Accelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBDArticle Published on 2023-04-012023-07-08 Journal: Journal of biomolecular structure & dynamics [Category] COVID19(2023년), [키워드] COVID-19 MD simulations SARS-CoV-2 Spike RBD. [DOI] 10.1080/07391102.2022.2036640 PMC 바로가기
Exploration of Potent Antiviral Phytomedicines from Lauraceae Family Plants against SARS-CoV-2 Main ProteaseArticle Published on 2022-12-142023-07-11 Journal: Viruses [Category] COVID19(2023년), [키워드] cassameridine cassythicine docking laetanine litseferine main protease. MD simulations SARS-CoV-2 [DOI] 10.3390/v14122783 PMC 바로가기
Exploring the multiple conformational states of RNA genome through interhelical dynamics and network analysisArticle Published on 2022-11-012023-07-10 Journal: Journal of molecular graphics & modelling [Category] COVID19(2023년), [키워드] Interhelical dynamics MD simulations network analysis RNA SARS-CoV-2. [DOI] 10.1016/j.jmgm.2022.108264 PMC 바로가기
Structural Reshaping of the Zinc-Finger Domain of the SARS-CoV-2 nsp13 Protein Using Bismuth(III) Ions: A Multilevel Computational StudyArticle Published on 2022-10-032022-11-16 Journal: Inorganic chemistry [Category] COVID19(2023년), SARS, 변종, [키워드] analyses anti-SARS-CoV-2 Anti-SARS-CoV-2 Activity classical decrease degrade domain Effect Efficacy Evidence evidenced extension feature Helicase hydrophobic immune Interaction Ion MD simulations MIF Modification molecular molecular interaction non-structural protein nsp12 protein nsp13 Occurrence pandemic Protein provide Research responsible SARS-COV-2 infection the SARS-CoV-2 the vaccine therapeutic strategy variants [DOI] 10.1021/acs.inorgchem.2c02685 PMC 바로가기
Systematic virtual screening in search of SARS CoV-2 inhibitors against spike glycoprotein: pharmacophore screening, molecular docking, ADMET analysis and MD simulationsArticle Published on 2022-10-012022-11-15 Journal: Molecular diversity [Category] COVID19(2023년), SARS, 치료제, [키워드] absence acting acute respiratory syndrome Amino acid Analysis Anti-viral binding site catalytic coronavirus disease Coronavirus-2 COVID-19 distribution docking score effective Entry inhibitor glycoprotein host cell in silico inhibitor Interaction less Ligand MD simulation MD simulations medications metabolism molecular molecular docking nucleic acid offered performed Precision research finding residue SARS CoV-2 spike spike glycoprotein spike glycoprotein. stability starting point target Toxicity viral entry Virtual screening [DOI] 10.1007/s11030-022-10394-9 PMC 바로가기
Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2SARS-CoV-2의 RNA 의존성 RNA 중합효소의 강력한 억제제로서 인공적으로 확장된 유전 정보 시스템(AEGIS)Article Published on 2022-09-012022-09-11 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 유전자 메커니즘, 치료제, [키워드] AEGIS affected Antiviral agents antiviral agents. binding binding site candidate COVID-19 drug Economy examined genetic information help host cells identify in vivo Infection Information Systems inhibit inhibitor ligands MD simulations mechanism molecular docking monophosphate nucleotide nucleotides Original position outbreak pandemic potential therapeutic agent potential therapeutic agents RdRP RDV Remdesivir Replication responsible RNA RNA-dependent RNA polymerase SARS-CoV-2 SARS-COV-2 infection sequence shown the SARS-CoV-2 therapeutic toxicities Toxicity Transmission unavailability Viral RNA virus [DOI] 10.1080/07391102.2021.1883112 PMC 바로가기 [Article Type] Article
Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods철저한 구조 기반 가상 스크리닝, 분자 역학 시뮬레이션을 사용하여 B.1.617.2(델타), AY.1(델타 플러스) 및 C.37(람다) SARS-CoV-2 변이체에서 중요한 스파이크 돌연변이를 타겟팅하기 위한 전산 용도 변경 접근 방식 및 MM-PBSA 방법Article Published on 2022-08-012022-09-11 Journal: Computers in biology and medicine [Category] COVID19(2023년), SARS, 변종, 신약개발, [키워드] ACE-2 acute respiratory syndrome acute respiratory syndrome coronavirus angiotensin angiotensin-converting enzyme 2 approach Area atovaquone AY.1 B.1.617.2 binding affinity binding site candidate causative agent complex Complexes complexes Compound contagious contribute coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 Critical Delta delta variant Delta variants docking result docking results drug Drug repurposing drug-likeness drugs eight enzyme FDA approved drug FDA approved Drugs followed by genomic help heparin highest binding affinity Host hydrogen Hydrogen bond identify in silico inhibiting inhibitor inhibitors interact Interaction interactions Lambda Ligand MD simulation MD simulations molecular molecular docking molecular dynamics Molecular dynamics simulation Molecular mechanics morbidity and mortality mortality rates Mutation mutations Praziquantel Protein Proteins RBD Receptor-binding domain reported Research researcher residue SARS-CoV-2 SARS-CoV-2 RBD SARS-CoV-2 variant selected severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 Simulation spike spike mutation Spike protein stability surface surface area targets the receptor-binding domain the spike protein variant variants variants of concern viral cell Virtual screening virtual screening. VoC was done was performed wild type Wuhan Wuhan, China [DOI] 10.1016/j.compbiomed.2022.105709 PMC 바로가기 [Article Type] Article
A Multistage In Silico Study of Natural Potential Inhibitors Targeting SARS-CoV-2 Main ProteaseSARS-CoV-2 주요 프로테아제를 표적으로 하는 천연 잠재적 억제제에 대한 다단계 인실리코 연구Article Published on 2022-07-292022-09-11 Journal: International Journal of Molecular Sciences [Category] COVID19(2023년), SARS, 치료제, [키워드] ADMET battle binding binding mode Characteristics choice co-crystallized Compound compounds conducted COVID-19 determine determined by DFT docking exhibited FIVE in silico in vitro in vivo inhibitor Ligand M pro main protease MD simulations metabolite metabolites molecular molecular docking molecular dynamics natural natural antiviral PDB PDB ID performed pharmacophoric positive Potential protease SARS-CoV-2 SARS-CoV-2 main protease selected similarity simulation studies Simulation study structural similarity. Structure targeting the SARS-CoV-2 thermodynamic Toxicity was determined [DOI] 10.3390/ijms23158407 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
Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms항체가 있는 SARS-CoV-2 스파이크 변이체 복합체에서 결합 및 알로스테리의 돌연변이 프로파일링을 위한 형태 역학 및 섭동 기반 네트워크 모델링 통합: 돌연변이 탈출 메커니즘의 로컬 및 글로벌 결정인자 균형 조정Article Published on 2022-07-102022-09-11 Journal: Biomolecules [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, [키워드] Affect allosteric communication Analysis antibodies antibody Antibody binding antibody combination antibody escape approach balancing binding binding affinity binding energy binding hotspots binding interaction change Complexes complexes conformational conformational dynamics conserved cross-reactive determinant determined by dominant dynamic network modeling Dynamics Effect Efficiency energetics escape escape mutant escape mutants Factors flexibility fluctuation host receptor identify Interaction interactions Local MD simulations mechanism modeling modulate Mutation mutational profiling mutations network neutralization neutralize omicron pattern predict Profiling Protein protein folding protein stability residue SARS-CoV-2 spike SARS-CoV-2 spike protein single antibody spike spike plasticity Spike protein stability suggested the antibody the SARS-CoV-2 ultrapotent antibodies. variant [DOI] 10.3390/biom12070964 PMC 바로가기 [Article Type] Article