyrimidines are heterocycles with a broad spectrum of antiviral activity. We have synthesized a new family of azolo[1,5-a]pyrimidines and their condensed polycyclic analogs by cyclocondensation reactions and direct CH-functionalization and studied their anticoagulant properties. Five compounds among 1,2,4-triazolo[1,5-a]pyrimidin-7-ones and 5-alkyl-1,3,4-thiadiazolo[3,2-a]purin-8-ones demonstrated higher anticoagulant activity than the reference drug, dabigatran etexilate. Antithrombin activity of lead compounds was confirmed using lipopolysaccharide (LPS) treated blood to mimic conditions of cytokine release syndrome. The studied compounds affected only the thrombin time value, reliably increasing it 6.5–15.2 times as compared to LPS-treated blood.
ARTICLE | doi:10.20944/preprints202111.0329.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Machine Learning; Deep Learning; Molecular Modeling; Virtual Screening; Drug Discovery
Online: 18 November 2021 (13:59:09 CET)
Virtual screening - predicting which compounds within a specified compound library bind to a target molecule, typically a protein - is a fundamental task in the field of drug discovery. Doing virtual screening well provides tangible practical benefits, including reduced drug development costs, faster time to therapeutic viability, and fewer unforeseen side effects. As with most applied computational tasks, the algorithms currently used to perform virtual screening feature inherent tradeoffs between speed and accuracy. Furthermore, even theoretically rigorous, computationally intensive methods may fail to account for important effects relevant to whether a given compound will ultimately be usable as a drug. Here we investigate the virtual screening performance of the recently released Gnina molecular docking software, which uses deep convolutional networks to score protein-ligand structures. We find, on average, that Gnina outperforms conventional empirical scoring. The default scoring in Gnina outperforms the empirical AutoDock Vina scoring function on 89 of the 117 targets of the DUD-E and LIT-PCBA virtual screening benchmarks with a median 1% early enrichment factor that is more than twice that of Vina. However, we also find that issues of bias linger in these sets, even when not used directly to train models, and this bias obfuscates to what extent machine learning models are achieving their performance through a sophisticated interpretation of molecular interactions versus fitting to non-informative simplistic property distributions.
ARTICLE | doi:10.20944/preprints202111.0125.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: artificial intelligence; de novo design; fragment-based drug discovery; HIV-1 inhibitors; pseudo natural products
Online: 8 November 2021 (09:23:49 CET)
The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are only a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, new novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual-focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available at https://figshare.com/s/ceb58d58e8f5585ce67e.
ARTICLE | doi:10.20944/preprints202111.0108.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Plasmodium; malaria; type III beta phosphatidylinositol 4-kinase; virtual screening; homology modeling; molecular dynamics
Online: 5 November 2021 (08:44:31 CET)
Plasmodium species that cause malaria, a disease responsible for about half a million deaths per annum despite concerted efforts to combat it. The causative agent depends on type III beta phosphatidylinositol 4-kinase (PPI4K) during the development of merozoite. PPI4K is the only clinically validated Plasmodium kinase so far and its inhibitors are effective both in vitro and in vivo. In this work, a small library of ~22 000 fragments was virtually screened using PPI4K homology model to discover potential ligands of the enzyme. 16 virtual hits were selected based on ≤ -9.0 kcal/mol binding energy cut off and were subjected to similarity and substructure searching after they had passed PAINS screening. The derivatives obtained showed improved binding energies, which ranged from -10.00 to -13.80 kcal/mol. Moreover, the topmost ranking compound 31, with interesting drug-like quality was stable within the protein’s binding cavity during the 10 ns molecular dynamics simulation period. In addition, analysis of its binding pose revealed some unique binding interactions with PPI4K active site residues as the basis for the observed improved binding affinity. Overall, compound 31 appears to be a viable starting point for the development of PPI4K inhibitors with antimalarial activity.
ARTICLE | doi:10.20944/preprints202111.0105.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: quorum sensing; furanones; biofilm
Online: 4 November 2021 (16:18:19 CET)
Clinical evidence has shown that bacterial infections are more difficult to eradicate when form-ing a biofilm aggregate than when are produced by bacteria in planktonic form. Therefore, com-pounds that inhibit biofilm formation could be used against severe infections. It has been re-ported that bromo 2-(5H) furanones inhibited biofilm formation by their anti-quorum sensing properties. To determine if the 2-(5H) furanone moiety is essential to induce inhibition of biofilm formation, we evaluated ten halogen 2-(5H) furanones derivates previously synthesized. Besides evaluating the inhibition of biofilm formation, we assessed pyocyanin production, swarming motility, and transcription of essential QS genes: rsaL, rhlA, pqsA and phz1 genes. Our results showed that although three bromo-furan-2(5H)-one-type derivatives (A1-A3) and two bromo-4-(phenylamino)-furan-2(5H)-one-type compounds (B2 and B6) inhibited the biofilm formation in both P. aeruginosa PA14 (reference) and PA64 (drug-resistant) strains only the furanones A1-A3 were efficient to inhibit QSS.
