ARTICLE | doi:10.20944/preprints202007.0558.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; protein protein interactions; virtual screening; docking; molecular dynamics; zinc
Online: 23 July 2020 (12:27:23 CEST)
The outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19, has caused a global health crisis. Unfortunately, only a few treatments have proved to be effective, and their worldwide distribution remains as a challenge. Due to the urgency of the situation, drug repurposing remains as the fastest way to identify possible therapeutic options. Recent studies have shown that the stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS coronavirus is a valid strategy to inhibit viral replication, but no study up to date has been done in SARS-CoV-2. In this work, a novel protocol for the discovery of PPIs stabilizers is presented and applied to SARS-CoV-2 N protein with a drug repurposing approach. This enabled us to identify that catechin, a structural motif present in widely distributed natural products, might be a privileged scaffold for this type of stabilization. Since many of the compounds presented in this work are generally considered nutraceuticals and have also been exhaustively studied, even though some of them contain PAINS substructures, could be good candidates for the SARS-CoV-2 nucleocapsid inhibition and be considered for further in vitro testing against COVID-19.
Tue, 21 July 2020
ARTICLE | doi:10.20944/preprints202007.0495.v1
Subject: Chemistry, 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.
Mon, 20 July 2020
Subject: Chemistry, 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.
Sun, 19 July 2020
ARTICLE | doi:10.20944/preprints202007.0424.v1
Subject: Chemistry, 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.
Thu, 16 July 2020
ARTICLE | doi:10.20944/preprints202007.0350.v1
Subject: Chemistry, 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.
Sun, 12 July 2020
Online: 12 July 2020 (12:19:00 CEST)
Background and Objectives: Therapeutic applications of stem cells are considered as an appropriate alternative in the treatment of many diseases, but the reduction in their survival after transplantation limit their clinical application that can be enhanced by chemical preconditioning. The present study investigated the effect of all-trans retinoic acid on survival, migration and angiogenesis of adipose derived stem cells in amelioration of cisplatin-induced acute kidney injury (AKI). Methods: Sprague-Dawley rats (180–220 g) (n=150) were divided into 5 major groups, 30 rats each. Group I: (negative control group). Group II: (Cisplatin ‘CIS’-treated group). Group III: (cisplatin and all-trans retinoic acid group). Group IV: (cisplatin and MSCs group). Group V: (cisplatin, ATRA and MSCs group). Ten rats were sacrificed at different time intervals in all groups at days 3, 7 and 11. Kidney tissue and blood samples were obtained. Renal function tests and oxidative stress parameters were studied; Molecular studies in addition to histopathological scoring systems for renal injury were analyzed. Results: ADMSCs isolation and characterization was done. ADMSCs preconditioning with ATRA enhanced the kidney function after cisplatin through decreasing serum creatinine and microalbuminuria, increasing creatinine clearance and return the antioxidant balance by decreasing NO and increasing SOD. ATRA also could reduce the inflammation, apoptosis and stimulate the angiogenesis by decreasing TGFB1, caspase-3 and increasing HIF1. The use of ADMSCs pretreated with ATRA was associated with significantly regenerative changes in kidney. Conclusion: ATRA increased ADMSCs viability and efficacy that leaded to amelioration of kidney functions through the reduction of oxidative stress, increase of antioxidant enzyme activity and reduction of apoptosis.
Sat, 11 July 2020
REVIEW | doi:10.20944/preprints202007.0222.v1
Subject: Chemistry, Medicinal Chemistry Keywords: ROS; oxidative stress; catalytic antioxidants; superoxide dismutase; catalase; peroxidase; manganese; salen-type ligands; animal studies
Online: 11 July 2020 (03:30:41 CEST)
Manganosalen complexes are coordination compounds that possess a chelating salen-type ligand, a class of bis-Schiff bases obtained by condensation of salicylaldehyde and a diamine. They may act as catalytic antioxidants mimicking both the structure and the reactivity of the native antioxidant enzymes active site. Thus, manganosalen complexes have shown to exhibit superoxide dismutase, catalase, and glutathione peroxidase activities, and they could potentially facilitate the scavenging of excess ROS, thereby restoring the redox balance in the damaged cells and organs. Initial catalytic studies compared the potency of these compounds as antioxidants in terms of rate constants of the chemical reactivity against ROS, giving catalytic values approaching and even exceeding that of the native antioxidative enzymes. Although most of these catalytic studies lack of biological relevance, subsequent in vitro studies have confirmed the efficiency of many manganosalen complexes in oxidative stress models. These synthetic catalytic scavengers, cheaper than natural antioxidants, have accordingly attracted intensive attention for the therapy of ROS-mediated injuries. The aim of this review is to focus on in vivo studies performed on manganosalen complexes and their activity on the treatment of several pathological disorders associated with oxidative damage. This disorders, ranging from the prevention of fetal malformations to the extension of lifespan, include neurodegenerative, inflammatory and cardiovascular diseases, tissue injury, and other damages related to liver, kidney or lungs.
Tue, 30 June 2020
ARTICLE | doi:10.20944/preprints202006.0358.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Enzyme inhibition; Secondary Metabolites; In-silico Analysis; Molecular docking; Drug candidates
Online: 30 June 2020 (08:11:28 CEST)
Metabolic enzymes are often targeted for drug development programs of metabolic diseases such as diabetes and its complications. Many secondary metabolites isolated from natural products have shown therapeutic action against these enzymes. However, some commercially available synthetic drugs have shown unfriendly impacts with various side effects. Thus, this research has focused on a comprehensive study of secondary metabolites showing better inhibitory activities towards metabolic enzymes such as α-amylase, α-glucosidase, aldose reductase, and lipase. Further receptor-based virtual screening was performed against the various secondary metabolites database designed in-silico. Using Gold combined with subsequent post-docking analyses, the score was obtained as methyl xestospongic ester (Gold score 65.83), 2,″4″-O-diacetylquercitrin (Gold score 65.15), kaempferol-3-O-neohesperidoside (Gold score 53.37) and isosalvianolic acid C methyl ester (Gold score 53.44) for lipase, aldol reductase, α-amylase, and α-glucosidase, respectively. Besides, vitexin and isovitexin for α-amylase; N-trans-Caffeoyl-tyramin for α-glucosidase; purpurolide F and schaftoside for lipase; acteoside and orientin for aldose reductase could be potential drugs for respective enzymes based on in-silico analyses, supported by experimental IC50 values reported. They could bind to the competitive sites of the various targets of metabolic enzymes, and finally, toxicity analysis using ProTox-II was also performed.
Sun, 28 June 2020
ARTICLE | doi:10.20944/preprints202006.0326.v1
Subject: Chemistry, Medicinal Chemistry Keywords: 2019-nCoV; 3CLpro protein; Cat's Claw; Uncaria tomentosa; Molecular Modeling
Online: 28 June 2020 (09:05:54 CEST)
COVID-19 is a novel severe acute respiratory syndrome coronavirus. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CLpro) bound to a synthetic inhibitor which represents a major druggable target. The druggability of Mpro could be used for discovering drugs to treat coronavirus disease 2019. It was carried out a multi-level computational study to evaluate the potential anti-viral properties of the components of the medicinal herb Uncaria tomentosa (Cat´s claw) focusing on the inhibition of Mpro. The in-silico approach starts with protein-ligand docking of 26 Cat’s claw key components followed by ligand pathway calculations, molecular dynamics simulations and MM-GBSA calculation of the free energy of binding for the best docked candidates. The structural bioinformatics approaches led to the identification of three bioactive compounds of Uncaria tomentosa (Speciophylline, Cadambine and Proanthocyanidin B2) with potential therapeutic effects by strong interaction with 3CLpro. Additionally, in silico drug-likeness indices for these components were calculated and show good predicted therapeutic profiles of these phytochemicals. Our findings suggest the potential effectiveness of Cat's claw as complementary and/or alternative medicine for COVID-19 treatment.
Fri, 24 April 2020
ARTICLE | doi:10.20944/preprints202004.0448.v1
Subject: Chemistry, Medicinal Chemistry Keywords: acetyleugenol; Acacia nilotica; anti-tuberculosis; Serine/Threonine kinases; multi-drug resistant TB
Online: 24 April 2020 (14:12:33 CEST)
Acetyleugenol is a phytochemical compound with broad effect against infectious diseases and tumors. Here, we extracted, characterized and elucidated the structure of acetyeugenol, for the first time, from the leaves of Acacia nilotica (L.)―a well-known medicinal plant. The broad antibacterial potential of acetyleugenol was first confirmed against seven bacterial pathogenic isolates with best activity against Proteus sp., Salmonella typhi, Staphylococcu aureus, and Streptococcus pneumonia, which showed similar or better zone of inhibition to that of the control amoxicillin. To further investigate its effect against Mycobacterium tuberculosis, acetyleugenol and its indole and phenyl analogs were subjected to molecular docking experiments against two potential tuberculosis drug targets―MtPknE and MtPknB Ser/Thr protein kinases. The results reveal that all of the analogs have improved docking scores comparing to the acetyleugenol. The indole analogs EUG-1 and EUG-3 were more effective with better docking scores for MtPknE with –11.08 and –10.05 kcal/mol, respectively. Similar results were obtained for the MtPknB. In contrast, only the EUG-2 phenyl analog has given rise to similar docking scores for both targets. This opens the door for further comprehensive studies on these acetyleugenol analogs with in vitro and in vivo experiments to validate and get more insights into their mechanisms of action.
Sun, 19 April 2020
ARTICLE | doi:10.20944/preprints202004.0334.v1
Subject: Chemistry, Medicinal Chemistry Keywords: SARS-COV-2; folding/unfolding; antiparasitic; molecular docking; molecular dynamics; COVID-19; Ivermectin
Online: 19 April 2020 (06:56:09 CEST)
The global pandemic caused by the new SARS-COV-2 coronavirus makes it necessary to search for drugs for its control. Within of this research it has been known that the ivermectin drug, a FDA-approved drugs which is formulated as an 80:20 mixture of ivermectin B1a and B1b and used commonly for parasitic infections, has an inhibitory effect on viruses, includes SARS-COV-2 at in vitro level. In the particular case of SARS-COV-2 its mechanism of action remains elusive and controversial. Interestingly, the energy of interaction of ivermectin with any of the proteins the SARS-CoV-2 and the possible structural alterations at the protein level that this drug can cause have not been reported. In this sense, we carried out a bioinformatics study with docking strategies and molecular dynamics to predict the binding and disturbance induced by ivermectin in proteins associated with SARS-CoV-2. We use DockThor and Molegro docking scores. The DockThor server and myPresto software were used to build complexes and dynamics studies, respectively. The results obtained suggested that ivermectin is capable of docking with the 3CL protease and the HR2 domain, and may promote structural changes in these proteins by inducing unfolding/folding. Specifically, ivermectin brings protease to a significantly more deployed conformational state and the HR2 domain to a more compact state compared to the native state. Finally, it is shown that B1a and B1b macrocyclic lactones have a behavior different from to each target protein. These results suggest a possible inhibitory effect against SARS-CoV-2 due to a synergistic role of this drug to spontaneously bind to two important proteins involve in the proliferation of this virus. However, more studies are required on this possible mechanism of action.
Tue, 7 April 2020
ARTICLE | doi:10.20944/preprints202004.0084.v1
Subject: Chemistry, Medicinal Chemistry Keywords: in silico repositioning; dual inhibitor; Covid-19; 3CLpro; PLpro; remdesivir
Online: 7 April 2020 (10:44:11 CEST)
Aims: In late December 2019, early reports predicted the onset of a potential Coronavirus outbreak in china, given the estimate of a reproduction number for the 2019 Novel Coronavirus (COVID-19). Because of high ability of transmission and widespread prevalence, the mortality of COVID-19 infection is growing fast worldwide. Absent of an anti-COVID-19 has put scientists on the urge to repurpose already approved therapeutics or to find new active compounds against coronavirus. Here in this study, a set of computational approaches were performed in order to repurpose antivirals for dual inhibition of the frontier proteases involved in virus replication, papain-like protease (PLpro; corresponding to nsp3) and a main protease (Mpro), 3C‑like protease (3CLpro; corresponding to nsp5). Materials and Methods: In this regard, a rational virtual screening procedure including exhaustive docking techniques was performed for a database of 160 antiviral agents over 3CLpro and PLpro active sites of SARS-CoV-2. The compounds binding energies and interaction modes over 3CLpro and PLpro active sites were analyzed and ranked with the aid of free Gibbs binding energy. The most potent compounds, based on our filtering process, are then proposed as dual inhibitors of SARSC-CoV-2 proteases. Key findings: Accordingly, seven antiviral agents including two FDA approved (Nelfinavir, Valaganciclovir) and five investigational compounds (Merimepodib, Inarigivir, Remdesivir, Taribavirine and TAS106-106) are proposed as potential dual inhibitors of the enzymes necessary for RNA replication in which Remdesivir as well as Inagrivir have the highest binding affinity for both of the active sites. Significance: The mentioned drug proposed to inhibit both PLpro and 3CLpro enzymes with the aim of finding dual inhibitors of SARSC-CoV-2 proteases.
ARTICLE | doi:10.20944/preprints202004.0079.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; Nigella Sativa; 6LU7; 2GTB; molecular docking; MOE software
Online: 7 April 2020 (08:58:42 CEST)
The spread of the global COVID-19 pandemic, the lack of specific treatment and the urgent situation requires use of all resources to remedy this scourge. In the present study, using molecular docking, we identify new probable inhibitors of COVID-19 by molecules from Nigella sativa L, which is highly reputed healing herb in North African societies and both Islamic and Christian traditions. The discovery of the Mpro protease structure in COVID-19 provides a great opportunity to identify potential drug candidates for treatment. Focusing on the main proteases in CoVs (3CLpro/Mpro) (PDB ID 6LU7 and 2GTB); docking of compounds from Nigella Sativa and drugs under clinical test was performed using Molecular Operating Environment software (MOE). Nigelledine docked into 6LU7 active site gives energy complex about -6.29734373 Kcal/mol which is close to the energy score given by chloroquine (-6.2930522 Kcal/mol) and better than energy score given by hydroxychloroquine (-5.57386112 Kcal/mol) and favipiravir (-4.23310471 kcal/mol). Docking into 2GTB active site showed that α- Hederin gives energy score about-6.50204802 kcal/mol whcih is better energy score given by chloroquine (-6.20844936 kcal/mol), hydroxychloroquine (-5.51465893 kcal/mol)) and favipiravir (-4.12183571kcal/mol). Nigellidine and α- Hederin appeared to have the best potential to act as COVID-19 treatment. Further, researches are necessary to testify medicinal use of identified and to encourage preventive use of Nigella Sativa against coronavirus infection.
Wed, 25 March 2020
ARTICLE | doi:10.20944/preprints202003.0372.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; SARS-CoV-2; Marine natural product; Virtual screening; Docking
Online: 25 March 2020 (08:23:57 CET)
The current emergency due to the worldwide spread of the COVID-19 caused by the new SARS-CoV-2 is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness was not yet assessed. The main protease (Mpro) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpro inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpro inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.
