X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturationArticle Published on 2022-09-032022-11-16 Journal: Nature Communications [Category] SARS, 변종, [키워드] Analysis Antiviral binding C-terminal C-terminally capture catalytic cause cleavage cleavage site cleavage sites Complete complex coronavirus 2 COVID-19 enzyme event form Interaction M pro maturation mutant non-structural protein pathogen plasticity polyprotein polyproteins Prevent protease provide representing respiratory responsible SARS-CoV-2 specificity substrates the SARS-CoV-2 therapeutic unique X-ray X-ray crystallographic structure [DOI] 10.1038/s41467-022-32854-4 PMC 바로가기
Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complexSARS-COV-2 NSP1–5'-UTR 복합체의 확장 된 앙상블 시뮬레이션Research Article Published on 2022-01-192022-09-10 Journal: PLoS Computational Biology [Category] SARS, 유전자 메커니즘, [키워드] 5’-untranslated region acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 Analysis Author bind binding block C-terminal causative pathogen characteristic cluster analysis complex Consistency coronavirus COVID-19 cryo cryo-EM Efficiency electron density ENCODE evade experimental evidence experiments Extended flexible Host host cells host immunity host mRNA human cell increase infected cells interactions intrinsically investigated involved mechanism modulate molecular dynamics Molecular dynamics simulation molecular mechanism mutant N-terminal nonstructural protein 1 nsp1 open pandemic of COVID-19 performed predicted Protein Recognition recognize reported residue residues respiratory ribosome RNA SARS-CoV-1 SARS-CoV-2 SARS-CoV-2-infected cells selective severe acute respiratory syndrome Coronavirus Simulation solvent suggested the SARS-CoV-2 translate translation Viral Viral RNA virus X-ray crystallographic structure [DOI] 10.1371/journal.pcbi.1009804 PMC 바로가기 [Article Type] Research Article
In silico evaluation of the interaction between ACE2 and SARS-CoV-2 Spike protein in a hyperglycemic environmentArticle Published on 2021-11-242022-10-29 Journal: Scientific Reports [Category] COVID-19, MERS, SARS, [키워드] ACE2 ACE2 receptor Analysis approach computational analysis Computational biology and bioinformatics condition Contact decrease Diabetes Mellitus endocrinology entry routes evaluate human ACE2 human ACE2 receptor Hydrogen bond Interaction interactions lysine Molecular medicine outcome polar Protein reduced residue salt bridges SARS-CoV-2 significantly spike susceptible the Spike undergo van der Waal virus was performed X-ray crystallographic structure [DOI] 10.1038/s41598-021-02297-w PMC 바로가기 [Article Type] Article
Structure-based drug design of an inhibitor of the SARS-CoV-2 (COVID-19) main protease using free software: A tutorial for students and scientistsResearch article Published on 2021-06-012022-10-05 Journal: European journal of medicinal chemistry [Category] SARS, 신약개발, [키워드] AutoDock AutoDock vina coronavirus COVID-19 disseminate drug drug candidate drug design experimental validation help homologous information inhibitor Interaction Main protease (Mpro) inhibitor modify molecular docking Molecular modeling tutorial MPro pandemic Pandemics peptide Peptide inhibitor protease protocol provide SARS Coronavirus SARS-CoV SARS-CoV-2 SARS-CoV-2 Mpro structure-based design Structure-based drug design (SBDD) structures the SARS-CoV-2 UCSF Chimera X-ray X-ray crystallographic structure [DOI] 10.1016/j.ejmech.2021.113390 [Article Type] Research article
Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulationSupervised Molecular Dynamics 시뮬레이션을 통해 알려진 SARS-CoV-2 Papain-like proteinase 억제제의 결합 해제 경로 풀기Research Article Published on 2021-05-192022-09-10 Journal: PLoS ONE [Category] SARS, 치료제, [키워드] activity Behavior can be used characterized complex COVID-19 disease Critical Dynamics enzyme event inhibitor inhibitors molecular dynamics Papain Papain-like protease pathway Pathways PLPro Potential potential molecular protease Protein proteinase recent residue residues SARS-CoV-2 SARS-CoV-2 virus targets the SARS-CoV-2 virus therapy for COVID-19 Treatment X-ray crystallographic structure [DOI] 10.1371/journal.pone.0251910 PMC 바로가기 [Article Type] Research Article
Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulationComputational Biology Published on 2021-04-132022-10-28 Journal: PeerJ [Category] COVID-19, [키워드] 3CL-Pro adopted analyzed antiviral drug approach AutoDock binding caused chemotypes Compound compounds computation conformational coronavirus coronavirus diseases COVID-19 COVID-19 pandemic crystal structures crystallographic structure demonstrated develop deviation Diversity docking drug candidate effective FDA-approved drug fluctuation Frame global effort globe Gromacs High-resolution identification in silico indicated inhibitor insight interval library Ligand ligands main protease molecular docking Molecular dynamics simulation molecular target MPro oral bioavailability other molecules over parameters performed pharmacokinetic Physicochemical properties predicted profiles protease protein-ligand protein-ligand interaction protein-ligand interactions Result RMSD RMSF Safe SARS-CoV-2 selected small molecule target protein the SARS-CoV-2 the SARS-CoV-2 virus Toxicity trajectory treat Vina viral disease Virtual screening while X-ray crystallographic structure [DOI] 10.7717/peerj.11261 PMC 바로가기 [Article Type] Computational Biology
Repurposing of approved drugs with potential to interact with SARS-CoV-2 receptorResearch Article Published on 2021-03-292022-10-04 Journal: Biochemistry and Biophysics Reports [Category] 신약개발, [키워드] Abstract ACE ACE1 ACE2 addition Amino acid Analysis angiotensin approved drug binding Cell comparable coronavirus 2 COVID-19 distribution domain Drug repurposing entry of SARS-CoV-2 enzyme epithelial expression homolog host cells host-virus interaction human cells human lung Image Infection Interaction interfere low expression organized peptidase predict primary sequence Proteins RBD receptor Receptor binding domain Region reported repurposing respiratory S protein same order SARS-CoV-2 SARS-CoV-2 receptor SARS-CoV-2 spike protein similarities similarity spike glycoprotein Spike protein the SARS-CoV-2 tissue Transmission variety viral spike protein X-ray crystallographic structure [DOI] 10.1016/j.bbrep.2021.100982 PMC 바로가기 [Article Type] Research Article
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing siteArticle Published on 2020-11-182022-10-04 Journal: Nature Communications [Category] SARS, 변종, 치료제, [키워드] Antiviral antiviral drug autocleavage binding C-terminal catalytic cause cleavage conformational change coronavirus 2 COVID-19 Critical cysteine protease determine Drug discovery Enzyme mechanisms event feature identify M pro maturation mechanism molecular docking mutant Mutation nonstructural protein occur pathogen physiological polyproteins protease replicase polyprotein representing respiratory responsible SARS-CoV-2 SARS-CoV-2 main protease sequence subsequent the disease therapeutic viral replication wild-type wild-type SARS-CoV-2 X-ray crystallographic structure X-ray crystallography [DOI] 10.1038/s41467-020-19662-4 PMC 바로가기 [Article Type] Article
Computational Evaluation of the Inhibition Efficacies of HIV Antivirals on SARS-CoV-2 (COVID-19) Protease and Identification of 3D Pharmacophore and Hit CompoundsResearch Article Published on 2020-09-212022-10-28 Journal: Advances in Pharmacological and Pharmaceutical Sciences [Category] COVID-19, [키워드] acute respiratory syndrome analysed anti-HIV drug antiviral drugs AutoDock binding affinity binding score carried classification Compound compounds Computational study coronavirus coronavirus disease COVID-19 derivation Discovery Studio docked docking study drug Efficacy eight evaluate evaluated Health practitioner HIV HIV treatment hydrophilic identification identify In silico methods in vivo inhibit inhibition Interaction majority medication molecular Novel coronavirus parameters Patient performed pharmaceutical pharmacophore protease Protease inhibitor Protein Data Bank reported researcher Ritonavir SARS-CoV-2 SARS-CoV-2 protease spread of COVID-19 Structure the SARS-CoV-2 these compound these compounds treat Vaccine was obtained web server X-ray crystallographic structure [DOI] 10.1155/2020/8818008 PMC 바로가기 [Article Type] Research Article
Structure-Based Drug Design of an Inhibitor of the SARS-CoV-2 (COVID-19) Main Protease Using Free Software: A Tutorial for Students and Scientistspreprint Published on 2020-08-122022-10-31 Journal: ChemRxiv [Category] COVID-19, [키워드] AutoDock coronavirus COVID-19 disseminate drug drug candidate drug design experimental validation Free help homologous information inhibitor Interaction M pro modify molecular docking pandemic Pandemics peptide Peptide inhibitor protease provide SARS Coronavirus SARS-CoV SARS-CoV M SARS-CoV-2 scientist structure-based design structures student supplementary material the SARS-CoV-2 tutorial UCSF Chimera X-ray X-ray crystallographic structure [DOI] 10.26434/chemrxiv.12791954 PMC 바로가기 [Article Type] preprint