Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics ApproachArticle Published on 2022-01-012022-10-30 Journal: Molecules [Category] COVID-19, SARS, [키워드] Analysis Antiviral agents attachment bind binding energy binding site Bromelain Cell COVID-19 Critical determine deviation docking domain fluctuation fruit hACE2 human Angiotensin-converting enzyme human cell in silico inhibit interact Interaction MD simulation Molecular dynamics simulation Mutation peptide peptide-protein interaction radius of gyration RBD RBD binding RBD mutation RBD variant recent receptor Receptor-binding domain residue responsible RMSD RMSF SARS-CoV-2 SARS-CoV-2 variant SARS-CoV-2 variants spike glycoprotein Spread the RBD the SARS-CoV-2 trajectory [DOI] 10.3390/molecules27010260 PMC 바로가기 [Article Type] Article
Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injuryOriginal Article Published on 2021-12-292022-10-30 Journal: Journal of Advanced Veterinary and Animal Research [Category] COVID-19, [키워드] active site acute respiratory syndrome Algorithm Analysis apigenin candidate cardiac injury complexes Compound conducted coronavirus defined deviation distribution docking drug drug design exhibited fluctuation forms H-bonds hACE2 hACE2 receptor human Angiotensin-converting enzyme Hydrogen bond hydrophobic interaction Injury Ligand ligands material MDs mechanism metabolism molecular molecular docking Molecular dynamic parameter polar profile profiles programming Protein Quantitative quantum tunneling quercetin receptor Research resulting RMSD RMSF SARS-CoV-2 selected selective Simulation solvent subsequent suggested supramolecular docking target specificity the binding affinity were used [DOI] 10.5455/javar.2021.h544 PMC 바로가기 [Article Type] Original Article
Molecular docking of SARS-COV-2 Spike epitope sequences identifies heterodimeric peptide-protein complex formation with human Zo-1, TLR8 and brain specific glial proteinsSARS-COV-2 스파이크 에피토프 서열의 분자 도킹으로 인간 Zo-1, TLR8 및 뇌 특이적 신경교 단백질과의 이종이량체 펩티드-단백질 복합체 형성 확인Article Published on 2021-12-012022-09-11 Journal: Medical Hypotheses [Category] SARS, 유전자 메커니즘, [키워드] allele asphyxia binding Blood brain barrier blurred vision Brain Brain infection cause clinical observation clinical observations complex death deviation docking epitope epitope peptide Epitopes experiment Glia glial cell headache heterodimeric HLA-DRB1 Human brain human population Hypothesis identify immunogenic induce infect Infection Inflammation Interaction Loss of Smell mechanism modify molecular molecule NDRG2 neurological abnormalities neurological abnormality observation observations peptide peptides performed Protein Proteins question receptor respiratory tract illness RMSD root S100B SARS-CoV-2 SARS-COV-2 infection selected sequence specific protein spike spike epitopes Spike protein structures Symptoms tested the Spike TLR TLR8 Toll-like receptor VCAM1 virus working hypothesis zonula zonula occludens [DOI] 10.1016/j.mehy.2021.110706 PMC 바로가기 [Article Type] Article
De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations딥 러닝, 도킹 및 분자 역학 시뮬레이션을 사용하여 SARS-CoV-2 치료에서 새로운 프로테아제 억제제 후보의 새로운 설계Article Published on 2021-12-012022-09-11 Journal: Computers in biology and medicine [Category] SARS, 치료제, [키워드] Analysis antiviral drugs AutoDock AutoDock vina binding binding affinities binding affinity binding site candidate clinical trial Compound Critical Cys145 deep deep learning deviation docking docking result docking results Efficacy fluctuation free energy Free energy calculation hydrogen Hydrogen bond identify in-silico In-vitro inhibiting inhibitor Interaction ligands main protease MET molecular molecular docking molecular dynamic simulation molecular dynamics MPro network predicted protease Protease inhibitor Proteases required residues resulting RMSD RMSF root Root-mean-square deviation SARS-CoV-2 SARS-CoV-2 main protease selected statistical analyses statistical analysis strong interaction Support the SARS-CoV-2 transfer Treatment were used [DOI] 10.1016/j.compbiomed.2021.104967 PMC 바로가기 [Article Type] Article
dockECR: Open consensus docking and ranking protocol for virtual screening of small moleculesdockECR: 소분자의 가상 스크리닝을 위한 개방형 합의 도킹 및 순위 지정 프로토콜Article Published on 2021-12-012022-09-11 Journal: Journal of molecular graphics & modelling [Category] SARS, 치료기술, 치료제, [키워드] accelerate addition applied approaches AutoDock AutoDock vina average Candidates co-crystallized complement Consensus crystal structure docking eight emerging disease evaluated Exponential consensus ranking Frame information Interaction library molecular molecular docking molecular dynamics Molecular dynamics simulation molecular dynamics simulations molecules Open source predicted protease Protein Protein target protocol ranking residue RMSD SARS-CoV-2 SARS-CoV-2 main protease SARS-CoV-2 virus small molecule targets the SARS-CoV-2 virus Treatment Virtual screening was used were used [DOI] 10.1016/j.jmgm.2021.108023 PMC 바로가기 [Article Type] Article
Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysisArticle Published on 2021-11-152022-10-04 Journal: Scientific Reports [Category] MERS, SARS, 신약개발, [키워드] acid addition Alpha Analysis cholesterol Cluster Computational biology and bioinformatics decrease drug Drug development Dynamics evaluated exhibit form gallstone heptad repeat higher affinity host cell Hydrogen bond in-silico interact Interaction membrane membranes molecular docking monomer Numerous Physicochemical properties prefusion Protein protein sequences random reduce reduction in Region remained residue RMSD RMSF SARS-CoV-2 SARS-COV-2 infection severity shown spike tension the SARS-CoV-2 the Spike trajectory treat Ursodeoxycholic acid Viral hepatitis was performed [DOI] 10.1038/s41598-021-01705-5 PMC 바로가기 [Article Type] Article
In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2Article Published on 2021-11-012022-10-04 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, [키워드] ADME ADME/T ADP Analysis approach binding binding free energy caused combination therapy Compound coronavirus 2 coumarin COVID-19 COVID-19 infection derivative develop docked docking docking result docking score drug Drug repurposing drug-likeness endoribonuclease enzyme FIVE help identification IMPROVE in silico information inhibitor inhibitory activity Ligand LLC MD simulation molecular pandemic performed protease Protein provide radius of gyration receptor receptor protein respiratory RMSD SARS CoV-2 SARS-CoV-2 Seven stability therapy Treatment USA Virtual screening virus was performed were used WHO [DOI] 10.1080/07391102.2020.1808075 PMC 바로가기 [Article Type] Article
Structural Insights on the SARS-CoV-2 Variants of Concern Spike Glycoprotein: A Computational Study With Possible Clinical ImplicationsGenetics Published on 2021-10-222022-10-31 Journal: Frontiers in Genetics [Category] COVID-19, [키워드] Affect Alpha Breakthrough infection change clinical Cluster comparable concern conformational conformational epitopes Contact Coronavirus disease 2019 CoV COVID-19 cross-reactivity determine driving Endemic endemic HCoV Epitopes HCoV 229E help HKU1 immune infections insight MERS Model Modification NL63 OC43 pandemic performed Phylogenetic Protein Reinfection resulting RMSD S1-NTD SARS CoV SARS-CoV-2 SARS2 similarity spike spike glycoprotein Spike protein subsequent the SARS-CoV-2 the spike protein Transmissibility variant variants of concern viral infection viral pathogenesis virulence VoC [DOI] 10.3389/fgene.2021.773726 PMC 바로가기 [Article Type] Genetics
Investigating Fungi-Derived Bioactive Molecules as Inhibitor of the SARS Coronavirus Papain Like Protease: Computational Based StudyMedicine Published on 2021-10-212022-10-31 Journal: Frontiers in Medicine [Category] COVID-19, [키워드] amino acid residues analyses Analysis Antiviral antiviral therapy approach Auto-dock binding affinity candidate carcinogenicity catechin caused Compound compounds Computational approaches concerning COVID-19 COVID-19 pandemic Critical death develop deviation effective effort fluctuation fungi Gromacs growth hydrogen bonds infections inhibitor Interaction investigated less Like molecule outcomes Papain Papain-like protease PLPro protease Protease inhibitor radius of gyration RMSD RMSF SARS Coronavirus SARS-CoV-2 screened selected the binding affinity time-consuming Toxicity WHO World Health Organization [DOI] 10.3389/fmed.2021.752095 PMC 바로가기 [Article Type] Medicine
Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL pro)SARS-COV-2를 표적으로하는 약물 재생 연구 : 약물 표적 3C 유사 프로테아제 (3CL Pro)에 대한 앙상블 도킹 접근법Article Published on 2021-09-012022-08-31 Journal: Journal of biomolecular structure & dynamics [Category] SARS, 신약개발, 치료제, [키워드] 3CL pro 3CLpro 6LU7 acute respiratory syndrome Analysis anti-bacterial Anti-viral anti-viral drug apo form approach approved binding candidate causative agent caused cleavage Clustering conformation conformational conformations coronavirus 2 COVID-19 COVID-19 pandemic cryptic pockets crystal structure cumulative database death disease docking drug Drug administration Drug repurposing drug target food Food and Drug Administration high-resolution crystal structure HIV in silico main protease Markov modeling Novel coronavirus PDB PDB ID polyprotein protease repurposing respiratory responsible RMSD RNA viruses SARS-CoV SARS-CoV-2 screened selected Severe acute respiratory syndrome state Structure Support target treating COVID-19 Variation Viral was used [DOI] 10.1080/07391102.2020.1792344 PMC 바로가기 [Article Type] Article