Sat, 29 February 2020
ARTICLE | doi:10.20944/preprints202002.0453.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Michael acceptor; safe covalent drugs; oxidative stress inducers; trans-cinnamaldehyde; curcumin; colorectal cancer
Online: 29 February 2020 (04:22:03 CET)
Curcumin and trans-cinnamaldehyde are acrolein-based Michael acceptor compounds that are commonly found in domestic condiments, and known to cause cancer cell death via redox mechanisms. Based on the structural features of these compounds we designed and synthesized several 2-cinnamamido-N-substituted-cinnamamide (bis-cinnamamide) compounds. One of the derivatives, (Z)-2-[(E)-cinnamamido]-3-phenyl-N-propylacrylamide 1512 showed a moderate antiproliferative potency (HCT-116 cell line inhibition of 32.0 µM), good selectivity profile (no inhibition of normal cell lines), and proven cellular activities leading to apoptosis. SAR studies led to more than 10-fold increase in activity. Our most promising compound, [(Z)-3-(1H-indol-3-yl)-N-propyl-2-[(E)-3-(thien-2-yl)propenamido)propenamide] 4112 killed colon cancer cells at IC50 = 0.89 µM (Caco-2), 2.85 µM (HCT-116) and 1.65 µM (HT-29), while exhibiting much weaker potency on C-166 and BHK normal cell lines (IC50 = 71 µM and 77.6 µM, respectively). Cellular studies towards identifying the compounds mechanism of cytotoxic activities revealed that apoptotic induction occurs in part as a result of oxidative stress. Importantly, the compounds showed inhibition of cancer stem cells that are critical for maintaining the potential for self-renewal and stemness. The results presented here show discovery of covalently-acting Michael addition compounds that potently kill cancer cells by a defined mechanism, with minimal effect on normal noncancerous cell.
Fri, 28 February 2020
ARTICLE | doi:10.20944/preprints202002.0438.v1
Subject: Chemistry, Medicinal Chemistry Keywords: COVID-19; Simeprevir; Protease inhibitor; Virtual screening; Docking
Online: 28 February 2020 (13:14:38 CET)
Coronavirus disease 2019 (COVID-19) has been first appeared in Wuhan, China but its fast transmission, led to its widespread prevalence in various countries and make it a global concern. In addition, lack of a definitive treatment is another concern that needs to be attention. Researchers have come up with several options, which are not certain, but protease inhibitor and some antiviral agent are in the forefront. In this study a virtual screening procedure employing docking of different databases including 1615 FDA approved drugs was used to identify new potential small molecule inhibitors for protease protein of COVID-19. The docking result indicates that among all, simeprevir (Hepatitis C virus (HCV) NS3/4A protease inhibitor) could fit well to the binding pocket of protease and because of some other positive features including ADME profile, might be a helpful treatment option for COVID-19.
Wed, 19 February 2020
REVIEW | doi:10.20944/preprints202002.0271.v1
Subject: Chemistry, Medicinal Chemistry Keywords: composites; nanoparticles; photodynamic therapy; photosensitizer; titanium dioxide
Online: 19 February 2020 (10:44:08 CET)
Metallic nanoparticles (NPs), among polymeric NPs, liposomes, micelles, quantum dots, dendrimers, or fullerenes, are becoming more and more important due to their potential use in the novel medical therapies. Titanium dioxide (titanium(IV) oxide, titania, TiO2) is an inorganic compound that owes its recent rise in scientific interest to photoactivity. After the illumination in aqueous media with UV light, TiO2 produces an array of reactive oxygen species (ROS). The capability to produce ROS and thus induce cell death has found application in the photodynamic therapy (PDT) for the treatment of a wide range of maladies, from psoriasis to cancer. Titanium dioxide NPs were studied as photosensitizing agents in the treatment of malignant tumors as well as in photodynamic inactivation of antibiotic-resistant bacteria. Both TiO2 NPs themselves, as well as their composites with other molecules, can be successfully used as photosensitizers in PDT. Moreover, various organic compounds can be grafted on TiO2 NPs, leading to hybrid materials. These nanostructures can reveal increased light absorption allowing their further use in targeted therapy in medicine. In order to improve efficient anticancer therapy, many approaches utilizing titanium dioxide were tested. The most significant studies are discussed in this review.
Mon, 27 January 2020
REVIEW | doi:10.20944/preprints202001.0324.v1
Subject: Chemistry, Medicinal Chemistry Keywords: natural products; sirtuin; drug discovery; epigenetics; structure–activity relationship
Online: 27 January 2020 (09:21:29 CET)
Natural products have been used for the treatment of human diseases since ancient history. Over time, due to the lack of precise tools and techniques for the separation, purification, and structural elucidation of active constituents in natural resources there has been a decline in financial support and efforts in characterization of natural products. Advances in the design of chemical compounds and the understanding of their functions is of pharmacological importance for the biomedical field. However, natural products regained attention as sources of novel drug candidates upon recent developments and progress in technology. Natural compounds were shown to bear an inherent ability to bind to biomacromolecules and cover an unparalleled chemical space in comparison to most libraries used for high-throughput screening. Thus, natural products hold a great potential for the drug discovery of new scaffolds for therapeutic targets such as Sirtuins. Sirtuins are Class III histone deacetylases that have been linked to many diseases such as Parkinson`s disease, Alzheimer’s disease, type II diabetes, and cancer linked to aging. In this review, we examine the revitalization of interest in natural products for drug discovery and discuss natural product modulators of Sirtuins that could serve as a starting point for the development of isoform selective and highly potent drug-like compounds.
Fri, 24 January 2020
ARTICLE | doi:10.20944/preprints202001.0279.v1
Subject: Chemistry, Medicinal Chemistry Keywords: NS3 inhibitors; allosteric inhibitors; NS4A; peptidomimetics; imidazole; hepatitis C virus; molecular dynamics; Flaviviridae; DSLS; binding assay
Online: 24 January 2020 (11:11:46 CET)
The non-structural protein NS3/4A protease is a critical factor for hepatitis C virus (HCV) maturation that requires activation by NS4A. Synthetic peptide mutants of NS4A were found to inhibit NS3 function. The bridging from peptide inhibitors to heterocyclic peptidomimetics of NS4A has not been in consideration in literature, and therefore, we decided to explore this strategy to develop a new class of NS3 inhibitors. In this report, a structure-based design approach was used to convert the bound form of NS4A into 1H-imidazole-2,5-dicarboxamide derivatives as first generation peptidomimetics. This scaffold mimics the buried amino acid sequence Ile-25` to Arg-28` at the core of NS4A21`-33` needed to activate the NS3 protease. Some of the synthesized MOC compounds were able to compete with and displace NS4A21`-33` for binding to NS3. For instance, N5-(4-guanidinobutyl)-N2-(n-hexyl)-1H-imidazole-2,5-dicarboxamide (MOC-24) inhibited the binding of NS4A21`-33` with a competition IC50 of 1.9 ± 0.12 µM in a fluorescence anisotropy assay, stabilized the denaturation of NS3 by increasing the aggregation temperature by ΔTagg 0.6 ± 0.140 ℃. MOC-24 also inhibited NS3 protease activity in a fluorometric assay. Molecular dynamics simulations rationalized the structure-activity relationship (SAR) differences between the active MOC-24 and the inactive MOC-26. Our data shows that MOC compounds are possibly the first examples of NS4A peptidomimetics that demonstrated promising activities against NS3 proteins.
Fri, 17 January 2020
ARTICLE | doi:10.20944/preprints202001.0182.v1
Subject: Chemistry, Medicinal Chemistry Keywords: dinoflagellate; Karenia mikimotoi; glycolipids; monogalactosyldiacylglycerol; monogalactosylmonoacylglycerol; polyunsaturated fatty acid methyl ester; Staphylococcus aureus; Escherichia coli; Candida albicans; anti-inflammatory activity
Online: 17 January 2020 (09:18:08 CET)
A New monogalactosyldiacylglycerol (MGDG), a known monogalactosylmonoacylglycerol (MGMG) and a known polyunsaturated fatty acid methyl ester (PUFAME) were isolated from the marine dinoflagellate Karenia mikimotoi. The planar structure of the glycolipids was elucidated using MS and NMR spectroscopic analyses and comparisons to the known glycolipid to confirm its structure. The isolation of PUFAME strongly supports the polyunsaturated fatty acid fragment of these glycolipids. The relative configuration of the sugar was deduced by comparisons of 3JHH values and proton chemical shifts with those of known glycolipids. All isolated compounds MGDG, MGMG and PUFAME (1-3) were evaluated for their antimicrobial and anti-inflammatory activity. All compounds modulated macrophage responses, with compound 3 exhibiting the greatest anti-inflammatory activity.
Thu, 9 January 2020
Subject: Chemistry, Medicinal Chemistry Keywords: high-frequency near-infrared diode laser; osteoarthritis; inflammation; matrix metalloproteinase; human chondrocyte
Online: 9 January 2020 (12:22:18 CET)
High-frequency near-infrared diode laser provides high peak output, low heat accumulation, and efficient biostimulation. Although these characteristics are considered suitable for osteoarthritis (OA) treatment, the effect of high-frequency near-infrared diode laser in in vitro or in vivo OA models has not yet been reported. Therefore, we aimed to assess the biological effects of high-frequency near-infrared diode laser irradiation on IL-1β-induced chondrocyte inflammation in an in vitro OA model. Normal Human Articular Chondrocyte-Knee (NHAC-Kn) cells were stimulated with human recombinant IL-1β and irradiated with high-frequency near-infrared diode laser (910 nm, 4 or 8 J/cm2). The mRNA and protein expression of relevant inflammation- and cartilage destruction-related proteins was analyzed. IL-1β treatment significantly increased the mRNA levels of IL-1β, IL-6, TNF-α, MMP-1, MMP-3, and MMP-13. High-frequency near-infrared diode laser irradiation significantly reduced the IL-1β-induced expression of IL-1β, IL-6, TNF-α, MMP-1, and MMP-3. Similarly, high-frequency near-infrared diode laser irradiation decreased the IL-1β-induced increase in protein expression and secreted levels of MMP-1 and MMP-3. These results highlight the therapeutic potential of high-frequency near-infrared diode laser in OA.
ARTICLE | doi:10.20944/preprints202001.0081.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Berberine; Lipophilic substituent; Anti-cancer activity; Photocytotoxicity; Reactive oxygen species
Online: 9 January 2020 (11:30:40 CET)
The objective of this study was to synthesize 9-/13-position substituted berberine derivatives and evaluated their cytotoxic and photocytotoxic effects against three human cancer cell lines. Among all the synthesized compounds, 9-O-dodecyl- (5e), 13-dodecyl- (6e) and 13-O-dodecyl-berberine (7e) exhibited stronger growth inhibition against three human cancer cell lines, (HepG2, HT-29 and BFTC905), in compare with structurally related berberine (1). These three compounds also showed the photocytotoxicity in human cancer cells in a concentration-dependent and light dose-dependent manner. Through flow cytometry analysis, we found out a lipophilic group at 9-/13-position of berberine may have facilitated its penetration into test cell and hence enhanced its photocytotoxicity on human liver cancer cell HepG2. Further, in cell cycle analysis, 5e, 6e and 7e induced HepG2 cells to arrest at S phase and caused apoptosis upon irradiation. In addition, photodynamic treatment of berberine (1) and its derivatives 5e, 6e and 7e again showed a significant photocytotoxic effects on HepG2 cells, induced remarkable cell apoptosis, greatly increased intracellular ROS level and the loss of mitochondrial membrane potential. These results over and again confirmed that berberine derivatives 5e, 6e and 7e greatly enhanced photocytotoxicity. Taking together, the test data led us to conclude that berberine derivatives with a dodecyl group at 9-/13-position could be great candidates for the anti-liver cancer medicines developments.
Sun, 29 December 2019
ARTICLE | doi:10.20944/preprints201912.0387.v1
Subject: Chemistry, Medicinal Chemistry Keywords: 3,4-DHPEA-EA; C2C12 myocytes; olive oil; antioxidant; skeletal muscle
Online: 29 December 2019 (13:55:48 CET)
Oleuropein, glycosylated secoiridoid present in the olive leaves, is known as an important antioxidant phenolic compound. We studied the antioxidant effect of low dose 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 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 suggest that growth arrest and cell dead of C2C12 proceeds via the JNK/c-Jun pathway. Moreover, we demonstrated that 3,4-DHPEA-EA(P) affects myogenesis of C2C12 cells; because the MyoD mRNA levels and the differentiation process are restored after treatment with 3,4-DHPEA-EA(P). Overall, the results indicate that 3,4-DHPEA-EA(P) prevents ROS-mediated degenerative process by functioning as an efficient antioxidant.
Fri, 13 December 2019
ARTICLE | doi:10.20944/preprints201912.0184.v1
Subject: Chemistry, Medicinal Chemistry Keywords: sponge; quorum sensing; quorum sensing inhibition; N-acyl homoserine lactone; Sarcotragus spinosulus; 3-Br-N-methyltyramine; 5,6-dibromo-N,N-dimethyltryptamine
Online: 13 December 2019 (12:12:54 CET)
Marine sponges, a well documented prolific source of natural products, harbors numerous microbial communities believed to possess N-acyl homoserine lactones (AHLs) mediated Quorum sensing (QS) as one of the mechanisms of interaction. Bacteria and eukaryotic organisms are known to produce molecules that can interfere with QS signaling, thus affecting microbial genetic regulation and function. In the present study, we established the potential for production of both QS signal molecules as well as QS interfering molecules (QSI) in the same sponge species Sarcotragus spinosulus. A total of eighteen saturated acyl chain AHLs were identified along with six putative unsaturated acyl chain AHLs. Bioassay guided purification led to the isolation of two brominated metabolites with QS-interfering activity. The structures of these compounds were elucidated by comparative spectral analysis of 1HNMR and HR-MS data and was identified as 3-Br-N-methyltyramine (1) and 5,6-dibromo-N,N-dimethyltryptamine (2). The QSI activity of compounds 1 and 2 were evaluated using reporter gene assays for long- and short-chain signals (E. coli pSB1075 and E. coli pSB401) and was confirmed by measuring dose dependent inhibition of proteolytic activity and pyocyanin production in P. aeruginosa PAO1. The obtained results showed the co-existence of QS and QSI in S. spinosulus, a complex network which may mediate the orchestrated function of the microbiome within the sponge holobiont.
Sun, 8 December 2019
ARTICLE | doi:10.20944/preprints201912.0099.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Leishmania; thiochromenes; benzothiopyrans; cytotoxicity
Online: 8 December 2019 (15:54:40 CET)
As a part of our ongoing effort in the search for promising antileishmanial agents based on the thiochroman scaffold, we prepared a series of substituted 2H-thiochromenes. Thirty-three compounds were evaluated against intracellular amastigotes forms of L. (V) panamensis. Twelve compounds were active with EC50 values lower than 40 μM, and among those three compounds displayed the highest antileishmanial activity with EC50 values below 10 uM. Cytotoxicity was determined against human U-937 macrophages; thus, compounds having electrophilic alkenes (α,β-unsaturated carbonyl, or nitriles) displayed the highest antileishmanial activity but also moderate to high cytotoxicities. Based on SAR analysis, compounds 8d and 10, which differ only in the hydroxy group at C4, were selected as the most promising compounds in this library because good antiparasitic activity and Selectivity Index.
