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Preprint ARTICLE | doi:10.20944/preprints202309.2078.v1

High-molecular-weight dissolved organic matter enhanced phosphorus availability in paddy soils: Evidence from field and microcosm experiments

Hai-Bo Wang, Xi-Peng Liu, Bing-Jie Jin, Yu-Chen Shu, Cheng-Liang Sun, Yong-Guan Zhu, Xian-Yong Lin

Subject: Environmental And Earth Sciences, Soil Science Keywords: Soil phosphorus availability; Dissolved organic matter; Organic fertilizer; Competitive adsorption; Molecular weight

Online: 3 October 2023 (03:36:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.2178.v1

Expression, characterisation, homology modelling and molecu-lar docking of a novel M17 family leucyl-aminopeptidase from Bacillus cereus CZ

Jie Liu, Tangbing Cui

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: leucyl-aminopeptidase; Bacillus cereus; expression; homology modeling; molecular docking

Online: 2 October 2023 (11:18:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0052.v1

Molecular Mimicry between SARS-CoV-2 proteins and human self-antigens related with autoimmune central nervous system (CNS) disorders

Elisa Gouvea Gutman, Renan Amphilophio Fernandes, Jéssica Vasques Raposo-Vedovi, Andreza Lemos Salvio, Larissa Araujo Duarte, Caio Faria Tardim, Vinicius Gabriel Coutinho Costa, Valeria Coelho Santa Rita Pereira, Marcos Martins Da Silva, Fabrícia Lima Fontes-Dantas³, Soniza Vieira Alves-Leon

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: COVID-19; SARS-CoV-2; Molecular mimicry; immune tolerance; autoimmune disorders; central nervous system.

Online: 2 October 2023 (11:10:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0061.v1

Handheld Ultra-Fast duplex PCR assays and Lateral flow detection and identification of Leishmania parasites for cutaneous leishmanisis diagnosis

Insaf Bel Hadj Ali, Yusr Saadi Ben Aoun, Zeineb Hammami, Oumayma Rhouma, Ahmed Sahbi Chakroun, Ikram Guizani

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Cutaneous leishmaniases; Molecular diagnosis; Point of care; Leishmania; Molecular target; Palm PCR; Duplex PCR; Lateral Flow immunoassay

Online: 2 October 2023 (09:43:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0042.v1

A Molecular Dynamics Simulation Study of In- and Cross-Plane Thermal Conductivity of Bilayer Graphene

Rafat Mohammadi, Mohammad Reza Ghaderi, Ebrahim Hajian

Subject: Engineering, Mechanical Engineering Keywords: bilayer graphene; in-plane and cross-plane thermal conductivities; non-equilibrium molecular dynamics; anisotropic thermal transport

Online: 2 October 2023 (05:09:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0013.v1

The Reversal Effect of P-Glycoprotein-Mediated Tumor Multidrug Resistance by Pyxinol and 24S-Pyxinol Amino Acid Ester Derivatives

Luying Tan, Peng Gao, Zhuoqiao Li, Chencheng Gao, Xiaoyu Geng, Qianyun Wang, Daohao Tang, Fang Wang, Jinping Liu

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: tumor multidrug resistance; P-glycoprotein; pyxinol amino acid ester derivatives; molecular docking; metabolomics

Online: 1 October 2023 (08:32:50 CEST)

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(1) Background: The typical transporter protein, P-glycoprotein (P-gp), has been proven to be associated with multidrug resistance (MDR). Pyxinol and 24S-Pyxinol amino acid ester derivatives had been demonstrated to be promising P-gp inhibitors for reversal of tumor MDR in KBV cells, however, their roles in MDR reversal in other tumor-resistant cells are still unclear. (2) Methods: In the present study, we synthesized 40 amino acid ester derivatives of Pyxinol and 24S-Pyxinol. The MDR reversal effects of these derivatives were evaluated in A549/Tax, MCF-7/ADR, and HCT-8/VCR cells using the CCK-8 assay. Subsequently, western blot assay, intracellular Rhodamine123 (Rh123) accumulation assay and P-gp ATPase activity assay were utilized to investigate the effects of active compound on P-gp. Molecular docking was used to predict the possible binding patterns of active compound to P-gp. Moreover, based on UPLC-Q/TOF-MS cellular metabolomics technology to identify endogenous differential metabolites and metabolic pathways associated with tumor MDR effects of the active compound. (3) Results: The results of the CCK-8 assay showed that compounds 8, 14, 16, 17, 18, 23, 25, 34, 36, 37 exhibited strong MDR reversal effect in A549/Tax, MCF-7/ADR and HCT-8/VCR cells, which were screened by reversal fold (RF) greater than 5. Among them, 10 μM of derivative 37 (new compound) showed the outstanding activity (RF: 15.31) in reversing MDR in A549/Tax cells. Compound 37 could act as a substrate for P-gp and inhibit the efflux function of P-gp by competitively binding to the binding site of antitumor drugs. Meanwhile, the molecular docking results confirmed that compound 37 was identified to under-go high-affinity binding to the drug binding site of P-gp. In addition, 14 endogenous differential metabolites and 6 metabolic pathways involved closely associated with the reversal of tumor MDR effects of compound 37 were identified. (4) Conclusions: Overall, a new candidate compound 37 (24S-3-L-threonyl-Pyxinol) could be provided for reversing tumor MDR by this study.

Preprint ARTICLE | doi:10.20944/preprints202309.2103.v1

Developments in Genetics – a Better Management of Ovarian Cancer Patients

Ovidiu Virgil Maioru, Viorica Elena Radoi, Laurentiu Camil Bohîlțea, Madalin Codrut Coman, Anca Elena Eftenoiu, Andra Dan, Livia Mălina Burtavel, Iulian Andrei Hotinceanu, Emilia Maria Severin

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Ovarian; Molecular; Genetics; Pathways; Diagnosis; Screening; Panel

Online: 29 September 2023 (12:00:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.2043.v1

Snapshot of the Phylogenetic Relationships among Avian Pox-Viruses Circulating in Portugal between 2017 and 2023

Daniela Santos, Teresa Fagulha, Margarida Dias Duarte, Ana Duarte, Fernanda Ramos, Sílvia C Barros, Tiago Luís, Ana Margarida Henriques

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Avipoxvirus; molecular characterization; phylogenetic analysis; viral introduction; Portugal

Online: 29 September 2023 (08:32:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1917.v1

In Silico Drug Re-Purposing Studies for the Discovery of Novel MbtA Inhibitors

Gourav Rakshit, Abanish Biswas, Venkatesan Jayaprakash

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Mycobacterium; Antibiotic resistance; Drug re-purposing; MbtA; Siderophores; Molecular Docking; Molecular Dynamics; PCA analysis

Online: 28 September 2023 (13:28:39 CEST)

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Tuberculosis (TB) continues to pose a global health challenge, exacerbated by the rise of drug-resistant strains. The development of new TB therapies is an arduous and time-consuming process. To expedite the discovery of effective treatments, computational structure-based drug re-purposing has emerged as a promising strategy. From this perspective, conditionally essential targets present a valuable opportunity, and the mycobactin biosynthesis pathway stands out as a prime example highlighting the intricate response of Mycobacterium tuberculosis (Mtb) to changes in iron availability. This study focuses on the re-purposing and revival of FDA-approved drugs (library) as potential inhibitors of MbtA, a crucial enzyme in mycobactin biosynthesis in Mtb conserved among all species of mycobacteria. Literature suggests this pathway to be associated with drug efflux pumps, which potentially contribute to drug resistance. This makes it a potential target for antitubercular drug discovery. Herein we utilized cheminformatics and structure-based drug repurposing approaches, viz., molecular docking, dynamics, and PCA analysis, to decode the intermolecular interactions and binding affinity of the FDA-reported molecules against MbtA. The virtual screening revealed ten molecules with significant binding affinities and interactions with MbtA. These drugs, originally designed for different therapeutic indications (4: antiviral, 3: anticancer, 1: CYP450 inhibitor, 1: ACE inhibitor, and 1: leukotriene antagonist), are repurposed as potential MbtA inhibitors. Furthermore, our study explores the binding modes and interactions between these drugs and MbtA, shedding light on the structural basis of their inhibitory potential. Principal component analysis highlighted significant motions in MbtA-bound ligands, emphasizing the stability of the top Protein-Ligand Complexes (PLCs). This computational approach provides a swift and cost-effective method for identifying new MbtA inhibitors, which can subsequently undergo validation through experimental assays. This streamlined process is facilitated by the fact that these compounds are already FDA-approved and have established safety and efficacy profiles. This study has the potential to lay the groundwork for addressing the urgent global health challenge at hand, specifically in the context of combating Antimicrobial Resistance (AMR) and Tuberculosis (TB).

