Targeting SARS-CoV-2 nucleocapsid oligomerization: Insights from molecular docking and molecular dynamics simulationsSARS-CoV-2 뉴클레오캡시드 올리고머화 표적화: 분자 도킹 및 분자 역학 시뮬레이션의 통찰력Article Published on 2022-04-012022-09-11 Journal: Journal of biomolecular structure & dynamics [Category] COVID19(2023년), SARS, 유전자 메커니즘, 치료법, [키워드] Analysis anti-N drugs antiviral drug antiviral drugs binding binding affinity C-terminal C-terminal domain caused complex complexes Compound computational approach COVID-19 CTD distribution drug drugs effective examined filament FIVE followed by free energy free energy landscape highest binding affinity hydrogen Hydrogen bond increase indicated infect inhibitor insight MD simulation molecular molecular docking molecular dynamics Molecular dynamics simulation N protein nucleocapsid oligomerization outbreak packaged parameter PCA PDB population distribution potential mechanism potential mechanisms Protein Rapamycin Replication RMSD RMSF Sapanisertib SARS-CoV-2 nucleocapsid SARS-CoV-2 virus self-assembly Silmitasertib stability targeting the SARS-CoV-2 virus Transcription Viral protein Viral RNA virions [DOI] 10.1080/07391102.2020.1839563 PMC 바로가기 [Article Type] Article
501Y.V2 spike protein resists the neutralizing antibody in atomistic simulations501Y.V2 스파이크 단백질은 원자 시뮬레이션에서 중화 항체에 저항합니다.Article Published on 2022-04-012022-09-11 Journal: Computational biology and chemistry [Category] COVID19(2023년), SARS, 변종, 진단, [키워드] 501Y.V2 antibody resistance atomic B.1.351 backbone binding caused CCS changed complex complexes COVID-19 pandemic COVID-19 vaccine design deaths distribution distributions experiment free energy free energy landscape indicated lead molecular molecular dynamics Mutation neutralizing antibody observation outbreak Protein reduced RMSD S protein SARS-CoV-2 SARS-CoV-2 variant significantly SMD SMD simulations spike Spike protein the mean variant wild-type [DOI] 10.1016/j.compbiolchem.2022.107636 PMC 바로가기 [Article Type] Article
Plant-Derived Antiviral Compounds as Potential Entry Inhibitors against Spike Protein of SARS-CoV-2 Wild-Type and Delta Variant: An Integrative in SilicoApproachSARS-CoV-2 야생형 및 델타 변이체의 스파이크 단백질에 대한 잠재적 진입 억제제로서의 식물 유래 항바이러스 화합물: SilicoApproach의 통합Article Published on 2022-03-082022-09-11 Journal: Molecules [Category] SARS, 변종, 신약개발, 진단, 치료제, [키워드] antagonists Antiviral Antiviral agents antiviral drug antiviral drugs approach approaches binding affinities binding affinity binding energy binding free energies binding free energy binding interaction carried complexes Compound compounds controls Corilagin country COVID-19 COVID-19 infection Delta delta variant develop docking Efficacy exhibited experimental validation explained FIVE free energies glycoprotein greater H-bonds hydrogen hydrophobic interaction hydrophobic interactions Hypericin in silico India lead Ligand ligands Lupeol molecular molecular docking molecular dynamics molecular dynamics and simulations Molecular modeling mutated phytochemical compounds plant compound Potential Protein Research resulting RMSD RMSF S protein SARS-CoV-2 SARS-CoV-2 spike SARS-CoV-2 variant second wave selected several variant several variants spike spike glycoprotein Spike protein stability target proteins therapeutic intervention Transmissibility Vaccine Virtual screening virulence was performed while wild-type wild-type SARS-CoV-2 [DOI] 10.3390/molecules27061773 PMC 바로가기 [Article Type] Article
A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main proteaseFDA 승인 약물의 다단계 가상 스크리닝은 SARS-COV-2 주 프로테아제의 잠재적 억제제를 보여줍니다.Article Published on 2022-03-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, 치료제, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus Analysis antiviral target applied approach approved binding mode caused Compound coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 COVID-19 treatment crystal structure crystal structures docking drug drug candidate drug candidates Drug repurposing extension FDA-approved drug filtration FIVE flavonoid followed by free energy functional protein H-bond health emergency identify inhibitor inhibitors inhibitors of SARS-CoV-2 M pro maturation MD simulations molecular molecular docking molecular dynamics pharmacophore Potential protease protease inhibitors protein-ligand interaction protocol reported repurposing respiratory responsible reveal RMSD SARS-CoV-2 SARS-CoV-2 main protease severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 trajectory Treatment Viral Virtual screening [DOI] 10.1080/07391102.2020.1837680 PMC 바로가기 [Article Type] Article
