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Preprint ARTICLE | doi:10.20944/preprints202401.0588.v1

Phytoene Desaturase (Pds) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

Fernanda dos Santos Nascimento, Marcelly Santana Mascarenhas, Samantha Costa Boaventura, Carla Catharina Hora Souza, Andresa Priscila de Souza Ramos, Anelita de Jesus Rocha, Julianna Matos da Silva Soares, Leandro Eugenio Cardamone Diniz, Tiago Antônio De Oliveira Mendes, Claudia Fortes Ferreira, Edson Perito Amorim

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Gene composition; phytoene desaturase; molecular marker; genetic improvement; Musa spp.

Online: 8 January 2024 (11:27:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0576.v1

Study on the Effects of Wettability and Pressure in Shale Matrix Nanopores Imbibition during Shut-in Process by Molecular Dynamics Simulations

Wen Jiang, Weifeng Lv, Ninghong Jia, Xiaoqing Lu, Lu Wang, Kai Wang, Yuhao Mei

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: imbibition; shut-in pressure; wettability; micro-mechanism; molecular dynamics simulation

Online: 8 January 2024 (07:23:49 CET)

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Shut-in after fracturing is generally adopted for wells in shale oil reservoirs, and imbibition occurring in matrix nanopores has been proven as an effective way to improve recovery. In this research, the molecular dynamics (MD) simulation was used to investigate the effects of wettability and pressure on nanopores imbibition during shut-in for a typical shale reservoir Jimsar. The results indicate that the microscopic advancement mechanism of the imbibition front is the competitive adsorption between “interfacial water molecules” at the imbibition front and “adsorbed oil molecules” on the pore wall. The essence of spontaneous imbibition involves the adsorption and aggregation of water molecules onto the hydroxyl groups on the pore wall. The flow characteristics of shale oil suggest that the overall push of the injected water to the oil phase is the main reason for the displacement of adsorbed oil molecules. Thus, shale oil especially the heavy hydrocarbon component in the adsorbed layer tends to slip on the walls. However, the weak slip ability of heavy components on the wall surface is an important reason that restricts the displacement efficiency of shale oil during spontaneous imbibition. The effectiveness of spontaneous imbibition is strongly dependent on the hydrophilicity of the matrix pore's wall. The better hydrophilicity of the matrix pore's wall facilitates higher levels of adsorption and accumulation of water molecules on the pore wall and requires less time for “interfacial water molecules” to compete with adsorbed oil molecules. During the forced imbibition process, the pressure difference acts on both the bulk oil and the boundary adsorption oil, but mainly on the bulk oil, which leads to the occurrence of wetting hysteresis. Meanwhile, shale oil still existing in the pore always maintains a good stratified adsorption structure. Because of the wetting hysteresis phenomenon, as the pressure difference increases, the imbibition effect gradually increases, but the actual capillary pressure gradually decreases and there is a loss in the imbibition velocity relative to the theoretical value. Simultaneously, the decline in hydrophilicity further weakens the synergistic effect of pressure difference because of the more pronounced wetting hysteresis. Thus, selecting an appropriate well pressure enables cost savings and maximizes the utilization of the formation's natural power for EOR.

Preprint REVIEW | doi:10.20944/preprints202401.0454.v1

Recent Advances on Therapy of Slowing Progression of Dia-betic Kidney Disease

Na Wang, Chun Zhang

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: DKD; molecular mechanisms; ACEI/ARB; SGLT2i; NS-MRAs; GLP-1RAs

Online: 5 January 2024 (10:38:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0481.v1

Development of a Real-Time PCR Assay for Early Detection of the Eucalyptus Pathogen Quambalaria eucalypti

Roberto Faedda, Gabriela B. Silva

Subject: Biology And Life Sciences, Life Sciences Keywords: Quambalaria eucalypti; Quambalaria shoot blight; qPCR; diagnostics; molecular detection; Eucalyptus.

Online: 5 January 2024 (10:13:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202310.0701.v3

An In-Depth Insight into Clinical, Cellular and Molecular Factors in COVID19-Associated Cardiovascular Ailments for Identifying Novel Disease Biomarkers, Drug Targets and Clinical Management Strategies

Muneera Altaweel, Abdulmohsen AlMusaad, Gousay Alkhazmari, Hussain Alrowaily, Maram AlSubaiee, Mareyah Alshaikh Husain, Nouf Alomayrin, Rafyel Al Muaiweed, Norah Aleid, Abdulrahman A Alarfaj, Sarah AlMukhaylid, Zainab Albahrani, Aftab Ahmed Jalbani, Zafar Iqbal

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Cardiovascular diseases; COVID-19; pathophysiology; molecular pathogenesis; personalized cardiovascular medicine

Online: 20 December 2023 (10:57:30 CET)

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Background: COVID-19 was initially identified as a respiratory system disorder, but it has been discovered to interact with and influence the cardiovascular system. COVID-19-associated cardiovascular (CV) complications are common, resulting in high acute phase mortality and a large number of morbidities in the chronic phase, thus severely impacting patients' quality of life and health outcomes. Nevertheless, clinical, cellular, and molecular biological factors underlying the pathophysiology of cardiovascular complications associated with COVID-19 are poorly understood. Objective: This review investigates putative underlying clinical factors as well as cellular and molecular biological mechanisms by which COVID-19 leads to acute CV complications, including state-of-the-art genomic sequencing-based findings, assessing the long-term CV consequences of COVID-19, and aiming to shed light on developing strategies for differential diagnosis, risk prognostic stratification, prevention, and clinical management of CV sequlea in COVID-19 patients. Methods: For this purpose, a through review of literature and published data was carried out from first report of COVID-19 till October 2023 to find out a comprehensive account of clinical, cellular and molecular genetic factors underlying COVID-19-associated cardiovascular diseases. Results: We found that the relationship between COVID-19 and CV risk is complex and multifaceted. In addition to acute COVID-19 detertriuos effects, COVID-19 survivors may experience long-term CV effects. We provide a detailed account of the involvement of a large number of genomic alterations, microRNAs, and novel viral as well as host proteins in CVDs associated with COVID-19, which has helped identify some novel drug targets to treat COVID-19-related cardiovascular complications. Conclusions: The relationship between COVID-19 and CV risk is complex and multifaceted. While COVID-19 primarily affects the respiratory system, it can also significantly affect CV health. as compared to classical cardiovascular diseases, there are new clinical, cellular and molecular biological factors in CVDs related to COVID-19, that need specific diagnostic assays, prognostic stratification and treatment modules. Therefore, specail care is must taken to treat cardiovascular diseases associated with COVID-19.