Preprint REVIEW | doi:10.20944/preprints202308.0706.v2

Dr Jekyll and Mr Hyde: From Two Branches of Immune Response to Three Types of Interferon Response

Brent Brown, Chinua Imarogbe, Ingo Fricke, Pascal Mensah

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Interferon; Innate; Adaptive; Genetic; Molecular

Online: 26 September 2023 (11:35:53 CEST)

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Interferons were the original prototype cytokine system discovered in 20th-century research. As the name implies, they were originally thought to be synthesised and secreted between cells. Thanks to technological advances, the processes involved in protein secretion can be explained comparatively more clearly at both the genetic and biochemical levels. The discovery of interferon (IFN) occurred when genetic research was still in its infancy. Franklin and Wilkins discovered the structure and function of deoxyribonucleic acid (DNA) at the same time as Crick and Watson; however, Isaacs and Lindemann, two scientists, described the first IFN in 1957. Mutations can be caused by inherent genetic protein synthesis and during infection as well as within IFN regulation pathways affecting cell proliferation. This remains central to host cell IFN synthesis and effects through IFN protein receptor subunits defined by 6 protein domains. Type II IFN is key to immune cell function secreted by a variety of immune cells, mainly natural killer (NK) as well as T cells. Single–stranded and/or double–stranded RNA/DNA viruses, as well as bacterial infections (e.g., Escherichia coli) and fungal infections (e.g., Aspergillus), also affect IFN regulation. Pathogenic proteins utilise intra/extracellular proteins that sense foreign antigens like Toll–like Receptors (TLRs), affected by mutations within the human cellular IFN transduction pathways. Since the discovery of the third IFN type in 2003, when immune cell phenotypes were further characterised, questions remain about the immunological mechanisms contributing to the regulation of the innate and adaptive host immune system. Alterations in the synthesis of type I/II/III host IFNs can differentially and beneficially alter homeostatic cellular pathways in pathological disease, with type I IFN being synthesised in cancer as well as by homeostatic cells. Therefore, considered here are the overall IFN molecular, cell regulatory mechanisms in the context of immune cell research developments.

Preprint ARTICLE | doi:10.20944/preprints202309.1706.v1

Multi-faceted Exploration of Novel Isoxazolidine Derivatives: Synthesis, Characterization, Molecular Docking, Dynamic Simulation, and Computational Investigations

Sabir Mohammed Salih, Huda A. Basheer, Jesus Vicente de Julián-Ortiz, Haydar A. Mohammad-Salim

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: isoxazolidine derivatives; 1,3-dipolar cycloaddition; α-aryl-N-methyl nitrones; Density Functional Theory (DFT); Electron Localization Function (ELF); CDFT indices; docking; molecular dynamics; EGFR; binding energy

Online: 26 September 2023 (04:37:56 CEST)

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Preprint REVIEW | doi:10.20944/preprints201902.0122.v6

The Future of Leishmaniasis Treatment: Protein Targets and Beyond

Carlos A. Padilla, María J. Álvarez, Emmanuel Campo, José G. Severiche, Aldo F. Combariza

Subject: Biology And Life Sciences, Biophysics Keywords: Leishmania; Trypanosoma; Molecular Dynamics; Theoretical Chemistry

Online: 22 September 2023 (11:07:35 CEST)

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Preprint CONCEPT PAPER | doi:10.20944/preprints202309.1514.v1

Development of Photonic Multi-Sensing Systems Based on Molecular Gates Biorecognition and Plasmonic Sensors: The PHOTONGATE Project

Oscar Nieves Paniagua, David Ortiz de Zárate, Elena Aznar, Isabel Caballos, Eva Garrido, Ramón Martínez Mañez, Fabian Dortu, Damien Bernier, Beatriz Mengual-Chuliá, F. Xavier López-Labrador, Jens J. Sloth, Katrin Löschner, Lene Duedahl-Olesen, Natalia Prado, Martín Hervello, Armando Menéndez, Rainer Gransee, Thomas Klotzbuecher, Maria Clara Henriques Baptista Gonçalves, Fahimeh Zare, Ana Fuentes López, Isabel Fernández-Segovia, José M. Barat, Jaime Salcedo, Sara Recuero, Santiago Simón, Ana Fernández Blanco, Sergio Peransi, Maribel Gómez-Gómez, Amadeu Griol

Subject: Physical Sciences, Optics And Photonics Keywords: Photonics; Molecular gates; Localized surface plasmonic resonance (LSPR); porous silica; bio-sensing; microfluidics; respiratory viruses; chemical contaminants

Online: 22 September 2023 (08:28:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1376.v1

Circulation of Dengue Virus Serotype 1 genotype V and Dengue Virus Serotype 2 genotype III in Tocantins State, Northern Brazil, 2021-2022

Ueric José Borges de Souza, Ygor da Silva Miranda Macedo, Raíssa Nunes dos Santos, Franciano Dias Pereira Cardoso, Jucimária Dantas Galvão, Evgeni Evgeniev Gabev, Ana Cláudia Franco, Paulo Michel Roehe, Fernando Rosado Spilki, Fabrício Souza Campos

Subject: Biology And Life Sciences, Virology Keywords: DENV; Genomic surveillance; Epidemiology; molecular clock; SNPs; arboviruses

Online: 20 September 2023 (10:42:22 CEST)

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The dengue virus (DENV) is an arbovirus belonging to the Flaviviridae family; the species comprises four antigenically distinct serotypes (DENV–1, DENV–2, DENV–3, and DENV–4), which are further subdivided into genotypes. The virus is transmitted to humans through mosquito bites, primarily from the Aedes spp. genus. Dengue is endemic in various parts of the world, including tropical and subtropical regions of Asia, Latin America, Africa, and Oceania. In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of arboviral disease cases, particularly dengue. This study aimed to monitor DENV circulation within the state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. During this period, both DENV-1 and DENV-2 serotypes were identified. Our findings confirm the circulation of DENV serotypes 1 and 2 in Tocantins, affecting males and females equally, with younger age groups (4 to 43 years old) being the most susceptible. Phylogenetic analysis revealed that the circulating viruses belong to DENV–1 genotype V American and DENV–2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 Genotype V sequenced here is closely related to genomes previously sequenced in the state of São Paulo. Regarding DENV-2 genotype III genomes, these are clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. In both cases, our results suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the significant impact of major population centers in Brazil on virus dispersion, including other Latin-American countries and the USA. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here reveal the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of the DENV and the ongoing significance of surveillance efforts in supporting public health policies.

Preprint ARTICLE | doi:10.20944/preprints202309.1298.v1

Molecular Epidemiology of Staphylococcus aureus in Oral and Rectal Swabs from Bats in Pakistan

S Attaullah, Shahzad Ali, Kendra L. Phelps, Kevin J. Olival

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: antibiotic resistance; Chiroptera; Staphylococcus aureus; microbiota; molecular identification; risk factors; bacteria

Online: 20 September 2023 (04:52:53 CEST)

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In Pakistan, bats are one of the dominant mammals that play an important role in the ecosystem in terms of pollination, seed dispersal, and control of pest insects. Bats have also played an im-portant role in the emergence and transmission of zoonotic pathogens; however, most current studies focus on viral pathogens, not potential bacterial pathogens. This study was designed to estimate the prevalence and antibiotic profiling of Staphylococcus (S.) aureus in oral and rectal samples from bats captured in northern Pakistan and to determine the factors associated with in-fection. Two hundred individual bats of five species: Pipistrellus javanicus (n = 17), Pipistrellus pipistrellus (n = 10), Rhinopoma microphyllum (n = 48), Rousettus leschenaultii (n = 124), and Scotophilus kuhlii (n = 1) were captured for non-lethal collection of oral and rectal samples to iso-late S. aureus. Bats were sampled from three sites: a natural cave, a man-made castle, and an an-imal shed, in Khyber Pakhtunkhwa and Punjab provinces. Oral (n = 200) and rectal (n = 200) swabs were collected from each individual bat using sterile cotton swabs specifically for use in bacteriological studies. Each isolate of bacteria was identified by using phenotypic tests and con-firmed as S. aureus based on PCR assay. Out of a cumulative four hundred samples, 80 swabs were positive for S. aureus including 47 rectal and 33 oral swabs. Prevalence of S. aureus infection varied significantly among species, with Rousettus leschenaultii exhibiting the highest prevalence (n = 77; 37.90%). In addition to bat species, prevalence varied significantly among habitats but not between sex, age class, or reproductive status. This study confirmed the occurrence of S. aureus in oral and rectal microbiota of bats in Pakistan. Importantly, S. aureus isolates showed resistance to tetracycline, gentamicin, and erythromycin and carried resistant genes such as TetK, TetM, Erma, and aacA-D. In this regard, efforts should be taken to educate the local communities on how to minimize exposure to an antibiotic-resistant bacterial pathogen through contact with bats while simultaneously increasing the awareness of protecting bats as a vital component of our ecosystem.