ARTICLE | doi:10.20944/preprints202111.0072.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: antimalarial drugs; artemisinins; ACTs; resistance; amino-artemisinins, pharmacokinetics; metabolism; Cmax; drug efficacy
Online: 3 November 2021 (09:10:50 CET)
Because of the need to replace the current clinical artemisinins in artemisinin combination therapies, we are evaluating fitness of amino-artemisinins for this purpose. These include the thiomorpholine derivative artemiside obtained in one scalable synthetic step from dihydroartemisinin (DHA) and the derived sulfone artemisone. We have recently shown that artemiside undergoes facile metabolism via the sulfoxide artemisox into artemisone and thence into the unsaturated metabolite M1; DHA is not a metabolite. Artemisox and M1 are now found to be approximately equipotent with artemiside and artemisone in vitro against asexual P. falciparum (Pf) blood stage parasites (IC50 1.5 – 2.6 nM). Against Pf NF54 blood stage gametocytes, artemisox is potently active (IC50 18.9 nM early-stage, 2.7 nM late-stage). Comparative drug metabolism and pharmacokinetic (DMPK) properties were assessed via po and iv administration of artemiside, artemisox and artemisone in a murine model. Following oral administration, the composite Cmax value of artemiside plus its metabolites artemisox and artemisone formed in vivo is some 2.6-fold higher than that attained following administration of artemisone alone. Given that efficacy of short half-life rapidly-acting antimalarial drugs such as the artemisinins is associated with Cmax, it is apparent that artemiside will be more active than artemisone in vivo, due to additive effects of the metabolites. As is evident from earlier data, artemiside indeed possesses appreciably greater efficacy in vivo against murine malaria. Overall, the higher exposure levels of active drug following administration of artemiside coupled with its synthetic accessibility indicate it is much the preferred drug for incorporation into rational new artemisinin combination therapies.
REVIEW | doi:10.20944/preprints202111.0020.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Neocarya macrophylla; Chrysobalanaceae; antivenom; analgesic; anti-inflammatory; antimicrobial; antioxidant; catechin; stigmasterol
Online: 1 November 2021 (13:06:02 CET)
Neocarya macrophylla (Sabine) Prance (Nm, Chrysobalanaceae) is used traditionally as food, for medicinal spiritual and industrial purposes. It is also used as soap, dye, glue, fodder, termite repellent, firewood and for structural materials. Few studies on the physicochemical, nutritional contents, phytochemical and pharmacological activities have validated the benefits of Nm to humanity as food, in cosmetics and pharmaceutical products. The major bioactive constituents identified in the plant so far are steroids and flavonoids (such as stigmasterol, quercetin, catechin and its related glycosides). Extracts of the plant have shown good antivenom, antimicrobial, analgesic, anti-inflammatory, antimycobacterial, anthelmintic and antioxidant activities. Acute toxicity studies conducted have confirmed the plant to be toxic. More studies on the plant are required in order to exploit other biological activities as claimed by traditional healers and also to isolate more bioactive compounds. In addition, the safety and tolerability assessment of Nm should be undertaken due to its widespread usage.
ARTICLE | doi:10.20944/preprints202010.0576.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Antimalarial; Erythrina fusca; Phaseolin; Molecular docking; Phytochemical analysis
Online: 21 October 2021 (12:08:52 CEST)
The exploration of alternative antimalarial therapeutics is a requisite for the emergence of resistance against Artemisinin. Considering the required cost and time length of classical small molecule drug discovery process, phytochemical screening of traditionally used medicinal plant which are repertoire of active compounds with antimalarial activity has become popular. To investigate the antimalarial property of traditionally used medicinal plants, a number of Erythrina spp have been reviewed systematically where less studied E. fusca has been selected for further analysis. Phytochemical investigation yielded five compounds namely; Phaseolin, Phytol, β-amyrin, Lupeol, and Stigmasterol. In-vitro antimalarial drug sensitivity HRP-II ELISA was carried out against chloroquine (CQ) sensitive 3D7 and CQ-resistant Dd2 strains. Extracts showed significant antimalarial activity against 3D7 and Dd2 strains (IC50 4.94 – 22 µg/mL) and these compounds have been reported here for the first time. Molecular docking analysis showed high binding energy (−9.0 ± 0.32 kcal/mole) indicating high degree of interaction between Phaseolin and 14 clinically important Plasmodium falciparum proteins at the active site. Stable interaction was also observed between ligand and protein from molecular dynamics simulation analysis with high free energy (−75.156 ± 11.459) that substantiates the potential of Phaseolin as an antimalarial drug candidate.