Preprint REVIEW | doi:10.20944/preprints202312.1401.v1

Crafting Genetic Diversity: Unlocking the Potential of Protein Evolution

Vamsi Krishna Gali, Kang Lan Tee, Tuck Seng Wong

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Protein engineering; directed evolution; genetic diversity; random mutagenesis; molecular cloning

Online: 19 December 2023 (10:45:59 CET)

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Preprint REVIEW | doi:10.20944/preprints202311.1355.v1

Molecular Characteristics of Tumor Cell: Recent Advances and Challenges

Abas Mahammed Abdi

Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: ; cancer; NK cells; macrophages; T cells; immunotherapy; molecular characterization

Online: 21 November 2023 (15:27:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0114.v1

Identification of Aggregation Processes in Hexamethylenetetramine Aqueous Solutions: A Comprehensive Raman and Acoustic Spectroscopic Study Combined with Molecular Orbital Calculations

Stefanos Tsigoias, Michael G. Papanikolaou, Themistoklis A. Kabanos, Angelos G. Kalampounias

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: Raman; Ultrasonic relaxation spectroscopy; Molecular orbital calculations; Hexamethylenetetramine; Aggregation mechanism

Online: 2 November 2023 (08:17:34 CET)

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Raman scattering has been employed to study in detail the concentration dependence of the vibrational modes for the hexamethylenetetramine (HMTA) aqueous solutions. The formation of protonated and/or aggregated species has been clarified by comparing the experimental with the theoretically predicted vibrational spectra by means of quantum mechanical calculations. The analysis has shown that the vibrational modes of the solutions arise from a contribution of the vibrational modes of the HMTA self-aggregates and hetero-aggregates of HMTA with water molecules that are formed in the low- and intermediate-concentration region, respectively. The protonation of HMTA is ruled out due to the large differences between the experimental and the theoretically calculated spectra of the protonated molecules of HTMA in the fingerprint region. In the low-concentration solutions, the hetero-aggregation reaction of HMTA with water is the dominant mechanism, while at higher concentrations a self-aggregation mechanism occurs. Ultrasonic absorption and velocity measurements were carried out for hexamethylenetetramine aqueous solutions. The acoustic spectra reveal the presence of only one single Debye-type relaxation process that is assigned to the aggregation mechanism of HMTA. The sound absorption data follow two different dependencies on HMTA mole fraction. The crossover 0.018 mole fraction signifies two separate regions with distinct structural characteristics. The relaxation mechanism observed in dilute solutions is attributed to hetero-association of HMTA with water molecules, while at higher concentrations the observed relaxation process is assigned to the self-association reaction of HMTA molecules. This structural transformation is also reflected in several physicochemical properties of the system, including the kinematic viscosity, the mass density, the sound speed, and the adiabatic compressibility of the HMTA aqueous solutions. The combination of vibrational and acoustic spectroscopies with molecular orbital calculations allowed us to disentangle the underlying processes and to elucidate the observed relaxation mechanism in the HMTA aqueous solutions.

Preprint ARTICLE | doi:10.20944/preprints202311.0001.v1

Epidemiology of Antimicrobial Resistance Genes in Staphyloccocus aureus Isolates from a Public Database in a One Health Perspective – Sample Origin and Isolates Geographical Distribution

Francesca Zaghen, Valerio Massimo Sora, Gabriele Meroni, Giulia Laterza, Piera Anna Martino, Alessio Soggiu, Luigi Bonizzi, Alfonso Zecconi

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: S. aureus; One Health; antimicrobial resistance; molecular epidemiology; geographical distribution.

Online: 1 November 2023 (09:41:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1852.v1

Challenges to Cannabis sativa Production from Pathogens and Microbes – the Role of Molecular Diagnostics and Bioinformatics

ZAMIR PUNJA, Dieter Kahl, Ron Reade, Yu Xiang, Jack Munz, Punya Nachappa

Subject: Biology And Life Sciences, Plant Sciences Keywords: bioinformatics; cannabis; hemp; hop latent viroid; molecular diagnostics; plant pathogens

Online: 30 October 2023 (09:54:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0464.v1

Prevalence and Genetic Characterization of Morphologically Indistinguishable Sarcocysts of Sarcocystis cruzi in Cattle and Sarcocystis poephagicanis in Yaks

Kui Tang, Danqu Lamu, Tao Qin, Zhe Liao, Mingzhu Zhang, Zhipeng Wu, Shuangsheng Deng, Jianping Tao, Junjie Hu

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Sracocystis cruzi; Sarcocystis poephagicanis; cattle; yak; morphological and molecular characterization

Online: 9 October 2023 (10:36:54 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/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/preprints202308.1696.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 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/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 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/preprints202307.0010.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/preprints202306.2214.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 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 ARTICLE | doi:10.20944/preprints202305.1768.v1

Ammonia and Humidity Sensing by Phthalocyanine-Corrole complex Heterojunction Devices

Lorena Di Zazzo, Sujithkumar Ganesh Moorthy, Rita Meunier-Prest, Corrado Di Natale, Roberto Paolesse, Marcel Bouvet

Subject: Chemistry And Materials Science, Nanotechnology Keywords: corrole; phthalocyanine; gas sensor; organic heterojunction; conductometric transducer; molecular material

Online: 25 May 2023 (08:31:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1546.v1

Novel Oleanolic Acid-Phtalimidines Tethered 1,2, 3 Triazole Hy-Brids As Promising Antibacterial Agents: Design, Synthesis, In Vitro Experiments and In Silico Docking Studies

Ghofrane Lahmadi, Mabrouk Horchani, Amal Dbeibia, Abdelkarim Mahdhi, Anis Romdhane, Ata Martin Lawson, Adam Daïch, Abdel Halim Harrath, Hichem Ben Jannet, And Mohamed Othman

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: Oleanolic acid; phtalimidines; triazole; click chemistry; antibacterial activity; molecular docking

Online: 23 May 2023 (03:33:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1530.v1

Drought-Responsive Genes in Tomato: Meta-Analysis of Gene Expression using Machine Learning

Rabiul Haq Chowdhury, Fatiha Sultana Eti, Md. Atiqur Rahman Bhuiyan, Shipan Das Gupta, Mehede Hassan Rubel

Subject: Biology And Life Sciences, Plant Sciences Keywords: Abiotic stresses; Molecular breeding; Machine learning; Responsive genes; Adapted crops

Online: 22 May 2023 (15:29:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1304.v1

Molecular Networks of Platinum Drugs and Arsenic Trioxide and Its Interaction With microRNAs in Cancer

Shihori Tanabe, Eger Boonstra, Taehun Hong, Sabina Quader, Ryuichi Ono, Horacio Cabral, Kazuhiko Aoyagi, Hiroshi Yokozaki, Hiroki Sasaki

Subject: Biology And Life Sciences, Life Sciences Keywords: drug resistance; cisplatin; arsenic; tumor microenvironment; microRNA; molecular pathway network

Online: 18 May 2023 (08:41:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0281.v1

Computational Characterization of the Binding Properties of the HIV1-Neutralizing Antibody PG16 and Design of PG16-Derived CDRH3 Peptides

Manuel Deubler, Lucas Weißenborn, Simon Leukel, Anselm H.C. Horn, Jutta Eichler, Heinrich Sticht

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Antibody; PG16; HIV-1; peptides; antibody mimetic peptides; molecular dynamics

Online: 5 May 2023 (03:08:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.1066.v1

Unveiling the Intimate Mechanism of the Crocin Antioxidant Properties by Radiolytic Analysis and Molecular Simulations

Sarah Al Gharib, Pierre Archirel, Daniel Adjei, Jacqueline Belloni, Mehran Mostafavi

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: crocin; antioxidant properties; pulse radiolysis; gamma radiolysis; molecular simulation; mechanism.