Wed, 4 December 2019
ARTICLE | doi:10.20944/preprints201912.0049.v1
Subject: Chemistry, Medicinal Chemistry Keywords: natural product; drug discovery; protoflavonoid; continuous-flow chemistry; oxime; antitumor; antiviral; epstein-barr virus; lytic cycle
Online: 4 December 2019 (11:40:33 CET)
Protoflavones, a rare group of natural flavonoids with a non-aromatic B-ring, are best known of their antitumor properties. The protoflavone B-ring is a versatile moiety that may be explored for other pharmacological purposes, but common cytotoxicity of these compounds is a limitation to such efforts. Protoapigenone was previously found to be active against the lytic cycle of Epstein-Barr virus (EBV). Further, the 5-hydroxyflavone moiety is a known pharmacophore against HIV-integrase. The aim of this work was to prepare a series of less cytotoxic protoflavone analogs, and to study their antiviral activity against HIV and EBV. Twenty-seven compounds including 18 new derivatives were prepared from apigenin through oxidative de-aromatization and subsequent continuous-flow hydrogenation, deuteration, and/or 4′-oxime formation. One compound was active against HIV at the micromolar range, and 3 compounds showed significant activity against the EBV lytic cycle at the medium-low nanomolar range. Among these, protoapigenone 1′-O-isopropyl ether (6) was identified as a promising lead due to its 73-times selectivity of its antiviral over its cytotoxic effect, which exceeds that of protoapigenone by 2.4-times. Our results open new opportunities to design new, potent and safe anti-EBV agents based on the natural protoflavone moiety.
Sat, 30 November 2019
REVIEW | doi:10.20944/preprints201911.0392.v1
Subject: Chemistry, Medicinal Chemistry Keywords: fungal pathogens; antifungal agents; natural products
Online: 30 November 2019 (11:30:19 CET)
In this review, we discuss novel natural products discovered within the last decade that are reported to have antifungal activity against pathogenic species. Nearly a hundred natural products were identified that originate from bacteria, alga, fungi, sponges and plants. Fungi were the most prolific source of antifungal compounds discovered during the period of review. The structural diversity of these antifungal leads encompasses all the major classes of natural products including polyketides, shikimate metabolites, terpenoids, alkaloids and peptides.
Fri, 29 November 2019
ARTICLE | doi:10.20944/preprints201911.0375.v1
Subject: Chemistry, Medicinal Chemistry Keywords: synthesis; 2-mercaptabezimidazole; sulfonamide; molecular docking study; α-amylase; sa
Online: 29 November 2019 (10:28:22 CET)
In the search of potent α-amylase inhibitors, we have synthesized seventeen derivatives of 2-mercaptobenzimidazole bearing sulfonamide (1-17) and evaluated for their α-amylase inhibitory potential. All compounds display a variable degree of α-amylase activity having IC50 values ranging between 0.90 ± 0.05 to 11.20 ± 0.30 µM when compared with the standard drug acarbose having IC50 value 1.70 ± 0.10 µM. Compound 1, 2, 11, 12 and 14 having IC50 values 1.40 ± 0.10, 1.30 ± 0.05, 0.90 ± 0.05, 1.60 ± 0.05 and 1.60 ± 0.10 µM respectively were found many folds better than the standard drug acarbose. The remaining analogs showed good inhibitory potentials. All the synthesized compounds were characterized by HREI-MS, 1H and 13C-NMR. Structure activity relationship (SAR) has been recognized for all newly synthesized analogs. Through molecular docking study, binding mode of active analogs with α-amylase enzyme was confirmed.
Wed, 27 November 2019
ARTICLE | doi:10.20944/preprints201911.0339.v1
Subject: Chemistry, Medicinal Chemistry Keywords: human albumin; hydrogen bonds; hp contacts; π- π / cation-π interactions; bonds roughness; decay curve; power spectrum; interaction between amino-acids
Online: 27 November 2019 (09:35:09 CET)
In this paper we review dynamics and roughness of bonds in proteins on example of albumin, that is important from the physiological point of view. We have performed computer simulations of albumin chain. Statistics were collected by performing many simulations realizations for each experimental setting. We concentrate on hydrogen bonds, cation-π and π- π interactions and NP contacts. Histograms of hydrogen bonds length are positively skewed in contrary to histograms of interactions and HP contacts that are negatively skewed. Scaling exponents of power spectra of energies of bonds / interactions /contacts are in range -0.2 to -0.5 and significantly differ between various hydrogen bonds or interactions. Varying scaling of such spectra can be used to classify between distinct bonds or contacts. Concerning particular amino-acids, largest amount of HBO H20 bonds are between Glutamate (GLU) amino-acids and water particle, while large amount of HBO bonds are formed with Lysine (LYS). For HP contacts the mayor role plays Phenylalanine (PHE) and Leucine (LEU) amino-acids. From decay curves HBO H2O bonds decays in fastest rate, while HBO bonds and HP contacts at slowest rate. We present as well decay curves of bonds formed by particular amino-acids, that gives interesting results.
Sun, 24 November 2019
Subject: Chemistry, Medicinal Chemistry Keywords: myricetin; ferulic acid; antiviral activity; microscale thermophoresis; molecular docking
Online: 24 November 2019 (16:29:54 CET)
A variety of myricetin derivatives bearing ferulic acid amide scaffolds were designed and synthesized. The structures of all title compounds were determined by 1 H NMR, 13 C NMR, 19 F NMR and HRMS. Preliminary bioassays suggested that some of the target compounds exhibited remarkable antiviral activities. In particular, compound 4l possessed significant protection activity against tobacco mosaic virus (TMV), with an half maximal effective concentration (EC50) value of 196.11 μg/mL, which was better than commercial agent ningnamycin (447.92 μg/mL). Meanwhile, microscale thermophoresis (MST) indicated that compound 4l have strong binding capability to tobacco mosaic virus coat protein (TMV-CP) with dissociation constant (Kd) values of 0.34 μmol/L, which was better than ningnamycin (0.52 μmol/L). These results suggest that novel myricetin derivatives bearing ferulic acid amide scaffolds may be considered as an activator for antiviral agents.
Subject: Chemistry, Medicinal Chemistry Keywords: myricetin; ferulic acid; antiviral activity; microscale thermophoresis; molecular docking
Online: 24 November 2019 (04:18:53 CET)
A variety of myricetin derivatives bearing ferulic acid amide scaffolds were designed and synthesized. The structures of all title compounds were determined by 1 H NMR, 13 C NMR, 19 F NMR and HRMS. Preliminary bioassays suggested that some of the target compounds exhibited remarkable antiviral activities. In particular, compound 4l possessed significant protection activity against tobacco mosaic virus (TMV), with an half maximal effective concentration (EC50) value of 196.11 μg/mL, which was better than commercial agent ningnamycin (447.92 μg/mL). Meanwhile, microscale thermophoresis (MST) indicated that compound 4l have strong binding capability to tobacco mosaic virus coat protein (TMV-CP) with dissociation constant (Kd) values of 0.34 μmol/L, which was better than ningnamycin (0.52 μmol/L). These results suggest that novel myricetin derivatives bearing ferulic acid amide scaffolds may be considered as an activator for antiviral agents.
Thu, 7 November 2019
ARTICLE | doi:10.20944/preprints201911.0071.v1
Subject: Chemistry, Medicinal Chemistry Keywords: NMDAR; amantadine; dansyl; fluorescent ligand; energy minima; molecular modelling; fluorescent bioassay
Online: 7 November 2019 (04:17:07 CET)
Excitotoxicity related to the dysfunction of the N-methyl-d-aspartate receptor (NMDAR) has been indicated to play an integral role in the pathophysiology of multiple disease states, including neurodegenerative disorders such as Parkinson’s disease. There is a notable gap in the market for novel NMDAR antagonists, however current methods to analyze potential antagonists rely on indirect measurements of calcium flux and hazardous radioligand binding assays. Recently, a fluorescent NMDAR ligand, N-adamantan-1-yl-dimethylamino-1-naphthalenesulfonic acid, known as AM-DAN was developed by our group. Additional studies on this ligand is necessary to evaluate its potential as a biological tool in NMDAR research. Therefore, this study was aimed at conducting structural analyses, fluorescence experiments, high-accuracy NMDAR molecular modelling and NMDAR phencyclidine (PCP) site competition binding studies using AM-DAN. Results revealed that AM-DAN has appropriate structural properties, significant fluorescent ability in various solvents and is able to bind selectively and compete for the PCP-binding site of the NMDAR. Therefore, AM-DAN holds promise as a novel fluorescent ligand to measure the affinity of prospective drugs binding at the NMDAR PCP-site and may circumvent the use of radioligands.
Tue, 5 November 2019
ARTICLE | doi:10.20944/preprints201911.0043.v1
Subject: Chemistry, Medicinal Chemistry Keywords: hydrogen peroxide response; layer-by-layer; multilayer thin film; glucose sensitive; stimuli-sensitive
Online: 5 November 2019 (03:12:59 CET)
Glucose-sensitive films were prepared by the layer-by-layer (LbL) deposition of poly(ethyleneimine) (H-PEI) solution and DNA solution (containing glucose oxidase (GOx)). H-PEI/DNA+GOx multilayer films were constructed using electrostatic interactions. The (H-PEI/DNA+GOx)5 film was then partially decomposed by hydrogen peroxide (H2O2). The mechanism for the decomposition of the LbL film was considered to involve a more reactive oxygen species (ROS) that was formed by the reaction of hemin and H2O2, which then caused nonspecific DNA cleavage. GOx present in the LbL films reacts with glucose to generate hydrogen peroxide. Therefore, decomposition of the H-PEI/DNA+GOx)5 film was observed when the thin film was immersed in a glucose solution. A (H-PEI/DNA+GOx)5 film exposed to a glucose solution for periods of 24, 48 72, and 96 h indicated decomposition of the film increased with the time. The rate of LbL film decomposition increased with the glucose concentration. At pH and ionic strength close to physiological conditions, it was possible to slowly decompose the LbL film at a sub-millimolar glucose concentration.
Wed, 16 October 2019
ARTICLE | doi:10.20944/preprints201910.0174.v1
Subject: Chemistry, Medicinal Chemistry Keywords: AQP3 protein; molecular docking; molecular dynamics; MM-GBSA analysis; pharmacophore-based filter
Online: 16 October 2019 (04:37:31 CEST)
Aquaporin-3 (AQP3) is one of the aquaglyceroporins, which is expressed in the basolateral layer of the skin membrane. Studies have reported that human skin squamous cell carcinoma overexpresses AQP3 and inhibition of its function may alleviate skin tumorigenesis. In the present study, we have applied a virtual screening method that encompasses filters for physicochemical properties and molecular docking to select potential hit compounds that bind to the Aquaporin-3 protein. Based on molecular docking results, the top 20 hit compounds were analyzed for stability in the binding pocket using unconstrained molecular dynamics simulations and further evaluated for binding free energy. Furthermore, examined the ligand-unbinding pathway of the inhibitor from its bound form to explore possible routes for inhibitor approach to the ligand-binding site. With a good docking score, stability in the binding pocket, and free energy of binding, these hit compounds can be developed as Aquaporin-3 inhibitors in the near future.
Sun, 15 September 2019
ARTICLE | doi:10.20944/preprints201909.0152.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chlorophyll; carotenoids; methanol; photo-protection; phytoextraction; Portulaca oleracea
Online: 15 September 2019 (15:04:55 CEST)
The chlorophyll is one of the most important natural pigments used extensively in the food industry. Two important factors for the production of chlorophyll are the use of plants rich in chlorophyll and efficiency of extraction method. Present investigation was performed to compare the extraction of photosynthetic pigments by using solvents of different chemical nature. The purslane plants with different growth behavior viz. Scrollable and standing were grown under shade and sunshine stress condition. Different solvents including diethyl ether, 5% ethanol, pure acetone, 20% acetone, pure methanol and 10% methanol were used to extract chlorophyll and carotenoids from the purslane plant. The results indicated that stress, growth type and different solvents had a significant effect on the extraction of chlorophyll and carotenoids. Different trend was observed in extraction rate for chlorophylls and carotenoids. Among the solvents, pure methanol was the best for extraction of chl a. Methanol and acetone were appropriate solvents to achieve the highest amount of chlorophyll from plant tissues. Among different solvents, pure methanol for chl a, pure acetone and methanol for carotenoids were best solvent for purslane plant with a growing type scrollable of under shade.
Fri, 13 September 2019
ARTICLE | doi:10.20944/preprints201909.0130.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Synthesis; triazinoindole; thiosemicarbazide; alpha-glucosidase; molecular docking study; SAR
Online: 13 September 2019 (10:54:30 CEST)
New class of triazinoindole bearing thiosemicarbazide (1-25) was synthesized and evaluated for α-glucosidase inhibitory potential. All synthesized analogues exhibited excellent inhibitory potential having IC50 values ranging from 1.30 ± 0.01 to 35.80 ± 0.80 µM when compared with the standard acarbose having IC50 value 38.60 ± 0.20 µM. Among series the analogues 1 and 23 was found the most potent having IC50 values 1.30 ± 0.05 and 1.30 ± 0.01 µM respectively. Structure activity relationship (SAR) was mainly based upon by bring about difference of substituents on phenyl rings. To confirm the binding interactions, molecular docking study was performed. Synthesized analogues were characterized through HREI-MS, 1H and 13C-NMR analysis.
Thu, 5 September 2019
ARTICLE | doi:10.20944/preprints201909.0063.v1
Subject: Chemistry, Medicinal Chemistry Keywords: FABP4; A-FABP; aP2; antidiabetes; antiobesity; antiatherosclerosis; anticancer; computational tools; computer-aided drug discovery
Online: 5 September 2019 (15:39:58 CEST)
Small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have got interest following the recent publication of their pharmacologically beneficial effects. Recently it comes out that FABP4 is an attractive molecular target for the treatment of type 2 diabetes, other metabolic diseases, and some type of cancers. In the past years, hundreds of effective FABP4 inhibitors have been synthesized and discovered but, unfortunately, none of them is in the clinical research phase. The field of computer-aided drug design seems to be promising and useful for the identification of FABP4 inhibitors; hence, different structure- and ligand-based computational approaches were already performed for their identification. In this paper, we searched for new potentially active FABP4 ligands in the Marine Natural Products (MNP) database. 14,492 compounds were retrieved from this database and filtered through a statistical and computational filter. Seven compounds were suggested by our methodology to possess a potential inhibitory activity upon FABP4 in the range of 79–245 nM. ADMET properties prediction were performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives; from these analyses, three molecules resulted as excellent candidates for becoming new drugs.
Mon, 2 September 2019
ARTICLE | doi:10.20944/preprints201909.0024.v1
Subject: Chemistry, Medicinal Chemistry Keywords: JBIR-99; high-speed counter-current chromatography; polyketide; NMR spectroscopy; mass spectroscopy; X-ray crystallography; Meyerozyma guilliermondii
Online: 2 September 2019 (11:20:28 CEST)
JBIR-99 is a secondary metabolite of marine fungi that has been shown to possess strong antibiotic activity. An efficient approach using a combination of size exclusion chromatography with a Sephadex LH-20 and high-speed counter-current chromatography (HSCCC) has been successfully developed for the isolation and purification of a polyketide from the solid-state fermentation of Meyerozyma guilliermondii. The active compound was isolated with purity >95% by HSCCC using an optimized solvent system composed of petroleum ether–ethyl acetate– 95% ethanol–water (5:3:5:3, v/v/v/v) after size exclusion chromatography. This compound was successfully purified in the quantity of 68 mg from 120 mg of the crude extract. The structure of JBIR-99 was elucidated and assigned by 1D, 2D NMR spectroscopic, and positive HRESITOFMS. Moreover, the relative configuration of compound JBIR-99, displaying a quite complex multi-ring structure, is determined by X-ray crystallography for the first time. The purification method developed for JBIR-99 will facilitate the further investigation and development of this antibiotic agent as a lead compound. Furthermore, it is suggested that the combination of size exclusion chromatography and HSCCC could be more widely applied for the isolation and purification of polyketides from marine fungi.