REVIEW | doi:10.20944/preprints202110.0243.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: fluorine-18; prosthetic group; 18F-fluoroglycosylation; positron emission tomography; PET
Online: 18 October 2021 (11:10:02 CEST)
In the field of 18F-chemistry for the development of radiopharmaceuticals for positron emission tomography (PET), various labeling strategies by the use of prosthetic groups have been im-plemented, including chemoselective 18F-labeling of biomolecules. Among those, chemoselec-tive 18F-fluoroglycosylation methods focus on the sweetening of pharmaceutical radiochemistry by offering a highly valuable tool for the synthesis of 18F-glycoconjugates with suitable in vivo properties for PET imaging studies. A previous review covered the various 18F-fluoroglycosylation methods that have been developed and applied as of 2014 [Maschauer and Prante, BioMed. Res. Int. 2014, 214748]. This paper is an updated review, providing the recent progress in 18F-fluoroglycosylation reactions and the preclinical application of 18F-glycoconjugates, including small molecules, peptides, and high-molecular-weight proteins.
ARTICLE | doi:10.20944/preprints202109.0188.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: pyrazolo-pyrido-pyrimidines; cytotoxicity; tumor cell lines; SAR; in silico docking.
Online: 10 September 2021 (15:07:59 CEST)
To explore a new set of anticancer agents, a novel series of pyrazolo[4,3-e]pyrido[1,2-a]pyrimidine derivatives 7a-l have been designed and synthesized via cyclocondensation reactions of pyrazolo-enaminone 5 with a series of arylidene malononitriles; compound 5 was obtained from 5-amino-4-cyanopyrazole (3). The structures of the target compounds 7a-l were investigated by spectral techniques and elemental analysis (IR, UV-Vis, 1H NMR, 13C NMR and ESI-MS). All compounds were evaluated for their in vitro cytotoxicity employing a panel of different human tumor cell lines, A375, HT29, MCF7, A2780, FaDu as well as non-malignant NIH 3T3 and HEK293 cells. It has been found that the conjugate 7e was the most active towards many cell lines with EC50 values ranging between 9.1 and 13.5 µM, respectively. Moreover, in silico docking studies of 7e with six anticancer drug targets, i.e. DHFR, VEGFR2, HER-2/neu, hCA-IX, CDK6 and LOX also was performed, in order to gain some insights into their putative mode of binding interaction and to estimate the free binding energy of this bioactive molecule.
ARTICLE | doi:10.20944/preprints202108.0424.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: hydrazone; Candida species; antifungal agents; Candida albicans; Candida glabrata
Online: 23 August 2021 (10:29:47 CEST)
The treatment of benzylidenemalononitriles 3a-c with phenylhydrazines 4a-n in refluxing ethanol did not provide pyrazole derivatives but furnished hydrazones 1a-o. The structure of hydrazones was secured by X-Ray analysis. Newly synthesized hydrazones 1a-o were tested against 8 Candida spp. strains in a dose response assay to determine the minimum inhibitory concentration (MIC99). Five compounds 1c, 1d, 1i, 1k and 1l were identified as promising antifungal agents against Candida spp. (C. albicans SC5314, C. glabrata, C. tropicalis, C. parapsilosis and C. glabrata (R azoles)) with MIC99 values ranging from 16 to 32 µg/mL. To further evaluate the antifungal potential of the active compounds, they have been assayed against a mammalian cell line HEK293 to determine general cell toxicity and on NCI-60 cancer cell lines panel, demonstrating selectivity antifungal activity over cytotoxicity.
ARTICLE | doi:10.20944/preprints202108.0359.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 1, 2, 4-Triazine; Lanosterol 14a-demethylase (CYP51); Drug Resistance; Molecular Docking; Molecular Dynamic Simulation.
Online: 17 August 2021 (12:27:02 CEST)
This research aims to find out whether the synthetic 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a We are interested in using molecular docking and molecular dynamics modelling to investigate the interaction between the derivatives of 1, 2, 4-triazine and the resulting lanosterol 14 - demethylase (CYP51) of Candida albicans The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identifying the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.
ARTICLE | doi:10.20944/preprints202105.0106.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: ecdysterone; metabolites; excretion profile; urinary pharmacokinetics
Online: 6 May 2021 (15:20:04 CEST)
Ecdysterone is a phytosteroid widely discussed for its various pharmacological, growth-promoting and anabolic effects mediated by activation of estrogen receptor beta (ERbeta). Performance-enhancement in sports was demonstrated recently, and ecdysterone was consequently included in the Monitoring Program to detect potential patterns of misuse in sport. Only few studies on the pharmacokinetics of ecdysterone in humans have been reported so far. In this study, post-administration urines in twelve volunteers (single dose of 50 mg of ecdysterone) were analyzed using dilute-and-inject liquid chromatography-tandem mass spectrometry. Identification and quantitation of ecdysterone and of two metabolites, 14-deoxy ecdysterone and 14-deoxy poststerone was achieved. Ecdysterone was the most abundant analyte present in post-administration urines, detected for more than 2 days with a maximum concentration (Cmax) in the 2.8-8.5 h urines (Cmax = 4.4-30.0 µg/mL). The metabolites 14-deoxy ecdysterone and 14-deoxy poststerone were detected later reaching the maximum concentrations at 8.5-39.5 h (Cmax = 0.1-6.0 µg/mL) and 23.3-41.3 h (Cmax = 0.1-1.5 µg/mL), respectively. Cumulative urinary excretion yielded average values of 18%, 2.3% and 1.5% for ecdysterone, 14-deoxy ecdysterone and 14-deoxy poststerone, respectively. Ecdysterone and 14-deoxy ecdysterone were excreted following first order kinetics with half-lives calculated with three hours, while pharmacokinetics of 14-deoxy poststerone needs further evaluation.