Online: 27 April 2023 (09:55:53 CEST)

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Preprint REVIEW | doi:10.20944/preprints202304.0694.v1

Medical Applications of Molecular Biotechnologies in the Context of the Hashimoto’s Thyroiditis

Maria Trovato, Andrea Valenti

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Hashimoto’s thyroiditis; molecular biotechnologies; clinical trials studies; hygiene hypothesis; parvoviruses

Online: 21 April 2023 (08:48:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0209.v1

Uncovering Taste-Active Metabolites in Chili Sauce Fermentation Through Metabolomics and Web-based Computing Tools Analysis

Jiaqi Wang, Sen Mei, Chi Jin, Muhammad Aamer Mehmood, Qing Zhang, Tao Hu, Weili Li, Tao Wu

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: chili sauce; Lactiplantibacillus plantarum; feature-based molecular network; metabolomics; taste

Online: 13 March 2023 (03:09:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202302.0059.v1

Exploring the Unbinding Mechanism of Drugs from SERT via Molecular Dynamics Simulation and its Implication in Antidepressants

Xin-Guan Tan, Xue-Feng Liu, Xin Li, Ming-Hui Pang, Yu-Qing Wang, Yun-Jie Zhao

Subject: Biology And Life Sciences, Biophysics Keywords: hSERT; comprehensive molecular dynamics (MD) simulation; drug design; MM/GBSA

Online: 3 February 2023 (06:16:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0168.v1

Aquaporin-2 Interaction with Cortisol Modulates its Water Permeability. Perspectives for Corticosteroids Non-genomic Effects

Robin Mom, Stéphane Réty, Daniel Auguin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: AQP2; cortisol; corticosteroid; non-genomic effects; molecular dynamics; water permeability

Online: 9 December 2022 (02:31:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202208.0217.v1

Ferromagnetic Coupling and Single-Ion Magnet Phenomenon in Mononuclear Ruthenium(Iii) Complexes Based on Guanine Nucleobase

Marta Orts-Arroyo, Nicolás Moliner, Francesc Lloret, José Martínez-Lillo

Subject: Chemistry And Materials Science, Inorganic And Nuclear Chemistry Keywords: Ruthenium; crystal structures; ferromagnetic coupling; molecular magnetism; single-ion magnet.

Online: 11 August 2022 (11:41:41 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0442.v1

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples

Karen Marcela Jiménez, Dora Janeth Fonseca-Mendoza, Adrien Morel, Oscar Ortega-Recalde, Nora Contreras, Camilo Andres Velandia-Piedrahita, Adriana Steevens, Luisa Caldas, Juan Pablo Ribón, Martha Sanchez, Carlos Martín Restrepo, Rodrigo Cabrera

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; molecular diagnostic; SARS-CoV-2; Real-time PCR

Online: 29 July 2022 (03:10:47 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0078.v2

Mitochondrial Damage-Associated Molecular Patterns Content in Extracellular Vesicles Promotes Early Inflammation in Neurodegenerative Disorders

Claudia Deus, Henrique Tavares, Margarida Beatriz, Sandra Mota, Carla Lopes

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Extracellular vesicles; neurodegenerative disorders; mitochondrial damage-associated molecular patterns; inflammation

Online: 6 July 2022 (09:16:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0099.v1

SARS-CoV-2 Shielding Effect of Chitosan Derivatives: An in-silico Prospective

Poonam Das, Sabuj Sahoo, Sanatan Majhi, George rout Kerry, Atala Bihari Jena

Subject: Biology And Life Sciences, Virology Keywords: Chitosan; mHTCC; SARS-CoV-2; S protein; ACE2; Molecular interaction

Online: 7 June 2022 (09:05:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0143.v1

Immunoinformatic Guided Rational Design of a Next Generation Multi Epitope Based Peptide Vaccine against Marburg Virus Disease Combined with Molecular Docking Studies

Mujahed Mustafa, Shaza Shantier

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Marburg virus disease (MVD); Vaccine design; Immunoinformatic; Molecular Docking Study.

Online: 10 May 2022 (14:16:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0005.v1

Metabolomic Comparison Using Streptomyces spp as a Factory of Secondary Metabolites

Rene Flores Clavo, Alana Kelyene Pereira, Nataly Ruiz Quiñones, Jonas Henrique Costa, Taícia Pacheco Fill, Fabiana Fantinatti Garboggini

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: genome mining; marine environments; molecular networking; bacterial extremophiles; secondary metabolites

Online: 1 April 2022 (10:21:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202202.0222.v1

Identification of CT Attenuation Values that Could be Predictive of Necrosis (N-CTav) in Hepatocellular Carcinoma Tumors after Lenvatinib Treatment and the Association between the N-CTav Occupancy Rate in the Tumor and Maintenance of Complete Response with Lenvatinib Treatment

Makoto Chuma, Hideki Yokoo, Atsushi Hiraoka, Kazuhiko Ueda, Takahiro Yokoyama, Kunihiko Tsuji, Noritomo Shimada, Haruki Uojima, Satoshi Kobayashi, Nobuhiro Hattori, Tomomi Okubo, Masanori Atsukawa, Toru Ishikawa, Koichi Takaguchi, Akemi Tsutsui, Hidenori Toyoda, Toshifumi Tada, Yoshinori Saito, Shunji Hirose, Takaaki Tanaka, Kazuhisa Takeda, Masako Otani, Zenjiro Sekikawa, Tsunamasa Watanabe, Hisashi Hidaka, Manabu Morimoto, Kazushi Numata, Tatehiro Kagawa, Michiie Sakamoto, Takashi Kumada, Shin Maeda

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: hepatocellular carcinoma; lenvatinib; molecular targeted agents; complete response; CT value

Online: 18 February 2022 (04:05:18 CET)

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Purpose: To assess the utility of measurement of the computed tomography (CT) attenuation value (CTav) in predicting tumor necrosis in hepatocellular carcinoma (HCC) patients who achieve a complete response (CR), defined using modified Response Evaluation Criteria in Solid Tumors (mRECIST), after lenvatinib treatment. Method: We compared CTav in arterial phase CT images with postoperative histopathology in four patients who underwent HCC resection after lenvatinib treatment, to determine CTav thresholds indicative of histological necrosis (N-CTav). Next, we confirmed the accuracy of the determined N-CTav in 15 cases with histopathologically proven necrosis in surgical specimens. Furthermore, the percentage of the tumor with N-CTav, i.e. the N-CTav occupancy rate, assessed using Image J software in 30 tumors in 12 patients with CR out of 571 HCC patients treated with lenvatinib, and its correlation with local recurrence following CR were examined. Results: Receiver operating characteristic (ROC) curve analysis revealed an optimal cut-off value of CTav of 30.2 HU, with 90.0% specificity and 65.0% sensitivity in discriminating between pathologically identified necrosis and degeneration, with a CTav of less than 30.2 HU indicating necrosis after lenvatinib treatment (N30-CTav). Furthermore, the optimal cut-off value of 30.6% for the N30-CTav occupancy rate by ROC analysis was a significant indicator of local recurrence following CR with 76.9% specificity and sensitivity (area under the ROC curve; 0.939), with the CR group with high N30-CTav occupancy (>30.6%) after lenvatinib treatment showing significantly lower local recurrence (8.3% at 1 year) compared with the low (<30.6%) N30-CTav group (P<0.001, 61.5% at 1 year). Conclusion: The cut-off value of 30.2 HU for CTav (N30-CTav) might be appropriate for identifying post-lenvatinib necrosis in HCC, and an N30-CTav occupancy rate of >30.6% might be a　predictor of maintenance of CR. Use of these indicators have the potential to impact systemic chemotherapy for HCC.