Sun, 25 August 2019
ARTICLE | doi:10.20944/preprints201908.0253.v1
Subject: Chemistry, Medicinal Chemistry Keywords: halogen bonding; fluorine; iodine; pentafluorosulfanyl; titration; ab initio calculation; NMR study; drug design
Online: 25 August 2019 (15:41:59 CEST)
The activation of halogen bonding by the substitution of the pentafluorosulfanyl (SF5) group was studied using a series of SF5-substituted iodobenzenes. The simulated electrostatic potential values of SF5-substituted iodobenzenes, ab initio molecular orbital calculations of intermolecular interactions of SF5-substituted iodobenzenes with pyridine, and the 13C NMR titration experiments of SF5-substituted iodobenzenes in the presence of pyridine or tetra (n-butyl) ammonium chloride (TBAC) indicated the obvious activation of halogen bonding, although this was highly dependent on the position of SF5-substitution on the benzene ring. 3,5-Bis-SF5-iodobenzene was the most effective halogen bond donor followed by o-SF5-substituted iodobenzene, while the m- and p-SF5 substitutions did not activate the halogen bonding of iodobenzenes. The 2:1 halogen bonding complex of 3,5-bis-SF5-iodobenzene and 1,4-diazabicyclo[2.2.2]octane (DABCO) was also confirmed. Since SF5-containing compounds have emerged as promising novel pharmaceutical and agrochemical candidates, the 3,5-bis-SF5-iodobenzene unit should be an attractive fragment of rational drug design capable of halogen bonding with biomolecules.
Wed, 21 August 2019
ARTICLE | doi:10.20944/preprints201908.0223.v1
Subject: Chemistry, Medicinal Chemistry Keywords: LSD1; molecular inhibitors; thieno[3,2-b]pyrrole-5-carboxamide derivatives; Molecular docking; 3D-QSAR; Molecular dynamics simulations
Online: 21 August 2019 (09:54:43 CEST)
Histone Lysine Specific Demethylase 1 (LSD1) is overexpressed in many cancers and become a new target for anticancer drugs. In recent years, the small molecule inhibitors with various structures targeting LSD1 have been reported. Here we report the binding interaction modes of a series of thieno[3,2-b]pyrrole-5-carboxamides LSD1 inhibitors using molecular docking, three dimensional quantitative structure-activity relationship (3D-QSAR). Comparative molecular field analysis (CoMFA q2=0.783, r2=0.944, r2pred=0.851) and Comparative molecular similarity indices analysis (CoMSIA q2=0.728, r2=0.982, r2pred=0.814) were used to establish 3D-QSAR models, which had good verification and prediction capabilities. Based on the contour maps and the information of molecular docking, 8 novel small molecules were designed in silico, among which compounds D4, D5 and D8 with high predictive activity were subjected to further molecular dynamics simulations (MD), and their possible binding modes were explored. It was found that Asn535 plays a crucial role in stabilizing the inhibitors. Furthermore, the ADME and bioavailability prediction for D4, D5 and D8 were carried out. The results would provide valuable guidance for designing new reversible LSD1 inhibitors in the future.
Sun, 11 August 2019
ARTICLE | doi:10.20944/preprints201908.0127.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Cucurbitaceae; cucurbitacines; triterpenic saponines; cell cancer lines; antiproliferative activities
Online: 11 August 2019 (08:50:51 CEST)
There are many species of endemic plants from Mexico, without food or commercial use, but with different applications in traditional medicine and valuable for their content of secondary metabolites. In this sense, we found two species of Cucurbitacea family plants natives of southeast and gulf of México, with traditionally use how soap and laundry agent, control of some pests, and it has also been used how infusion for the treatment of different types of dermatitis and stomachache. In the present work, we evaluate the antiproliferative activity in vitro, of six crude organic extracts, tested against six human tumor cell lines, A549 (lung), HBL-100 (breast), HeLa (cervix), SW1573 (lung), T-47D (breast) and WiDr (colon), the results indicated that at least three extracts from both species presents an interesting antiproliferative activity on five tumor cell lines.
ARTICLE | doi:10.20944/preprints201908.0124.v1
Subject: Chemistry, Medicinal Chemistry Keywords: plasmonics; nanomedicine; theranostics; copper; VEGF; glioblastoma; differentiated neuroblastoma; peptidomimetics; qPCR; actin.
Online: 11 August 2019 (07:13:00 CEST)
Angiogenin (ANG), an endogenous protein that plays a key role in cell growth and survival, has been scrutinised here as promising nanomedicine tool for the modulation of pro-/ anti-angiogenic processes in brain cancer therapy. Specifically, peptide fragments from the putative cell membrane binding domain (residues 60-68) of the protein were used in this study to obtain peptide-functionalised spherical gold nanoparticles (AuNPs) of about 10 nm and 30 nm in optical and hydrodynamic size, respectively. Different hybrid biointerfaces were fabricated by peptide physical adsorption (Ang60-68) or chemisorption (the cysteine analogous Ang60-68Cys) at the metal nanoparticle surface, and the cellular assays were performed in the comparison with ANG-functionalised AuNPs. Cellular treatments were performed both in basal and in copper-supplemented cell culture medium, to scrutinise the synergic effect of the metal, which is another known angiogenic factor. Two brain cell lines were investigated in parallel, namely tumour glioblastoma (A172) and neuron-like differentiated neuroblastoma (d-SH-SY5Y). Results on cell viability/proliferation, cytoskeleton actin, angiogenin translocation and VEGF release pointed to the promising potentialities of the developed systems as anti-angiogenic tunable nanoplaftforms in cancer cells treatment.
Fri, 19 July 2019
ARTICLE | doi:10.20944/preprints201907.0220.v1
Subject: Chemistry, Medicinal Chemistry Keywords: diversity; fragment-based drug discovery; library design; library size
Online: 19 July 2019 (07:54:41 CEST)
Fragment-based drug discovery (FBDD) has become a major strategy to derive novel lead candidates for various therapeutic targets, as it promises efficient exploration of chemical space by employing fragment-sized (MW < 300) compounds. One of the first challenges in implementing a FBDD approach is the design of a fragment library, and more specifically, the choice of its size and individual members. A diverse set of fragments is required to maximise the chances of discovering novel hit compounds. However, the exact diversity of a certain collection of fragments remains underdefined, which hinders direct comparisons among different selections of fragments. Based on structural fingerprints, we herein introduced quantitative metrics for the structural diversity of fragment libraries. Structures of commercially available fragments were retrieved from the ZINC database, from which libraries with sizes ranging from 100 to 100,000 compounds were selected. The selected libraries were evaluated and compared quantitatively, resulting in interesting size-diversity relationships. Our results demonstrated that while library size does matter for its diversity, there exists an optimal size for structural diversity. It is also suggested that such quantitative measures can guide the design of diverse fragment libraries under different circumstances.
Thu, 18 July 2019
ARTICLE | doi:10.20944/preprints201907.0215.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Platinum, N-heterocyclic carbene ligand, anticancer activity, DNA interaction, optical tweezers technique, liquid phase AFM microscop
Online: 18 July 2019 (10:17:27 CEST)
A platinum (II) complex stabilized by a pyridine and a N-heterocyclic carbene ligand featuring an anthracenyl moiety was prepared. The compound was fully characterized and its molecular structure was determined by single-crystal X-ray diffraction. The compound demonstrated high in vitro antiproliferative activities against cancer cell lines with IC50 ranging from 10 to 80 nM. The presence of the anthracenyl moiety on the NHC Pt complex was used as a luminescent tag to probe the metal interaction with the nucleobases of the DNA through a pyridine-nucleobase ligand exchange. Such interaction of the platinum complex with DNA was corroborated by optical tweezers techniques and liquid phase AFM microscopy. The results revealed a two-state interaction between the platinum complex and the DNA strands. This two-state behaviour was quantified from the different experiments due to contour length variations. At 24h incubation, the stretching curves revealed multiple structural breakages, and AFM imaging revealed a highly compact and dense structure of platinum complexes bridging the DNA strands.
Fri, 21 June 2019
REVIEW | doi:10.20944/preprints201906.0219.v1
Subject: Chemistry, Medicinal Chemistry Keywords: phytochemistry; biological activities; Apocynaceae family
Online: 21 June 2019 (18:28:55 CEST)
This review aims at studying the phytochemistry and biological activities of some selected Apocynaceae plants. Eleven members of this family were reviewed for their phytochemistry and biological activities. Interestingly, the commonly isolated compounds reported from Mondia whitei (Hook.f.) Skeels, Secondatia floribunda A. DC, Carissa carandas, Tabernaemontana divaricate, Nerium oleander, Wrightia tinctoria, T. divaricate, Alstonia scholaris, Carrisa spinarum Linn, Thevetia peruviana and Caralluma lasiantha were triterpenoids, flavonoids, phytosterols, cardiac glycosides and lignans. All of them exhibited remarkable biological activities, mostly similar to each other. This review provides a detailed insight into the pharmacological activities of these selected members of this family.
Fri, 10 May 2019
ARTICLE | doi:10.20944/preprints201905.0131.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Citrus aurantium L. blossoms; total phenolics; ultrasonic-assisted extraction; Box-Behnken design; free radical scavenging activity; anti-HMG-CoA reductase activity
Online: 10 May 2019 (14:41:59 CEST)
The objective of this study was to develop an ultrasonic-assisted procedure for the extraction of total phenolics from Citrus aurantium L. blossoms (CAB) and evaluate the free radical scavenging activity, anti-HMG-CoA reductase activity of total phenolics. In this work, a Box-Behnken design based on the single-factor experiments was used to explore the optimum extraction process. Under the optimum conditions (extraction solvent 70.31% ethanol, extraction temperature 61.94 °C, extraction time 51.73 min and liquid-to-solid ratio 35.63 mL/g), the extraction yield of total phenolics was 95.84 mg gallic acid equivalents (GAE)/g dry matter (DM), which was highly consistent with the theoretical value (96.12 mg GAE/g DM). The total phenolic extract showed excellent free radical scavenging properties against DPPH·, ABTS+·, ·OH and ·O2-, with the IC50 values of 197.007, 83.878, 218.643 and 158.885 μg/mL, respectively, and the extracts also showed good inhibition of HMG-CoA reductase activity, with the IC50 value of 117.165 μg/mL. Total phenolics from CAB could be a potential source of natural free radical scavenger and HMG-CoA reductase inhibitor.
Mon, 6 May 2019
REVIEW | doi:10.20944/preprints201905.0066.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chitin; chitosan; cosmetics; biodegradability; biomaterials; polysaccharides; green technology; marine cosmetic ingredients; marine green source; marine resources
Online: 6 May 2019 (12:37:44 CEST)
Huge amounts of chitin and chitosans can be found in the biosphere as important constituent of the exoskeleton of many organisms, as well as waste by worldwide seafood companies. Nowadays, politicians, environmentalists, and industrialists encouraged the use of these marine polysaccharides as renewable source, particularly when developed by alternative eco-friendly processes, especially in the production of regular cosmetics. The aim of this review is to outline the physicochemical and biological properties and the different bioextraction methods of chitin and chitosans sources, focusing on enzymatic deproteinization, bacteria fermentation, and enzymatic deacetylation methods. Thanks to their biodegradability, non-toxicity, biocompatibility, and bioactivity, the application of these marine polymers is widely used in the contemporary manufacturing of biomedical and pharmaceutical products. In the end, advanced cosmetic products based on chitin and chitosans are presented, analyzing different therapeutic aspects about skin, hair, nail, and oral care. The innovative formulations described can be considered as excellent solutions regarding problems in the various body anatomical sectors.
ARTICLE | doi:10.20944/preprints201905.0046.v1
Subject: Chemistry, Medicinal Chemistry Keywords: aminopeptidases; inhibitors; aminophosphonate; phenylglycine analogues; fluorine substituted; molecular modeling
Online: 6 May 2019 (10:16:45 CEST)
Inhibitory activity of 14 phosphonic analogues of phenylglycine, substituted in aromatic ring by fluorine and chlorine, was determined towards porcine aminopeptidase N. The obtained data served as a basis for studying their interaction with the enzyme as modelled by the use of Schrödinger Release 2018 program. The observed linearity between modelled Gibbs free energy differences and inhibitory constants indicated the usefulness of this program. The obtained binding mode was compared with this modelled for bovine lens leucine aminopeptidase. Although both enzymes differ in the number of zinc ions present in the active site, they are considered to exhibit similar activity towards substrates and inhibitors. Our studies seem to support that supposition since the modes of binding of the studied inhibitors are quite similar. Additionally, inhibitory activity of the phosphonic analogues of phenylglycine towards barley aminopetpidase was determined showing that this enzyme could be considered as neutral aminopeptidase.
Subject: Chemistry, Medicinal Chemistry Keywords: azolines synthesis; quorum sensing; Chromobacterium violaceum CV026; molecular docking; molecular dynamics
Online: 6 May 2019 (08:59:08 CEST)
The increasingly common occurrence of antibiotic-resistant bacteria has become an urgent public health issue. There are currently some infections without any effective treatment, which require new therapeutic strategies. An attractive alternative is the design of compounds capable of disrupting bacterial communication known as quorum sensing (QS). In gram-negative bacteria, such communication is regulated by acyl-homoserine lactones (AHLs). QS allows bacteria to proliferate before expressing virulence factors. Our group previously reported that hexyloxy phenyl imidazoline (9) demonstrated 71% inhibitory activity of QS at 100 µM (IC50=90.9 µM) in Chomobacterium violaceum, a gram-negative bacterium. The aim of the present study was to take 9 as a lead compound to design and synthesize three 2-imidazolines (13-15) and three 2-oxazolines (16-18), to be evaluated as quorum sensing inhibitors on C. violaceum CV026. We were looking for compounds with a higher affinity towards the Cvi receptor of this bacterium and the ability to inhibit QS. The binding mode of the test compounds on the Cvi receptor was explored with docking studies and molecular dynamics. It was found that 8-pentyloxyphenyl-2-imidazoline 13 reduced the production of violacein (IC50=56.38 µM) without affecting bacterial growth, suggesting inhibition of quorum sensing. Indeed, compound 13 is apparently one of the best QS inhibitors known to date. Molecular docking revealed the affinity of compound 13 for the orthosteric site of the N-hexanoyl homoserine lactone (C6-AHL) on the CviR protein. Ten aminoacid residues in the active site of C6-AHL interacted with 13, and 7 of these are the same as those interacting with AHL. Contrarily, 8-octyloxyphenyl-2-imidazoline 14, 8-decyloxyphenyl-2-imidazoline 15 and 9-decyloxyphenyl-2-oxazoline 18 bound only to an allosteric site and thus did not compete with C6-AHL for the orthosteric site.
Wed, 24 April 2019
ARTICLE | doi:10.20944/preprints201904.0262.v1
Subject: Chemistry, Medicinal Chemistry Keywords: total synthesis; antitumor activity; structure-activity relationship
Online: 24 April 2019 (05:29:48 CEST)
(-)-Zeylenone is a promising cytotoxic agent，which is a natural product isolated from Uvaria grandiflora Roxb. Though substantial antitumor mechanism has been researched , little has focused on its enantiomer (+)-Zeylenone.This article will try to find a gram scale synthesis method of (+)-Zeylenone and explain the structure-activity relationship of this kind of compound. Total synthesis of (+)-zeylenone was completed in 13 steps with quinic acid as starting material in 8.8% overall yield. The highlight of the route was the control of the three carbon’s chirality by clever use of single step dihydroxylation under the direction of the key C-3 chirality. In addition, zeylenone derivatives were designed and synthesized and their antitumor activity were evaluated against three human cancer cell lines using the CCK8 assay. Structure-activity relationship suggested compounds with both two absolute configurations exhibited good activity. Besides, hydroxyls at C-1/2 position were crucial for the activity and esterification of C-1 hydroxyl with large groups made the activity disappeared. Hydroxyl at C-3 position was also important as proper ester substituent could increase the potency.