COMMUNICATION | doi:10.20944/preprints202104.0518.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: insect neuropeptides; pyrokinins; trans peptide bond; imidazoline ring; SPOS;
Online: 19 April 2021 (21:18:57 CEST)
A facile solid-phase synthetic method for incorporating the imidazoline ring motif, a surrogate for a trans peptide bond, into bioactive peptides is reported. The example described is the synthesis of an imidazoline peptidomimetic analog of an insect pyrokinin neuropeptide via a cyclization reaction of an iminium salt generated from the preceding amino acid and 2,4-diaminopropanoic acid (Dap).
COMMUNICATION | doi:10.20944/preprints202104.0368.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: CySSG; prodrug; glutathione; orally; bioavailable
Online: 14 April 2021 (11:40:14 CEST)
Cysteine-glutathione mixed disulfide (CySSG), a prodrug of glutathione (GSH) --the “Master Antioxidant”, was found to be orally bioavailable in mice, and protected against a toxic dose of acetaminophen. If oral bioavailability can also be demonstrated in humans, this suggests a wide range of applicability for CySSG.
ARTICLE | doi:10.20944/preprints202012.0588.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Trazodone; drug design; dissolution; crystal structure; solid-state NMR (SSNMR) spectroscopy; GIPAW calculation
Online: 23 December 2020 (13:42:36 CET)
New pharmaceutically acceptable salts of trazodone for the treatment of central nervous system disorders are synthesized and described. Each salt (trazodone hydrogen bromide and trazodone 1-hydroxy-2-naphthoate) was obtained by two or three different methods leading to the same crystalline form. Although trazodone salts are poorly crystalline, single-crystal X-ray diffraction data for trazodone 1-hydroxy-2-naphthoate were collected and analyzed as well as compared to the previously described crystal structure of commercially available trazodone hydrochloride. The powder samples of all new salts were characterized by Fourier transform infrared spectroscopy and 13C solid-state nuclear magnetic resonance spectroscopy. Spectroscopic studies were supported by gauge including projector augmented wave (GIPAW) calculations of carbon chemical shielding constants. The main goal of our research was to find salts with better physicochemical properties and to make an attempt to associate them with both the anion structure and the most prominent interactions exhibited by the protonated trazodone cation. The dissolution profiles of trazodone from tablets prepared from various salts with lactose monohydrate were investigated. The studies revealed that salts with simple anions show a fast release of the drug while the presence of more complex anion, more strongly interacting with the cation, effects a slow-release profile of the active substance and can be used for the preparation of the tables with a delay or prolonged mode of action.
ARTICLE | doi:10.20944/preprints202011.0446.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Alkaloids; Anti-Onchocercal; Bisindoles; Docking; Homology Modeling; Monoindoles.
Online: 17 November 2020 (11:13:54 CET)
A new iboga-vobasine-type isomeric bisindole alkaloid named voacamine A (1), along with eight known compounds, voacangine (2), voacristine (3), coronaridine (4), tabernanthine (5), iboxygaine (6), voacamine (7), voacorine (8), and conoduramine (9), were isolated from the stem bark of Voacanga africana. The structures of the compounds were determined by comprehensive spectroscopic analyses (1D- and 2D-NMR). Compounds 1, 2, 3, 4, 6, 7 and 8 were found to inhibit the motility of both the microfilariae (Mf) and adult male worms of Onchocerca ochengi, in a dose-dependent manner, but were only moderately active on the adult female worms upon biochemical assessment at 30 μM drug concentrations. The IC50 values of the isolates are 2.49-5.49 µM for microfilariae and 3.45-17.87 µM for adult males. Homology modeling was used to generate a 3D model of the the O. ochengi thioredoxin reductase target and docking simulation attempted to offer an explanation of the anti-onchocercal structure-activity relationship (SAR) of the isolated compounds. These alkaloids are new potential leads for the development of antifilirial drugs. The results of this study validate the traditional use of V. africana in the treatment of human onchocerciasis.
REVIEW | doi:10.20944/preprints202011.0005.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: aminoacyl-tRNA synthetase, small molecule inhibitors, human diseases
Online: 2 November 2020 (09:09:37 CET)
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for translating amino acids for protein synthesis. Their function in pathogen-derived infectious diseases has been well established, which has led to development of small molecule therapeutics. The applicability of ARS inhibitors for other human diseases such as fibrosis has recently been explored in the clinical setting. There are active studies to find small molecule therapeutics for cancers. Studies on central nervous system (CNS) disorders are burgeoning as well. In this regard, we present a concise analysis of the recent development of ARS inhibitors based on small molecules from the discovery research stage to clinical studies as well as a recent patent analysis from the medicinal chemistry point of view.