Preprint REVIEW | doi:10.20944/preprints202202.0004.v1

Mapping Spatiotemporal Heterogeneity in Tumour Progression by Integrating High-Throughput Imaging and Omics Analysis

Pooja Annasaheb Patkulkar, Ayalur Raghu Subbalakshmi, Mohit Kumar Jolly, Sanhita Sinharay

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Spatial transcriptomics; Molecular imaging; single-cell RNA-seq; intratumoral heterogeneity

Online: 1 February 2022 (11:08:51 CET)

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Preprint REVIEW | doi:10.20944/preprints202201.0084.v1

Yeast Hybrids in Brewing

Matthew J. Winans

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: hybrid; lager; yeast; introgression; interspecific; domestication; phylogeny; brewing; molecular; genomics

Online: 6 January 2022 (11:55:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0254.v1

Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields With and Without NBFIX and ECC Corrections

Natalia Lukasheva, Dmitry Tolmachev, Hector Martinez-Seara, Mikko Karttunen

Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: Peptides and proteins; Counterions; Ions; Carboxyls; Molecular dynamics; Force fields

Online: 15 December 2021 (11:14:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0506.v1

A Retrospective Cohort Study of the Clinical Features, Pathological Characteristics, and Molecular Classification in Reproductive Age Patients with Endometrial Cancer who Experienced Unsuccessful Fertility-sparing Treatment

Tong Yu, Xi-Wen Zhang, Ping-Li Sun, Abdulkarim Mohamed Farah, Yan Jia

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: endometrial cancer; fertility-sparing management; molecular classification; reproductive age; pregnancy

Online: 26 November 2021 (12:42:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0329.v1

Virtual Screening with Gnina 1.0

Jocelyn Sunseri, David Koes

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Machine Learning; Deep Learning; Molecular Modeling; Virtual Screening; Drug Discovery

Online: 18 November 2021 (13:59:09 CET)

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Preprint REVIEW | doi:10.20944/preprints202110.0113.v1

Factorization in Molecular Modeling and Belief Propagation Algorithms

Pu Tian

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: Factorization; molecular modeling; belief propagation; sum-product; local distribution theory

Online: 7 October 2021 (10:31:52 CEST)

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Working Paper ARTICLE

Dual Effects of Vericiguat on Osteoclast Differentiation and Bone Resorption via a Balance between VASP and NF-κB Pathways

Kaiqiang Sun, Fanqi Kong, Feng Lin, Fudong Li, Jingchuan Sun, Changzhen Ren, Bing Zheng, Jiangang Shi

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Vericiguat; osteoclast (OCs), MAPK, NF-κB; RANKL; AKT, molecular mechanism

Online: 8 September 2021 (13:02:05 CEST)

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Preprint REVIEW | doi:10.20944/preprints202108.0489.v1

Heat Stress and its Impact on Plant Function: An Update

Anand Kumar, Prashant Kaushik

Subject: Biology And Life Sciences, Plant Sciences Keywords: Heat stress; molecular responses; morphological responses; physiological process; reproductive activity

Online: 25 August 2021 (11:46:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0604.v2

RT-qPCR Diagnostics: The “Drosten” Sars-Cov-2 Assay Paradigm

Stephen Bustin, Sara Kirvell, Jim F Huggett, Tania Nolan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; reverse transcription; qPCR; SARS-CoV-2; molecular diagnosis

Online: 3 August 2021 (15:34:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0155.v1

Long-Range Static and Dynamic Previtreous Effects in Supercooled Squalene - Impact of Strong Electric Field

Szymon Starzonek, Aleksandra Drozd-Rzoska, Sylwester J. Rzoska

Subject: Physical Sciences, Acoustics Keywords: molecular liquid; nonlinear dielectric effect; glass transition; ODIC; pretransitional effect

Online: 6 July 2021 (13:34:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202106.0297.v1

A Functional Study of the TatD DNases of Trueperella pyogenes and the Conformational Analysis of Luteolin as an Inhibitor

Zehui Zhang, Yinfeng Liang, Lihui Yu, Menghan Chen, Yuru Guo, Zhiruo Kang, Chenghu Qu, Chunlian Tian, Dexian Zhang, Mingchun Liu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Trueperella pyogenes; TatD DNases; luteolin; DNA hydrolysis; molecular modeling; SPR

Online: 10 June 2021 (14:13:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0211.v1

Evaluation of SYK Gene as a Prognostic Biomarker and Suggested Aromatic Potential Phytochemicals to Halt the Colorectal Cancer

Partha Biswas, Dipta Dey, Atikur Rahman, Md. Aminul Islam, Tasmina Ferdous Susmi, Md. Abu Kaium, Md. Nazmul Hasan, MD. Hasanur Rahman, Shafi Mahmud, Md. Abu Saleh, Priyanka Paul, Md Rezanur Rahman, Md. Ataur Rahman, Han Gyeul Song, Bonglee Kim

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Colorectal cancer; SYK; Prognostic Significance; Genetic Alteration; Molecular dynamics simulations

Online: 10 May 2021 (15:20:54 CEST)

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Background: Colorectal cancer is considered the third most fetal among all type of cancer. Spleen tyrosine kinase (SYK) is a non-receptor type tyrosine-protein that plays crucial role in signaling mediated via immune receptor. We adopted an onco-informatics analysis to evaluate the SYK expression and prognostic value of SYK in colorectal cancer, and identification of potential phytochemicals which may inhibit overexpression of SYK protein as well as minimized colorectal cancer. Materials & Methods: Differential expression of SYK gene was analyzed using the several transcriptomic databases including Oncomine, UALCAN, GENT2 and GEPIA2. The server, cBioPortal was used to analyze mutation and copy number alterations whereas GENT2, GEPIA, OncoLnc and PrognoScan were employed to examine the survival rate. A protein-protein interaction network of SYK and co-expressed genes of SYK was conducted via GeneMANIA. Considering SYK gene encoding protein as drug target, selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. YASARA molecular dynamics simulators were applied for the post validation of the molecular docking data. Results: We have observed significant overexpression of mRNA expression levels of SYK gene colorectal adenocarcinoma (COAD) samples compared with normal tissues. Significant methylation level and various genetic alterations are assembled in SYK gene which can lead to the development of colorectal cancer. As a result, lower level of SYK expression was related to the more chances of patients’ survival by which all the outcomes from the multiple bioinformatics platforms and web resources have demonstrated the significant evidences that the SYK kinsase can possess as a potential biomarker for the treatment of colorectal cancer. Here, aromatic phytochemicals namely, Kaempferol and Glabridin targeting SYK showed more stability compared to controls and may be useful for the treatment of colorectal cancer. Conclusion: Our study showed dysregulated expression of SYK in colorectal cancer and potentiality to act as a biomarker for the prognosis of CRC. Moreover, we have shown phytochemicals (Kaempferol and Glabridin) target SYK as potential treatment strategies and drug repositioning potentiality in colorectal cancer.

