Virtual Screening and Quantum Chemistry Analysis for SARS-CoV-2 RNA-Dependent RNA Polymerase Using the ChEMBL Database: Reproduction of the Remdesivir-RTP and Favipiravir-RTP Binding Modes Obtained from Cryo-EM Experiments with High Binding AffinityArticle Published on 2022-09-202022-11-15 Journal: International Journal of Molecular Sciences [Category] SARS, 신약개발, 치료법, 치료제, [키워드] acute respiratory syndrome adopted affinity Analysis anti-SARS-CoV-2 anti-viral activity approved binding affinity binding free energy ChEMBL Chemistry clinical development Compound coronavirus coronavirus disease COVID-19 Cryo-electron microscopy cryo-EM cryo-EM structure database docking drug drug candidates drug library drug repositioning drugs dsRNA fragment molecular orbital calculation Frequency frequency analysis interactions mode molecular Novel coronavirus ONIOM geometry optimization calculation pathogenic PDB performed predicted quantum quantum chemistry calculation RdRP reported reproduction RNA RNA-dependent RNA polymerase SARS-CoV-2 Screening screenings significantly suggested Treatment Virtual screening was performed [DOI] 10.3390/ijms231911009 PMC 바로가기
In Silico Study towards Repositioning of FDA-Approved Drug Candidates for Anticoronaviral Therapy: Molecular Docking, Molecular Dynamics and Binding Free Energy CalculationsArticle Published on 2022-09-142022-11-15 Journal: Molecules [Category] SARS, 신약개발, 치료제, [키워드] AAK1 addition Anti-COVID-19 Anti-SARS-CoV-2 Activity applied binding binding free energy binding pattern calculation candidate Combination complexes computational modeling digoxin drug drug repositioning drugs Dynamics energy Enzymes evaluated exhibited FDA-approved drug Free greater in silico inhibitor inhibitors methodology molecular molecular docking molecular dynamic simulations MPro niclosamide ouabain PLPro Proscillaridin protease Protein provide RdRP repositioning RNA-dependent RNA polymerase SARS-CoV-2 SARS-CoV-2 main protease screened suggested target targets tested to define [DOI] 10.3390/molecules27185988 PMC 바로가기
Repurposing vilanterol as a novel potential antifungal for Candida albicans: In-silico & in-vitro approachResearch article Published on 2022-09-012022-10-05 Journal: Medicine in Drug Discovery [Category] 신약개발, [키워드] Acridine orange and Ethidium bromide Alter Amino acids CYSCystine Analysis AO/EBAcridine orange and Ethidium bromide approach binding binding free energy C. albican C. albicans Candida Candida albican carried cause cell membrane chronic Conditions obstructive pulmonary disease Clinical and Laboratory Standards Institute clinical study CLSIClinical and Laboratory Standards Institute complex Computational drug Concentration COPDchronic Conditions obstructive pulmonary disease Cystine demethylase diffusion Dimethyl sulfoxide disrupt DMSODimethyl sulfoxide docking method dose drug drug interaction Drug screening drugs Erg11pLanosterol 14-alpha demethylase FDAThe United States Food and Drug Administration fluorescent fungicidal fungicidal activity glycine GLYGlycine Health High-throughput virtual screening HISHistidine histidine HTVSHigh-throughput virtual screening humans In-vitro infect infections inhibitory concentration initial Interaction lanosterol Lanosterol 14-alpha demethylase MDSMolecular Dynamics Simulations MICMinimum inhibitory concentration Microscopy Minimum inhibitory concentration MMGBSAMolecular mechanics energies with generalized born surface area Molecular dynamics simulation molecular dynamics simulations Molecular mechanics energies with generalized born surface area mortality rate PBSPhosphate buffer saline PDBProtein Data Bank Phenylalanine PHEPhenylalanine Phosphate buffer saline Phosphatidylcholines Picoseconds POPCPhosphatidylcholines Protein Data Bank psPicoseconds repurposing Safe SDStandard deviation Serine SERSerine SPStandard-precision Standard deviation Standard-precision tested The United States Food and Drug Administration tyrosine TYRTyrosine Variable-dielectric surface generalized born model 2.0 VSGB 2.0Variable-dielectric surface generalized born model 2.0 XPXtra-precision Xtra-precision Yeast extract/peptone/dextrose YPDYeast extract/peptone/dextrose [DOI] 10.1016/j.medidd.2022.100137 [Article Type] Research article