REVIEW | doi:10.20944/preprints202010.0551.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: cannabinoids; Δ9-tetrahydrocannabinol; cannabidiol; non-cannabinoids; flavonoids; terpenes; secondary metabolites
Online: 27 October 2020 (11:45:28 CET)
The Cannabis plant (Cannabis sativa L.) produces an estimated 545 chemical compounds of different biogenetic classes. In addition to economic value, many of these phytochemicals have medicinal and physiological activity. The plant is most popularly known for its two most prominent and most studied secondary metabolites— Δ9-Tetrahydrocannabinol (Δ9-THC) and Cannabidiol (CBD). Both Δ9-THC and CBD have a wide therapeutic window across many ailments and form part of a class of secondary metabolites called cannabinoids—of which approximately over 104 exist. This review will focus on non-cannabinoid metabolites of Cannabis sativa that also have therapeutic potential, some of which share medicinal properties similar to those of cannabinoids. The most notable of these non-cannabinoid phytochemicals are flavonoids and terpenes. We will also discuss future directions in cannabis research and development of cannabis-based pharmaceuticals. Caflanone, a flavonoid molecule with selective activity against the human viruses including the coronavirus SARS-COV2, and certain cancers, is one of the most promising non-cannabinoid molecules that is being advanced into clinical trials. As validated by thousands of years of the use of cannabis for medicinal purposes, vast anecdotal evidence abounds on the medicinal benefits of the plant. These benefits are attributed to the many phytochemicals in this plant, including non-cannabinoids. The most promising non-cannabinoids with potential to alleviate global disease burdens are discussed.
ARTICLE | doi:10.20944/preprints202009.0391.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Diabetes mellitus; oxidative stress; alpha-glucosidase; alpha-amylase; Salvia aurita; abietane diterpenes
Online: 17 September 2020 (09:03:16 CEST)
Diabetes mellitus (DM) is one of the most dangerous metabolic diseases with high rate of mortality worldwide. It is well known that insulin resistance and deficiency in insulin production from pancreatic β-cells are the main characteristic of DM. Due to the detrimental side effects of the current treatment, there is a considerable need to develop new effective antidiabetic drugs, especially alpha-glucosidase and alpha-amylase inhibitors with lesser adverse effects. These inhibitors are known to be directly involved in the delay of carbohydrate digestion, resulting in a reduction of glucose absorption rate and consequently reduce the post-prandial raise of plasma glucose, which can reduce the risk of long-term diabetes complications. Hence, natural products are well-known sources for the discovery of new scaffold for drugs discovery, including new antidiabetic drugs. The phytochemical investigation of Salvia aurita collected from Hogobach pass, Eastern Cape, South Africa (SA), yielded four known abietane diterpenes namely carnosol (1), rosmanol (2), 7-methoxyrosmanol (3), 12-methoxycarnosic acid (4) and one flavonoid named 4,7-dimethylapigenin (5). Structural characterization of these isolated compounds was conducted using 1 and 2D NMR, in comparison with reported spectroscopic data. These compounds are reported for the first time from S. aurita. The biological evaluation of the isolated compound against alpha-glucosidase exhibited strong inhibitory activities for 3 and 2 with IC50 values of 4.2 ± 0.7 and 16.4 ± 1.1 µg/mL respectively, while 4 and 1 demonstrated strong alpha-amylase inhibitory activity amongst the isolated compounds with IC50 of 16.2 ± 0.3 and 19.8 ± 1.4 µg/mL. Molecular docking analysis confirms strong inhibitory activity of 3 against alpha-glucosidase. Additionally, excellent antioxidant capacities were displayed by 2, 1 and 3 respectively as ORAC (25789.9 ± 10.5; 23961.8 ± 14.1; 23939.3 ± 2.4) µM TE/g; 1 and 2 as FRAP (3917.8 ± 2.1; 1522.3 ± 0.9) µM AAE/g; 5 and 2 as TEAC (3190.4 ± 2.8; 2055.0 ± 2.6) µM TE/g. The methanolic extract of S. aurita is a rich source of abietane diterpenes with excellent antioxidant and anti-diabetic activities that can be useful to modulate oxidative stress, and might possibly be excellent candidates for the management of diabetes. This is the first scientific report on the phytochemical isolation and biological evaluation of alpha-glucosidase and alpha-amylase inhibitory activities of Salvia aurita.