Fri, 29 March 2019
Online: 29 March 2019 (09:13:02 CET)
Astragalus is a very interesting plant genus well-known for content of flavonoids, triterpenes and polysaccharides. Its secondary metabolites are described as biologically active compounds showing a number of activities, like immunomodulating, antibacterial, antiviral and hepatoprotective. This inspired us to analyze the Bulgarian endemic A. aitosensis (Ivanisch.) to obtain deeper information about its phenolic components. We used extensive chromatographic separation of A. aitosensis extract to obtain seven phenolic compounds (1–7), which were identified using combined LC-MS and NMR spectral studies. The 1D and 2D NMR analysis and HR-MS allowed us to resolve the structures of known compounds 5–7 as isorhamnetin-3-O-robinobioside, isorhamnetin-3-O-(2,6-di-O-α-rhamno-pyranosyl-β-galactopyranoside), and alangiflavoside, respectively, and further comparison of these spectral data with available literature helped us with structural analysis of newly described flavonoid glycosides 1–4. These were described in plant source for the first time.
Tue, 19 March 2019
Subject: Chemistry, Medicinal Chemistry Keywords: Simaroubaceae; Picrasma javanica; quassionoids; phytochemicals; pharmacological properties
Online: 19 March 2019 (10:49:34 CET)
Picrasma javanica Blume or also known as Picrasma nepalensis or Picrasma philippinensis is a plant belongs to the Simaroubaceae family, which is known for its secondary metabolites namely quassinoids with various pharmacological properties including antitumor, antimalarial and antiviral. The plant traditionally used as medicine for different diseases in Myanmar, Thailand and Indonesia. The purpose of this study is to discern the phytochemical constituents and pharmacological activities of Picrasma javanica. The background, phytochemical constituents and pharmacological benefits of Picrasma javanica were reviewed and supported from previous studies, including in vivo and in vitro studies. The literature used in the review comprises of published books, journals, reviews and articles published from the year of 1969 to 2018, which are available in ScienceDirect, PubMed, Scopus and GoogleScholar. Chemical structures presented in this paper are either drawn with ACD/ChemSketch. Picrasma javanica possesses several phytochemical constituents, including quassinoids, alkaloids and triterpenoids. Compounds of the plant were isolated and studied for their pharmacological activities such as antimalarial, antiproliferative, antiviral, antimicrobial and membrane stabilising activity. Most importantly, these studies showed that the key players for the pharmacological benefits are quassinoids and alkaloids present in the plant.Picrasma javanica indeed has therapeutic potentials which may be beneficial for people. However, further extensive studies must be done on the plant as the detailed information on its pharmacological activities are still lacking.
Fri, 15 March 2019
ARTICLE | doi:10.20944/preprints201903.0166.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Structure-based design; glycogen phosphorylase inhibitor; glycogen metabolism; type 2 diabetes; X-ray crystallography; N-acyl-β-D-glucopyranosylamine
Online: 15 March 2019 (14:06:06 CET)
Structure-based design and synthesis of two biphenyl-N-acyl-β-D-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented. X-ray crystallography revealed the importance of structural water molecules and that the inhibitory efficacy correlates with the degree of disturbance caused by the inhibitor binding to a loop crucial for the catalytic mechanism. The in silico derived models of the binding mode generated during the design process corresponded very well with the crystallographic data.
Wed, 27 February 2019
ARTICLE | doi:10.20944/preprints201902.0248.v1
Subject: Chemistry, Medicinal Chemistry Keywords: 10-methoxycanthin-6-one; quaternization; antibacterial; SARs
Online: 27 February 2019 (05:08:02 CET)
Natural products are an important source of antibacterial agents. Canthin-6-one alkaloids have displayed potential antibacterial activity based on our previous work. In order to improve the activity, twenty-two new 3-N-benzylated 10-methoxy canthin-6-ones were designed and synthesized through quaternization reaction. The in vitro antibacterial activity against three bacteria was evaluated by double dilution method. Four compounds (6f, 6i, 6p and 6t) displayed 2-fold superiority (minimum inhibitory concentration (MIC) = 3.91 µg/mL) against agricultural pathogenic bacteria R. solanacearum and P. syringae than agrochemical propineb. Moreover, the structure–activity relationships (SARs) were also carefully summarized in order to guide the development of antibacterial canthin-6-one agents.
Wed, 6 February 2019
ARTICLE | doi:10.20944/preprints201902.0064.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Dopamine receptors, Molecular Docking, Molecular Dynamics, Receptor-Ligand Interactions
Online: 6 February 2019 (13:54:13 CET)
Background: Selectively targeting dopamine receptors has been a persistent challenge in the last years for the development of new treatments to combat the large variety of diseases evolving these receptors. Although, several drugs have been successfully brought to market, the subtype-specific binding mode on a molecular basis has not been fully elucidated. Methods: Homology modeling and molecular dynamics were applied to construct robust conformational models of all dopamine receptor subtypes (D1-like and D2-like receptors). Fifteen structurally diverse ligands were docked to these models. Contacts at the binding pocket were fully described in order to reveal new structural findings responsible for DR sub-type specificity. Results: We showed that the number of conformations for a receptor:ligand complex was associated to unspecific interactions > 2.5 Å and hydrophobic contacts, while the decoys binding energy was influenced by specific electrostatic interactions. Known residues such as 3.32Asp, the serine microdomain and the aromatic microdomain were found interacting in a variety of modes (HB, SB, π-stacking). Purposed TM2-TM3-TM7 microdomain was found to form a hydrophobic network involving Orthosteric Binding Pocket (OBP) and Secondary Binding Pocket (SBP). T-stacking interactions revealed as especially relevant for some large ligands such as apomorphine, risperidone or aripiprazole. Conclusions: This in silico approach was successful in showing known receptor-ligand interactions as well as in determining unique combinations of interactions, key for the design of more specific ligands.
Wed, 30 January 2019
ARTICLE | doi:10.20944/preprints201901.0307.v1
Subject: Chemistry, Medicinal Chemistry Keywords: molecular docking; fluoroquinolones; antimicrobial activity
Online: 30 January 2019 (09:31:52 CET)
An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds.A restricted hybrid HF-DFT calculation was performed in order to obtain the most stable conformer of each ligand and a series of DFT calculations using the B3LYP levels with 6-31G* basis set has been conducted. The docking studies of the quinolone compounds will be performed with the CLC Drug Discovery Workbench to identify and visualize the ligand-receptor interaction mode.
Fri, 4 January 2019
ARTICLE | doi:10.20944/preprints201901.0046.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Keywords: methotrexate, cubic phase, magnetocubosomes, monoolein, liquid crystalline phase, drug delivery system, alternating magnetic field
Online: 4 January 2019 (14:32:38 CET)
The release profiles of methotrexate, an anticancer drug, from the monoolein liquid crystalline cubic phases were studied. The cubic phases were used either in the form of a lipidic film deposited onto a glassy carbon electrode surface or in the dispersed form of magnetocubosomes, which are considered a prospective hybrid drug delivery system. Commonly, cubosomes or liposomes are employed, but not in the case of toxic methotrexate, known to block receptors responsible for folate transport into the cells. The release profiles of the drug from the lipidic films were monitored electrochemically and described using the Higuchi model. They were also modified via changes in temperature; the release was faster, although deviating from the model when the temperature was increased. Magnetocubosomes - cubic phase nanoparticles containing hydrophobic magnetic nanoparticles placed in an alternating magnetic field of low frequency and amplitude, stimulated drug release from the suspension, which was monitored spectroscopically. These new biocompatible hybrid materials are very promising, allowing to control the release of the drug at the appropriate sites, but do require further investigations into their in vitro cytotoxicity and in vivo biodistribution.
Tue, 18 December 2018
ARTICLE | doi:10.20944/preprints201812.0214.v1
Subject: Chemistry, Medicinal Chemistry Keywords: αβ motif; Abu; chlorotoxin; Cys; disulfide bond; insectotoxin; isosteric substitution; L-α-aminobutyric acid; molecular dynamics; Ser
Online: 18 December 2018 (04:46:38 CET)
Chlorotoxin (CTX) is a 36–amino acid peptide with 8 Cys residues that forms four Cys-Cys bonds. It has high affinity for the glioma-specific chloride channel and matrix metalloprotease-2. Structural and binding properties of CTX analogs with various Cys residue substitutions with L-a-aminobutyric acid (Abu) have been previously reported. Using 4.2 ìs molecular dynamics, we compared the conformational and essential space sampling of CTX and analogs [Abu/Ser2,19]CTX, [Abu/Ser5,28]CTX, [Abu/Ser16,33]CTX, [Abu/Ser20,35]CTX, and [Abu/Ser2,5,16,19,20,28,33,35]CTX. The native and substituted peptides maintained a high degree of a-helix propensity from residues 8 through 21, with the exception of [Ser5,28]CTX and [Abu16,33]CTX. In agreement with previous circular dichroism spectropolarimetry results, the C-terminal b-sheet content varied less from residues 25 through 29 and 32 through 36 and was well conserved in all analogs, except: [Abu16,33]CTX, [Ser20,35]CTX, [Abu2,5,16,19,20,28,33,35]CTX, and [Ser2,5,16,19,20,28,33,35]CTX. The Cys16-Cys33 and Cys20-Cys35 Cys-Cys bonds appear to be required to maintain the ab-motif of CTX. Their selective substitution with Ser16,33 however, may mitigate the destabilizing effect of Cys16-Cys33 substitution by the formation of an inter residue H-bond from OgH of Ser16 to OgH of Ser33 bridged by a water molecule. All peptides shared considerable sampled conformational space, which explains the retained receptor binding of the nonnative analogs.
Mon, 3 December 2018
ARTICLE | doi:10.20944/preprints201812.0027.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Rumex tunetanus; Phenolic compounds; Metabolic profiling; Antioxidant activity; RP-UHPLC-ESI-QTOF-MS
Online: 3 December 2018 (13:58:52 CET)
The present study was designed to investigate the bioactive compound in Rumextunetanus extracts (polygonaceae), a plant growing in GarâaSejnane region (NW-Tunisia). Hydro-methanol extracts of flowers and stems of Rumextunetanus were analyzed by RP-UHPLC-ESI-QTOF-MS in the negative mode to identify the maximum of bioactive compounds. Applied the aforementioned method, a total of 60 bioactive compounds were characterized for the first time in Rumextunetanus between them, 18 photochemical were firstly identified in the Polygonaceae family in negative ionization mode. Quantification of the identified compounds revealed that quercetin-3-O-glucuronide and (-)-epicatechingallate were the most abundant phenolic compounds in flowers and stems, respectively. Moreover, positive correlations were found between the antioxidant activity measured by DPPH and FRAP assays with the total phenolic compounds (r = 0.98; r = 0.99, respectively) and the abundance of some phenolic subfamilies such as hydroxycinnamic acids, hydroxybenzoic acids, flavonols and flavones with r > 0.86. The compounds displaying significant (P < 0.01) and good correlations with the antioxidant activity (r > 0.93) were hydroxybenzoic acid, rutin, quercetin-3-O-glucuronide, quercetin-3-O-glucoside, quercetin and luteolin-7-O-rutinoside. In addition, the flowers and stems of Rumex tunetanus showed different bioactive compound profiles and significant antioxidant properties of extracts. These results highlight the potential of the RP-UHPLC-ESI-QTOF-MS and MS/MS system to identify untargeted metabolic profiling of Rumex tunetanus. Overall, these results contribute to the clear explanation of the past and current usage of genus Rumex in folk medicine. Future investigations are necessary to develop purified antioxidant extracts, with the application of more selective extraction techniques.
Mon, 26 November 2018
ARTICLE | doi:10.20944/preprints201811.0574.v1
Subject: Chemistry, Medicinal Chemistry Keywords: activity cliff; activity landscape plotter; epigenetics; docking; drug discovery; D-tools; molecular dynamics; Epi-polypharmacology; SmART; structure-activity relationships
Online: 26 November 2018 (07:14:05 CET)
In this work we discuss the insights from activity landscape, docking and molecular dynamics towards the understanding of the structure-activity relationships of dual inhibitors of major epigenetic targets: lysine metiltransferase (G9a) and DNA metiltranferase 1 (DNMT1). The study was based on a novel data set of 50 published compounds with reported experimental activity for both targets. The activity landscape analysis revealed the presence of activity cliffs, e.g., pairs of compounds with high structure similarity but large activity difference. Activity cliffs were further rationalized at the molecular level by means of molecular docking and dynamics simulations that led to the identification of interactions with key residues involved in the dual activity or selectivity with the epigenetic targets.
Fri, 16 November 2018
REVIEW | doi:10.20944/preprints201811.0409.v1
Online: 16 November 2018 (11:34:24 CET)
G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, G-quadruplex structure regulates transcription, translation, splicing, telomere stability etc. Changes in its structure and stability lead to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/ other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.
ARTICLE | doi:10.20944/preprints201811.0371.v1
Subject: Chemistry, Medicinal Chemistry Keywords: biosynthesis; nanoparticles; plant extracts; Citrus reticulata
Online: 16 November 2018 (04:33:22 CET)
Biosynthesis of nanoparticles for delivery of therapeutic agents has introduced new opportunities in upgrading medical treatment. Plant extracts contains different capping and reducing agents naturally thus provided simpler and less expensive way to synthesize AgNPs. In present work, Citrus reticulata mediated stabilised AgNPs was synthesized. Optimum concentration of reactants was achieved by varying the amount of extracts (1-11 ml) and AgNO3 concentration (0.5-3 mM). Surface Plasmon peak of Citrus reticulata mediated AgNPs was determined by UV-visible spectrophotometer and functional groups of capping agents were examined by FTIR analysis. Surface Plasmon peaks of Citrus reticulata fresh peel, seed, and juice extracts were observed at 420 nm. But in dry peel extract, absorption peak of AgNPs appeared at 410 nm. Colour of different extracts was changed after the reduction of AgNO3 to AgNPs by reducing agents present in the extracts. FTIR analysis showed band peaks at 3316 cm-1 correspond to amide (N-H and O-H) stretching vibrations while alkanes peaks was observed at 1638 cm-1 which showed C=C stretching aromatic ring (flavonoids). Furthermore, Citrus reticulata fresh peel mediated AgNPs showed impressive stability up-to 112 days. In conclusion, Citrus reticulata fresh peel extract provided an excellent source of reducing agents for synthesizing stabilized AgNPs.
Wed, 14 November 2018
ARTICLE | doi:10.20944/preprints201811.0330.v1
Subject: Chemistry, Medicinal Chemistry Keywords: hyperpigmentation; tyrosinase inhibitors; 3-(2,4-dihydroxyphenyl)propionic acid; structure-activity relationship study; B16-F10 cellular melanogenesis inhibition
Online: 14 November 2018 (09:59:45 CET)
Compounds with tyrosinase inhibitory efficacy could be effective as depigmenting agents. Although a large number of natural and synthetic tyrosinase inhibitors have been reported, few of them are used as skin-whitening agents due to poor activity and safety concerns. 3-(2,4-Dihydroxyphenyl)propionic acid (DPPA), a naturally occurring compound isolated from Ficus carica, was previously discovered as a moderate tyrosinase inhibitor. In this study, the structure-activity relationship study of DPPA was conducted. Compound 3g, with the 2,4-resorcinol subunit and terminal hydrophobic di-butylamino group, was identified with low nanomolar enzymatic IC50 value. Additionally, compound 3g could effectively reduce melanin levels in B16-F10 melanoma cells treated with α-melanocyte-stimulating hormone (α-MSH) without affecting cell viability and proliferation. All these results indicated that compound 3g could be considered as a promising candidate for the treatment of diseases associated with hyperpigmentation.
