Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like proteaseOriginal Article Published on 2023-10-052024-09-05 Journal: Cellular and Molecular Life Sciences [Category] update2024, [키워드] binding free energy cooperativity Entropy contribution Papain-like protease Regional improvement of inhibitor [DOI] 10.1007/s00018-023-04985-4 PMC 바로가기 [Article Type] Original Article
Molecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 Mpro: an in silico approach towards drug repurposingArticle Published on 2023-06-012023-07-08 Journal: Journal of biomolecular structure & dynamics [Category] COVID19(2023년), [키워드] binding free energy coronavirus Drug discovery MM-PBSA Molecular dynamics simulation SARS-CoV-2 Mpro [DOI] 10.1080/07391102.2022.2059008
Structure-based design of promising natural products to inhibit thymidylate kinase from Monkeypox virus and validation using free energy calculationsArticle Published on 2023-05-012023-06-09 Journal: Computers in biology and medicine [Category] Fulltext, 원숭이두창, [키워드] binding free energy Bioactivity drugs molecular screening Monkeypox TMPK. [DOI] 10.1016/j.compbiomed.2023.106797 PMC 바로가기
Implications of SARS-CoV-2 spike protein interactions with Zn-bound form of ACE2: a computational structural studyArticle Published on 2023-02-012024-09-05 Journal: Biometals : an international journal on the role of metal ions in biology, [Category] update2024, [키워드] binding free energy Metalloproteins monoclonal antibodies SARS-CoV-2 Spike protein Zinc parameterization Zinc-bound ACE2 [DOI] 10.1007/s10534-023-00491-z PMC 바로가기 [Article Type] Article
Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2Article Published on 2022-12-012022-11-16 Journal: Journal of molecular graphics & modelling [Category] COVID19(2023년), SARS, 변종, 치료기술, [키워드] ACE2 ACE2 receptor Affect angiotensin-converting enzyme 2 Area B.1.1.529 binding binding efficiency binding free energy conformation domain dominant explicit full-length glycans glycoprotein host cells hydrophobic interaction infect Infection initiated Interaction interactions ions Mechanics MMPBSA molecular dynamics Molecular dynamics simulation molecular dynamics simulations mutated Mutation omicron Omicron variant performed RBD RBD-ACE2 receptor residue Salt Bridge SARS-CoV-2 SARS-CoV-2 spike glycoprotein Simulation spike spike glycoprotein strain surface the receptor-binding domain trajectory variant variant of SARS-CoV-2 variants wild-type [DOI] 10.1016/j.jmgm.2022.108286 PMC 바로가기
Computational investigation of natural compounds as potential main protease (Mpro) inhibitors for SARS-CoV-2 virusArticle Published on 2022-12-012023-07-10 Journal: Computers in biology and medicine [Category] COVID19(2023년), [키워드] binding free energy DFT calculation dynamics simulation Main proteases (M(pro)) omicron [DOI] 10.1016/j.compbiomed.2022.106318 PMC 바로가기
Elucidation of the inhibitory activity of ivermectin with host nuclear importin α and several SARS-CoV-2 targetsArticle Published on 2022-11-012022-11-15 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 치료제, [키워드] 3CL pro 3CLpro acting antiviral activity approach binding binding free energy complex COVID-19 dimeric docked complexes docking explained FDA-approved drug FIVE heterodimeric Host in vitro activity inhibit inhibitor inhibitory activity Ivermectin MD simulation molecular molecular docking Molecular dynamics simulation molecular mechanism nuclear previous study protease Proteins reached Replication responsible SARS-CoV-2 SARS-CoV-2 replication shown Structural analysis structural property target translocation variety virus with COVID-19 [DOI] 10.1080/07391102.2021.1911857 PMC 바로가기
In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 bindingSARS-CoV-2 스파이크 단백질 N501Y 및 N501T 돌연변이가 인간 ACE2 결합에 미치는 영향에 대한 실리코 분석Article Published on 2022-11-012022-09-11 Journal: Journal of molecular graphics & modelling [Category] COVID19(2023년), SARS, 변종, [키워드] Analysis analyzed anti-SARS-CoV-2 antibodies Anti-viral drugs antisense attachment binding binding energy binding free energy classic Dynamics Effect Effect of mutations on binding energy effective free energy hACE2 hACE2 receptor hACE2-SARS-CoV-2 spike protein binding. handling highlight Host human ACE2 maintain molecular molecular dynamics molecular dynamics simulations Mutation N501Y N501Y and N501T mutations nine outcome predicted Protein binding raised Replication SARS CoV SARS-CoV-2 SARS-CoV-2 mutations SARS-CoV-2 spike protein Spike protein survival Transmissibility treatment strategy Vaccines virus [DOI] 10.1016/j.jmgm.2022.108260 PMC 바로가기 [Article Type] Article
Decoding the effects of spike receptor binding domain mutations on antibody escape abilities of omicron variantsArticle Published on 2022-10-302022-11-15 Journal: Biochemical and Biophysical Research Communication [Category] COVID19(2023년), SARS, 변종, 진단, [키워드] affinities antibodies antibody Antibody binding antibody escape appear approach approved binding affinity binding free energy cause Coverage COVID19 decrease Effect evaluate globe hotspot immune evasion immunogenic Immunogenic hotspot immunoinformatics K417N monoclonal antibody mutant Mutation mutations omicron Omicron variant Omicron variants Omicron variants. Point mutation RBD mutation RBD-specific antibody recent Receptor binding domain reduce reduction in REGN10987 residue selection pressure significantly single mutation the binding affinity therapeutic vaccination variants [DOI] 10.1016/j.bbrc.2022.08.050 PMC 바로가기
When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative AccuracyArticle Published on 2022-10-112022-11-16 Journal: Journal of chemical theory and computation [Category] COVID19(2023년), SARS, 변종, [키워드] Accuracy ACE2 active against acute respiratory syndrome affinity angiotensin-converting enzyme 2 antibodies antibody applied Beta binding binding free energy biological processe calculation complex coronavirus coronavirus disease Delta delta variant Diversity dust effective estimate host cell Immune escape immune response information methodology molecular omicron Perspective Predictive principle receptor robust SARS-CoV-2 Support the binding affinity the receptor-binding domain Therapies Transmissibility variant variants widespread wild type [DOI] 10.1021/acs.jctc.2c00604 PMC 바로가기