In Silico Screening of Bioactive Compounds of Representative Seaweeds to Inhibit SARS-CoV-2 ACE2-Bound Omicron B.1.1.529 Spike Protein TrimerArticle Published on 2022-02-172022-10-30 Journal: Marine Drugs [Category] COVID-19, COVID19(2023년), SARS, [키워드] Corallina officinalis Sargassum wightii ACE2 Alpha Alter Angiotensin-converting enzyme antibody antiviral drug B.1.1.529 BNT162b2 caffeic acid Compound compounds COVID-19 develop dietary supplement drug evade immunization infecting inhibit inhibitor inhibitory effect Interaction less manifested molecular docking analysis MOST mutated Mutation neutralization omicron omicron B.1.1529 Omicron variant Pathogenesis patients pharmacological phloretin PROTECT protein domains RBD receptor residue RMSD Sargassum SARS-CoV-2 SARS-CoV-2 variant SARS-CoV-2 variants Screening seaweed Seaweeds severe disease spike spike glycoprotein suggested supported the receptor-binding domain therapeutic Transmissibility Transmission treat Treatment trimeric variant B.1.617.2 [DOI] 10.3390/md20020148 PMC 바로가기 [Article Type] Article
Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main proteaseBiochemistry Published on 2022-02-082022-10-28 Journal: PeerJ [Category] COVID-19, COVID19(2023년), MERS, SARS, [키워드] adopted Analysis Anti-SARS-CoV-2 Activity Antiviral approach approved backbone binding binding energy Compound compounds Concentration contributing to COVID-19 dataset demonstrated determine deviation docking docking score drug Drug discovery electrostatic examined Factor feasible filtration highest Hydrogen bond IC50 indicated M pro main protease molecular Molecular dynamics simulation Molecular modeling pandemic polyprotein Precision Prevent protease reduction Result Ritonavir RMSD SARS-CoV-2 SARS-CoV-2 infections selected Spread tested the SARS-CoV-2 therapy virus multiplication [DOI] 10.7717/peerj.12929 PMC 바로가기 [Article Type] Biochemistry
Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2Article Published on 2022-02-042022-10-29 Journal: International Journal of Molecular Sciences [Category] COVID-19, COVID19(2023년), SARS, [키워드] activities addition analogue anticancer Antiviral binding binding affinity binding pocket Cancer Compound compounds COVID-19 Curcumin DDX3 demonstrated deviation disease dual inhibitor Dynamics effective Essential global pandemic hydrogen bond interactions inhibitor inhibitory activity Interaction main protease MDs molecular Molecular dynamics simulation natural compound analogues radius of gyration residue retrieved RMSD SARS-CoV-2 SARS-CoV-2 main protease shown Simulation stability [DOI] 10.3390/ijms23031771 PMC 바로가기 [Article Type] Article
A dynamic simulation study of FDA drug from zinc database against COVID-19 main protease receptorCOVID-19 주요 프로테아제 수용체에 대한 아연 데이터베이스에서 FDA 약물의 동적 시뮬레이션 연구Article Published on 2022-02-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] COVID19(2023년), MERS, SARS, 치료제, [키워드] accelerate approved binding calculated clinical study Compound compounds contagious COVID-19 database death drug drug candidate enzyme FDA FDA drugs FDA-approved drug FDA-approved drugs global public health globe Glu166 identify in silico Approach in vitro in vivo Initially lead library main protease MD simulation molecular molecular docking molecular dynamic simulation molecular dynamics MPro outbreak PCA protease provide receptor Research residue responsible RMSD RMSF SARS-CoV-2 selected Seven Spread trajectory was used Zinc ZINC database zinc database. [DOI] 10.1080/07391102.2020.1821785 PMC 바로가기 [Article Type] Article
Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2Molecular Biosciences Published on 2022-01-272022-10-31 Journal: Frontiers in Molecular Biosciences [Category] COVID-19, [키워드] acute respiratory syndrome addition affected Against allergenicity antimicrobial peptide binding binding energy binding free energy calculate complexes coronavirus deviation docked docking docking result docking scores domain drug candidate Dynamics effective exacerbated fluctuation Future Health host cell HPEPDOCK Hydrogen bond in vitro in vivo inhibit lack molecular molecular dynamics mortality rate non-allergenic non-toxic pandemic peptide peptide-protein docking peptides predicted radius of gyration RBD RMSD RMSF SARS-CoV-2 selected Spike protein Spread suggested the RBD the SARS-CoV-2 the Spike Toxicity Transmission Vaccines virus [DOI] 10.3389/fmolb.2021.791642 PMC 바로가기 [Article Type] Molecular Biosciences
In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19Article Published on 2022-01-062022-10-28 Journal: Pharmaceutics [Category] COVID-19, [키워드] 2-deoxy-D-glucose 2-deoxyglucose Analysis binding binding energy calculated cancer cell cell death cells combat Controller COVID-19 D-glucose Density functional theory calculations Deprivation drug effective Effectiveness electron density Emergency use fructose-6-phosphate Glucose-6-phosphate Hydrogen bond India Infection information inhibit inhibitor intervene investigated lack main protease of SARS-CoV-2 MD simulation metabolism molecular molecular docking molecular dynamics simulations MPro nCoV Novel coronavirus occur occurred parameter Patient phosphorylated protease reported resulting RMSD RMSF SARS-CoV-2 second wave shaking the binding affinity trajectory viral infection was performed Wuhan, China [DOI] 10.3390/pharmaceutics14010135 PMC 바로가기 [Article Type] Article