Virtual screening, molecular dynamics and structure-activity relationship studies to identify potent approved drugs for Covid-19 treatmentCOVID-19 치료를위한 강력한 승인 약물을 확인하기위한 가상 스크리닝, 분자 역학 및 구조-활성 관계 연구Article Published on 2021-10-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, 치료제, [키워드] Accuracy active site applied approach approved approved drug approved drugs best binding energy binding energy prediction binding free energy binding site Bromocriptine candidate Complexes COVID-19 COVID-19 treatment Cys145 determined by dominant drug drug design Drug screening drugs Ergotamine facilitate FDA FDA approved drug food free energies His41 hydrogen hydrogen bonding hydrophobic hydrophobic interactions identify Interaction MD simulation MD simulations MLR MM/PBSA molecular molecular docking molecular dynamics MPro Multiple linear regression offer Pattern recognition performed predicted Principal component principal component analysis protease Protein Quantitative receptor residues SAR SARS-CoV-2 SARS-CoV-2 main protease selected drug selected drugs Simeprevir similarity stability structural–activity relationship. Tadalafil the SARS-CoV-2 Treatment [DOI] 10.1080/07391102.2020.1794974 PMC 바로가기 [Article Type] Article
The Se–S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study엡셀렌 유사 억제제에 의한 SARS-CoV-2 주요 프로테아제의 공유 결합 억제 메커니즘에서 Se-S 결합 형성: 전산 연구Article Published on 2021-09-102022-09-10 Journal: International Journal of Molecular Sciences [Category] SARS, 신약개발, 치료제, [키워드] antiviral therapies apo form bond canonical catalytic dyad Combination complex covalent bond DFT Donor drug Ebselen Formation functional H-bond His41 hydrogen hydroxyl hydroxyl group inhibition inhibition mechanism knowledge less M pro mechanism member molecular dynamics Molecular dynamics simulation performed position potential energy potential energy surface protease Protease inhibitor SARS-CoV-2 SARS-CoV-2 main protease Se–S covalent bond selective Selenium sulfur theory [DOI] 10.3390/ijms22189792 PMC 바로가기 [Article Type] Article
Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations분자 역학 및 결합 자유 에너지 시뮬레이션을 통한 PF-07321332 SARS-CoV-2 프로테아제 억제제의 결합 메커니즘 탐색Article Published on 2021-08-242022-09-10 Journal: International Journal of Molecular Sciences [Category] SARS, 치료제, [키워드] α-ketoamide 3CL pro 3CL Protease affinity Analysis Antiviral binding binding affinity binding energy binding mechanism calculated catalytic dyad caused chymotrypsin complexes Compound coronavirus coronavirus disease COVID-19 Cys145 demonstrated disrupt docking Dynamics energy Free global public health His41 Interaction Ligand Lopinavir LOPINAVIR AND RITONAVIR low potency main protease MD simulation molecular Novel coronavirus novel coronavirus disease optimization PF-07321332 protease remained residue respiratory Respiratory Coronavirus Ritonavir SARS-CoV-2 SARS-CoV-2 protease severe acute respiratory coronavirus severe acute respiratory coronavirus 2 Simulation trajectory [DOI] 10.3390/ijms22179124 PMC 바로가기 [Article Type] Article
Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics SimulationsArticle Published on 2021-08-172022-10-28 Journal: Biology [Category] COVID-19, [키워드] Leucas zeylanica acute respiratory syndrome addition Amino acid Analysis antiviral drug approach assist azetidin-2-one binding affinity binding pockets biological activity Candidates catalytic Characteristics Chemical complex complexes Compound compounds conserved coronavirus COVID-19 Cys145 dataset docked docking drug design Dynamics effective Effects Efficacy exhibited fluctuations gas chromatography–mass spectrometry GC-MS highest docking scores His41 Hydrogen bond impacted inhibitor inhibitors inhibitory activity Interaction Laboratory Leuca Ligand M pro main protease metabolite molecular molecular docking molecular docking analysis Molecular dynamics simulation phytochemical protease Protein protein sequence radius of gyration Research rigidity SARS-CoV-2 SARS-CoV-2 main protease simple Simulation stability targeting the SARS-CoV-2 therapeutic thermal stability Toxicity transmission rate vaccination variations was used were assessed were used [DOI] 10.3390/biology10080789 PMC 바로가기 [Article Type] Article
Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro)분자 역학 시뮬레이션과 결합 된 약물 재검사 및 가상 스크리닝 전략 SARS-COV-2 주요 프로테아제 (3CLPRO)에 대한 강력한 억제제를 확인했습니다.Article Published on 2021-08-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] MERS, SARS, 신약개발, [키워드] 3CLpro accelerate anti-HIV drugs approach approved binding binding free energy Care catalytic dyad Combined confirmed case coronavirus Cys145 database death disease dissemination drug Drug screening drug-repurposing Epidemic FDA FIVE free energy Health care Health care system His41 HIV idea in viral infection rate inhibit inhibitor inhibitors intensity maturation molecular dynamics Molecular dynamics simulation pandemic pathway protease public health raised Replication reported Research saquinavir SARS-CoV-2 SARS-CoV-2 main protease screened spread to TCM tested these compound these compounds Traditional Chinese medicine traditional Chinese medicines Vaccine Viral Virtual screening virtual screening. [DOI] 10.1080/07391102.2020.1779128 PMC 바로가기 [Article Type] Article