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: SARS-CoV-2; zinc; zn; zinc-deficiency; cytokine storm
Online: 8 September 2020 (10:09:19 CEST)
Since the discovery of the first reported case with Zinc-deficiency in Iran1 by Prasad et al. in 1961, the knowledge on Zinc has increased significantly. Zinc is the second most abundant common trace mineral in the human body, responsible for vital biological functions from cell growth and development to cell homeostasis and immune response 2,3. Up to a fifth of the global population is estimated to suffer from different degrees of Zinc deficiency4. In the western world, Zinc deficiency is more prevalent among the geriatric population3, vegans/vegetarians, and people with certain underlying conditions4such as liver cirrhosis, inflammatory bowel disease, and various auto-immune disorders4,5. Zinc and Zinc deficiency has been associated with several infectious diseases 2,3. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is responsible for the ongoing pandemic belongs to the family of coronaviruses. SARS-CoV-2 has a high genetic similarity to another family member, SARS-CoV, which caused the first major epidemic of the 21st century6,7. Currently, there is no evidence linking the anti- SARS-CoV-2 response and the element Zinc. Herein and in light of the SARS-CoV-2 pandemic, we marshal the evidence associating the element Zinc with the anti-viral and antibacterial immune response as well as the cytokine storm and lung injury. Such a revisit of the precedent evidence may inspire further investigation assessing the relationship between Zincemia status and the anti-viral response in SARS-CoV-2 patients.
ARTICLE | doi:10.20944/preprints202007.0558.v2
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; protein protein interactions; virtual screening; docking; molecular dynamics; zinc
Online: 2 September 2020 (09:48:48 CEST)
The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: cannabis; cannabinergic; drug; FDA-approved; medical conditions; pharmaceutical-grade; phytocannabinoid
Online: 31 August 2020 (10:38:32 CEST)
Despite the surge in the research of cannabis chemistry and its biological and medical activity, only a few cannabis-based pharmaceutical-grade drugs have been developed and marketed to date. Not many of these drugs are Food and Drug Administration (FDA)-approved and some are still going through regulation processes. Active compounds including cannabinergic compounds (i.e., molecules targeted to modulate the endocannabinoid system) or analogs of phytocannabinoids (cannabinoids produced by the plant) may be developed into single-molecule drugs. However, since in many cases treatment with whole plant extract is preferred over treatment with a single purified molecule, some more recently developed cannabis-derived drugs contain several molecules. Different combinations of active plant ingredients (API) from cannabis with proven synergy may be identified and developed as drugs to treat different medical conditions. However, possible negative effects between cannabis compounds should also be considered, as well as the effect of the cannabis treatment on the endocannabinoid system. FDA registration of single, few or multiple molecules as drugs is a challenging process and certain considerations that should be reviewed in this process, including issues of drug-drug interactions, are also discussed here.
ARTICLE | doi:10.20944/preprints202008.0667.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Ovarian cancer; drug resistance; apoptosis; proteomics; combination; cytotoxicity; artemisinin; oleanolic acid; platinum drugs; cisplatin
Online: 30 August 2020 (12:06:32 CEST)
Background: In the present study, cisplatin, artemisinin and oleanolic acid were evaluated alone and in combination, on human ovarian A2780, A2780ZD0473R and A2780cisR cancer cell lines with aim of overcoming cisplatin resistance and side effects. Methods: Cytotoxicity was assessed by MTT reduction assay. CI values were used as a measure of combined drug effect. MALDI TOF/TOF MS/MS and 2-DE gel electrophoresis were used to identify protein biomarkers in ovarian cancer and to evaluate combination effects. Results: Synergism from combinations was dependent on concentration and sequence of administration. Generally, bolus was most synergistic. 49 proteins differently expressed by 2 ≥ fold were: CYPA, EIF5A1, Op18, p18, LDHB, P4HB, HSP7C, GRP94, ERp57, mortalin, IMMT, CLIC1, NM23, PSA3,1433Z, and HSP90B were down-regulated, whereas hnRNPA1, hnRNPA2/B1, EF2, GOT1, EF1A1, VIME, BIP, ATP5H, APG2, VINC, KPYM, RAN, PSA7, TPI, PGK1, ACTG and VDAC1 were up-regulated, while TCPA, TCPH, TCPB, PRDX6, EF1G, ATPA, ENOA, PRDX1, MCM7, GBLP, PSAT, Hop, EFTU, PGAM1, SERA and CAH2 were not-expressed in A2780cisR cells. The proteins were found to play critical roles in cell cycle regulation, metabolism and biosynthetic processes and drug resistance and detoxification. Conclusion: Results indicate that appropriately sequenced combinations of cisplatin with ART and OA may provide a means to reduce side effects and circumvent platinum resistance.
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: XPAzf; Zn; Cd; GSNO; H2O2; oxidation
Online: 24 August 2020 (09:50:12 CEST)
Tetrathiolate zinc fingers are potential targets of oxidative assault under cellular stress conditions. We used the synthetic 37-residue peptide representing the tetrathiolate zinc finger domain of the DNA repair protein XPA, acetyl-DYVICEECGKEFMSYLMNHFDLPTCDNCRDADDKHK-amide (XPAzf) as a working model to study the reaction of its Zn(II) complex (ZnXPAzf) with hydrogen peroxide and S-nitrosoglutathione (GSNO), as oxidative and nitrosative stress agents, respectively. We also used the Cd(II) substituted XPAzf (CdXPAzf) to assess the situation of cadmium assault, which is accompanied by oxidative stress. Using electrospray mass spectrometry (ESI-MS), HPLC, and UV-vis and circular dichroism spectroscopies we demonstrated that even very low levels of H2O2 and GSNO invariably cause irreversible thiol oxidation and concomitant Zn(II) release from ZnXPAzf. In contrast, CdXPAzf was more resistant to oxidation, demonstrating the absence of synergy between cadmium and oxidative stresses. Our results indicate that GSNO cannot act as a reversible modifier of XPA, and rather has a deleterious effect on DNA repair.