Preprint REVIEW | doi:10.20944/preprints202105.0008.v1

Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential

Bruna Brasil Brandão, Ankita Poojari, Atefeh Rabiee

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Adipose Tissue, Development, Molecular Circuits, Secretome, Thermogenesis, Metabolism, Obesity, Therapy

Online: 3 May 2021 (15:58:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202101.0151.v1

Nanobodies Provide Insight Into the Molecular Mechanisms of the Complement Cascade and Offer New Therapeutic Strategies

Alessandra Zarantonello, Henrik Pedersen, Nick Stub Laursen, Gregers R Andersen

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: complement system; proteolytic cascade; convertase; inhibitor; structural biology; molecular mechanism

Online: 8 January 2021 (11:54:36 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0797.v1

Tackling the Moving Mutant Target: Taxifolin Derivatives as Novel Putative E571K Exportin-1 Inhibitors for KRAS-mutant Lung Adenocarcinoma Therapy

Temidayo Adigun, Oluwatobi Medayedupin, Ireoluwa Joel, Idowu Fakolujo, Bankole Ofeniforo, Faith Bankole, Adedayo Omoniyi, Olalekan Ogunro, Adebimpe Agunlejika, Oluwatobi Omoyeni, Joy Bamidele, Adetola Ajayi

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: KRAS-mutant lung adenocarcinoma; E571K exportin-1; Taxifolin; Molecular modelling

Online: 31 December 2020 (12:25:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0708.v1

Phytochemicals as Therapeutics Against COVID-19: An In-Silico Study

Debraj Koiri, Ditam Chakraborty, Pranotosh Das, Rajkumar Rana, Soumyanil Chatterjee, Tanmoy Das, Paltu Kumar Dhal

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Phytochemicals; SARS-CoV-2; S-Protein; Molecular docking; ACE 2

Online: 28 December 2020 (16:51:12 CET)

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Preprint REVIEW | doi:10.20944/preprints202012.0681.v1

Understanding Root Rot Disease in Agricultural Crops

Bruce A. Williamson-Benavides, Amit Dhingra

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Fungi; oomycetes; resistance; susceptibility; molecular mechanisms; quantitative trait loci; mapping

Online: 28 December 2020 (11:12:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0326.v1

On the Size Effect of Additives in Amorphous Shape Memory Polymers

Elias M. Zirdehi, Hakan Dumlu, Gunther Eggeler, Fathollah Varnik

Subject: Physical Sciences, Condensed Matter Physics Keywords: Shape memory polymers; Size effect of additives; Molecular dynamics simulations

Online: 14 December 2020 (12:02:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202012.0013.v1

Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus Thermoproteolyticus as Possible Antibacterial Agents

Emilio Lamazares, Desmond MacLeod-Carey, Fernando P. Miranda, Karel Mena-Ulecia

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Thermolysin; Antibacterial agents; Docking; Molecular dynamics; MM-PBSA, ADME-Tox.

Online: 1 December 2020 (10:48:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202011.0146.v4

The Role of Divalent Transition Metal Ions in the Binding of Fur Dimer to DNA: Binding of Mn²⁺ and Co²⁺ to EC Fur dimer-DNA Complex

Mazen Hamed, Salih Jabour

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ferric Uptake Regulation; Fur, Iron(II), Molecular dynamics; DNA; protein

Online: 10 November 2020 (12:23:58 CET)

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Preprint REVIEW | doi:10.20944/preprints202002.0261.v2

Phase Transitions in Virology

Ricard Sole, Josep Sardanyes, Santiago F. Elena

Subject: Biology And Life Sciences, Virology Keywords: epidemics; molecular replicators; mutation; quasispecies; recombination; self-assembly; phase transitions

Online: 29 October 2020 (09:30:44 CET)

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Viruses have established symbiotic relationships with almost every other living organism on Earth and at all levels of biological organisation, from other viruses up to entire ecosystems. In most cases, peacefully coexisting with their hosts, but in most relevant cases, parasitising them and inducing diseases. Viruses are playing an essential role in shaping the eco-evolutionary dynamics of their hosts, and have been also involved in some of the major evolutionary innovations either by working as vectors of genetic information or by being themselves coopted by the host into their genomes. Viruses can be studied at different levels of biological organisation, from the molecular mechanisms of genome replication, gene expression and encapsidation, to global pandemics. All these levels are different and yet connected through the presence of threshold conditions allowing for the formation of a capsid, the loss of genetic information or epidemic spreading. These thresholds, as it occurs with temperatures separating phases in a liquid, define sharp qualitative types of behaviour. These {\em phase transitions} are very well known in Physics. They have been studied by means of simple, but powerful models able to capture their essential properties, allowing to understand them. Can the physics of phase transitions be an inspiration for our understanding of viral dynamics at different scales? Here we review well-known examples of transition phenomena in virology and their simplest mathematical modelling approaches. We suggest that the advantages of abstract, simplified pictures used in Physics are also the key to properly understand the origins and evolution of complexity in viruses. By means of several examples, we explore this multilevel landscape and how minimal models provide deep insights into a diverse array of problems. The relevance of these transitions in connecting dynamical patterns across levels and their evolutionary and clinical implications are outlined.

Preprint ARTICLE | doi:10.20944/preprints202010.0472.v1

In-silico Characterization and Comparative Analysis of BLB Disease Resistance Xa genes in Oryza sativa

Muhammad Anas Ramzan, Hasib Asghar, Abdul Rehman, Muhammad Rashid, Ljupcho Jankuloski

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: BLB Resistance; Xa genes; Xoo; Molecular characterization; Rice; LRR; S_TKc

Online: 23 October 2020 (09:13:39 CEST)

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Working Paper REVIEW

The Alterations of Cellular Signaling Pathways in the Host Cell upon the High Pathogenic Coronaviruses Infection, SARS-CoV and MERS-CoV. What Could Be Expected from the SARS-CoV-2?

Nima Hemmat, Zahra Asadzadeh, Noora Karim-ahangar, Hajar Alemohammad, Basira Najafzadeh, Afshin Derakhshani, Amir Baghbanzadeh, Hossein Bannazadeh Baghi, Darya Javadrashid, Souzan Najafi, Meriadeg Ar Gouilh, Behzad Baradaran

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration

Online: 21 September 2020 (04:17:24 CEST)

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Working Paper ARTICLE

Inclusion of Different Molecular Weight Condensed Tannin on Ruminal Fermentation and Milk Fatty Acid Profile of Dairy Goats

Siwaporn Paengkoum, Anan Petlum, Pramote Paengkoum

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: CTs molecular weight; ruminal fermentation; bio-hydrogenation; milk compositions; goat

Online: 20 September 2020 (14:44:56 CEST)

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Working Paper REVIEW

Application of Quantum Computing to Biochemical Systems: A Look to the Future

Hai-Ping Cheng, Erik Deumens, James Freericks, Chenglong Li, Beverly Sanders

Subject: Biology And Life Sciences, Biophysics Keywords: computational molecular biology, biochemistry, quantum computing, hybrid quantum-classical algorithms

Online: 24 August 2020 (09:37:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0562.v1

Discovery of Unusual Cyanobacterial Tryptophan-containing Anabaenopeptins by MS/MS Based Molecular Networking

