Possibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation studySARS-COV-2 주 프로테아제를위한 용도로 인한 약물로서 HIV-1 프로테아제 억제제-임상 시험 약물의 가능성 : 분자 도킹, 분자 역학 및 결합 자유 에너지 시뮬레이션 연구Article Published on 2021-09-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, 치료제, [키워드] active site Amino acid amino acids Antiviral bind binding binding free energy binding mechanism clinical trial complexes COVID-19 COVID-19 pandemic develop docking result docking results drug Drug repurposing enzyme form free energy Free energy calculations help HIV-1 HIV-1 protease clinical trial drugs in silico inhibitor inhibitors inhibitors of SARS-CoV-2 Initially Interaction intermolecular interaction intermolecular interactions key amino acid key amino acids M pro MD simulations molecular molecular basis molecular docking molecular dynamics overcome performed protease Repurposed drug Repurposed drugs RMSD RMSF SARS-CoV-2 SARS-CoV-2 main protease SARS-CoV-2 virus SARS-COV-2Mpro Scientific community strong interaction the SARS-CoV-2 the SARS-CoV-2 virus therapeutic agents TMC310911 Trial Wuhan Wuhan, China [DOI] 10.1080/07391102.2020.1786459 PMC 바로가기 [Article Type] Article
Camphor, Artemisinin and Sumac Phytochemicals as inhibitors against COVID-19: Computational approachResearch article Published on 2021-09-012022-10-05 Journal: Computers in biology and medicine [Category] SARS, 치료제, [키워드] 6LU7 Analysis Antiviral treatment approach binding site Bioavailability Camphor caused compounds condition coronavirus coronavirus SARS-CoV-2 COVID-19 death docked docking drug effective enzyme Hinokiflavone indicate Infection Infectious disease inhibitor molecular molecular docking myricetin parameter PCA PDB performed pharmacokinetic phytochemical radius of gyration RMSD SARS-CoV-2 SARS-CoV-2 main protease stability Structure Sumac temperature Therapies these compound this new coronavirus [DOI] 10.1016/j.compbiomed.2021.104758 [Article Type] Research article
Development of Effective Therapeutic Molecule from Natural Sources against Coronavirus ProteaseArticle Published on 2021-08-302022-10-29 Journal: International Journal of Molecular Sciences [Category] COVID-19, MERS, SARS, [키워드] addition Administered amino acid residue Antiviral agents binding binding domain can be used complex complexes coronavirus disease correlated Course COVID-19 COVID-19 patients demonstrated development disease docked docking docking result docking score drug candidate drug design effective exhibited flavonols Free energy calculations in silico in silico Approach inhibitor inhibitory Interaction investigated involved less Ligand M pro MPro MDs MM/GBSA molecular Molecular dynamics simulation molecular target molecule Mutation myricetin Myricitrin natural natural products protein-ligand interaction reduced Remdesivir residue RMSD RMSF rutin SARS-CoV-2 SARS-CoV-2 main protease SARS-CoV-2 Mpro selected Source stability Treatment Vaccine [DOI] 10.3390/ijms22179431 PMC 바로가기 [Article Type] Article
An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 VariantsPharmacology Published on 2021-08-202022-10-31 Journal: Frontiers in Pharmacology [Category] COVID-19, [키워드] antiviral activity antiviral property approaches approved bind binding binding affinity binding site Bromelain changes in complex complexes COVID-19 destabilized Dynamics enzyme exhibited hACE2 human Angiotensin-converting enzyme in vitro in vivo increases in indicated inhibitor inhibitory effect Interaction molecular molecular docking Molecular dynamics simulation Mutation mutations new SARS-CoV-2 new virus Novel coronavirus potential mechanism Potential treatment Prevent Protein RBD RBD protein RBD proteins RBD variant Receptor-binding domain remained required Research resulting RMSD SARS-CoV-2 SARS-CoV-2 variants shown Simulation Spread stability the receptor-binding domain the SARS-CoV-2 treat Treatment variant variants viral spike protein virus while [DOI] 10.3389/fphar.2021.717757 PMC 바로가기 [Article Type] Pharmacology
Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach분자 도킹, 분자 역학 시뮬레이션 및 MM-PBSA 접근 방식을 사용한 SARS-CoV-2 약물 표적에 대한 천연 억제제 식별Cellular and Infection Microbiology Published on 2021-08-122022-09-11 Journal: Frontiers in Cellular and Infection Microbiology [Category] MERS, SARS, 치료제, [키워드] (RdRp) 10-hydroxyaloin A active site Against Amino acid amino acid residue Analysis anti-SARS-CoV-2 bind binding site complex complexes Compound Cys145 docking score drug drugable targets Dynamics Efficacy experimental validation free energy Gibbs free energy hydrogen identification in silico in vitro in vivo inhibitor isoquercetin lead M pro MD simulation molecular molecular docking molecular dynamics MPro natural parameter physiochemical properties physiochemical property plant Principal component principal component analysis protease RdRP responsible Result RMSD RMSF RNA-dependent RNA polymerase SARS-CoV-2 SARS-CoV-2 spike screened Simulation spike stable complex target target protein the SARS-CoV-2 the Spike was performed [DOI] 10.3389/fcimb.2021.730288 PMC 바로가기 [Article Type] Cellular and Infection Microbiology
Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19분자 도킹, 결합 모드 분석, 분자 역학 및 SARS-COV-2 주요 프로테아제에 대한 선택적 전위 항 바이러스제의 ADMET/독성 특성의 예측 : CovID-19에 대항하기위한 약물 용도를 향한 노력Article Published on 2021-08-012022-08-31 Journal: Molecular diversity [Category] SARS, 신약개발, 치료제, [키워드] active site Amino acid amino acid residue amino acid residues Analysis Antiviral antiviral agent Antiviral agents antiviral drug antiviral molecules ARB Arbidol AutoDock binding carried Chloroquine complex COVID-19 crystal structure Cys145 digestion direction docking Docking studies docking study drug design Drug discovery drug target Dynamics/simulation study effort enzyme exhibited FDA-approved drug FDA-approved drugs Glu166 glycyrrhizin GS441524 HCQ HIS163 Hydroxychloroquine in silico indicated inhibitory Interaction lead Ligand M pro mechanism molecular molecular docking molecular docking studies Molecular docking study molecular dynamics molecules MPro not need polyprotein Potential Potential antiviral agents present protease Protein provide RDV reason reason for Remdesivir RMSD SARS-CoV-2 SARS-CoV-2 main protease SARS-CoV-2 main protease (Mpro). selected selective stability starting point starting points suggested tested Toxicity Viral [DOI] 10.1007/s11030-021-10188-5 PMC 바로가기 [Article Type] Article
Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2SARS-CoV-2의 뉴클레오캡시드 인단백질의 RNA 결합 도메인을 표적으로 하는 잠재적 억제제의 가상 스크리닝 및 역학Article Published on 2021-08-012022-09-11 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 유전자 메커니즘, 치료법, [키워드] Antiviral binding binding domain binding energy binding free energy calculated coronavirus coronavirus disease COVID-19 database databases docking docking process docking score docking scores drug exonuclease fluctuation genetic material hotspot inhibitor Interaction Ligand mechanism molecular molecular dynamics Molecular dynamics simulation N protein nucleocapsid Nucleocapsid phosphoprotein nucleocapsid phosphoprotein. outbreak pandemic Potential treatment Precision PubChem PubChem database remained required RMSD RMSF RNA SARS-CoV-2 selected Site target target protein transcribed Transcription unique viral replication virion Virtual screening virus zidovudine [DOI] 10.1080/07391102.2020.1778536 PMC 바로가기 [Article Type] Article
Therapeutic development by repurposing drugs targeting SARS-CoV-2 spike protein interactions by simulation studiesResearch article Published on 2021-08-012022-10-05 Journal: Saudi Journal of Biological Sciences [Category] 신약개발, [키워드] affected Analysis antiviral drugs binding energy conducted Corona COVID-19 COVID-19 disease deviation docking Doxorubicin drug drugs drugs targeting evaluate Exemestane fluctuation Gatifloxacin gyration host cell Hydrogen bond in silico inhibit Interaction Interpretation MDs molecular interaction Molecular simulation pandemic pathogenic Prevent radius RBD complex reference Research respiratory Respiratory illness RMSD RMSF root SARS-CoV-2 SARS-CoV-2 spike protein Simulation study Spike protein Spread square suggested the SARS-CoV-2 therapeutic molecules transmitted virus spike protein Wuhan, China [DOI] 10.1016/j.sjbs.2021.04.057 [Article Type] Research article
Structural and conformational analysis of SARS CoV 2 N-CTD revealing monomeric and dimeric active sites during the RNA-binding and stabilization: Insights towards potential inhibitors for N-CTDRNA- 결합 및 안정화 동안 SARS COV 2 N-CTD의 구조적 및 구조적 분석 단량체 및 이량 체 활성 부위를 나타냅니다. N-CTD에 대한 잠재적 억제제에 대한 통찰력Article Published on 2021-07-012022-08-31 Journal: Computers in biology and medicine [Category] SARS, 치료법, 치료제, [키워드] active site active sites acute respiratory syndrome acute respiratory syndrome coronavirus advent Analysis Antiviral binding binding site boceprevir C terminal C-terminal domain Cefoperazone Ceftaroline Ceftaroline fosamil complex conformational conformational change coronavirus correlated CTD Degradation dimer dimeric docking domain drug dynamic Dynamic cross-correlation matrix (DCCM) exonuclease explain FDA-approved drug FDA-approved drugs fluctuation genomic RNA Health help Host hosts independent inhibitor insight involved leads molecular molecular dynamics Molecular dynamics (MD) Molecular mechanics Molecular mechanics/generalized born model and solvent accessibility (MM/GBSA) monomer monomeric N protein N-terminal domain NTD nucleases nucleocapsid Nucleocapsid C terminal domain (N-CTD) PC1 PCA Prevent Protease inhibitor PROTECT Protein protein-ligand interaction residue respiratory ribonucleoprotein RMSD RMSF RNA SARS CoV SARS-CoV-2 Schrodinger severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) solvent stability subunit the N protein Viral viral genome viral genomic RNA Virtual screening virus [DOI] 10.1016/j.compbiomed.2021.104495 PMC 바로가기 [Article Type] Article
Exploring the potential of novel phenolic compounds as potential therapeutic candidates against SARS-CoV-2, using quantum chemistry, molecular docking and dynamic studies양자 화학, 분자 도킹 및 동적 연구를 사용하여 SARS-CoV-2에 대한 잠재적인 치료 후보로서 새로운 페놀 화합물의 잠재력 탐색Article Published on 2021-07-012022-09-11 Journal: Bioorganic & medicinal chemistry letters [Category] SARS, 치료제, [키워드] ADMET Analysis binding affinity candidate chain complex Compound compounds distributions electrostatic hydrogen hydrogen bond interaction hydrophobic in vitro in vivo indicate inhibitor inhibitors Interaction intermolecular interaction intermolecular interactions investigated Ligand molecular molecular docking molecular dynamic simulations molecular dynamics Molecular dynamics simulation nsp13 Phenolic compounds Protein RMSD RMSF SARS-CoV-2 SARS-CoV-2 protein stability Structure structures synthetic therapeutic virus [DOI] 10.1016/j.bmcl.2021.128079 PMC 바로가기 [Article Type] Article