ARTICLE | doi:10.20944/preprints202008.0306.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Glycyrrhiza uralensis; Glycyrol; Liquiritigenin; cholinesterases; human monoamine oxidases; kinetics; docking simulation.
Online: 13 August 2020 (12:11:26 CEST)
Eight compounds were isolated from the roots of Glycyrrhiza uralensis and tested for cholinesterase (ChE) and monoamine oxidase (MAO) inhibitory activities. Glycyrol (GC) effectively inhibited butyrylcholinesterase (BChE) and acetylcholinesterase (AChE) with IC50 values of 7.22 and 14.77 µM, respectively, and also moderately inhibited MAO-B (29.48 µM). Six of the other seven compounds only weakly inhibited AChE and BChE, whereas liquiritin apioside moderately inhibited AChE (IC50 = 36.68 µM). Liquiritigenin (LG) potently inhibited MAO-B (IC50 = 0.098 µM) and MAO-A (IC50 = 0.27 µM), and liquiritin, a glycoside of LG, weakly inhibited MAO-B (> 40 µM). GC was a reversible, noncompetitive inhibitor of BChE with a Ki value of 4.47 µM, and LG was a reversible competitive inhibitor of MAO-B with a Ki value of 0.024 µM. Docking simulations showed that the binding affinity of GC for BChE (-7.8 kcal/mol) was greater than its affinity for AChE (-7.1 kcal/mol), and suggested that GC interacted with BChE at Thr284 and Val288 by hydrogen bonds (distances: 2.42 and 1.92 Å, respectively) beyond the ligand binding site of BChE, but that GC did not form hydrogen bond with AChE. The binding affinity of LG for MAO-B (-8.8 kcal/mol) was greater than its affinity for MAO-A (-7.9 kcal/mol). These findings suggest GC and LG should be considered promising compounds for the treatment of Alzheimer’s disease with multi-targeting activities.
ARTICLE | doi:10.20944/preprints202008.0112.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: AKT/PI3K signaling pathway; apoptosis; human hepatocarcinoma HepG2 cells; migration activity; proliferation; oxidative stress; ROS level; uvaol
Online: 5 August 2020 (05:58:26 CEST)
Natural products have a significant role in the development of new drugs, being relevant the pentacyclic triterpenes extracted from Olea europaea. Anticancer effect of uvaol, a natural triterpene, has been scarcely studied. The aim of this study was to understand the anticancer mechanism of uvaol in HepG2 cell line. Cytotoxicity results showed a selectivity effect of uvaol with higher influence in HepG2 than WRL68 cells used as control. Uvaol presented anti-migratory capacity in HepG2, supported by the morphological changes and higher HSP-60 expression. This compound also induced arrest in G0/G1 phase and an increase in apoptosis rate. These results are supported by decreased Bcl-2 expression and down-regulation of AKT/PI3K signaling pathway. A reduction in reactive oxygen species levels in HepG2 cells was observed. Altogether, results showed anti-proliferative and pro-apoptotic effect of uvaol on hepatocellular carcinoma, constituting an interesting challenge in the development of new treatments against this type of cancer.
ARTICLE | doi:10.20944/preprints202008.0077.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: anti-oxidant activity; anti-oxidant enzymes, anti-proliferative activity; maslinic acid; melanoma; Olea europaea; ROS levels
Online: 4 August 2020 (04:57:13 CEST)
Maslinic acid (MA) is a natural triterpene from Olea europaea whose pharmacological functions have been showed. The objective of this study was to examine MA effect on cell viability (by MTT assay), reactive oxygen species (ROS levels, by flow cytometry) and key anti-oxidant enzyme activities (by spectrophotometry) in murine skin melanoma (B16F10) cells compared to healthy cells (A10). MA induced cytotoxic effects in cancer cells (IC50 42 µM) whereas no effect was found in A10 cells treated with MA (up to 210 µM). In order to produce a stress situation in cells, 0.15 mM of H2O2 were added. Under stressful conditions, MA protected both cell lines against oxidative damage, decreasing intracellular ROS, being higher in B16F10 than in A10 cells. The treatment with H2O2 and without MA produced different responses in anti-oxidant enzymes activities depending on cell line. In A10 cells, all enzymes were up-regulated, but in B16F10 cells only superoxide dismutase, glutathione S-transferase and glutathione peroxidase increased their activities. MA restored the enzyme activities to similar levels than control group in both cell lines, highlighting that in A10 cells the highest MA doses induced values lower than control. Overall, these findings demonstrate the great anti-oxidant capacity of MA.