Preprint BRIEF REPORT | doi:10.20944/preprints202309.1217.v1

Occurrence of Anthracnose Caused by Colletotrichum gloeosporioides on Lucky Bamboo in China

Qin Xiong, Yaxin Zhang, Xueying Wang, Yulin Qian, Wei Wu, Jinwen Li, Qirui Zeng

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Dracaena braunii; Colletotrichum gloeosporioides; internal transcribed spacer (ITS); glyceraldehyde-3-phosphate dehydrogenase (GAPDH); molecular characterization; pathogenicity test

Online: 19 September 2023 (13:29:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1250.v1

Evolution of Intrinsic Disorder in Protein Loops

Fizza Mughal, Gustavo Caetano-Anollés

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chronology; early evolution; flexibility; intrinsically disordered region; loop prototype; molecular function; protein evolution; protein structure; structural domain

Online: 19 September 2023 (11:22:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1302.v1

Molecular Identification of Xanthomonas oryzae pv. oryzae and Bacterial Leaf Blight Resistance Genes Xa5, and Xa21 in Cultivated Rice Accessions Benin

Chimène Nadège Mahoussi Nanoukon, Koffi David Hambada Montcho, Antoine Abel Missihoun, Kéllya Laurinzo Déguénon, Bignon Meyrix Paméla Franzel Loumédjinon, Emilienne ZINSOU, Emilienne Zinsou, Réel Gael Fael Hougbélagnon, Amed Havivi, Lamine Baba-Moussa, Lambert Gustave Djédatin

Subject: Biology And Life Sciences, Plant Sciences Keywords: Bacterial blight; Xanthomonas oryzae pv. oryzae; molecular characterization; resistance genes

Online: 19 September 2023 (11:00:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1275.v1

OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria

Alexandre Le Loarer, Laurent Dufossé, Jérome Bignon, Michel Frédérich, Allison Ledoux, Mireille Fouillaud, Anne Gauvin-Bialecki

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: OSMAC method; marine-derived actinobacteria; molecular network; natural product; specialized metabolites; cytotoxic activity; antiplasmodial activity

Online: 19 September 2023 (08:50:39 CEST)

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Preprint REVIEW | doi:10.20944/preprints202309.1260.v1

Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS): Myth or Reality? The State of the Art on a Controversial Disease

Saverio La Bella, Giovanna Scorrano, Marta Rinaldi, Armando Di Ludovico, Francesca Mainieri, Marina Attanasi, Alberto Spalice, Francesco Chiarelli, Luciana Breda

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: PANDAS; Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections; PANDAS syndrome; neuropsychiatric disorder; streptococci; molecular mimicry; CaM kinase; striatal cholinergic interneurons; obsessive-compulsive disorder; streptococcal infection; tic; tics

Online: 19 September 2023 (07:09:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1225.v1

Exploration of Temperature-Induced Quantum Proton Tunneling Probability in PCR-Mediated DNA Amplification

Joseph De Luna

Subject: Physical Sciences, Biophysics Keywords: genetics; molecular biology; biophysics; quantum mechanics

Online: 19 September 2023 (05:18:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1199.v1

Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design

Haiyan Jin, Jongwan Kim, Onju Lee, Hyein Kim, Kyoung Tai No

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: protein-protein interaction; fragment molecular orbital method; polo-like kinase 1; molecular dynamics simulation

Online: 19 September 2023 (03:58:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0795.v1

Prediction of Thermostability of Enzymes Based on the AAindex Database and Machine Learning

Gaolin Li, Lili Jia, Kang Wang, Tingting Sun, Jun Huang

Subject: Chemistry And Materials Science, Chemical Engineering Keywords: Artificial Intelligence; Machine Learning; Thermostability; Molecular Dynamics Simulation; Extended Sequence; Directed Evolution

Online: 12 September 2023 (16:57:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0673.v2

Immunopathogenesis of Orthopoxviridae: Insights into Immunology from Smallpox to Monkeypox (Mpox)

Brent Brown, Chinua Imarogbe, Ingo Fricke, Alexander Gonzalez, Pascal Mensah

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Orthopoxvirus; Molecular; Health; Immunology; Monkeypox; Smallpox; Innate; Adaptive; Cells

Online: 12 September 2023 (02:45:52 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0695.v2

Filoviridae: Insights into Immune Responses to Ebolavirus

Brent Brown

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Adaptive; Ebola; Filoviridae; Immunology; Innate; Molecular

Online: 12 September 2023 (02:40:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0233.v1

Adsorption of the Low Density Lipoproteins on the Azobenzene-containing Polymer Brush: Modelling by the Coarse-grained Molecular Dynamics

Jaroslav Ilnytskyi, Dmytro Yaremchuk, Orest Komarytsia

Subject: Physical Sciences, Condensed Matter Physics Keywords: low density lipoproteins; hemoperfusion; azobenzene; adsorption; molecular dynamics

Online: 6 September 2023 (15:11:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0323.v1

utPCR: A Strategy for Highly Specific and Absolutely Quantitative Detection of Single Molecules within Only Minutes

Rui Wang, Ying Liu, Shuaiwei Chen, Linlin Bai, Kaiming Guo, Yanan Pang, Feng Qian, Yongfang Li, Li Ding, Yongming Wang

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Ultrafast PCR; droplet digital PCR (ddPCR); single-molecule detection; bloodstream infection; absolute quantification; molecular diagnosis

Online: 6 September 2023 (04:20:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints202309.0163.v1

Medical Application of Molecular Hydrogen to Diabetic Kidney Disease: Therapeutic Potential through Improvements in Mitochondrial Function

Shin-ichi Hirano, Yusuke Ichikawa, Bunpei Sato, Yoshiyasu Takefuji, Fumitake Satoh

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: molecular hydrogen; diabetic kidney disease; mitochondrial dysfunction; oxidative stress; in-flammation; reactive oxygen species; medical application

Online: 4 September 2023 (11:16:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1958.v1

Geometrical Selection of GaN Nanowires Grown by Plasma-Assisted MBE on Polycrystalline ZrN Layers

Karol Olszewski, Marta Sobanska, Vladimir G. Dubrovskii, Egor D. Leshchenko, Aleksandra Wierzbicka, Zbigniew R. Zytkiewicz

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: GaN nanowires; ZrN buffer layers; molecular beam epitaxy; nanowire orientation; geometrical selection

Online: 30 August 2023 (04:11:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1885.v1

A Comprehensive Comparative Analysis of Deep Learning based Feature Representations for Molecular Taste Prediction

Yu Song, Sihao Chang, Jing Tian, Weihua Pan, Lu Feng, Hongchao Ji

Subject: Chemistry And Materials Science, Food Chemistry Keywords: Cheminformatics; Taste prediction; Machine learning; Deep learning; Molecular feature representation

Online: 29 August 2023 (03:06:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1856.v1

In Vitro and In Silico Evaluation of the Anti-leishmanial Activity of Novel Synthetic Chalcones

Fernando Ferreira Leite, Luis Cezar Rodrigues, Bruno Hanrry Melo De Oliveira, Gabrielly Diniz Duarte, Maria Denise Leite Ferreira, Natália Ferreira De Sousa, Shayenne Eduarda Ramos Vanderley, Leonardo Lima Cardoso, Tatjana Souza Lima Keesen, Rodrigo Santos Aquino De Araújo, Luciana Scotti, Marcus Tullius Scotti, Francisco Jaime Bezerra Mendonça-Junior

Subject: Biology And Life Sciences, Parasitology Keywords: chalcones; anti-leishmanial activity; molecular docking; molecular dynamic

Online: 28 August 2023 (10:27:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1696.v1

Molecular Resonance Imaging of the CAIX expression in Mouse Mammary Adenocarcinoma Cells

Claudia Quattrociocchi, Alberto Mangia, Silvio Aime, Valeria Menchise, Daniela Delli Castelli

Subject: Biology And Life Sciences, Life Sciences Keywords: MRI; Molecular Imaging; CAIX; Breast cancer; Gd-contrast agent; liposomes

Online: 24 August 2023 (09:39:11 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1723.v1

Research Progress on the Effect of Nitrogen on Rapeseed between Seed Yield and Oil Content and Its Regulation Mechanism

Jiarong Zhu, Wenjun Dai, Biyun Chen, Guangqin Cai, Xiaoming Wu, Guixin Yan

Subject: Biology And Life Sciences, Plant Sciences Keywords: rapeseed; nitrogen; yield; oil content; molecular mechanisms

Online: 24 August 2023 (07:24:14 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1673.v1

An integrative taxonomic analysis of Honduran Central America parasite isolated from non-ulcerated cutaneous leishmaniasis points to Leishmania (Leishmania) poncei n. sp. (Kinetoplastea: Trypanosomatidae)

Fernando Tobias Silveira, Thiago Vasconcelos dos Santos, Gabriela Venícia Aruajo Flores, Carmen Maria Sandoval Pacheco, Wilfredo H. Sosa Ochoa, Edivaldo Costa Sousa, Concepcion Zuniga Valeriano, Vania Lucia Ribeiro Da Matta, Claudia Maria Castro Gomes, Patricia K Ramos, Luciana V Lima, Marliane B Campos, Carlos Eduardo P Corbett, Márcia Dalastra Laurenti