Thu, 8 November 2018
ARTICLE | doi:10.20944/preprints201811.0221.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Fatty Acid Amide Hydrolase; cannabinoid; carboxamide inhibitors; 3D-QSAR; CoMSIA.
Online: 8 November 2018 (14:52:23 CET)
Fatty Acid Amide Hydrolase (FAAH) is one of the enzymes responsible of endocannabinoids metabolism. The inhibition of FAAH is a useful and indirect strategy to raise endogenous cannabinoid concentrations, which would be useful for the treatment of various pathological processes in which cannabinoid concentrations are lowered. In the present work, we present an extensive 3D-QSAR/CoMSIA study on a series of 90 irreversible inhibitors of FAAH of pyrimidinyl-piperazine-carboxamide structure. The final model obtained was extensively validated (q2 = 0.734; r2test = 0.966; r2m = 0.723), and based on the information derived from the contour maps we reported a series of 10 new compounds designed as powerful FAAH inhibitors (pIC50 of the best-proposed compounds = 12.196; 12.416).
Tue, 6 November 2018
ARTICLE | doi:10.20944/preprints201811.0137.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Streptomyces; angucycline; saquayamycin; cytotoxicity
Online: 6 November 2018 (10:55:42 CET)
Four angucycline glycosides including three new compounds landomycin N (1), galtamycin C (2) and vineomycin D (3), and a known homologue saquayamycin B (4), along with two alkaloids 1-acetyl-β-carboline (5) and indole-3-acetic acid (6), were identified from the fermentation broth of an intertidal sediments derived Streptomyces sp. Their structures were mainly established by IR, HR-ESI-MS, 1D and 2D NMR techniques. Among the isolated angucyclines, saquayamycin B displayed potent cytotoxic activity against hepatoma carcinoma cells HepG-2, SMMC-7721 and plc-prf-5, with IC50 values 0.135, 0.033 and 0.244 μM respectively, superior to positive drug doxorubicin. Saquayamycin B treatment to SMMC-7721 cells led to the typical morphological signs of apoptosis in 4',6-diamidino-2-phenylindole (DAPI) staining experiment.
Fri, 2 November 2018
ARTICLE | doi:10.20944/preprints201811.0008.v1
Subject: Chemistry, Medicinal Chemistry Keywords: neuroinflammation; microglia; carbon-11; radiochemistry; positron emission tomography
Online: 2 November 2018 (02:55:47 CET)
Positron emission tomography (PET) imaging of Colony Stimulating Factor 1 Receptor (CSF1R) is a new strategy for quantifying both neuroinflammation and inflammation in the periphery since CSF1R is expressed on microglia. AZ683 has high affinity for CSF1R (Ki = 8 nM; IC50 = 6 nM) and >250-fold selectivity over 95 other kinases and, in this paper, we report the radiosynthesis of [11C]AZ683 and initial evaluation of its use in CSF1R PET. [11C]AZ683 was synthesized by 11C-methylation of the desmethyl precursor with [11C]MeOTf in 3.0% non-corrected activity yield (based upon [11C]MeOTf), >99% radiochemical purity and high specific activity. Preliminary PET imaging with [11C]AZ683 revealed no brain uptake in rodents and nonhuman primates suggesting that [11C]AZ683 is a poor candidate for imaging neuroinflammation, but that it could still be useful for peripheral imaging of inflammation.
Thu, 1 November 2018
ARTICLE | doi:10.20944/preprints201810.0768.v1
Subject: Chemistry, Medicinal Chemistry Keywords: silybin; prostate cancer; 2,3-dehydrosilybin; cell proliferation; cell apoptosis.
Online: 1 November 2018 (18:16:29 CET)
As part of our ongoing silybin project, this study aims to introduce a basic nitrogen-containing group to 7-OH of 3,5,20-O-trimethyl-2,3-dehydrosilybin or 3-OH of 5,7,20-O-trimethyl-2,3-dehydrosilybin via an appropriate linker for in vitro evaluation as potential anti-prostate cancer agents. The synthetic approaches to 7-O-substituted-3,5,20-O-trimethyl- 2,3-dehydrosilybins through a five-step procedure and to 3-O-substituted-5,7,20-O-trimethyl-2,3- dehydrosilybins via a four-step transformation have been developed. Thirty-two nitrogen-containing derivatives of silybin have been achieved through these synthetic methods for the evaluation of their antiproliferative activities towards both androgen-sensitive (LNCaP) and androgen-insensitive prostate cancer cell lines (PC-3 and DU145) using WST-1 cell proliferation assay. These derivatives exhibited greater in vitro antiproliferative potency than silybin. Among them, 11, 29, 31, 37, and 40 were identified as five optimal derivatives with IC50 values in the range of 1.40–3.06 µM, a 17- to 52-fold improvement in potency as compared with silybin. All these five optimal derivatives can arrest the PC-3 cell cycle in the G0/G1 phase and promote PC-3 cell apoptosis. Derivatives 11, 37, and 40 are more effective than 29 and 31 in activating PC-3 cell apoptosis.
Wed, 17 October 2018
ARTICLE | doi:10.20944/preprints201810.0381.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Biginelli reaction; dihydropyrimidin-2-thiones; synthesis, virtual screening, drug design; LaSOM 282
Online: 17 October 2018 (09:34:06 CEST)
The Biginelli reaction is a highly versatile reaction, which leads to dihydropyrimidinones/thiones. This scaffold is reported as being a privileged structure due to its ability to interact with biological targets. Synthesis of ethyl 4-(2-fluorophenyl)-6-methyl-2-thioxo-1-(p-tolyl)-1,2,3,4-tetrahydropyrimidine-5-carboxylate was achieved through the Biginelli reaction using a functionalized thiourea. In silico studies demonstrated that the compound title showed good potential for interacting with ecto-5’-nucleotidase, which has been considered as a target in designs for anti-cancer drugs.
ARTICLE | doi:10.20944/preprints201810.0375.v1
Subject: Chemistry, Medicinal Chemistry Keywords: endophytic fungi; sesterterpene; cytotoxic activity; pancreatic cancer
Online: 17 October 2018 (06:39:51 CEST)
As a part of our ongoing research on endophytic fungi, we have isolated a sesterterpene mycotoxin, fusaproliferin (FUS), from Fusarium solani strain associated with the plant Aglaonema hookerianum Schott. FUS showed rapid and sub-micromolar IC50 against pancreatic cancer cell lines. Time dependent survival analysis and microscopy imaging showed rapid morphological changes in cancer cell lines 4 hours after incubation with FUS. This provides a new chemical scaffold that can be further developed to obtain more potent synthetic agents against pancreatic cancer.
Tue, 16 October 2018
REVIEW | doi:10.20944/preprints201810.0360.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Molecular Dynamics, CoSolvent Molecular Dynamics, Drug design, Fragment Screening, Docking
Online: 16 October 2018 (12:15:17 CEST)
Molecular dynamics(MD) simulations are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals the solvent structure and preferential interaction sites (hot spots) on the protein surface. This information is largely transferable across all classes of protein ligands (from water to drugs) and can be used very effectively to understand ligand recognition and improve the predictive capability of well-established methods such as molecular docking. MD simulations for protein and drug or drug-like compounds are now being used but are still computationally expensive and can only be applied to specific cases. On the other hand, MDmix simulations can now be used in SBDD and we will describe the latest developments and implementations. We expect to see an increase in the application of these techniques to a plethora of protein targets to identify new drug candidates with the advent of new tools and faster computers.
ARTICLE | doi:10.20944/preprints201810.0355.v1
Subject: Chemistry, Medicinal Chemistry Keywords: assay; diarrhea; isolate; hydrolysis; proteins; inhibition zone
Online: 16 October 2018 (11:26:59 CEST)
The study compared antibacterial potential of hydrolysates of casein and alpha-lactalbumin from cow and goat milk on diarrhea-causing Escherichia coli and Staphylococcus aureus. Milk samples were aseptically obtained from lactating cows and goats. The samples were skimmed; casein was isolated using acetic acid and alpha-lactalbumin by filtrate thermoprecipitation at 75 °C. 50% of each isolate was reconstituted in a buffer and hydrolyzed with papain at 55 °C for 2 hours. The hydrolysates were heated to 75 °C to inactivate papain, cooled and their antibacterial activity determined by disc diffusion method. Results showed alpha-lactalbumins had higher degrees of hydrolysis and antibacterial activity than caseins; goat alpha-lactalbumin had the highest antibacterial activity with mean inhibition zones of 19.60 mm and 19.50 mm on E. coli and S. aureus. Cow alpha-lactalbumin inhibited E. coli more than S. aureus with inhibition zones of 16.80 mm and 12.50 mm. Cow and goat milk casein hydrolysates inhibited E. coli with mean inhibition zones of 8.00 mm and 10.90 mm and inhibited S. aureus with inhibition zones of 4.13 mm and 1.90 mm respectively. The research showed that the milk hydrolysates can be a source of antibiotics for diarrhea treatment. Research should be done to establish the peptide fractions associated with the observed bioactivity.
Fri, 28 September 2018
ARTICLE | doi:10.20944/preprints201809.0564.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Pritimerin; target fishing; druggability; network pharmacology
Online: 28 September 2018 (11:54:58 CEST)
Pristimerin (PM) is a naturally occurring quinonemethide triterpenoid compound that isolated from the Celastraceae and Hippocrateaceae families. Its anticancer effects have attracted a great deal of attention, but the mechanisms of action remain obscure. In this study, we screened for the active compounds of Pristimerin using a drug-likeness approach. Potential protein targets of Pristimerin were predicted by PharmMapper and Coremine database. Candidate protein targets were then uploaded to GeneMANIA and GO pathway analysis. Finally, compound-target, target-pathway, and compound-target-pathway networks were constructed using Cytoscape 3.3. The results showed that Pristimerin had good drug ability and identified 13 putative protein targets. Network analysis revealed that these targets are associated with cancer, inflammation and other physiological processes. In summary, Pristimerin is predicted to target a variety of proteins and pathways to form a network that exerts systemic pharmacological effects.
Mon, 3 September 2018
ARTICLE | doi:10.20944/preprints201809.0048.v1
Subject: Chemistry, Medicinal Chemistry Keywords: pretargeting; Fusarinine C; rituximab; click chemistry; multimerization; PET; gallium-68
Online: 3 September 2018 (15:55:44 CEST)
Among extensive studies on click chemistry the inverse electron-demand Diels-Alder reaction between 1,2,4,5-tetrazine (Tz) and trans-cyclooct-2-en (TCO) has gained increasing attraction due to its exceptionally fast reaction kinetics and high selectivity for in vivo pretargeting applications including PET imaging. The facile two-step approach utilizing TCO-modified antibodies as targeting structures has not made it into clinic though as the increase in blood volume from mice to human seems to be the major limitation. This study aimed to show if the design of multimeric Tz-ligands by chelator scaffolding can improve the binding capacity and may lead to enhanced PET imaging with gallium-68. For this purpose we utilized the macrocyclic siderophore Fusarinine C (FSC) which allows to conjugate up to three Tz-residues due to three primary amines available for site specific modification. The resulting mono- di- and trimeric conjugates were radiolabelled with gallium-68 and characterized in vitro (logD, protein binding, stability, binding towards TCO modified rituximab (RTX)) and in vivo (biodistribution- and imaging studies in normal BALB/c mice using a simplified RTX-TCO tumour surrogate). The 68Ga-labelled FSC-based Tz-ligands showed suitable hydrophilicity, high stability, high targeting specificity and the binding capacity to RTX-TCO was increased by the grade of multimerization. Corresponding in vivo studies showed a multimerization typical profile but generally suitable pharmacokinetics with low accumulation in non-targeted tissue. Imaging studies in RTX-TCO tumour surrogate bearing BALB/c mice confirmed this trend and revealed improved targeting by multimerization as increased accumulation in RTX-TCO positive tissue was observed.
Thu, 30 August 2018
ARTICLE | doi:10.20944/preprints201808.0516.v1
Subject: Chemistry, Medicinal Chemistry Keywords: ALK5 inhibitor; TGF-β; kinase assay; selectivity; docking
Online: 30 August 2018 (05:52:08 CEST)
The transforming growth factor-β (TGF-β), in which overexpression have been associated with various diseases, has become an attractive molecular target for the treatment of cancers. Three series of 3-substituted-4-(quinoxalin-6-yl) pyrazoles 14a–h, 15a–h, 16a–h, 22a, 22b, 22d, 23a, 23b, 23d, 24b, and 24d were synthesized and evaluated for their activin receptor-like kinase 5 (ALK5) and p38α mitogen activated protein (MAP) kinase inhibitory activity in an enzymatic assays. Among these compounds, the most active compound 16f inhibited ALK5 phosphorylation with an IC50 value of 0.28 µM, with 98% inhibition at 10 µM. Compound 16f also had good selectivity index of >35 against p38α MAP kinase, with 9.0-fold more selective than clinical candidate, compound 3 (LY-2157299). Molecular docking study was performed to identify the mechanism of action of the synthesized compounds and their good binding interactions were observed. ADMET prediction of good active compounds showed that these ones possess good pharmacokinetics and drug-likeness behavior.
Wed, 29 August 2018
REVIEW | doi:10.20944/preprints201808.0488.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Sarcophyton; Sinularia; Lobophytum; new compounds; anti-microbial; anti-inflammatory; anti-tumoral
Online: 29 August 2018 (09:03:48 CEST)
Work reviews the new isolated isolated cembranoid diterpene derivatives from species belonging to the family Alcyoniidae, which comprises the genera Sarcophyton, Sinularia, and Lobophytum as well as their biological properties, during 2016–2017. The compilation permitted to conclude that much more new cembranoid diterpenes were found in the soft corals of the genus Sarcophyton sp. (33 new compounds) than in those belonging to the genera Lobophytum (17) or Sinularia (8). Several methods have been used for identifying these new compounds, after extraction with organic solvents and fractionation. The fractions obtained, in some cases, were followed by TLC, and again subjected to chromatographic procedures, including semi-preparative HPLC. Beyond the chemical composition, the biological properties were also evaluated, namely anti-microbial against several Gram-positive and Gram-negative bacteria and fungi, anti-inflammatory and anti-tumoral against several types of cancer cells. Although the biological activities detected in almost all samples, they were not outstanding ones.
Mon, 27 August 2018
ARTICLE | doi:10.20944/preprints201808.0463.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Factor Xa ( F-Xa), Cardiovascular diseases (CD), Coronary heart disease (CHD), Tissue plasminogen activator (t-PA), Urokinase (UK), Streptokinase (SK), N,N-Dimethyl formamide (DMF)
Online: 27 August 2018 (14:54:10 CEST)
A new series of 1,3,4-oxadiazoles derivatives was synthesized, characterized and evaluated for their in vitro and in vivo anti-thrombotic activity. Compounds (3a-3i) exhibited significant clot lysis with respect to negative control and reference drug streptokinase (30,000 IU) while enhanced clotting time (CT) values were observed (130-342 sec) for these tested compounds than the standard drug heparin (110 sec.). High affinity towards 1NFY with greater docking score was observed for the compounds (3a, 3i, 3e, 3d and 3h) than the control ligand RPR200095. In addition, very good inhibitory potential against factor Xa (F-Xa) was observed with higher docking scores (5612-6270) with ACE values (–189.68 to –352.28 kcal/mol) than the control ligand RPR200095 (Docking score 5192; ACE –197.81 kcal/mol. In vitro, in vivo and in silico results proposed that these newly synthesized compounds can be used as anti-coagulant agents.
