A computational drug repurposing approach in identifying the cephalosporin antibiotic and anti-hepatitis C drug derivatives for COVID-19 treatmentCOVID-19 치료를 위한 세팔로스포린 항생제 및 항 C형 간염 약물 유도체 식별을 위한 컴퓨터 약물 용도 변경 접근법Article Published on 2021-03-012022-08-31 Journal: Computers in biology and medicine [Category] MERS, SARS, 신약개발, 치료제, [키워드] active site acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 amalgam Analysis antibiotic antiviral agent Antiviral agents approach backbone atom Bacterial bacterial pneumonia Bank binding binding free energy caused Ceftaroline Ceftaroline fosamil Chemical complex Computational drug coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 Critical Cys145 database death derivative drug Drug repurposing free energy Free energy calculations Glu166 Gly143 HCV hepatitis C hepatitis C virus His41 hydrogen Hydrogen bond hydrogen bonds identify indicated indication information inhibitor inhibitors Interaction investigated M pro MD simulations molecular molecular dynamics offer pharmacokinetic Pneumonia potential energy Preclinical Testing profiles Protease inhibitor Protein repurposing residue respiratory RMSD SARS-CoV-2 SARS-CoV-2 main protease Seven severe acute respiratory syndrome Coronavirus Side effects suggested supported telaprevir Treatment Virtual screening [DOI] 10.1016/j.compbiomed.2020.104186 PMC 바로가기 [Article Type] Article
Identification of FDA approved drugs and nucleoside analogues as potential SARS-CoV-2 A1pp domain inhibitor: An in silico study잠재적인 SARS-CoV-2 A1pp 도메인 억제제로서 FDA 승인 약물 및 뉴클레오시드 유사체 식별: 실리코 연구Article Published on 2021-03-012022-09-11 Journal: Computers in biology and medicine [Category] SARS, 신약개발, 치료제, [키워드] A1pp domain adenosine adenosine diphosphate Analysis approved binding binding affinity binding free energy biological activity citicholine conserved coronavirus crystal structure demonstrated deviation docking scores domain exhibited FDA FDA approved drug FDA approved Drugs FIVE fluctuation free energy free energy landscape gyration Host human coronavirus hydrogen Hydrogen bond hydrophobic identification in silico infect inhibit inhibitor Interaction intestine macro Macro domain molecular molecular dynamics Molecular dynamics simulation Molecular mechanics nadide nucleoside nucleoside analogue Nucleoside analogues offer Pathogenesis performed phosphatase positive control promote Protein radius radius of gyration reported respiratory tract ribose RMSD RMSF root mean square deviation root mean square fluctuation SARS-CoV-2 solvent stable complex substrate binding site surface area Therapeutic molecule Therapeutics these compound these compounds these viruses These viruses viral infection [DOI] 10.1016/j.compbiomed.2020.104185 PMC 바로가기 [Article Type] Article
Inhibitory efficiency of potential drugs against SARS-CoV-2 by blocking human angiotensin converting enzyme-2: Virtual screening and molecular dynamics study인간 안지오텐신 전환 효소-2를 차단하여 SARS-CoV-2에 대한 잠재적 약물의 억제 효율: 가상 스크리닝 및 분자 역학 연구Article Published on 2021-03-012022-08-31 Journal: Microbial pathogenesis [Category] SARS, 신약개발, 치료제, [키워드] ACE-2 ACE-2 receptor Analysis angiotensin anti-bacterial anti-viral drug Anti-viral drugs best bind binding affinity binding site block blocking Cefpiramide comprehensive analysis COVID-19 CPM drug effective Efficiency enzyme gyration highest binding affinity human Angiotensin-converting enzyme molecular molecular docking molecular dynamics Molecular dynamics simulation parameter radius of gyration receptor RMSD RMSF SARS-CoV-2 SARS-CoV-2 spike protein screened selected solvent Spike protein surface area Till Vaccine virus [DOI] 10.1016/j.micpath.2021.104762 PMC 바로가기 [Article Type] Article
Computational Determination of Potential Multiprotein Targeting Natural Compounds for Rational Drug Design Against SARS-COV-2Article Published on 2021-01-282022-10-30 Journal: Molecules [Category] COVID-19, [키워드] Against Analysis anti-SARS-CoV-2 binding binding energy binding free energy Candidates caused complex complexes Compound COVID-19 COVID-19 pandemic Critical database demonstrated Determination docking docking result drug effective enzyme Enzymes glycyrrhizin imperative inhibit investigated MD simulation mechanism Molecular dynamics simulation MPD3 MPro multiprotein inhibiting natural compounds natural natural antiviral PLPro Potential receptor receptors reported residue RMSD SARS-CoV-2 SARS-COV-2 infection selected stability targeting trajectory van der Waal Virtual screening virus [DOI] 10.3390/molecules26030674 PMC 바로가기 [Article Type] Article
Reverse vaccinology approach towards the in-silico multiepitope vaccine development against SARS-CoV-2SARS-CoV-2에 대한 in-silico 다중 에피토프 백신 개발을 위한 역백신학 접근법Research Article Published on 2021-01-232022-09-11 Journal: F1000Research [Category] 치료법, [키워드] acute respiratory syndrome adjuvant allergen allergenicity Antigen antigenicity approach B cell epitope B cell epitopes binding binding affinity C terminal CAI calculated caused codon adaptation index complex Corona virus coronavirus disease Coronavirus disease 2019 COVID-19 cytotoxic Cytotoxic T cell disease docked docking E. coli effective Epitopes experimental validation expression fatal COVID-19 GC content helper T cell human body immunization immunoinformatics in-silico membrane MHC molecular dynamics Molecular dynamics simulation molecular dynamics simulations multiepitope multiepitope based vaccine multiepitope vaccine Nidovirales nucleocapsid online tool pandemic pandemic coronavirus polyprotein predict predicted receptor reduction respiratory Result RMSD SARS-CoV-2 sequence Simulations spike Spread suggested T cell T cell epitopes the binding affinity tlr-3 Toxicity Vaccine vaccine candidate Vaccine development were used [DOI] 10.12688/f1000research.36371.1 PMC 바로가기 [Article Type] Research Article
Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting CoronavirusesMedicine Published on 2021-01-142022-10-31 Journal: Frontiers in Medicine [Category] COVID-19, [키워드] approach C-terminal domain (CTD) Cluster Contact CoV CoV spike protein CoV spike proteins CoVs generate HCoV 229E HKU1 Host Human Infection Lineage MERS Model modeling N-terminal domain (NTD) NL63 OC43 Other pandemic pattern performed Phylogenetic Protein relative RMSD RNA virus S1 domain S1-NTD SARS coronavirus 2 (SARS2) SARS CoV SARS1 SARS2 selected Seven similarity spike spike glycoprotein Spike protein viral pathogenesis viral surface virulence whole protein [DOI] 10.3389/fmed.2020.594439 PMC 바로가기 [Article Type] Medicine
Molecular Docking and Molecular Dynamics Aided Virtual Search of OliveNet™ Directory for Secoiridoids to Combat SARS-CoV-2 Infection and Associated Hyperinflammatory ResponsesMolecular Biosciences Published on 2021-01-072022-10-31 Journal: Frontiers in Molecular Biosciences [Category] COVID-19, [키워드] alleviate Anti-inflammatory anti-SARS-CoV-2 therapeutics AutoDock vina blocked combat complex correlated Cys145 docking drugs Dynamics FIVE fraction functional food Health help Hyperinflammatory hyperinflammatory responses IL1β IL6 IL6R indicated Inflammatory cytokine Interaction M pro main protease molecular molecular docking molecular dynamics non-toxic Oleaceae oleuropein olive oil olive secoiridoids Precision predicted Prevent protease receptor Replication residue response RMSD S protein SARS-CoV-2 SARS-CoV-2 entry SARS-COV-2 infection SARS-CoV-2 spike (S) protein stability structures supported the S protein the SARS-CoV-2 therapy TNFR1 TNFα viral disease virtual search [DOI] 10.3389/fmolb.2020.627767 PMC 바로가기 [Article Type] Molecular Biosciences
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease가상 현실의 대화형 분자 역학은 SARS-CoV-2 메인 프로테아제에 대한 유연한 기질 및 억제제 도킹을 위한 효과적인 도구입니다Article Published on 2020-12-282022-09-11 Journal: Journal of Chemical Information and Modeling [Category] SARS, 변종, 신약개발, 치료제, [키워드] approach backbone binding interactions build Community complexes COVID-19 creating crystal structure crystal structures crystallographic structure demonstrated docked docking Drug development Dynamics effective effort enzyme flexibility flexible focus hydrogen hydrogen bonds inhibitor MD simulation MD simulations Metrics molecular molecular dynamics MPro oligopeptide open physically PLOS protease Protein protein complex protein complexes Protein target protocol provide REALITY recommendation Research RMSD SARS-CoV-2 virus small molecule small molecule drug small molecule drugs software framework Structure structures substrate targets tested the SARS-CoV-2 the SARS-CoV-2 virus user Viral virtual reality [DOI] 10.1021/acs.jcim.0c01030 PMC 바로가기 [Article Type] Article
Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main ProteaseArticle Published on 2020-12-232022-10-28 Journal: Biology [Category] COVID-19, [키워드] affecting amino acid residue Analysis analyzed antibiotic anticancer Antiviral agents approach binding free energy binding interactions carried category China computational method conformational coronavirus coronavirus disease COVID-19 database determine docked docking scores drug Drug discovery Drug repurposing DrugBank database drugs E-pharmacophore hypothesis Effectiveness evaluate exhibited experimental drug Features generate human-to-human transmission hydrophobic interaction Hypothesis identity in vitro study in vivo inhibitor Interaction M pro MERS-CoV MM/PBSA molecular docking molecular dynamics Molecular dynamics simulation novel Novel coronavirus novel coronavirus disease Potential treatment repurposing required retrieved RMSD RMSF SARS-CoV SARS-CoV-2 SARS-CoV-2 main protease screened Screening selected sequence Seven simple specific treatment Spread stability suggested targeting the disease Treatment Virtual screening were used [DOI] 10.3390/biology10010002 PMC 바로가기 [Article Type] Article
Molecular docking and simulation investigation: effect of beta-sesquiphellandrene with ionic integration on SARS-CoV2 and SFTS virusesResearch Published on 2020-11-272022-10-30 Journal: Journal of Genetic Engineering & Biotechnology [Category] COVID-19, [키워드] ADME Analysis Beta-sesquiphellandrene binding pocket can be used caused complex computational analysis computational tool COVID-19 docked complex docking domain Drug discovery effective Fever glycoprotein in silico in silico Approach inhibitory effect Interaction lab membrane molecular docking pathogen polyprotein provide Result reveal RMSD RMSF SARS-CoV2 SFTS Simulation Spike protein syndrome the disease therapeutic Treatment viral disease virus viruses were used [DOI] 10.1186/s43141-020-00095-x PMC 바로가기 [Article Type] Research