Subject: Biology And Life Sciences, Parasitology Keywords: Non-ulcerated cutaneous leishmaniasis; visceral leishmaniasis; biological, epidemiological, clinical-immunological, and molecular taxonomic analysis; Leishmania (Leishmania) poncei; Honduras; Central America

Online: 24 August 2023 (03:43:47 CEST)

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Non-ulcerated cutaneous leishmaniasis (NUCL) is an atypical and peculiar clinical form of the disease that was first described by Ponce et al. (1988) in Honduras (Central America), where iso-lated or disseminated popular and/or nodular skin lesions are commonly seen in adolescents and young adults. Leishmania (L.) chagasi was then incriminated as the causal agent of the disease, as well as of American visceral leishmaniasis (AVL), although NUCL has been shown to be more prevalent than AVL in the region. Considering, however, the dubious taxonomic character of the causal agent of NUCL, as there is no evidence of this form of disease associated with L. (L.) cha-gasi in South America, this study aimed to carry out a retrospective taxonomic analysis on a se-ries of studies on the diagnostic approach to the Honduran parasite in loco (El Tigre island, Amapala municipality, west coast of Honduras), where taxonomic characters of a biological (in vitro and in vivo), epidemiological (vector and canine reservoir), clinical-immunological (im-munopathological features of in situ skin lesion and systemic infection) and molecular (ge-nomic/phylogenetic analyses) nature were considered. The findings, particularly those of mo-lecular nature, such as: the Honduran parasite showed to be more ancestral (molecular clock analysis of the DNA polymerase alpha subunit gene) than all viscerotropic ones [L. (L.) chagasi, L. (L.) donovani and L. (L.) infantum], as well as presenting an absolutely unprecedented structural variation on chromosome 17 and the highest frequency of genomic SNPs (more than twice the number seen in the Brazilian parasite), in addition to representing a different phylogenetic lin-eage (mainly in the NJ - RNA Pol II tree) from those viscerotropic ones, have pointed to the characterization of a new leishmanine parasite, Leishmania (Leishmania) poncei n. sp. (Kinetoplas-tea: Trypanosomatidae), in honor of Professor Ponce, who was the first researcher to describe NUCL in Honduras.

Preprint ARTICLE | doi:10.20944/preprints202308.1606.v1

Effect of Graphene on Nickel Surface Relaxation: Molecular Dynamics Simulation

Sergiy Konorev, Vitalii Yanchuk, Ivan Kruhlov, Andrii Orlov, Sergii Sidorenko, Igor Vladymyrskyi, Sergey Prikhodko, Svitlana Voloshko

Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: molecular dynamic simulation; interplane distance; graphene; surface relaxation; surface reconstruction; packing density

Online: 23 August 2023 (04:40:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1486.v1

Effectiveness of the use of Polymer in High Performance Concrete Containing Silica Fume

Alya Harichane, Nadhir Toubal Seghir, Paweł Niewiadomski, Lukasz Sadowski, Michał Cisiński

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: Polycarboxylate-ether superplasticizer (PCE); Rheology; Molecular architecture; High performance concrete; Carboxylic groups

Online: 22 August 2023 (12:15:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1503.v1

Neuroprotective Properties of Oleanolic Acid – Computational-Driven Molecular Research Combined with In Vitro and In Vivo Experiments

Katarzyna Stępnik, Wirginia Kukula-Koch, Wojciech Plazinski, Magda Rybicka, Kinga Gawel

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: molecular dynamic simulations; molecular docking; neuroprotection; acetylcholinesterase; zebrafish

Online: 22 August 2023 (08:58:41 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.1518.v1

A Molecular Modeling and Molecular Dynamics Simulations Investigation of the Potential Therapeutic Applications of Main Protease Inhibitors for SARS-CoV-2

Aganze Gloire-Aime Mushebenge, Samuel C. Ugbaja, Nonkululeko Avril Mbatha, Rene M. Khan, Hezekiel M. Kumalo

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: SARS-CoV-2; main protease; inhibitors; molecular modeling; molecular dynamics simulations; binding energy calculation; ADME properties; potential therapeutics; drug discovery

Online: 22 August 2023 (07:19:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1475.v1

Molecular and Pharmacokinetic Aspects of Acetylcholinesterase Inhibitory Potential of the Oleanane-type Triterpenes and Their Glycosides

Katarzyna Stępnik, Wirginia Kukula-Koch, Wojciech Płaziński

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: acetylcholinesterase inhibitory test; molecular docking; blood-brain barrier permeation; memory impairment; AChE inhibition kinetics

Online: 21 August 2023 (13:46:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1369.v1

Unraveling the role of molecular profiling in predicting treatment response in stage III colorectal cancer patients: Insights from the IDEA International Study

Ippokratis Messaritakis, Eleni Psaroudaki, Konstantinos Vogiatzoglou, Maria Sfakianaki, Pantelis Topalis, Ioannis Iliopoulos, Dimitrios Mavroudis, John Tsiaoussis, Nikolaos Gouvas, Maria Tzardi, Ioannis Souglakos

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: colorectal cancer; stage III; molecular profiling; IDEA study; whole exome sequencing; bioinfor-matics

Online: 18 August 2023 (10:51:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1329.v1

Atomic Insights into the Structural Properties and Displacement Cascades in Ytterbium Titanate Pyrochlore (Yb2Ti2O7) and High Entropy Pyrochlores

M. Mustafa Azeem, Qingyu Wang

Subject: Chemistry And Materials Science, Ceramics And Composites Keywords: molecular dynamics simulation; ytterbium pyrochlore oxides; nuclear waste substrate; displacement cascades; lattice constants; high entropy alloys; LAMMPS

Online: 18 August 2023 (07:22:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1208.v1

Complete Mitochondrial Genome Sequencing of the Calanoid Copepod Bestiolina similis (Sewell, 1914) from the Chennai Coast

Sivakumar Kandhasamy, MD Anwar Nawaz, Abdus Saboor

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Mitochondrial genome; Calanoida; Arthropod phylogeny; Molecular taxonomy; Chennai coast

Online: 16 August 2023 (11:18:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1143.v1

Photo-Programmable Processes in Bithiophene–Azobenzene Monolayers on Gold Probed by Simulations

Vladyslav Savchenko, Moufdi Hadjab, Alexander S. Pavlov, Olga Guskova

Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: photoisomerization; azobenzene; conjugated oligomer; molecular switch; chemisorbed monolayer; charge transfer; molecular modeling; organic electronics

Online: 16 August 2023 (10:28:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1098.v1

A Shortcut From Genome to Drug: The Employment of Bioinformatic Tools to Find New Targets for Gastric Cancer Treatment

Daiane M.S. Brito, Odnan G. Lima, Felipe P. Mesquita, Emerson L. da Silva, Maria E. A. de Moraes, Rommel M. R. Burbano, Raquel C. Montenegro, Pedro F.N. Souza

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Transcriptional meta-analysis; molecular docking; RT-qPCR; Bioinformatics; Structural-based virtual screening

Online: 15 August 2023 (11:47:28 CEST)

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Gastric cancer (GC) is a highly heterogeneous, complex disease and the fifth most common cancer worldwide (about one million cases and 784 000 deaths worldwide in 2018). CG is lately diagnosed and guarantees a poor prognosis for GC (the 5-year survival rate is less than 20%, but in early detection can reach 90%). This study evaluated the transcriptional profile in tumor gastric samples to find genes highly expressed during tumor establishment and use the related proteins as targets to find new anticancer molecules. Data was collected at Gene Expression Omnibus (GEO) bank to obtain 3 dataset matrices that analyze gastric tumor tissue versus normal gastric tissue, performed microarray using GPL570 platform, and from different sources. The genes found in silico analysis were confirmed in several lines of GC cells by RT-qPCR. The protein data bank was used to find the correspondent proteins. Then a structural-based virtual screening was done to find molecules, and docking analysis was done using the DockThor server. Our results of transcriptomic analysis, together with RT-qPCR, confirm the high expression of the genes AJUBA, FBXL13, CCDC69, CD80 and NOLC1 in GC lines. Based on that, the correspondent proteins were used in SBVS analysis. Five molecules, one each target, MCULE-2386589557-0-6, MCULE-7343047040-0-1, MCULE-5230409338-0-3, MCULE-9178344200-0-1 and MCULE -5881513100-0-29. All molecules have favorable pharmacokinetic, pharmacodynamic and toxicological properties. Molecular docking analysis revealed that the molecules interact with proteins in critical sites for their activity. Using a virtual screening approach, a molecular docking study was performed for proteins encoded by genes that play important roles in cellular functions for carcinogenesis. Combining a systematic collection of public microarray data with a comparative meta-profiling, RT-qPCR, SBVS, and molecular docking analysis provided a suitable approach to find genes involved in GC and work the correspondent protein to strive for new molecules with anticancer properties.

