Partial structure, dampened mobility, and modest impact of a His tag in the SARS-CoV-2 Nsp2 C-terminal regionOriginal Article Published on 2021-10-112022-10-31 Journal: European Biophysics Journal [Category] COVID-19, SARS, [키워드] assigned atomic level backbone C-terminal cleavage conformational conformations cryo-EM Defense eukaryotic cells flexible Host human protein information interact Interaction Intrinsically disordered proteins molecule N-terminal NMR spectroscopy not affect NSP2 nuclei Partial physiological predicted preference promote Protein Region regulate residues SARS-CoV-2 supplementary material targets the SARS-CoV-2 translation initiation Vesicle viral growth virus while X-ray crystallography [DOI] 10.1007/s00249-021-01575-9 PMC 바로가기 [Article Type] Original Article
Fragment-based in silico design of SARS-CoV-2 main protease inhibitorsSARS-CoV-2 주요 프로테아제 억제제의 단편 기반 in silico 설계Article Published on 2021-10-012022-09-11 Journal: Chemical biology & drug design [Category] SARS, 신약개발, 치료제, [키워드] 3CLpro approach AutoDock AutoDock vina binding binding affinity binding mode binding pocket co-crystallized Compound conformation conformations coronavirus Coronavirus COVID-19 crystal structure domain Drug discovery eight fragment fragment-based drug discovery generate Glide in silico inhibitor interactions linear combination linker main protease Mpro 3CLpro MD simulation MPro multivalency. Precision protease Protein Data Bank provided SARS-CoV-2 SARS-CoV-2 main protease SARS-CoV-2 replication screened selected small molecule Small molecules starting point Structure structures suggested therapeutic strategy were used X-ray X-ray crystal structure [DOI] 10.1111/cbdd.13914 PMC 바로가기 [Article Type] Article
A method for intuitively extracting macromolecular dynamics from structural disorderArticle Published on 2021-09-172022-10-29 Journal: Nature Communications [Category] COVID-19, SARS, [키워드] accounted Analysis approach conformations Cryo-electron microscopy cryo-EM structures disorder example Factors Hierarchical hypothese Implications information macromolecular molecular molecular mechanisms parameter Proteins Quantitative SARS-CoV-2 SARS-CoV-2 proteins STEAP4 Structural analysis structural biology Structure Structure determination structures temperature [DOI] 10.1038/s41467-021-25814-x PMC 바로가기 [Article Type] Article
Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics APIArticle Published on 2021-09-162022-10-29 Journal: Journal of Chemical Information and Modeling [Category] COVID-19, MERS, SARS, [키워드] Algorithm API assembly automated block bouton building can be used cells conformations Creative Common displaying downloaded Essential Giant GPU Graphics HIV implementation introduced limit memory molecular Molecular dynamics simulation platform presynaptic reduce reduced required SARS-CoV-2 significantly Structure structures View virus particle Visualization [DOI] 10.1021/acs.jcim.1c00743 PMC 바로가기 [Article Type] Article
Predicted pH-dependent stability of SARS-CoV-2 spike protein trimer from interfacial acidic groupsResearch Article Published on 2021-09-022022-10-31 Journal: Computational and Structural Biotechnology Journal [Category] COVID-19, [키워드] Abstract Acidic acidic pH Alter calculated calculation characterisation conformations Coronaviruses Cryo-electron microscopy Effect form group histidine insertion Mild modulated Neutral pH-dependence pre-fusion predicted protein electrostatics RBD Receptor binding Receptor binding domain reduce residues SARS-CoV-2 SARS-CoV-2 spike protein Spike protein spike trimer spike trimers stability Structure the SARS-CoV-2 transition trimer Trimers Vaccine design variant [DOI] 10.1016/j.csbj.2021.08.049 PMC 바로가기 [Article Type] Research Article
Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL pro)SARS-COV-2를 표적으로하는 약물 재생 연구 : 약물 표적 3C 유사 프로테아제 (3CL Pro)에 대한 앙상블 도킹 접근법Article Published on 2021-09-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, 치료제, [키워드] 3CL pro 3CLpro 6LU7 acute respiratory syndrome Analysis anti-bacterial Anti-viral anti-viral drug apo form approach approved binding candidate causative agent caused cleavage Clustering conformation conformational conformations coronavirus 2 COVID-19 COVID-19 pandemic cryptic pockets crystal structure cumulative database death disease docking drug Drug administration Drug repurposing drug target food Food and Drug Administration high-resolution crystal structure HIV in silico main protease Markov modeling Novel coronavirus PDB PDB ID polyprotein protease repurposing respiratory responsible RMSD RNA viruses SARS-CoV SARS-CoV-2 screened selected Severe acute respiratory syndrome state Structure Support target treating COVID-19 Variation Viral was used [DOI] 10.1080/07391102.2020.1792344 PMC 바로가기 [Article Type] Article
Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasionResearch Article Published on 2021-08-312022-10-31 Journal: eLife [Category] COVID-19, MERS, SARS, [키워드] absence acute respiratory syndrome Analysis Cell conformational conformational change conformations contagious control cell coronavirus COVID-19 Critical described endpoints energy landscapes fusion peptide glycan glycans glycosylation Host host cell induce Infection initial Invasion lack membrane membrane fusion pathogen post-translational modifications postfusion prefusion Protein provide regulate released remained reported reveal SARS-CoV-2 spike steric structural framework Structure the Spike transmembrane Transmission Vaccine viral genome viral particle virus was used while [DOI] 10.7554/eLife.70362 PMC 바로가기 [Article Type] Research Article
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 M proSARS-CoV-2 M pro를 표적으로 하는 새로운 비펩타이드성 억제제의 구조 기반 발견Article Published on 2021-08-232022-09-11 Journal: Journal of Chemical Information and Modeling [Category] SARS, 치료제, [키워드] 3CL pro activity acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 Analysis antiviral activity antiviral drug apo form binding free energy biochemical Candidates caused Compound conformations coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 Cytopathic effect develop docking drug energy transfer enzyme experiment form free energy half-maximal effective concentration half-maximal inhibitory concentration Health indicated inhibit inhibitor inhibitors ligands M pro maturation mechanism molecular molecular dynamics Molecular dynamics simulation nine novel Novel coronavirus novel coronavirus disease protease Protein ranged reduce Replication SARS-CoV-2 severe acute respiratory syndrome Coronavirus Spread Structure subsequent surface plasmon surface plasmon resonance targeting treat Treatment treatment of COVID-19 Vero E6 Vero E6 cell VERO E6 cells viral particle Viral particles Virtual screening virus [DOI] 10.1021/acs.jcim.1c00355 PMC 바로가기 [Article Type] Article
Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulationsResearch article Published on 2021-08-012022-10-05 Journal: Computers in biology and medicine [Category] SARS, 신약개발, [키워드] ACE2 proteins ACE2-RBD acute respiratory syndrome approach binding binding domain binding site caused Clustering analysis conformation conformational Conformational ensemble conformations Coronavirus-2 COVID-19 death docking scores drug drug design Drug repurposing drugs exhibited FDA approved drug help human ACE2 identify inhibiting Interaction investigated MD simulation MD simulations molecular Molecular dynamics simulation plasticity predicted RBD Receptor binding domain Respiratory disease responsible SARS-CoV-2 SARS-CoV-2 RBD SARS-CoV-2 receptor significantly Spike protein stability the RBD the SARS-CoV-2 Virtual screening virus infection were used worldwide pandemic [DOI] 10.1016/j.compbiomed.2021.104634 [Article Type] Research article
Mechanism of Ligand Recognition by Human ACE2 Receptor인간 ACE2 수용체에 의한 리간드 인식 메커니즘Article Published on 2021-05-272022-09-11 Journal: The journal of physical chemistry letters [Category] SARS, 신약개발, 치료제, [키워드] accelerated ACE2 ACE2 receptor active site acute respiratory syndrome addressed Amino acid angiotensin angiotensin converting enzyme angiotensin converting enzyme 2 binding conformational conformations coronavirus coronaviruses SARS-CoV Critical diabetes Diseases drug design drug target enzyme epithelial cell epithelial cells expected experimental structure expressed facilitate flexible heart heart failure homeostasis Human human ACE2 human ACE2 receptor human diseases hypertension inhibitor kidney Ligand Lungs mechanism MLN-4760 molecular molecular dynamics pancreas pulmonary diseases receptor Recognition Regulation renal Renin renin-angiotensin system SARS-CoV-2 Severe acute respiratory syndrome X-ray [DOI] 10.1021/acs.jpclett.1c01064 PMC 바로가기 [Article Type] Article