Subhasish Saha, Germana Esposito, Petra Urajova, Jan Mareš, Daniela Ewe, Alessia Caso, Marketa Macho, Katerina Delawska, Andreja Kust, Pavel Hrouzek, Josef Juran, Valeria Costantino, Kumar Saurav

Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Brasilonema; Anabaenopeptins; hexapeptides; tryptophan-containing peptides; molecular networking; antiproliferative activity

Online: 23 July 2020 (12:40:38 CEST)

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Working Paper ARTICLE

Synthesis, Antimicrobial Study and Molecular Docking Simulation of 3,4-Dimethoxy-β-nitrostyrene Derivatives as Candidate of PTP1B Inhibitor

Salman Alfarisi, Mardi Santoso, Alfinda Novi Kristanti, Ni Nyoman Tri Puspaningsih

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 3,4-dimethoxy-β-nitrostyrene derivatives; antimicrobial agent; PTP1B; molecular docking

Online: 20 July 2020 (11:31:48 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202007.0141.v3

Possible Cross-Reactivity Between SARS-CoV-2 Proteins, CRM197 and Proteins in Pneumococcal Vaccines May Protect Against Symptomatic SARS-CoV-2 Disease and Death

Robert Root-Bernstein

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19; pneumococcal vaccine; vaccination; cross-reactivity; protection; molecular mimicry; CRM197; rubella vaccine

Online: 4 September 2020 (10:45:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202006.0326.v1

Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat's claw) against the Main Protease 3CL^Pro of SARS-CoV-2 by Molecular Modeling

Andres F. Yepes-Pérez, Oscar Herrera-Calderon, José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala, Jean-Didier Maréchal, Wilson Cardona-G

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: 2019-nCoV; 3CLpro protein; Cat's Claw; Uncaria tomentosa; Molecular Modeling

Online: 28 June 2020 (09:05:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0186.v1

The Binding Mechanism of Coronavirus Disease 2019 with Human Angiotensin Converting Enzyme 2

Baliram Lone, Megha Lone

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Coronavirus disease 2019; SARS-CoV-2; ACE2; RBD; Molecular modelling

Online: 11 May 2020 (04:08:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0149.v1

Potential Inhibitors of SARS-CoV-2 Main Protease (M^pro) Identified from the Library of FDA Approved Drugs Using Molecular Docking Studies

Dipesh Verma, Srajan Kapoor, Satyajeet Das, Krishan Thakur

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: COVID-19; SARS-CoV-2; Mpro; Molecular docking; MM-GBSA

Online: 9 April 2020 (11:05:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202004.0079.v1

Identification of Compounds from Nigella Sativa as New Potential Inhibitors of 2019 Novel Coronasvirus (Covid-19): Molecular Docking Study

Salim Bouchentouf, Noureddine Missoum

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: COVID-19; Nigella Sativa; 6LU7; 2GTB; molecular docking; MOE software

Online: 7 April 2020 (08:58:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0277.v1

Anti-COVID-19 Effects of Ten Structurally Different Hydrolysable Tannins through Binding with the Catalytic-Closed Sites of COVID-19 Main Protease: An In-Silico Approach

Ibrahim Khalifa, Wei Zhu, Mohamed S. Nafie, Kunal Dutta, Chunmei Li

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: COVID-19; hydrolysable tannins; protease; molecular docking; structural-relationship activity

Online: 17 March 2020 (15:43:48 CET)

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Preprint ARTICLE | doi:10.20944/preprints201911.0375.v1

Synthesis of Diabetic II Inhibitors Based on 2-mercaptobenzimidazole and their Molecular Docking Study

Muhammad Taha, Fazal Rahim, Shawkat Hayat, Manikandan Selvaraj, Rai Khalid Farooq, Sayed Adnan Ali Shah, Zainul Amiruddin Zakaria

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: synthesis; 2-mercaptabezimidazole; sulfonamide; molecular docking study; α-amylase; sa

Online: 29 November 2019 (10:28:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0177.v1

The Effect of Co-Doping at the A-Site on the Structure and Oxide Ion Conductivity in (Ba_0.5-xSr_x)La_0.5InO_3-δ: A Molecular Dynamics Study

Kuk-Jin Hwang, Hae-Jin Hwang, Myung-Hyund Lee, Seng-Min Jeong, Tae Ho Shin

Subject: Chemistry And Materials Science, Electrochemistry Keywords: oxide ion conductivity; perovskite oxide; molecular dynamics simulation; ceramics electrolyte

Online: 16 October 2019 (04:55:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201903.0087.v2

Energy Conversion Monitoring in Skin Tissue: A More Sensitive Measure of Hypoxia Occurring With Sleep Disordered Breathing Than Pulse Oximetry

Guy M. Hatch, Liza Ashbrook, Aric A. Prather, Andrew D. Krystal

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: tissue hypoxia; sleep disordered breathing; primary snoring; molecular tissue oximeter

Online: 16 August 2019 (06:27:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0264.v1

Temporally and Spatially Resolved Emission Spectroscopy of Cyanide, Hydrogen and Carbon in Laser-Induced Plasma

Christian G. Parigger, Christopher M. Helstern, Ghaneshwar Gautam

Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: laser-induced plasma; atomic spectroscopy; molecular spectroscopy; cyanide; hydrogen; carbon

Online: 26 June 2019 (07:49:09 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201906.0140.v1

An Inactivation Switch Enables Rhythms in a Neurospora Clock Model

Abhishek Upadhyay, Michael Brunner, Hanspeter Herzel

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: circadian clock; mathematical modelling; molecular switch; Neurospora crassa; glucose compensation

Online: 15 June 2019 (14:36:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0207.v1

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia

Mariel C Isidra-Arellano, María del Rocio Reyero-Saavedra, María del Socorro Sánchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A Castro-Guerrero, David G Mendoza-Cozatl, Marc Libault, Oswaldo Valdés-López

Subject: Biology And Life Sciences, Plant Sciences Keywords: Phosphorus deficiency, common bean, rhizobia, molecular dialog, symbiosis, gene transcription

Online: 12 September 2018 (01:29:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0054.v1

Water Dispersible Few Layer Graphene Stabilized by a Novel Pyrene Derivative at Micromolar Concentration

Eunice Cunha, Maria Fernanda Proença, Maria Goreti Pereira, Maria José Fernandes, Robert Young, Karol Strutyński, Manuel Melle-Franco, Mariam Gonzales-Debs, Paulo Lopes, Maria da Conceição Paiva

Subject: Chemistry And Materials Science, Nanotechnology Keywords: few layer graphene production; aqueous suspension; pyrene derivative; molecular modelling

Online: 2 August 2018 (23:52:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0164.v1

Molecular Evolution in a Peptide-vesicle System

Christian Mayer, Ulrich Schreiber, Maria J. Dávila, Oliver J. Schmitz, Amela Bronja, Martin Meyer, Julia Klein, Sven W. Meckelmann

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Origin of life; evolution; molecular evolution; prebiotic chemistry; peptides; vesicles

Online: 19 March 2018 (13:01:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints201803.0050.v1

Facile Syntheses and Molecular-Docking of Novel Substituted 3,4-Dimethyl-1H-pyrrole-2-carboxamide/carbohydrazide Analogues with Antimicrobial and Antifungal Properties