Preprint ARTICLE | doi:10.20944/preprints202308.1075.v1

Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli

Siyanda S. Ngema, Solomuzi H. Khumalo, Michael C. Ojo, Ofentse J. Pooe, Tsolanku Sidney Maliehe, Albertus K. Basson, Evelyn Madoroba

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Nocardiopsis dassonvillei SOD(B)ST2SA2; Antibacterial activity; Molecular docking; Listeria monocytogenes

Online: 15 August 2023 (11:45:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0997.v1

An Integrated Computational and Experimental Approach to Formulate Tamanu Oil Bigels as Anti-Scarring Agent

Megha Krishnappa, Sindhu Abraham, Sharon Caroline Furtado, Shwetha Krishnamurthy, Aynul Rifaya, Kumarappan Chidamabaram, Parasuraman Pavadai

Subject: Medicine And Pharmacology, Pharmacy Keywords: Bigel; Calophyllum inophyllum; Calanolide A; Piscean collagen; Tamanu oil; Molecular Docking; ADMET

Online: 14 August 2023 (08:47:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0975.v1

H(N3)dap (Hdap = 2,6-diaminopurine) Recognition by Cu₂(EGTA): Structure, Physical Properties and DFT-Calculations of [Cu₄(μ-EGTA)₂(μ-H(N3)dap)₂(H₂O)₂]·7H₂O

Homa Mousavi, María Eugenia García-Rubiño, Duane Choquesillo-Lazarte, Alfonso Castiñeiras, Antonio Frontera, Juan Niclós-Gutiérrez

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Diaminopurine; Molecular recognition; supramolecular chemistry; Cu-chemistry; DFT calculations

Online: 14 August 2023 (04:17:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0933.v1

Precision Medicine in Pancreatic Ductal Adenocarcinoma: The Impact of Targeted Therapies on Survival of Patients Harboring Actionable Mutations

Anthony Tarabay, Alice Boileve, Cristina Smolenschi, Leony Antoun, Marine Valery, Alina Fuerea, Audrey Perret, Pascal Burtin, Simona Cosconea, Hichem Belkhodja, David Malka, Valérie Boige, Antoine Hollebecque, Michel Ducreux

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: PDAC; precision medicine; gene alterations; molecular profiling; molecular targeted therapies

Online: 11 August 2023 (11:06:09 CEST)

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Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of death by cancer worldwide. Mostly diagnosed with locally advanced or metastatic disease, patients lack treatment options. Gene alterations (GAs) are frequently observed in PDAC; some of which are considered for molecular targeted therapies (MTTs), with potential clinical benefits and im-proved outcomes. However, the applicability of molecular profiling (MP) for precision medicine in PDAC remains to be demonstrated. Methods: We conducted a retrospective analysis of all patients, aged ≥18 years with histologi-cally confirmed PDAC, who underwent tumor MP between 2010 and 2020 in our institution as part of personalized medicine trials. The primary study endpoint was overall survival (OS), and (minimal follow-up was 6 months after MP. Results: Of 115 eligible patients, MP was successful in 102 patients (89%). KRAS mutations were the most frequent GAs, mostly G12D. Based on ESCAT classification, actionable GAs were found in 29 patients (28%), involving mainly BRCA1 or BRCA2 (5 [18%]), HER2 (5 [18%]), MTAP (5 [18%]), and FGFR (3 [11%]). Only 12 of these 29 patients (41%, or 10% of the whole population) received MTTs, with a median progression-free survival of 1.6 months. Median OS was 19 months in patients with actionable GAs treated with MTTs (n=12 [11.8%]), 14 months in patients with actionable GAs treated with standard therapies (n=17 [16.7%]), and 17 months in patients without actionable GAs treated with standard therapies (n=73 [71.5%]; p=0.26). The absence of liver metastases was associated with better OS (HR=0.471, p=0.01). The highest OS following MTT was observed in patients with BRCA mutations treated with olaparib. Interpretation: Actionable GAs were found in more than a quarter of patients with advanced PDAC. Overall, targeting actionable GAs with MTTs was not associated with improved OS in this retrospective study with limited patient numbers. However, selected GA/MTT combinations (e.g., BRCA mutations/olaparib) were associated with a better outcome.

Preprint REVIEW | doi:10.20944/preprints202308.0887.v1

In Silico Drug Discovery: The Next Frontier in the Fight Against SARS-CoV-2

Calvin R. Wei, Godwin C. Lang’at

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Drug Discovery; Drug Repurposing; SARS-CoV-2; COVID; Molecular Docking; QSAR; Molecular Dynamic; Virtual Screening; Drug Design

Online: 11 August 2023 (09:03:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0879.v1

Enhanced risk stratification in early-stage endometrial cancer: Integrating Molucular-L1CAM Classification and Simplified L1CAM/p53 Categorization

Seungyeon Joe, Miseon Lee, Jun Kang, Joori Kim, Sook-Hee Hong, Sung Jong Lee, Keun Ho Lee, Ahwon Lee

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: early-stage endometrial cancer; molecular classification; L1CAM; risk stratification; prognosis

Online: 11 August 2023 (08:38:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.0768.v1

Adipose Tissue, Non-communicable Diseases and Physical Exercise: An Imperfect Triangle.

Francisco A Monsalve, Daniel R Gonzalez, Barbra Fernández Tapia, Fernando Delgado López

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: adipose tissue; adipocytokines; overweight; obesity; molecular mechanism; treatments; myocyotokines

Online: 10 August 2023 (05:04:41 CEST)

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Adipose tissue has acquired considerable importance due to its role in maintaining body homeostasis. Beyond storing energy, adipose tissue is essential in numerous processes of energy metabolism, food intake, endocrine and immunological functions as well as neromodulatory functions by secreting hormones that participate in the regulation of homeostasis and being responsive to soluble proteins secreted by other tissues. An imbalance of these functions will generate structural and functional changes in the adipose tissue, favouring the secretion of deleterious adipocytokines that benefit a pro-inflammatory state, allowing the development of metabolic and cardiovascular diseases. Obesity is a disease that has increased rapidly in recent decades and is caused by environmental, hormonal, and genetic factors, which probably work in combination. Environmental factors that contribute to the increase in obesity include decreased physical activity, associated with increased screen time, increased accessibility and consumption of foods rich in fats and sugars. Weight loss should be recommended for all obese patients and overweight patients with comorbidities. For many patients who need to lose weight for medical reasons, the initial goal is to lose 5-10% of their body weight in the first 6 months. A common theme worldwide has been the development of professional guidelines for the control and treatment of obesity and in Chile, the Chilean Society of Metabolic and Bariatric Surgery led the process of adopting the adult obesity clinical practice guideline, which establishes changes in the approach to managing obesity as a chronic disease, with an emphasis on multifactorial lifestyle interventions that include dietary changes, increased physical activity, and behavioural modifications. Pharmacotherapy, medical devices, and bariatric surgery are other options for patients who need additional interventions, so the objective of this review is to know the pathophysiological mechanisms of obesity from its origin to the current treatments available for treatment.

Preprint ARTICLE | doi:10.20944/preprints202308.0727.v1

A Novel Antimicrobial Peptide, Dermaseptin-SS1, with Anti-Proliferative Activity, Isolated from the Skin Secretion of Phyllomedusa tarsius

Xiaonan Ma, Yuping Chen, Anmei Shu, Yangyang Jiang, Xiaoling Chen, Chengbang Ma, Mei Zhou, Tao Wang, Tianbao Chen, Chris Shaw, Lei Wang

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: antimicrobial peptide; dermaseptin; molecular cloning; analogue design

Online: 9 August 2023 (10:45:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0694.v1

Calibration Technique for MBE Growth of Long Wavelength InAlAs/InGaAs Quantum Cascade Lasers

Piotr Gutowski, Iwona Sankowska, Maciej Bugajski, Grzegorz Sobczak, Aleksandr Kuźmicz, Kamil Pierściński

Subject: Chemistry And Materials Science, Nanotechnology Keywords: quantum cascade laser; molecular beam epitaxy; InAlAs/InGaAs

Online: 8 August 2023 (17:07:25 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.0434.v1

Assessing the Potential Contribution of in Silico Studies in Discovering Drug Candidates that Interact with Various SARS-CoV-2 Receptors

Aganze Gloire-Aimé Mushebenge, Samuel Chima Ugbaja, Nonkululeko Avril Mbatha, Hezekiel M. Kumalo

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: In silico studies; drug discovery; SARS-CoV-2; molecular docking; virtual screening; molecular dynamics simulations; drug candidates; antiviral activity; receptor-ligand complex; drug design

Online: 4 August 2023 (11:11:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0429.v1

Fibrinolytic Enzyme from Green Microalgae: A New Potential Drug for Thrombolytic Therapy?