Thu, 2 August 2018
REVIEW | doi:10.20944/preprints201808.0032.v1
Subject: Chemistry, Medicinal Chemistry Keywords: caffeine; methylxanthine; chlorogenic acid; caffeic acid; inflammation; antimutagen; anticancer; antioxidant
Online: 2 August 2018 (05:14:02 CEST)
Tea and coffee are the most commonly used beverages throughout the world. Both decoctions are rich in small organic molecules such as phenolics/polyphenolics, purine alkaloids, many methylxanthines, substituted benzoic and cinnamic acids. Many of these molecules are physiologically chemopreventive and chemoprotective agents against many severe conditions such as cancer, Alzheimer, Parkinsonism, inflammation, sleep apnea, cardiovascular disorders, bradycardia, fatigue, muscular relaxation, and oxidative stress. Caffeine, a purine alkaloid, is a common metabolite of both tea and coffee aqueous decoctions and its concentration in tea/coffee depends on the fermentation process, preparation of the water extract and quality of tea leaves/coffee beans. A 250 ml of a coffee cup contains 100-150 mg caffeine while the same volume of strong tea contains 25-40 mg caffeine. The present paper presents the potential of caffeine as a potent chemopreventive agent that can be used for numerous physiological disorders.
Wed, 1 August 2018
ARTICLE | doi:10.20944/preprints201808.0011.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chitosan; aldehydes; chalcone; MIC; anti-cancer activity
Online: 1 August 2018 (09:38:35 CEST)
Versatile hybrid organic polymers are prepared using two active intermediates such as cynuric chloride and chitosan derivatives. The prepared chalcones are characterized by using FT-IR, UV, and proton NMR, thermal analysis and Minimum inhibitory Concentration. Thermal stability of the synthesized hybrid polymer is found using TGA and the hybrid chitosan derivative chalcone is thermally stable up to 270 °C. The antimicrobial activity of the prepared chitosan containing chalcone moiety are find out using Minimum Inhibitory Concentration (MIC) method. The synthesized versatile chalcone shows excellent antimicrobial activity against gram-negative bacteria such as Pseudomonas aeruginosa; and Gram-positive bacteria Chalcone containing halogen moiety shows high activity (MIC 7.8 µg/mL) than the hydroxyl containing chalcone. Cytotoxicity activity of the synthesized composites shows high activity.
Sat, 28 July 2018
ARTICLE | doi:10.20944/preprints201807.0552.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Hedgehog signaling; Veratrum californicum; cyclopamine; HPLC-MS; Shh-Light II cells
Online: 28 July 2018 (23:25:31 CEST)
Veratrum californicum is a rich source of steroidal alkaloids such as cyclopamine, a known inhibitor of the Hedgehog (Hh) signaling pathway. Here we provide a detailed analysis of the alkaloid composition of V. californicum by plant part through quantitative analysis of cyclopamine, veratramine, muldamine and isorubijervine in the leaf, stem and root/rhizome of the plant. To determine if additional alkaloids in the extracts contribute to Hh signaling inhibition, we replicated the concentrations of these alkaloids observed in extracts using commercially available standards and compared the inhibitory potential of the extracts to alkaloid standard mixtures using Shh-Light II cells. Alkaloid combinations enhanced Hh signaling pathway antagonism compared to cyclopamine alone, and significant differences were observed in the Hh pathway inhibition between the stem and root/rhizome extracts and their corresponding alkaloid standard mixtures, indicating that additional alkaloids present in these extracts contribute to Hh signaling inhibition.
Mon, 23 July 2018
ARTICLE | doi:10.20944/preprints201807.0427.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Pharmacophore; 3D-QSAR; virtual screening; D3R selective antagonist; molecular docking; CNS-like
Online: 23 July 2018 (14:09:10 CEST)
The dopamine D3 receptor is an important CNS target for the treatment of a variety of neurological diseases. Selective dopamine D3 receptor antagonists modulate the improvement of psychostimulant addiction and relapse. In this study, five and six featured pharmacophore models of D3R antagonists were generated and evaluated with the post-hoc score combining two survival scores of active and inactive. Among Top 10 models, APRRR215 and AHPRRR104 were chosen based on the coefficient of determination (APRRR215: R2training = 0.80; AHPRRR104: R2training = 0.82) and predictability (APRRR215: Q2test = 0.73, R2predictive = 0.82; AHPRRR104: Q2test = 0.86, R2predictive = 0.74) of their 3D-quantitative structure–activity relationship models. Pharmacophore-based virtual screening of a large compound library from eMolecules (> 3 million compounds) using two optimal models expedited the search process 100-fold speed increase compared to the docking-based screening (HTVS scoring function in Glide) and identified a series of hit compounds having promising novel scaffolds. After the screening, docking scores, as an adjuvant predictor, were added to two fitness scores (from the pharmacophore models) and predicted Ki (from PLSs of the QSAR models) to improve accuracy. Final selection of the most promising hit compounds were also evaluated for CNS-like properties as well as expected D3R antagonism.
Mon, 16 July 2018
ARTICLE | doi:10.20944/preprints201807.0264.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Orotic hydrazide, Arylhydrazone, Mesenchymal Stem Cells, Proliferation
Online: 16 July 2018 (09:06:33 CEST)
Human mesenchymal stem cells (hMSCs) constitute of cells having potential of self-renewal and proliferation and are commonly isolated from bone marrow aspirates of large bones. The osteogenic potential of these stem cells has been extensively exploited by scientists during the last many years for the biological evaluation of synthetic scaffolds with applications in tissue engineering. Current work aimed to synthesize N-arylhydrazone derivatives of orotic acid and their evaluation as stimulators of human mesenchymal stem cells. Some of the analogs show good to moderate proliferation rate.
Sat, 14 July 2018
ARTICLE | doi:10.20944/preprints201807.0251.v1
Subject: Chemistry, Medicinal Chemistry Keywords: docking; epigenetics; epi-informatics; molecular interactions; molecular dynamics; natural products; flavonoids
Online: 14 July 2018 (17:45:16 CEST)
Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative and antineoplastic activities. Recently, different studies have shown that flavonoid have the potential to inhibit BET bromodomains. Previous reports suggest that flavonoids are putative inhibitors of the ZA channel due to their orientation and interactions with P86, V87, L92, L94 and N140. Herein, a comprehensive characterization of the binding mode of the biflavonoid amentoflavone and fisetin is discussed. To this end, both compounds were docked with BRD4 using four docking programs. Results were post-processed with protein-ligand interaction fingerprints. To gain further insights into the binding mode of the two natural products, docking results were further analyzed with molecular dynamics. Results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as basis for scaffold optimization and further characterization of flavonoids as BET inhibitors.
Fri, 13 July 2018
REVIEW | doi:10.20944/preprints201807.0226.v1
Subject: Chemistry, Medicinal Chemistry Keywords: galvanic replacement; photothermal therapy; drug delivery; nanoparticles; cancer treatment
Online: 13 July 2018 (05:11:21 CEST)
Owing to their unique physicochemical properties, nanoparticles are used in a variety of ways in the field of cancer treatment, including imaging, drug delivery, and photothermal and photodynamic therapies. The fascinating properties of nanoparticles are determined by their size, morphology, and constituent elements, and various synthetic methods and post-synthetic techniques have been applied to control these factors. Herein, we present examples of shape and composition control through galvanic replacement, a technique that exploits redox potential differences between elements to induce spontaneous ion-exchange and highlight its specific contributions to cancer treatment applications. The present article identifies the recent advances in nanoparticle formation techniques and discusses the future outlook of the field.
Fri, 6 July 2018
REVIEW | doi:10.20944/preprints201807.0116.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chemical space; chemoinformatics; data mining; databases; DNMT inhibitors; drug discovery; epi-informatics; molecular modeling; similarity searching; virtual screening
Online: 6 July 2018 (10:04:44 CEST)
Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling and other computational approaches that have been used to uncover natural products as inhibitors of DNA metiltransferases, a major family of epigenetic targets with significant potential for the treatment of cancer and several other diseases. Examples of these computational approaches include docking, similarity-based virtual screening, and pharmacophore modeling. It is also commented the chemoinformatic-based exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery and nutriepigenetics.
ARTICLE | doi:10.20944/preprints201807.0110.v1
Subject: Chemistry, Medicinal Chemistry Keywords: G-quadruplex; oxadiazole/pyridine polyheteroaryls; G4-ligands; FRET-melting; G4-FID; circular dichroism
Online: 6 July 2018 (08:28:22 CEST)
Acyclic olygoheteroaryl-based compounds represent a valuable class of ligands for nucleic acid recognition. In this regard, acyclic pyridyl polyoxazoles and polyoxadiazoles were recently identified as selective G-quadruplex stabilizing compounds with high cytotoxicity and promising anticancer activity. Herein, we describe the synthesis of a new family of polyheteroaryl oxadiazole/pyridine-ligands targeting DNA G-quadruplexes. In order to perform a structure-activity analysis identifying determinants of activity and selectivity, we followed a convergent synthetic pathway to modulate the nature and number of the heterocycles (1,3-oxazole vs 1,2,4-oxadiazole and pyridine vs benzene). Each ligand was evaluated towards secondary nucleic acid structures, which have been chosen as a prototype to mimic cancer-associated G-quadruplex structures (e.g., the human telomeric sequence, c-myc and c-kit promoters). Interesting, heptapyridyl-oxadiazole compounds showed preferential binding towards the telomeric sequence (22AG) in competitive conditions vs duplex DNA. In addition, G4-FID assays suggest a different binding mode from the classical stacking on the external G-quartet. Additionally, CD titrations in the presence of the two most promising compounds for affinity, TOxAzaPy and TOxAzaPhen, display a structural transition of 22AG in K-rich buffer. This investigation suggests that the pyridyl-oxadiazole motif is a promising recognition element for G-quadruplexes, combining seven heteroaryls in a single binding unit.
Tue, 3 July 2018
ARTICLE | doi:10.20944/preprints201807.0039.v1
Subject: Chemistry, Medicinal Chemistry Keywords: xanthohumol; biotinylated chalcones; anticancer activity; antioxidants
Online: 3 July 2018 (11:42:41 CEST)
Two biotinylated derivatives of the main hop chalcone xanthohumol (1) were prepared by a one-step synthesis via esterification using biotin and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC HCl) and 4-dimethylaminopyridine (DMAP) as coupling reagents. The products were characterized spectroscopically and their antiproliferative activity toward MCF-7, MCF-10A, HepG2, MDA-MB-231, 4T1 and Balb/3T3 cell lines was investigated using the SRB assay. For all three tested compounds the best activity was noted in the case of human (MCF-7) and mice (4T1) breast cancer cell lines (IC50 values < 9 μM). Both biotinylated derivatives showed higher anticancer activity than xanthohumol (1) towards all types of tested breast cancer cells. Double biotinylated xanthohumol (3) proved to be the most active in inhibiting cell growth, with IC50 values equal to 5.35 ± 1.5 μM for 4T1 and 8.03 ± 0.53 µM for MCF-7 cell lines. Compound 3 was also more active than 1 and 2 against liver cancer cells HepG2 (IC50 = 17.37 ± 5.1 μM), while the IC50 values for 1 and 2 were equal to 21.5 ± 2.7 and 22.1 ± 3.9 µM, respectively. 4‑O‑biotinylxanthohumol (2) was the second most active growth inhibitor, particularly with respect to MCF-7 (IC50 = 6.19 ± 1.7 μM) and 4T1 (IC50 = 6.64 ± 0.4 μM) cell lines. The antioxidant activity was evaluated using the 1.1-diphenyl-2-picrylhydrazyl radical (DPPH) method. All tested compounds (1-3) have antioxidant activity between 2.73 and 3.38 mM. It was reported for the first time that new prenylated chalcones containing the biotin moiety effectively inhibited proliferation of cancer cells in vitro.
Wed, 6 June 2018
REVIEW | doi:10.20944/preprints201806.0093.v1
Subject: Chemistry, Medicinal Chemistry Keywords: marine organisms; carbohydrate; glycoside; antioxidant; anticoagulant; anti-inflammatory; antitumor; antimicrobial
Online: 6 June 2018 (12:32:12 CEST)
The oceans harbor a great diversity of organisms, and have been recognized as an important source of new compounds with nutritional and therapeutic potential. Among these compounds, carbohydrate-based compounds are of particular interest because they exhibit numerous biological functions associated with their chemical diversity. This gives rise to new substances for the development of bioactive products. Many are the known applications of substances with glycosidic domains obtained from marine species. This review covers the structural properties and the current findings on the antioxidant, anti-inflammatory, anticoagulant, antitumor and antimicrobial activities of medium and high molecular-weight carbohydrates or glycosylated compounds extracted from various marine organisms.
Mon, 4 June 2018
ARTICLE | doi:10.20944/preprints201711.0091.v2
Subject: Chemistry, Medicinal Chemistry Keywords: asymmetrical mono-carbonyl analogs of curcumin (AMACs); synthesis; cytotoxicity, Vero; HeLa; MCF7; cell lines
Online: 4 June 2018 (08:19:03 CEST)
A series of novel asymmetrical mono-carbonyl analogs of curcumin (AMACs) were synthesized and evaluated for cytotoxic activity using the brine shrimp lethality test (BSLT) and the methyl thiazolyl tetrazolium assay against Vero, HeLa, and MCF7 cell lines. The structures of the synthesized compounds were confirmed by Fourier transform infrared spectrophotometry (FTIR), 1H-nuclear magnetic resonance (NMR), 13C-NMR, and mass spectral data. The results of the cytotoxicity evaluation showed that the synthesized compounds exhibited moderate to very high toxic activity in BSLT, requiring a concentration of 13.06–714.49 µg/mL to kill half the population. Most of the compound exhibited cytotoxic activity against HeLa cell lines, comparable to the activity of cisplatin with a concentration of the synthesized compounds required to inhibit 50% of the growth of the cell lines (IC50) value of 40.65–95.55 µM, and most of the compounds tested against MCF7 cell lines exhibited moderate to very high cytotoxic activity (IC50 value 7.86–35.88 µM). However, the selectivity index of the compounds was low, less than 1–1.96. Among the synthesized compounds, compound 1b showed the highest cytotoxicity and selectivity against MCF7 cell lines. Compound 1b could be considered for further development to obtain more active and selective chemotherapeutic agents against breast cancer.
Wed, 30 May 2018
ARTICLE | doi:10.20944/preprints201805.0437.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Jatropha pelargoniifolia; alkaloids; flavonoids; coumarinolignans; diterpenes; anti-inflammatory; antinociceptive; antipyretic; free radical scavenging
Online: 30 May 2018 (06:15:42 CEST)
Extensive phytochemical and chromatographic analysis of different root fractions of Jatropha pelargoniifolia Courb. (Euphorbiaceae) resulted in the isolation and identification of 22 distinct secondary metabolite compounds. Two new compounds, 6-hydroxy-8-methoxycoumarin-7-O-β-D-glycopyranoside and (3-(2-(methylamino) ethyl)-1H-indol-2-yl) methanol, were isolated and identified for the first time from a natural source. In addition, other known compounds, such as hovetricoside C and N-methyltryptamine were isolated from Euphorbiaceae, and hordenine, N-methyltyramine, their salts, cynaroside and linarin were identified in Jatropha spp. for the first time. Some isolated metabolites, such as β-sitosterol, β-sitosterol glucoside, curcusons D and C, naringenin, apigenin, cleomiscosins B and A, spruceanol, propacin, jatrophadiketone, and uracil were previously identified in various Jatropha species. The structures of the isolated compounds were determined using different spectroscopic techniques. The anti-inflammatory, antinociceptive, antipyretic, and antioxidant activities were evaluated for some adequately available isolated compounds. Compounds showed significant antinociceptive activity compared with the standard analgesic drug indomethacin. The edema size was significantly reduced (p< 0.05–0.001) in the animals treated with low doses (5 and 10 mg/kg) of the isolated compounds compared with those treated with a high dose (100 mg/kg) of standard anti-inflammatory drug (phenylbutazone). Furthermore, all tested compounds showed a significant (p< 0.05–0.001) reduction in the rectal temperature of hyper-thermic mice.