In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19Molecular Biosciences Published on 2021-07-052022-10-31 Journal: Frontiers in Molecular Biosciences [Category] COVID-19, [키워드] Allium analyses Analysis approaches binding free energy catalytic dyad Compound conformational changes coronavirus COVID-19 Curcuma Cys145 died drug Drug discovery drugs His41 hotspot humans identification identify in silico Interaction involved M pro main protease Molecular dynamics simulation natural natural medicinal plants over parameters plant Potential Potential treatment Protein researcher residue S-ACE2 screened Screening selected stability Structure-based virtual screening the binding affinity viral entry Virtual screening Zingiber [DOI] 10.3389/fmolb.2021.637122 PMC 바로가기 [Article Type] Molecular Biosciences
Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent InhibitorsArticle Published on 2021-06-262022-10-28 Journal: Biology [Category] COVID-19, [키워드] active site acute respiratory syndrome ADMET adverse effects Antiviral antiviral drug Asian binding affinity biological activity carcinogenicity caused Characteristics complex Complexes compounds coronavirus coronavirus disease COVID-19 Cys145 deviation disease docked drug drug candidate dynamics simulation effective Efficacy exhibited expressed fluctuation gallate high mortality rate His41 in viral inhibitor Laboratory M pro molecular docking Molecular dynamics simulation pathway pharmacological phytochemical phytochemicals plant plants potent profile protease Protein radius of gyration Replication reported retrieved SARS-CoV-2 Screening simple Spread supported targeting thermal stability these compound Toxicity Transcription treat Treatment Vaccine viral infection was used were assessed worldwide pandemic [DOI] 10.3390/biology10070589 PMC 바로가기 [Article Type] Article
Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like ProteaseChemistry Published on 2021-06-242022-10-31 Journal: Frontiers in Chemistry [Category] COVID-19, [키워드] 3-chymotrypsin-like protease 3CLpro activity Amino acid Antiviral catalytic catalytic activity catalytic dyad catalytic function catalytic rate caused changes in characterized cleavage Complete conformational coronavirus coronavirus disease Coronaviruses COVID-19 Cys145 death development dimeric dyad effective enzyme facilitated fold His41 Impact inactivation investigated mechanism observation Outbreaks pandemic Pandemics polyprotein polyproteins protease residue responsible SARS-CoV-2 SARS-CoV-2 protease secondary structure site-directed mutagenesis stability Substitution substitutions target tested thermodynamic thermodynamic stability variant variants was reduced were used wild-type [DOI] 10.3389/fchem.2021.692168 PMC 바로가기 [Article Type] Chemistry
Myricetin Inhibits SARS-CoV-2 Viral Replication by Targeting M pro and Ameliorates Pulmonary InflammationPharmacology Published on 2021-06-172022-10-31 Journal: Frontiers in Pharmacology [Category] COVID-19, [키워드] 3CLpro (Mpro) affected binding binding pocket compounds coronavirus disease COVID-19 develop drug drugs effective enzyme Health His41 hydrogen bonds IFN-γ IL-1α infiltration inflammatory cell inflammatory cytokines IL-6 inhibit inhibiting inhibitors interact M pro molecular docking myricetin Phe140 pulmonary pulmonary inflammation reported SARS-CoV-2 secretion selected Spread Symptomatic treatment targeting TNF-α [DOI] 10.3389/fphar.2021.669642 PMC 바로가기 [Article Type] Pharmacology
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2SARS-CoV-2의 주요 프로테아제에 대한 효과적인 항바이러스 파이토케미컬을 식별하기 위한 분자 모델링 접근법Article Published on 2021-06-012022-09-11 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 치료기술, 치료제, [키워드] Analysis Antiviral antiviral drugs Antiviral phytochemicals approach AutoDock AutoDock vina baicalin binding affinities binding energy can be used candidate COVID-19 Cys145 determine develop deviation docking effective FIVE fluctuation glabridin glucoside gold gyration His41 Hypericin identify inhibitor inhibitors Interaction interactions ligands Linear regression MD simulation MLR molecular molecular docking molecular dynamics molecular dynamics. Multiple Multiple linear regression Pattern recognition PCA performed predict Principal component principal component analysis protease Quantitative R 2 radius radius of gyration residues reveal RMSD RMSF root Root-mean-square deviation SARS-CoV-2 selected similarity solvent statistical analysis supported surface area target the binding affinity training set [DOI] 10.1080/07391102.2020.1761883 PMC 바로가기 [Article Type] Article