Yanara Alessandra Santana Moura, Ariadne Tennyle Vieira De Souza, Páblo Eugênio da Costa e Silva, Marllyn Marques Da Silva, Ana Lúcia Figueiredo Porto, Raquel Pedrosa Bezerra

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: thrombosis; kinetic parameters; cell growth; protein purification; biomass production; Chlorophyceae; agro-industrial sub-product; extraction methods; molecular weight; chromatography

Online: 4 August 2023 (10:49:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0305.v1

Coupled Electrostatic and Hydrophobic Destabilisation of the Gelsolin-Actin Complex Enables Facile Detection of Ovarian Cancer Biomarker Lysophosphatidic Acid

Katharina Davoudian, Shayon Bhattacharya, Damien Thompson, Michael Thompson

Subject: Physical Sciences, Biophysics Keywords: ovarian cancer; lysophosphatidic acid; gelsolin; actin; lipid-protein interaction; predictive molecular modelling

Online: 3 August 2023 (10:07:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0232.v1

BMAP-27 Peptide Reduces Proliferation and Increases Apoptosis in Primary and Metastatic Colon Cancer Cell Lines

Alakesh Das, Dikshita Deka, Nabajyoti Baidya, Antara Banerjee, Atil Bisgin, Suman Adhikari, Sheikh F. Ahmad, Asim K Duttaroy, Surajit Pathak

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Colon Cancer; Apoptosis; BMAP-27; Peptide therapy; Molecular Docking; MD-Simulation

Online: 2 August 2023 (13:22:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0231.v1

1-Piperidine Propionic Acid as an Allosteric Inhibitor of Protease Activated Receptor-2

Monica Chinellato, Matteo Gasparotto, Santina Quarta, Mariagrazia Ruvoletto, Alessandra Biasiolo, Francesco Filippini, Luca Spiezia, Laura Cendron, Patrizia Pontisso

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: G protein-coupled receptors, Protease Activated Receptor2; Allosteric modulator; 1-piperidinepropionic acid; Molecular Dynamics.

Online: 2 August 2023 (13:20:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0177.v1

Benzylfentanyl as a Surrogate Template for Fentanyl-Selective Imprinted Polymers

Md Ragib Hasan, David A. Spivak

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: fentanyl, benzylfentanyl; molecularly imprinted polymer (MIP); narcotics; molecular recognition

Online: 2 August 2023 (09:53:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0184.v1

Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Result in a Decrease in PCR Efficiency

Olga A. Zasedateleva, Sergey A. Surzhikov, Viktoriya E. Kuznetsova, Valeriy E. Shershov, Victor E. Barsky, Alexander S. Zasedatelev, Alexander V. Chudinov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: C5-modified dUTPs; A and B family DNA polymerases; PCR amplification; X-ray structure; molecular modeling; non-covalent interactions

Online: 2 August 2023 (08:21:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0141.v1

Design, BSA Binding, Stopped-Flow Kinetic, Mechanistic, Molecular Docking, and Biological Evaluation of Hy-droxychloroquine-Based Chitosan Nanoparticles for Enhancing Anticancer Activity in A549 Lung Cancer Cell Line

Rudi van Eldik, Fawzia I. Elshami, Hadeer A. Shereef, Ibrahim M El-Mehasseb, Shaban Y. Shaban

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: A549 lung cancer; nanoparticles; cell-penetration, drug affinity, dissociation constants; molecular docking; antibacterial; hydroxychloroquine

Online: 2 August 2023 (04:54:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.2118.v1

Antioxidant, Collagenase Inhibitory and Antibacterial Effects of Bioactive Peptides Derived from Enzymatic Hydrolysate of Ulva australis

You-An Kang, Ye-Jin Kim, Sang-Keun Jin, Hwa-Jung Choi

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: multi-functional properties; U. australis hydrolysate; peptide; molecular docking

Online: 1 August 2023 (03:27:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1891.v1

A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping to Advance Translational Mitogenomics

Jane Shen-Gunther, Rutger S. Gunther, Hong Cai, Yufeng Wang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics 1; hypervariable region 2; mitochondrial DNA 3; mitochondrial genomics 4; mitochondrial haplogroup 5; molecular anthropology 6; next generation sequencing 7; oncogenetics 8; phylogeography 9

Online: 27 July 2023 (09:29:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1457.v1

In Vitro and In Silico Analysis of Alpha-Amylase Inhibitory Activity of Ethanolic Extract of Adhatoda vasica Leaves

Chandrajeet Kumar Yadav, Sandhya KC, Shankar Thapa, Kamal Kandel, Laxmi Shrestha, Anjan Palikhey, Ashish Lamsal

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Anti-diabetic; Alpha amylase; Adhatoda vasica; Molecular docking

Online: 21 July 2023 (10:09:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1164.v1

The Norepinephrine Transporter - Gβγ Subunit Interaction Promotes Norepinephrine Efflux through the Transporter: In silico and Functional Studies

Luis Dinamarca-Villarroel, Angelica Fierro, Gonzalo E Torres

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Norepinephrine, Norepinephrine transporter, molecular dynamics, efflux, Gβγ subunit.

Online: 18 July 2023 (09:13:37 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202307.0953.v1

Response of Cultured Primary Human Gingival and Periodontal Ligament Cells to Angiotensin II and IL1β Challenges

Thais Francini Garbieri, Thiago José Dionísio, Bella Luna Colombini-Ishikiriama, Rafaela Alves da Silva, Vanessa Soares Lara, Sandra Helena Penha de Oliveira, Maria Helena Fernandes, Andrew Seth Greene, Carlos Ferreira Santos

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: Periodontium; Renin-Angiotensin System; Receptors; Angiotensin; Primary Cell Culture; Molecular Biology; Inflammation Mediators

Online: 14 July 2023 (11:15:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0605.v1

Insight and Recommendations for Fragile X Premutation Associated Conditions from the 5th International Conference on FMR1 Premutation

Flora Tassone, Dragana Protic, Emily Allen, Alison D. Archibald, Anna Baud, W Ted Brown, Dejan B. Budimirovic, Jonathan Cohen, Brett Dufour, Rachel Eiges, Nicola Elvassore, Lidia V. Gabis, Samantha J Grudzien, Deborah Hall, David Hessl, Abigail Hogan, Jessica Ezzell Hunter, Peng Jin, Poonnada Jiraanont, Jessica Klusek, R. Frank Kooy, Claudine M Kraan, Cecilia Laterza, Andrea Lee, Karen Lipworth, Molly Losh, Danuta Z Loesch, Reymundo Lozano, Marsha Mailick, Apostolos Manolopoulos, Verónica Martínez-Cerdeño, Yingratana Amabel McLennan, Robert M. Miller, Alice Montanaro, Matthew W. Mosconi, Sarah Potter, Melissa Raspa, Susan M. Rivera, Katharine Shelly, Peter K. Todd, Katarzyna Tutak, Jun Yi Wang, Anne C Wheeler, Tri Indah Winarni, Marwa Zafarullah, Randi Hagerman

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: FMR1 premutation; FXPAC; FXTAS; FXAND; FXPOI; FMR1 molecular and clinical

Online: 10 July 2023 (10:27:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0556.v1

Multi-scale Friction Simulation of Carbon Nanotube-Reinforced Nitrile Butadiene Rubber Composites Based on Molecular Dynamics and Finite Element Analysis

Ce Liang, Changgeng Shuai, Xue Yang

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: multi-scale model; CNT/NBR composites; molecular dynamics; finite element analysis; friction coefficient

Online: 10 July 2023 (07:10:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0482.v1

Discovery of TBX20 As a Novel Gene Underlying Atrial Fibrillation

Ning Li, Yan-Jie Li, Xiao-Juan Guo, Shao-Hui Wu, Wei-Feng Jiang, Dao-Liang Zhang, Kun-Wei Wang, Li Li, Yu-Min Sun, Ying-Jia Xu, Yi-Qing Yang, Xing-Biao Qiu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: cardiac arrhythmia; atrial fibrillation; medical genetics; molecular biology; linkage analysis; transcriptional regulation; TBX20; biological assay

Online: 7 July 2023 (10:53:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0483.v1

Photoswitchable Molecular Units with Tunable Non-Linear Optical Activity: A Theoretical Investigation

Aggelos Avramopoulos, Heribert Reis, Demeter Tzeli, Robert Zaleśny, Manthos Papadopoulos

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: (Hyper)polarizability; Density Functional Theory; Molecular Switches; Photochromism; Two-Photon absorption; Dithienylethene; bis(ethylene-1,2-dithiolato; Excited-state Energy Transfer

Online: 7 July 2023 (10:49:58 CEST)