Tue, 29 May 2018
ARTICLE | doi:10.20944/preprints201805.0419.v1
Online: 29 May 2018 (08:54:56 CEST)
A heterobifunctional reactive oxygen species (ROS)-responsive linker for directed drug assembly onto and delivery from a quantum dot (QD) nanoparticle carrier was synthesized and coupled to doxorubicin using EDC/sulfo-NHS coupling. The doxorubicin conjugate was characterized using 1H NMR and LC-MS and subsequently reacted under conditions of ROS formation (Cu2+/H2O2) resulting in successful and rapid thioacetal oxidative cleavage which was monitored using 1H NMR. The deprotected amine linker is amenable to peptide or protein conjugation prior to QD assembly or to direct conjugation to cognate reactive groups on ligands that cap the QD surface.
Mon, 14 May 2018
ARTICLE | doi:10.20944/preprints201805.0189.v1
Subject: Chemistry, Medicinal Chemistry Keywords: G-quadruplex DNA; interactions; berberine and palmatine analogues; chemotherapy; NMR; FRET and MST assays
Online: 14 May 2018 (11:44:10 CEST)
In this article/review, the selective interactions of several berberine and palmatine derivatives with various DNA G-quadruplex structures are reported. These derivatives were constructed starting from two natural compounds, berberine and palamatine, through specific synthetic passages following two different schemes for each of them and using several substituents. The details of these synthesis are also described. Indeed, the study of the interactions of these derivative compounds with various G-quadruplex forming sequences was carried out by means of various structural and biochemical techniques. The results show that the presence of suitable side chains are very useful to improve the interaction of the ligands with G-quadruplex structures. Thus, since G-quadruplex formation is promoted by these compounds, which have never been reported before, these may be tested as potential anticancer drugs.
Tue, 8 May 2018
ARTICLE | doi:10.20944/preprints201805.0133.v1
Subject: Chemistry, Medicinal Chemistry Keywords: antioxidant potential; molecular docking; molecular descriptors; binding free energy; free radicals; oxidative stress
Online: 8 May 2018 (15:38:38 CEST)
The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. The in silico study performed here was developed to evaluate the antioxidant potential of two molecules, ZINC08706191 (Z91) and ZINC08992920 (Z20), with recognized epithelial anticancer potential. Molecular docking, chemical-quantum calculations and Pearson's correlation were performed. The Z91 and Z20 molecules showed lower binding free energy (ΔG) values for the receptor-ligand interaction than the reference molecules (caffeine – CAF and ascorbic acid – AA), and better results for values of molecular descriptors correlated with ΔG, resulting in a decrease of ΔG. Strong correlations were observed between ΔG values for the five receptors evaluated and ΔG values of the potential epithelial anticancer activity available in literature. These results attest to the significant antioxidant potential of the Z91 and Z20 molecules and their strong relation with the potential epithelial anticancer activity and may be indicated for further analysis in relation to the control of oxidative stress and epithelial anticancer activity.
Fri, 4 May 2018
ARTICLE | doi:10.20944/preprints201805.0085.v1
Subject: Chemistry, Medicinal Chemistry Keywords: 7-acetamido-2-aryl-5-bromoindoles; trifluoroacetylation; cytotoxicity; apoptosis; tubulin polymerization; molecular docking
Online: 4 May 2018 (07:47:06 CEST)
Structurally related 7-acetyl-2-aryl-5-bromoindoles 2a–d and the 7-acetamido-2-aryl-5-bromoindoles 4a–d as well as their corresponding 3-trifluoroacetyl–substituted derivatives 5a–d and 5e–h were evaluated for potential antigrowth effect in vitro against the human lung cancer (A549) and cervical cancer (HeLa) cells. All of the 3-trifluoroacetyl–substituted 7-acetamido-2-aryl-5-bromoindoles 5e–h were found to be more active against both cell lines when compared to the chemotherapeutic drug, Melphalan. The most active compound 5g induced apoptosis in a caspase dependent manner for both cell lines. Compounds 5e–h were found to significantly inhibit tubulin polymerization. Molecular docking of 5g into the colchicine-binding site suggests that the compounds bind to tubulin by different type of interactions including pi-alkyl, amide-pi stacked and alkyl interactions as well as hydrogen bonding with the protein residues to elicit anticancer activity.
Mon, 23 April 2018
ARTICLE | doi:10.20944/preprints201804.0282.v1
Subject: Chemistry, Medicinal Chemistry Keywords: aminosteroid; aminocycloartane; alkaloid; 3D-QSAR; CoMFA; antitrypanosomal activity; cytotoxicity
Online: 23 April 2018 (11:02:16 CEST)
As part of our research for new leads against human African trypanosomiasis (HAT), we report on a 3D-QSAR study for antitrypanosomal activity and cytotoxicity of aminosteroid-type alkaloids recently isolated from the African medicinal plant Holarrhena africana A. DC. (Apocynaceae), some of which are strong trypanocides against Trypanosoma brucei rhodesiense (Tbr) with low toxicity against mammalian cells. Fully optimized 3D molecular models of seventeen congeneric Holarrhena alkaloids were subjected to a comparative molecular field analysis (CoMFA). CoMFA models were obtained for both, the anti-Tbr and cytotoxic activity data. Model performance was assessed in terms of statistical characteristics (R2, Q2 and P2 for partial least squares (PLS) regression, internal cross-validation (leave-one-out) and external predictions (test set), respectively, as well as the corresponding SDEP and F-values). With R2=0.99, Q2=0.83 and P2=0.79 for anti-Tbr activity and R2=0.94, Q2=0.64, P2=0.59 for cytotoxicity against L6 rat skeletal myoblasts, both models were of good internal and external predictive power. The regression coefficients of the models representing the most prominent steric and electrostatic effects on anti-Tbr and for L6 cytotoxic activity were translated into contour maps and analyzed visually, allowing suggestions for possible modification of the aminosteroids to further increase the antitrypanosomal potency and selectivity. Very interestingly, the 3D-QSAR model established with the Holarrhena alkaloids also applied to the antitrypanosomal activity of two aminocycloartane-type compounds recently isolated by our group from Buxus sempervirens L. (Buxaceae), which indicates that these structurally similar natural products share a common SAR and, possibly, mechanism of action with the Holarrhena steroids. This 3D-QSAR study has thus resulted in plausible structural explanations of the antitrypanosomal activity and selectivity of aminosteroid- and aminocycloartane-type alkaloids as an interesting new class of trypanocides and may represent a starting point for lead optimization.
Thu, 5 April 2018
REVIEW | doi:10.20944/preprints201804.0071.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Sulfenic acids; Sulfoxides; Sulfones; Disulfides; Alliin derivatives; Glycoconjugates; Pyrimidine derivatives.
Online: 5 April 2018 (16:30:18 CEST)
Sulfenic acids as small molecules are too unstable to be isolated and their transient nature offers the possibility to involve them in concerted processes that lead to the obtainment of functional groups such as sulfoxides, sulfones and disulfides. All these functions are present in a number of natural and synthetic drugs and can represent structural motives inducing biological relevant properties. In this small review the generation and reactions of sulfenic acid bearing naturally occurring residues are described. Carbohydrate and aminoacid-derived sulfenic acids have been used in concerted addition to triple bonds to obtain alliin derivatives and thiosugars in enantiomerically pure form. Glycoconjugates with sulfinyl, sulfonyl and disulfane functional groups and pyridine-derived disulfides have been obtained from bis and tris-sulfinyl precursors of sulfenic acids. Small families of such compounds have been subjected to preliminary biological tests. Starting from the evidence that the control of molecular architecture and the presence of suitable functional groups can play a significant role on the exhibition of biological properties, apoptotic effects on malignant cells by glycoconjugates and inhibitory activity against the important human pathogen S. aureus by pyrimidine-derived disulfides have been found.
Mon, 19 March 2018
ARTICLE | doi:10.20944/preprints201803.0142.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chitosan; thermoresponsive hydrogel; nitric oxide; s-nitrosothiols; biocompatibility; antimicrobial; Pseudomonas aeruginosa; pluronic F127
Online: 19 March 2018 (07:25:27 CET)
Nitric oxide (NO) is involved in physiological processes, including vasodilatation, wound healing and antibacterial activities. As NO is a free radical, designing drugs to generate therapeutic amounts of NO in controlled spatial and time manners is still a challenge. In this study, the NO donor S-nitrosoglutathione (GSNO) was incorporated into the thermoresponsive Pluronic F-127 (PL) - chitosan (CS) hydrogel, with an easy and economically feasible methodology. CS is a polysaccharide with known antimicrobial properties. Scanning electron microscopy, rheology and differential scanning calorimetry techniques were used for hydrogel characterization. The results demonstrated that the hydrogel has a smooth surface, thermoresponsive behavior and good mechanical stability. The kinetics of NO release and GSNO diffusion from GSNO-containing PL/CS hydrogel demonstrated a sustained NO/GSNO release, in concentrations suitable for biomedical applications. The GSNO-PL/CS hydrogel demonstrated a concentration-dependent toxicity to Vero cells, and antimicrobial activity to Pseudomonas aeruginosa (minimum inhibitory concentration and minimum bactericidal concentration values of 0.5 µg·mL-1 of hydrogel, which corresponds to 1 mmol·L-1 of GSNO). Interestingly, the concentration range in which the NO-releasing hydrogel demonstrated an antibacterial effect was not found to be toxic to the Vero mammalian cell. Thus, the GSNO-PL/CS hydrogel is a suitable biomaterial for topical NO delivery applications.
Wed, 7 March 2018
ARTICLE | doi:10.20944/preprints201803.0050.v1
Subject: Chemistry, Medicinal Chemistry Keywords: carboxamide; carbohydrazine; antibacterial; antifungal; molecular docking; Schiff base; NMR; IR
Online: 7 March 2018 (05:11:10 CET)
The article describes facile one-pot, hi-yielding reactions to synthesize substituted 3,4-dimethyl-1H-pyrrole-2-carboxamide (3a–m) and carbohydrazide analogues (5a–l) as potential antifungal and antimicrobial agents. The structural integrity and purity of the synthesized compounds were assigned based on appropriate spectroscopic techniques. Synthesized compounds were assessed in vitro for antifungal and antibacterial activity. The compound 5h, 5i and 5j were found to be the most potent against A. fumigatus, with MIC value of 0.031 mg/mL. The compound 5f bearing a 2,6-dichloro group on the phenyl ring was found to be the most active broad spectrum antibacterial agent with MIC value of 0.039 mg/mL. The mode of action of the most promising antifungal compounds (one representative from each series; 3j and 5h) was established by their molecular docking to the active site of sterol 14α-demethylase. Molecular docking studies revealed a highly spontaneous binding ability of the tested compounds in the access channel away from catalytic heme iron of the enzyme, which suggested that the tested compounds inhibit this enzyme and would avoid heme iron related deleterious side effects observed with existing antifungal compounds.
Thu, 1 March 2018
ARTICLE | doi:10.20944/preprints201803.0003.v1
Subject: Chemistry, Medicinal Chemistry Keywords: derivatives of N-phenylanthranilic acids; anti-inflammatory activity; flexible molecular docking; microsomal prostaglandin E synthase-1
Online: 1 March 2018 (04:58:58 CET)
The aim of the study was to determine the possibility of suppression of the prostaglandin synthesis by new derivatives of N-phenylanthranilic acids; they inhibit the activity of the microsomal prostaglandin E synthase-1 (mPGES-1) enzyme using the method of a flexible molecular docking. For the docking studies the crystallographic structural models with high resolution from Protein Data Bank were used: mPGES-1 in the complex with glutathione (pdb code 4AL0). A flexible molecular docking was carried out using the Molecular Operating Environment (MOE) software package. According to the results of the docking studies four scoring functions were calculated (Affinity dG Scoring, Alpha HB Scoring, London dG Scoring, GBVI/WSA dG Scoring). The values of the scoring functions calculated indicate the thermodynamic probability and energy favorability of forming complexes between molecules of the substances under research and the specified receptor, in which arrangement of ligands in the active site of the receptor and residues of amino acids of side chains are of similar geometry and types of binding of the known inhibitors of mPGES-1 determined on the basis of the crystallographic studies.
Thu, 22 February 2018
ARTICLE | doi:10.20944/preprints201802.0142.v1
Subject: Chemistry, Medicinal Chemistry Keywords: reactive selenium species; arylmethyl selenocyanate; cellular thiolstat; antimicrobial; anticancer; ESKAPE; multidrug resistance
Online: 22 February 2018 (11:34:22 CET)
Selenocyanates form an interesting class of organic selenium compounds as they serve as multifunctional agents (being the precursors of seleninic acids and diselenides in synthetic chemistry and as antimicrobial and cytotoxic agent in biology) and, due to their similarity with better known thiocyanates promise high biological activity. Yet whilst selenocyanates are common in synthetic chemistry, they are rarely considered in pharmaceutical design. Arylmethyl selenocyanates (1-13) have been synthesized and an insight into their structural properties using X-ray crystallography has been obtained. The compounds subsequently have been evaluated for their potential antimicrobial, nematicidal and cytotoxic activity. ADMET properties in vitro, using mutagenicity (AMES) and permeability (PAMPA) tests, have been determined. The compounds exhibit pronounced activity against various strains of bacteria (both Gram-positive and Gram-negative) and yeasts. Among them, benzylselenocyanate (1) represents the most active anti-ESKAPE agent, with potent antibacterial activity, especially against multidrug resistant MRSA strains (HEMSA 5). Our results demonstrate that the arylmethyl selenocyantes are not only non-mutagenic but also possess moderate cytotoxic activity against cancer cells.
Fri, 2 February 2018
ARTICLE | doi:10.20944/preprints201802.0021.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Keywords: one-pot synthesis; single crystal x-ray crystallography; oxovanadium(IV); zinc(II); spectroscopic studies; in vitro antibacterial studies.
Online: 2 February 2018 (16:00:10 CET)
Abstract Antibacterial activities can be improved using mixed ligands. Mixed ligands involved in this research are sodium sulfadiazine (Na-sfz) and dithiocarbamate (ai-dtc). One-pot synthesis was used to synthesize ligand of aniline dithiocarbamate (ai-dtc) and the corresponding coordination compounds of [VO(sfz)(ai-dtc)] and [Zn(sfz)(ai-dtc)]. Crystals of ai-dtc, which grew from the solution when refrigerated after five days, were diffracted with technique of single crystal x-ray crystallography to reveal the structure. Other characterization techniques involving physicochemical parameters, FT-IR, UV-Vis and NMR (1H NMR and 13C NMR) were carried out on ligands of ai-dtc, sfz and corresponding coordination compounds. Differences in results of FT-IR, UV-Vis and NMR between ligands and their respective metal ions confirmed the coordination. The in vitro antibacterial studies showed that the ligands (not the metal complexes) had modest activity against Gram negative bacteria: Staphylococcus aureus, whereas, the coordination compounds had modest activities against the Gram negative bacteria: Escherichia coli and Pseudomonas aeruginosa.