Assessment of a Computational Approach to Predict Drug Resistance Mutations for HIV, HBV and SARS-CoV-2Article Published on 2022-08-242022-11-15 Journal: Molecules [Category] SARS, 변종, 유전자 메커니즘, 치료제, [키워드] 3CLpro Accuracy antiviral drugs approach assessment binding free energy capsid demonstrated dependent on drug Drug discovery drug resistance effective Effectiveness emtricitabine experiment HBV HIV identify mechanism MM-GBSA Mutation mutations Nirmatrelvir performed predict predicted primary mechanism Protein Research residue residue scanning. resistance Rt SARS-CoV-2 selected sensitivity time-consuming treatment strategy Viral protein [DOI] 10.3390/molecules27175413 PMC 바로가기
Identification and Inhibition of the Druggable Allosteric Site of SARS-CoV-2 NSP10/NSP16 Methyltransferase through Computational Approaches컴퓨터 접근을 통한 SARS-CoV-2 NSP10/NSP16 메틸트랜스퍼라제의 약물 가능 알로스테릭 부위의 식별 및 억제Article Published on 2022-08-172022-09-11 Journal: Molecules [Category] SARS, 변종, [키워드] affected allosteric site antagonistic action assessment binding free energy caused complexes Compound COVID-19 COVID-19 pandemic Drug discovery drug library effort enzyme evaluated exhibited Health Host identification Infectious virus inhibition inhibitor inhibitors life life cycle methyl transferase methyltransferase molecular molecular docking molecular dynamics Molecular dynamics simulation molecular interaction Perspective proliferation PROTECT Research robust SARS-CoV-2 SARS-CoV-2 life cycle screened Simulation Site stability target the SARS-CoV-2 these compound these compounds variants Viral RNA was performed [DOI] 10.3390/molecules27165241 PMC 바로가기 [Article Type] Article
Exploring the mechanism of action of Xuanfei Baidu granule (XFBD) in the treatment of COVID-19 based on molecular docking and molecular dynamicsArticle Published on 2022-08-102022-11-16 Journal: Frontiers in Cellular and Infection Microbiology [Category] SARS, 유전자 메커니즘, [키워드] acting Activation alleviate Analysis analyzed Anti-inflammatory effects Apoptosis Baidu binding binding energy binding free energy bioinformatics Bioinformatics analysis carried chemotaxis clinical symptom Clinical symptoms Combination component Corona COVID-19 CSF2 database disease docking effective gene target GeneCard hydrogen bonds immune response Immunity IMPROVE Inflammation inflammatory cell Inflammatory factor Inflammatory response ingredient inhibiting Intersection KEGG Lymphocytes mechanism mechanism of action molecular molecular docking molecular dynamics monomer NLRP3 Pachypodol pandemic Patient platform Protein protein targets radius of gyration reduce Research residue SARS-COV-2 infection screened signaling pathway significantly solvent stability targets TCMSP database therapeutic treating COVID-19 Treatment was used White blood cell Xuanfei Baidu granule [DOI] 10.3389/fcimb.2022.965273 PMC 바로가기