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A series of derivatives, involving two dithienylethene (DTE), groups, connected by several molecular linkers (bis(ethylene-1,2-dithiolato)Ni- (NiBDT), naphthalene, quasilinear oligothiophene chains) are investigated with the aid of computational quantum chemistry methods. This involves the computation of the second- and third-order nonlinear optical properties, i.e. molecular hyperpolarizabilities of the designed/selected derivatives. These properties can be efficiently controlled by DTE switches, in connection with light of appropriate frequency. We found that NiBDT, as a linker, is associated with a greater contrast, in comparison to naphthalene, between the first and second hyperpolarizabilities of the “open-open” and the “closed-closed” isomers. This is explained by invoking the low lying excited states of NiBDT. It has been found that the second hyperpolarizability can be used as an index, which follows the structural changes induced by photochromism. The two-photon absorption, which is related to the imaginary part of second hyperpolarizability, has also been investigated for the S0S1 transition. Furthermore, the intramolecular excited-state energy transfer (EET) is studied as well as the overlap between the absorption and emission spectra of the donor and acceptor groups of the molecules. The electronic coupling, VDA, between the donor and acceptor fragments, as well as the emission spectrum of the donor and the absorption spectrum of the acceptor have been computed, assuming a Förster type transfer mechanism. EET is a critical factor governing the photochromism. Two methods were used to compute VDA, one based on linear response and one based on the distributed multipole analysis (DMA); both techniques give very similar results for the dominating Coulomb contribution. For NiBDT as the linker a low VDA value has been computed. We found that VDA is affected by the molecular geometry. Our results clearly show that the linker strongly influences the communication between the open-closed DTE groups and thus, photochromism. The present computations show that full photochromism is attained in derivatives where two DTE groups are linked by a tetrathiophene chain, in agreement with experiment. The sensitivity of molecular linear and nonlinear optical properties upon photochromism can assist with the identification of the molecular isomers.

Preprint ARTICLE | doi:10.20944/preprints202307.0489.v1

Autoantigens of Nervous System and Human Coronavirus Antigens: Is There a Possibility for Molecular Mimicry?

Natalia Y. Gavrilova, Muslimbek G. Normatov, Lidia A. Soprun, Vladimir J. Utekhin, Tamara V. Fedotkina, Leonid P. Churilov

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: molecular mimicry; post-COVID-19 syndrome; SARS-CoV-2; human coronaviruses; autoimmunity; autoantigens of nervous system

Online: 7 July 2023 (10:41:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.0229.v1

The Unmet Diagnostic and Treatment Needs in Large Cell Neuroendocrine Carcinoma of the Lung

Catalin Buium, Serban Negru, Diana Ionescu, Mircea Dediu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: large cell; neuroendocrine; lung cancer; pathology; molecular subtypes; diagnosis; treatment

Online: 4 July 2023 (12:28:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0218.v1

Interaction of Hoechst 33342 with Lipid Membranes at Different pH Values

Margarida M. Cordeiro, Hugo A. L. Filipe, Patrícia dos Santos, Jaime Samelo, João P. Prates Ramalho, Luís M. S. Loura, Maria J. Moreno

Subject: Biology And Life Sciences, Biophysics Keywords: biomembranes; cationic amphiphiles; fluorescent probe; membrane partition; molecular dynamics simulations; POPC

Online: 4 July 2023 (11:44:18 CEST)

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Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain DNA of living cells. To do so, it needs to interact with and permeate through cell membranes. The pH of biological media may vary quite significantly and this influences H33342 ionization state, and may change its rate of permeation through biomembranes. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics simulations. While probe insertion occurs for all ionization states, with similar overall equilibrium location, orientation was found to depend on the probe charge, with the neutral form lying mostly parallel and the doubly charged displaying a significant tilt relative to the membrane plane. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy of interaction is negative and is larger at lower pH values. This suggests efficient hydrogen bonding between the probe and the lipid, namely for the protonated +2 form. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from water and octanol partition. This highlights the distinction between lipophilicity and hydrophobicity, and the importance of considering association with lipid bilayers when predicting the affinity for biomembranes.

Preprint ARTICLE | doi:10.20944/preprints202307.0197.v1

Polymorph Dependent Initial Thermal Decay Mechanism of 1,1-Diamino-2,2-Dinitroethylene (FOX-7)

Huaiyu Jiang, Qingjie Jiao, Chaoyang Zhang

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: molecular dynamics; polymorph; thermal decomposition

Online: 4 July 2023 (11:34:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0096.v1

Mismatch Repair, p53, and L1 Cell Adhesion Molecule States Influence the Response to Chemotherapy in Advanced and Recurrent Endometrial Cancer

Jung Chul Kim, Byungsoo Ahn, Yong Jae Lee, Eun Ji Nam, Sang Wun Kim, Sunghoon Kim, Young Tae Kim, Eunhyang Park, Jung-Yun Lee

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: Endometrial neoplasms; molecular classification; Neural cell adhesion molecule L1 (L1CAM); Prognosis; Recurrence; Survival

Online: 4 July 2023 (03:52:30 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202307.0049.v1

N'-(5-bromofuran-2-carbonyl)isonicotinohydrazide

Ersya Yanu Ramadhani, Nur Pasca Aijijiyah, Eko Santoso, Lukman Atmaja, Mardi Santoso

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: furan carboxamide; organic synthesis; furoic acid; isoniazid; molecular docking; COX-2 inhibitor

Online: 3 July 2023 (10:19:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0010.v1

Use of Biomarkers to Improve 28-Day Mortality Stratification in Patients with Sepsis and SOFA≤6

Jaume Baldirà, Juan Carlos Ruiz-Rodríguez, Adolfo Ruiz-Sanmartin, Luis Chiscano, Alejandro Cortés, Diego Angeles-Sistac, Roser Ferrer-Costa, Imma Comas, Yolanda Villena, M.Nieves Larrosa, Juan José González-López, Ricard Ferrer

Subject: Medicine And Pharmacology, Emergency Medicine Keywords: Sepsis biomarkers; mortality; MR-proADM; SOFA score; Lactate; molecular diagnosis

Online: 3 July 2023 (08:10:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.2266.v1

Inherited Metabolic Diseases From Past to Present: A Bibliometric Analysis (1968-2023)

Banu Kadıoğlu Yılmaz, Ayşe Hümeyra Akgül

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Inherited metabolic disease; bibliometric study; newborn screening; gene therapy; metabolomics; molecular genetic analysis; phenylketonuria

Online: 30 June 2023 (14:24:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.2214.v1

Mechanistic Elucidation of Activation/Deactivation Signal Transduction within Neurotensin Receptor 1 Triggered by ‘Driver Chemical Groups’ of Modulators: A Comparative Molecular Dynamics Simulation

Xun Lu, Xinchao Shi, Jigang Fan, Mingyu Li, Yuxiang Zhang, Shaoyong Lu, Guanhuan Xu, Ziqiang Chen

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Neurotensin receptor 1; molecular dynamic simulation; signal transduction; selective interaction

Online: 30 June 2023 (10:36:29 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202305.0704.v2

Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties

Masahito Ohue, Yuki Kojima, Takatsugu Kosugi

Subject: Chemistry And Materials Science, Other Keywords: protein-protein interaction inhibitor; rule of five; rule of four; QEPPI; molecular generation; virtual chemical library

Online: 30 June 2023 (08:50:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1963.v1

Exploring Silybin B as a FOXM1 Inhibitor in Glioblastoma Stem Cells: Molecular Docking, ADMET, and Molecular Dynamics Approaches

Kumari Swati, Sameer Quazi, Rashi Srivastava, Siva Prasad Panda, Kirti Agrawal, Anand Parkash, Dhruv Kumar

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Glioblastoma Multiform (GBM); Cancer Stem Cella (CSC); Molecular Dynamics Simulation; In-silico; Phytochemical Screening; FOXM1; ADMET

Online: 28 June 2023 (08:23:27 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.1885.v1

Enigma of Pyramidal Neurons: Congruence to Molecular, Cellular, Physiological, Cognitive and Psychological Function

Victor Vasilyevich Dyakin

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: prevalent molecular chirality; bilaterality; pyramidal neuron; evolution

Online: 27 June 2023 (11:20:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1803.v1

Pattern Analysis of Galectin 1, 3, and 9 Serum Levels in Breast Cancer

Avery Funkhouser, Hayden Shuster, Julie Martin, W. Jeffery Edenfield, Anna Blenda

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: galectin; breast neoplasm; molecular subtype; oncotype; galectin-1; galectin-3; galectin-9

Online: 26 June 2023 (11:23:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1793.v1

Unleashing Black Sea Cucumber's Potential: Identifying Anti-Cancer Compounds Through In Silico Drug Discovery

Muhammad Fahrury Romdendine, Wisnu Ananta Kusuma, Annisa Annisa, Mala Nurilmala, Rizka Fitriani

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: bioactive compounds; black sea cucumbers; cancer; drug-target interactions; machine learning; molecular docking

Online: 26 June 2023 (10:36:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.1714.v1

Optimization of Mechanochemical Processes Toward Functional Nanocomposite Materials

MAMORU SENNA

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Charge transfer; Interparticle boundary; Metastable states; Molecular dispersion; Auto-liquefaction; Nanoglassy states:

Online: 25 June 2023 (05:02:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.1487.v1

Circular and Circulating DNA in IBD: from Pathogenesis to Potential Molecular Therapies

Federica Di Vincenzo, Ylenia Yadid, Valentina Petito, Valeria Emoli, Letizia Masi, Daniela Gerovska, Marcos Jesus Araúzo-Bravo, Antonio Gasbarrini, Birgitte Regenberg, Franco Scaldaferri

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: cell-free nucleic acids; cell-free DNA; circular DNA; microvescicles; inflammatory bowel disease; cGAS-STING; TLR9; oligonucleotides; bioinformatics; molecular therapies.