Jitendra D. Bhosale, Rajesh Dabur, Gopal P. Jadhav, R. S. Bendre

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: carboxamide; carbohydrazine; antibacterial; antifungal; molecular docking; Schiff base; NMR; IR

Online: 7 March 2018 (05:11:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints201709.0107.v2

Rosetta Mission: Electron Scattering Cross Sections—Data Needs and Coverage in BEAMDB Database

Bratislav P. Marinković, Jan Hendrik Bredehöft, Veljko Vujčić, Darko Jevremović, Nigel J. Mason

Subject: Physical Sciences, Atomic And Molecular Physics Keywords: electron scattering; cross sections; Rosetta mission; atomic and molecular databases

Online: 21 October 2017 (15:30:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201612.0089.v1

Selection of Prebiotic Molecules in Amphiphilic Environments

Christian Mayer, Ulrich Schreiber, Maria J. Davila

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: origin of life; selection; accumulation; prebiotic chemistry; molecular evolution; vesicles

Online: 16 December 2016 (08:46:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints201608.0118.v1

Uncovering Spatio-Temporal and Treatment-Derived Differences in the Molecular Physiology of a Model Coral-Dinoflagellate Mutualism with Multivariate Statistical Approaches

Anderson Mayfield

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: acclimation; coral reefs; endosymbiosis; molecular biology; multivariate statistics; temperature; upwelling

Online: 11 August 2016 (11:03:03 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/preprints202002.0053.v1

Laser-Plasma Spectroscopy of Hydroxyl with Applications

Christian G. Parigger, Christopher M. Helstern, Benjamin S. Jordan, David M. Surmick, Robert Splinter

Subject: Physical Sciences, Chemical Physics Keywords: plasma diagnostics; molecular spectra; diatomic molecules; plasma spectroscopy; laser spectroscopy; laser-induced breakdown spectroscopy; optical emission spectroscopy; molecular excitation temperature; combustion analysis; astrophysical spectroscopy

Online: 5 February 2020 (03:27:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0233.v1

MS-Based Approaches Enable the Structural Characterization of Transcription Factor / DNA Response Element Complex

Lukas Slavata, Josef Chmelik, Daniel Kavan, Ruzena Filandrova, Jan Fiala, Michal Rosulek, Hynek Mrazek, Zdenek Kukacka, Karel Valis, Petr Man, Michael Miller, William McIntyre, Daniele Fabris, Petr Novak

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transcription factor; protein; DNA; protein-nucleic acid cross-linking; quantitative cross-linking; transplatin; trans-dichlorodiamineplatinum(II); hydrogen-deuterium exchange; FOXO4; molecular modeling; molecular docking

Online: 22 July 2019 (08:03:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0035.v1

Targeting Mycobacterial Polyketide Synthase Pks13-TE Domain with Small Organic Molecular Scaffolds: QSAR-Driven Modelling Studies to Identify Novel Inhibitors

Jagriti Malhotra, Shovonlal Bhowmick, Mohammad K. Okla, Pritee Chunarkar Patil, Rupesh V. Chikhale

Subject: Medicinal Chemistry, Chemistry And Materials Science Keywords: Mycobacterial Polyketide Synthase; QSAR; Multiple Linear Regression; Docking; Molecular Dynamics Simulations

Online: 1 May 2024 (16:46:55 CEST)

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This study presents a detailed computational investigation aimed at identifying and evaluating potential small organic molecular scaffolds as inhibitors targeting the Pks13 protein, a critical enzyme in tuberculosis (TB) drug discovery. Our approach integrates multiple computational techniques, including quantitative structure-activity relationship (QSAR) modelling, compound library generation, molecular docking, biological activity prediction, re-evaluation of screened compounds, molecular dynamics (MD) analysis, and binding free energy estimation using the MM-GBSA approach. We developed a robust QSAR model using multiple linear regression (MLR) techniques, specifically tailored to predict the minimum inhibitory concentration (MIC) values of potential anti-TB agents. This model demonstrated excellent predictive performance, validated through rigorous internal and external validation procedures. Through molecular docking simulations, we identified five promising inhibitors Ethyl (R,Z)-2-(2-((2-chlorobenzyl) oxy)benzylidene)-5-(4-chlorophenyl)-7-methyl-3-oxo-2,3-dihydro-5H-thiazolo [3,2-a] pyrimidine-6-carboxylate (PKD1), (7R,9aR)-7-(2-hydroxyphenyl)-4-(2-methoxyphenyl)-3-methyl-7,8,9,9a-tetrahydroisoxazolo[5,4-b]quinolin-5(6H)-one (PKD2), (7-(4-methoxy phenyl)-2-methyl-3-phenylpyrazolo[1,5-a]pyrimidin-5-yl)(4-(3-(trifluoromethyl)phenyl) piperazin-1-yl)methanone (PKD3), (8S,10S)-10-(((2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl tetrahydro-2H-pyran-2-yl)oxy)-6,8,11-trihydroxy-8-(2-hydroxyacetyl)-1-methoxy-7,8,9,10-tetra-hydrotetracene-5,12-dione (PKD4), 3-(3,4-dimethylphenyl)-5-((2-(4-fluorophenyl)-2-oxoethyl) thio)-6-phenyl-2-thioxo-2,3,5,7a-tetrahydrothiazolo[4,5-d]pyrimidin-7(6H)-one (PKD5)with high binding affinities, prioritizing them based on their binding energies. These selected compounds were further assessed for their biological activity predictions, guiding the selection of candidates for experimental validation. Subsequent re-evaluation using absolute binding free energy estimation and MD simulations provided insights into the stability and dynamics of the protein-ligand complexes over time. Our findings highlighted the potential of identified compounds as stable binders within the Pks13-TE domain binding pocket, underscoring their viability as drug candidates. Additionally, binding free energy analysis using MM-GBSA reaffirmed the strong affinity of the proposed compounds towards Pks13. Our integrated computational approach offers a systematic and detailed framework for the identification and characterization of potential Pks13 inhibitors with specific relevance to TB drug discovery.

Preprint ARTICLE | doi:10.20944/preprints202404.1891.v1

[Fe^IIICl(TMPPH₂)][Fe^IIICl₄]₂: A Stand-Alone Molecular Nanomedicine that Induces High Cytotoxicity by Ferroptosis

Xiao Wang, Jia-Hao Feng, Chun-Mei Zeng, Ze-Sheng Zhang, Feng-Lin Cao, Wen-Hua Zhang, Jin-Xiang Chen, Yiming Mao, David James Young

Subject: Inorganic And Nuclear Chemistry, Chemistry And Materials Science Keywords: single-molecular nanomedicine; porphyrin ligand; chemodynamic therapy; ferroptosis; breast cancer therapy

Online: 29 April 2024 (09:55:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1678.v1

Hesperetin Inhibits Xanthine Oxidase Activity via Altering the Protein’s Secondary Structure and Suppressing Superoxide Anion Generation

Yinying Liu, Qiangqiang Chen, Hanyu Lu, Zhongxiang Fang, Shengmin Lu

Subject: Food Science And Technology, Biology And Life Sciences Keywords: Hesperetin; Xanthine oxidase; Inhibition kinetics; Interaction mechanism; Multi-spectroscopy; Molecular docking

Online: 25 April 2024 (16:01:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1547.v1