Urtica dioica Agglutinin: A plant protein candidate for inhibition of SARS-COV-2 receptor-binding domain for control of Covid19 InfectionUrtica dioica Agglutinin: Covid19 감염 통제를 위한 SARS-COV-2 수용체 결합 도메인 억제를 위한 식물성 단백질 후보Article Published on 2022-07-282022-09-11 Journal: PLoS ONE [Category] COVID19(2023년), MERS, SARS, 유전자 메커니즘, 진단, [키워드] ACE2 addition angiotensin Angiotensin-converting enzyme angiotensin-converting enzyme-2 Antiviral effect average bind binding binding affinity binding energy binding free energy binding site calculated Cell complex convalescent serum coronavirus docked docking docking result docking results domain Donor donors dynamic effective effective drug effective drugs ELISA ELISA assay enzyme exhibited free energy Gromacs host cell human cells IgG Infection inhibit inhibitory activity Interaction limitation MD simulation mechanism Medicine Medicines MTT Mutation peptide Prevent Previous studies Protein RBD RBD binding RBD complex RBD protein Receptor-binding domain Result S-protein Safe SARS-CoV SARS-CoV-2 Simulation spike Spike protein spike protein of SARS-CoV-2 stability the cell the RBD Toxicity Urtica Vaccine virus was performed was used [DOI] 10.1371/journal.pone.0268156 PMC 바로가기 [Article Type] Article
A ricin-based peptide BRIP from Hordeum vulgare inhibits M pro of SARS-CoV-2Hordeum vulgare의 리신 기반 펩타이드 BRIP는 SARS-CoV-2의 M pro를 억제합니다Article Published on 2022-07-272022-09-11 Journal: Scientific Reports [Category] COVID19(2023년), SARS, 변종, 치료제, [키워드] barley binding binding free energy binding site caused complex component components contributed COVID-19 cytotoxicity domains electrostatic free energy Hordeum identify in vitro inhibit inhibitor inhibitors inhibitory Interaction investigated M pro MD simulations molecular molecular docking molecular dynamics pandemic parameter peptide peptides Research ricin SARS-CoV-2 SARS-CoV-2 main protease stability suggested therapeutic potential thermodynamic Trajectories trajectory Van Van der Waals virus [DOI] 10.1038/s41598-022-15977-y PMC 바로가기 [Article Type] Article
Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort대규모 코호트에서 SARS-CoV-2에 대한 hACE2의 숙주 변이체의 도킹 특성 분석Article Published on 2022-07-112022-09-11 Journal: PLoS Computational Biology [Category] COVID19(2023년), SARS, 변종, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 analyzed angiotensin binding free energy caused coronavirus coronavirus disease COVID-19 COVID-19 infection Diagnosis docking free energy genetic diversity genomic data global health hACE2 Health Host human Angiotensin-converting enzyme Human angiotensin-converting enzyme 2 human cells individual individuals Interaction large cohort missense variant Mobility molecular molecular dynamics Molecular dynamics simulation molecular interaction Novel coronavirus novel coronavirus disease outbreak physical provided receptor SARS-CoV-2 SARS-CoV-2 entry SARS-CoV-2 infections selected severe acute respiratory syndrome Coronavirus Spike protein subject the spike protein UK biobank variant [DOI] 10.1371/journal.pcbi.1009834 PMC 바로가기 [Article Type] Article
Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approachA.30 변이체의 결합 및 동적 특징 조사 결과 hACE2에 대한 RBD의 더 높은 결합 및 중화 항체 탈출: 분자 시뮬레이션 접근Article Published on 2022-07-012022-09-11 Journal: Computers in biology and medicine [Category] COVID19(2023년), MERS, SARS, 변종, 진단, [키워드] A.30 variant ACE2 approach atomic binding binding affinity binding free energy calculated complex complexes coronavirus coronavirus disease cross-protective Deletion deletions Delta demonstrated dissociation Dissociation constant docking result domain drug Effects evade feature Free free energy global pandemic greater hACE2 help Host immune response Interaction interactions investigation mAb molecular Molecular simulation monoclonal antibodies mutated Mutation N terminal domain Neutralizing Neutralizing antibodies NTD omicron Omicron variants protein-protein docking RBD RBD complex reduce reported residue robust salt-bridge SARS-CoV-2 Simulation spike gene Spike protein Spread Substitution the spike protein variant variants variants of SARS-CoV-2 wild type [DOI] 10.1016/j.compbiomed.2022.105574 PMC 바로가기 [Article Type] Article