Online: 21 June 2023 (08:55:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1484.v1

Molecular Diet Analysis of Asian Clam for Estuarine Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Kanghui Kim, Gea-Jae Joo, Kwang-Seuk Jeong, Ye-Lim Lee, Donghyun Hong, Hyunbin Jo

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Corbicula fluminea; Nakdong River Estuary; eDNA metabarcoding; biodiversity; molecular diet analysis; next-generation sequencing; 18S V9

Online: 21 June 2023 (05:31:05 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.1276.v1

A Concise Review of Single-Molecule Magnets, Carbon Nanotubes and Hybrids Between Them

Mudasir A Yatoo, Faiza Habib, Ahmad Husain, Sharique Ahmad, Zubair Ahmad

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Molecular magnetism; single-molecule magnets; carbon nanotubes; single-molecule magnets-carbon nanotubes hybrids.

Online: 19 June 2023 (03:38:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1230.v1

Revealing the Genetic Code Symmetries through Computations Involving Fibonacci-like Sequences and Their Properties

Tidjani Négadi

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genetic code; symmetries; Fibonacci-like sequences; amino acids; ribonucleotides; patterns; hydrogen; atom; molecular mass

Online: 16 June 2023 (11:02:55 CEST)

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In this work, we present a new way to study the genetic code mathematical and chemical structure, based on the use of mathematical computations involving some few recently designed Fibonacci-like sequences, the “seeds” (“initial conditions”) of which are chosen according to the chemical and physical data of the three amino acids serine, arginine and leucine, playing a prominent role in a recent symmetry classification scheme of the genetic code. It appears that these mathematical sequences, of the same kind as the famous Fibonacci series, apart from their usual recurrence relations, are highly interwinned by many useful linear relationships. Using these sequences and also various sums or linear combinations of them, we derive several physical and chemical quantities of interest, as the number of total coding codons, 61, obeying various degeneracy patterns, the detailed number of hydrogen atoms, the detailed number of atoms (H/CNOS) and the integer molecular mass (or nucleon number), in the side chains of the 61 “amino acids”, also in various degeneracy patterns, in agreement with those described in the literature. Also, unexpectedly but interestingly, we find, as a by-product, an accurate description of the very chemical structure of the four ribonucleotides uridine monophosphate (UMP), cytidine monophosphate (CMP), adenosine monophosphate (AMP) and guanosine monophosphate (GMP), the building blocks of RNA whose groupings, in three units, constitutes the triplet codons. In summary, we find a full mathematical and chemical connection with the “ideal sextet’s classification scheme” mentioned above as well as with several others, notably, the Findley-Findley-McGlynn symmetrical classification. We organize the content of the text in such a way that, besides the presentation of several new research results, it has also an educational dimension. The paper could therefore be read and the computations easily worked out, also by non-experts with mathematical background.

Preprint ARTICLE | doi:10.20944/preprints202306.1190.v1

Decoding the Atomic Structure of Ga2Te5 PLD Films for Memory Applications using Diffraction and First-Principles Simulations

Andrey Tverjanovich, Chris J Benmore, Maxim Khomenko, Anton Sokolov, Daniele Fontanari, Sergei Bereznev, Maria Bokova, Mohammad Kassem, Eugene Bychkov

Subject: Chemistry And Materials Science, Electronic, Optical And Magnetic Materials Keywords: phase-change materials; synchrotron diffraction; first-principles molecular dynamics

Online: 16 June 2023 (08:26:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1178.v1

Implementing an On-Slide Molecular Classification of Gastric Cancer: A Tissue Microarray Study

Simona Costache, Rebecca De Havilland, Sofia Diaz McLynn, Maria Sajin, Sarah Wedden, Corrado D'Arrigo

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: gastric cancer; molecular classification; EBER; MMR; E-cadherin; beta-catenin; p53; Her2; PD-L1; Claudin18.2

Online: 16 June 2023 (05:46:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0990.v1

The copper(II)-Thiodiacetate (Tda) Chelate As Efficient Receptor of N9-(2-Hydroxyethyl)adenine (9heade). Synthesis, Molecular and Crystal Structures, Physical Properties and Dft Calculations of [Cu(tda)(9heade)(H2O)]·2H2O

Carmen Rosales-Martínez, Antonio Matilla-Hernández, Duane Choquesillo-Lazarte, Antonio Frontera, Alfonso Castiñeiras, Juan Niclós-Gutiérrez

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Copper(II); thiodiacetate chelate; synthetic adenine nucleoside; molecular and crystal structure; chelate-nucleoside recognition; water-mediated interligand interactions, physical properties; DFT calculations.

Online: 14 June 2023 (05:32:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0967.v1

A Computational (DFT) Study On The Anti-Malarial Drug: Lumefantrine

Ahmet Kunduracioglu

Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Lumefantrine; Anti-malarial activity; Spectral analysis; HOMO-LUMO; Molecular structure

Online: 14 June 2023 (03:28:53 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0960.v1

Autism spectrum disorder pathogenesis – a cross-sectional literature review

Agata Horecka-Lewitowicz, Olga Adamczyk-Gruszka, Dorota Kozieł, Hyebin Lim, Wojciech Lewitowicz, Piotr Lewitowicz

Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: keyword ASD, autism, Asperger syndrome, molecular sequencing

Online: 13 June 2023 (16:51:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0940.v1

18 Months Follow-Up of Deep Molecular Response 4.5 (MR4.5) with Nilotinib in Patients with Newly Diagnosed Chronic-Phase Chronic Myeloid Leukemia: A Prospective, Multi-Center Study in China

Bingbing Wen, Yuming Zhang, Haiqing Lin, Jin Lou, Chuangqing Tu, Yirong Jiang, Xiaolian Liu, Yan Chen, Huiqing He, Zelin Liu, Xiaoling Xie, Wangxiang Huang, Liping Pang, Xin Du

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: 18 months; deep molecular response; nilotinib; newly diagnosed; chronic-phase chronic myeloid leukemia

Online: 13 June 2023 (12:52:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0923.v1

Insight into the Clonal Lineage and Antimicrobial Resistance of Staphylococcus aureus from Vascular Access Infections before and during the COVID-19 Pandemic

Chih-Chen Kao, Chi-Hsiang Lai, Min Yi Wong, Tsung-Yu Huang, Yuan-Hsi Tseng, Yao-Kuang Huang

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: vascular access infections (VAIs); Staphylococcus aureus; antibiotic resistance; antibiotic resistance genes; multilocus sequence typing; molecular characterization

Online: 13 June 2023 (10:14:42 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0849.v1

Epigenetic Alterations That Are the Backbone of Immune Evasion in T-Cell Malignancies

Mihaela Andreescu

Subject: Medicine And Pharmacology, Hematology Keywords: Molecular biology; infectious diseases; clinical diagnostic; early detection; prognosis

Online: 12 June 2023 (14:31:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202306.0803.v1

Recent Advances in Machine Learning-Based Chemoinformatics: A Comprehensive Review

Sarfaraz K Niazi, Zamara Mariam

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: QSAR/QSPR; cheminformatics; small-molecules; AI/ML; molecular descriptors; biological activity; SAR; predictive modeling; computational validation

Online: 12 June 2023 (08:56:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0665.v1

Chemical Feedback in Templated Reaction-Assembly of Polyelectrolyte Complex Micelles: A Molecular Simulation Study of the Kinetics and Clustering

Christos Gioldasis, Apostolos Gkamas, Othonas Moultos, Costas Hristos Vlahos

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: Molecular Dynamics; polyelectrolytes; polymerization; self-assembly; graph theory

Online: 9 June 2023 (04:20:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0648.v1

Insights into the SARS-CoV-2 ORF6 Mechanism of Action

Elena Krachmarova, Peicho Petkov, Elena Lilkova, Nevena Ilieva, Miroslav Rangelov, Nadezhda Todorova, Kristina Malinova, Rossitsa Hristova, Genoveva Nacheva, Anastas Gospodinov, Leandar Litov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2 ORF6 – RAE1 binding; 3D molecular structure modelling; molecular dynamics simulations; cell cycle, cyclin E; R-loops; DNA replication stress

Online: 8 June 2023 (13:52:38 CEST)

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