Does Point of Care Testing Reduce Antibiotic Prescribing in Patients Presenting with Acute Sore Throat to Primary Care? A Prospective Test of Change

Rob Daniels, Esther Miles, Karen Button

Subject: Epidemiology And Infectious Diseases, Medicine And Pharmacology Keywords: Point-of-Care-Testing; GAS infections; molecular; quality improvement; antimicrobial stewardship

Online: 23 April 2024 (18:05:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0069.v1

Vesicle Morphogenesis in Amphiphilic Triblock Copolymer Solutions

Senyuan Liu, Mohammad Sadegh Samie, Radhakrishna Sureshkumar

Subject: Chemistry And Materials Science, Chemical Engineering Keywords: Triblock Copolymer; Micelle; Vesicle; Polymersome; Molecular Dynamics; Information Entropy; Nanomedicine; Biomimetic

Online: 2 April 2024 (02:33:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.1561.v1

Synthesis, In silico studies, and biological evaluation of newer N, N'-Phthaloyl GABA Aldehyde/ Aniline analogs as Anti-Epileptic

RAJAN KUMAR KURMI, Snigdha Srivastava, Reema Sinha Shina

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Docking, GABA-AT, QSAR, Epilepsy, Molecular Dynamics, synthesis and in vivo

Online: 26 March 2024 (11:27:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints202402.0801.v1

Chiral Jahn-Teller Distortion in Quasi-Planar Boron Clusters

Dongbo Zhao, Xin He, Yilin Zhao, Tianlv Xu, Shankai Hu, Paul W. Ayers, Shubin Liu

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: Jahn-Teller effect; Helical spin density; Helical molecular orbital; Boron clusters

Online: 14 February 2024 (11:26:08 CET)

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Preprint REVIEW | doi:10.20944/preprints202402.0158.v1

Environmental DNA: Enhancing Species Detection and Study Comparability with Synthetic DNA Tracers

George Stamatoyannopoulos, Thalia Papayannopoulou

Subject: Environmental And Earth Sciences, Environmental Science Keywords: eDNA; synthetic DNA; metabarcoding; DNA tracers; molecular standards; in-field controls

Online: 2 February 2024 (14:18:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.1394.v1

Effect of Cross Nano Wall Surface on the Onset Time of Explosive Boiling: A Molecular Dynamic Study

Rasoul Fallahzadeh, Fabio Bozzoli, Luca Cattani, Muhammad Waheed Azam

Subject: Engineering, Chemical Engineering Keywords: Explosive boiling; Molecular dynamics simulations; Liquid nanofilm; Nanostructurned surface; Onset time

Online: 18 January 2024 (11:02:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.2154.v1

Optimal Treatment Strategy for Oligo-Recurrence Lung Cancer Patients With Driver Mutations

Taimei Tachibana, Yosuke Matsuura, Hironori Ninomiya, Junji Ichinose, Masayuki Nakao, Sakae Okumura, Makoto Nishio, Norihiko Ikeda, Mingyon Mun

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: lung cancer; oligo-recurrence; driver mutation; local therapy; molecular targeted therapy

Online: 28 December 2023 (10:23:13 CET)

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Background: The efficacy of local therapies for lung cancer patients with postoperative oligo-recurrence has been reported. However, whether local therapies should be chosen over molecular targeted therapies for oligo-recurrence patients with driver mutations remains controversial. We hence aimed to investigate the optimal initial treatment strategy for oligo-recurrence in lung cancer patients with driver mutations. Methods: Among 2,152 patients with lung adenocarcinoma who underwent surgical resection at our institute between 2008 and 2020, 66 patients with driver mutations who experienced cancer oligo-recurrence after surgery, and were treated with local or molecularly targeted therapy as an initial therapy after recurrence were evaluated. Oligo-recurrence was characterized by the presence of 1 to 3 recurrent lesions. These patients were investigated focusing on their post-recurrence therapies and prognoses. Results: The median follow-up period was 71 months. Local and molecular targeted therapies were administered to 41 and 25 patients, respectively. The number of recurrence lesions tended to be lower in the initial local therapy group than in the molecular targeted therapy group. In the initial local therapy group, 23 patients (56%) subsequently received molecular targeted therapies. The time from recurrence to the initiation of molecular targeted therapy was significantly longer in the local therapy group than in the molecular targeted therapy group (p < 0.001). There was no significant difference in post-recurrence overall survival (hazard ratio, 1.429; 95% confidence interval, 0.701–2.912; log-rank, p = 0.324), and post-recurrence progression-free survival (hazard ratio, 0.799; 95% confidence interval, 0.459–1.390; log-rank, p = 0.426) in the initial local ablative therapy group compared with the initial molecular targeted therapy group. Conclusions: Local therapies as a first-line treatment did not show statistically significant differences in post-recurrence survival or progression-free survival compared with molecular targeted therapies. However, local therapies as an initial treatment should be considered preferably, as it can cure the recurrence and can delay the start of administration of molecular-targeted therapies.

Preprint ARTICLE | doi:10.20944/preprints202312.1822.v1

An Evaluation of the Anti-QS Activity and Virulence Factors Production Potential of Rhamnus cathartica L. against Some Gram-Positive and Gram-Negative Bacteria

Bashar IBRAHIM, AhuREİS REİS, Ulaş Evren ARIN, Muhammed Tilahun MUHAMMED, Ebru ONEM

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Quorum Sensing; Molecular Docking; Phytochemical; Rhamnus Cathartica L; Plant-Based Antimicrobial

Online: 26 December 2023 (01:47:16 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202312.1376.v1

Exploring FABP3 as a Potential Biomarker for Cardiac and Cerebral Injury Post-Stroke: Insights from Molecular Docking Studies with Natural Compounds

IVAN VITO FERRARI

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: heart fatty acid-binding protein; Morusin; molecular docking; FABP3; Resistomycin; pkCSM

Online: 19 December 2023 (09:45:41 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1849.v1

Characterization of Poultry Gelatins and Hydrolysates Prepared by a Biotechnological Method for Targeted Changes at the Molecular Level

Aneta Prokopová, Pavel Mokrejš, Robert Gál, Jana Pavlačková, Anna Hurajová

Subject: Chemistry And Materials Science, Biomaterials Keywords: antioxidant activity; biotechnology; functional groups; hydrolysate; microbial population; molecular weight; gelatin

Online: 29 November 2023 (11:01:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1620.v1

AI-based Nano-scale Material Property Prediction For Li-Ion Batteries

Mohit Anil Lal, Akashdeep Singh, Ryan Mzik, Amirmasoud Lanjan, Seshasai Srinivasan

Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Quantum Mechanics; Molecular Dynamics; battery materials; Artificial Intelligence; Machine Learning; Nanotechnology

Online: 28 November 2023 (01:40:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.1133.v1

Insight on the Structural and Dynamical Processes of Peptides by Means of Vibrational and Ultrasonic Relaxation Spectroscopies, Molecular Docking and DFT Calculations

Afrodite Tryfon, Panagiota Siafarika, Constantine Kouderis, Angelos G. Kalampounias

Subject: Chemistry And Materials Science, Physical Chemistry Keywords: glutathione; tripeptides; ultrasonic relaxation spectroscopy; molecular docking; self-association; proton-transfer

Online: 17 November 2023 (04:32:02 CET)

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