ARTICLE | doi:10.20944/preprints202007.0495.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: In silico target prediction; dihydrochalcones; SEA; SwissTargetPrediction; SuperPred; polyphamracology; virtual screening
Online: 21 July 2020 (13:43:40 CEST)
Natural products comprise a rich reservoir for innovative drug leads and are a constant source of bioactive compounds. To find pharmacological targets for new or already known natural products using modern computer-aided methods is a current endeavor in drug discovery. Nature’s treasures, however, could be used more effectively. Yet, reliable pipelines for large scale target prediction of natural products are still rare. We have developed an in silico workflow consisting of four independent, stand-alone target prediction tools and evaluated its performance on dihydrochalcones (DHCs) – a well-known class of natural products. Thereby, we revealed four previously unreported protein targets for DHCs, namely 5-lipoxygenase, cyclooxygenase-1, 17β- hydroxysteroid dehydrogenase 3, and aldo-keto reductase 1C3. Moreover, we provide a thorough strategy on how to perform computational target prediction and guidance on using the respective tools.
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 3,4-dimethoxy-β-nitrostyrene derivatives; antimicrobial agent; PTP1B; molecular docking
Online: 20 July 2020 (11:31:48 CEST)
A derivative series of 3,4-dimethoxy-β-nitrostyrene were synthesized and identified including new compound 6. The effect of antimicrobial activity of 3,4-alkyloxy modification of β-nitrostyrene was investigated. A molecular docking was also performed to obtain information about their interactions with Protein Tyrosine Phosphatase 1B (PTP1B). PTP1B containing cysteine 215 and arginine 221 as essential active residues plays a key role in signaling pathways that regulate various cell functions of microorganisms, which also act as negative regulator in signaling pathways of insulin that are involved in type 2 diabetes and other metabolic diseases. Compound 5 and 6 were the most potent as fragment of PTP1B inhibitor based on molecular docking, but compound 5 was more effective against Candida albicans. These compounds interact with serine 216 and arginine 221 residues. However, further research is needed to investigate their potential medicinal use.
ARTICLE | doi:10.20944/preprints202007.0424.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 4-Phenylbutyric acid; Colon-targeted drug delivery; Colitis; Prodrug; ER stress; Chemical chaperone
Online: 19 July 2020 (19:15:20 CEST)
An elevated level of endoplasmic reticulum (ER) stress is considered an aggravating factor for inflammatory bowel disease (IBD). To develop an ER stress attenuator that is effective against colitis, 4-phenylbutyric acid (4-PBA), a chemical chaperone that alleviates ER stress, was conjugated with acidic amino acids to yield a 4-PBA-glutamic acid conjugate (PBA-GA) and a 4-PBA-aspartic acid conjugate (PBA-AA). The PBA derivatives were converted to 4-PBA in the cecal contents, where the conversion was greater with PBA-GA. After oral administration of PBA-GA (oral PBA-GA), millimolar levels of PBA were accumulated in the cecum, whereas 4-PBA was not detected in the blood, indicating the targeting of PBA-GA to the large intestine. At concentrations in the cecum achievable by oral PBA-GA, 4-PBA effectively attenuated ER stress in human colon epithelial cells. In 2,4-dinitrobenzenesulfonic acid-induced colitis in rats, oral PBA-GA alleviated the damage and inflammation in the colon. Moreover, oral PBA-GA substantially reduced the elevated levels of ER stress marker proteins in the inflamed colon. Moreover, PBA-GA was as effective as the currently used anti-IBD drug, sulfasalazine. In conclusion, PBA-GA is a colon-targeted prodrug of 4-PBA and is effective against rat colitis probably through the attenuation of ER stress in the inflamed colon.
ARTICLE | doi:10.20944/preprints202007.0350.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 3,4-DHPEA-EA; C2C12 myocytes; olive oil; antioxidant; skeletal muscle
Online: 16 July 2020 (12:56:25 CEST)
Oleuropein, glycosylated secoiridoid present in olive leaves is known to be an important antioxidant phenolic compound. We studied the antioxidant effect of low doses of oleuropein aglycone (3,4-DHPEA-EA) and oleuropein aglycone peracetylated (3,4-DHPEA-EA(P)) in murine C2C12 myocytes treated with hydrogen peroxide (H2O2). Both compounds were used at a concentration of 10 μM and were able to inhibit cell death induced by the H2O2 treatment, with 3,4-DHPEA-EA(P) being more. Under our experimental conditions, H2O2 efficiently induced the phosphorylated-active form of JNK and of its downstream target c-Jun. We demonstrated, by Western blot analysis, that 3,4-DHPEA-EA(P) was efficient in inhibiting the phospho-active form of JNK. This data suggests that the growth arrest and cell death of C2C12 proceeds via the JNK/c-Jun pathway. Moreover, we demonstrated that 3,4-DHPEA-EA(P) affects the myogenesis of C2C12 cells; because MyoD mRNA levels and the differentiation process are restored with 3,4-DHPEA-EA(P) after treatment. Overall, the results indicate that 3,4-DHPEA-EA(P) prevents ROS-mediated degenerative process in a genomic and epigenomic manner by functioning as an efficient antioxidant.