Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs DesignSARS-COV-2의 주요 프로테아제 (MPRO)에 대한 HIV 프로테아제 억제제의 계산 시뮬레이션 : COVID-19 약물 설계에 대한 시사점Article Published on 2021-12-052022-08-31 Journal: Molecules [Category] 신약개발, 치료제, [키워드] amino acids Analysis anti-SARS-CoV-2 antiviral drug applied aromatic ring binding affinities binding affinity catalytic coronavirus disease Coronavirus disease 2019 COVID-19 darunavir docking Donor drug drug target experiment His41 HIV HIV protease inhibitor HIV-1 protease inhibitor homologous hydrogen Hydrogen bond hydrophobic inhibiting inhibitors inhibitory effect Inhibitory effects Interaction key amino acid Lopinavir LPV main protease (Mpro) mechanism mechanism of action molecular molecular dynamics molecular dynamics (MD) simulation MPro nelfinavir nonspecific pharmacophore protease Replication replication of SARS-CoV-2 residue ribavirin RTV SARS-CoV SARS-CoV-2 SARS-CoV-2 Mpro Simulation Treatment treatment of COVID-19 [DOI] 10.3390/molecules26237385 PMC 바로가기 [Article Type] Article
ZRC3308 Monoclonal Antibody Cocktail Shows Protective Efficacy in Syrian Hamsters against SARS-CoV-2 InfectionZRC3308 모노클로 날 항체 칵테일은 SARS-COV-2 감염에 대한 시리아 햄스터에서 보호 효능을 보여줍니다.Article Published on 2021-12-032022-09-01 Journal: Viruses [Category] SARS, 변종, 진단, [키워드] 1:1 antibody cocktail appear AY.1 B.1 B.1.1.7 B.1.351 B.1.617.2 binding affinities binding affinity circulation cocktail COVID-19 COVID-19 case COVID-19 treatment demonstrated effective epitope Epitopes hamster hamsters immune effector function in vitro mAb mAbs monoclonal antibody Neutralizing progressed Prophylactic Prophylaxis RBD of SARS-CoV-2 reduced SARS-CoV-2 SARS-COV-2 infection SARS-CoV-2 spike protein SARS-CoV-2 variant severe disease show Spike protein therapeutic activity therapy Treatment ZRC3308 [DOI] 10.3390/v13122424 PMC 바로가기 [Article Type] Article
DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteinsResearch article Published on 2021-12-012022-10-05 Journal: Computers in biology and medicine [Category] 유전자 메커니즘, [키워드] addition binding affinities binding energy binding mode conformation conformations correlation COVID-19 COVID-19 pandemic crystallographic structure dataset docking effective inhibitor effort Ensemble docking flexible highlight in silico inhibitor inhibitors Ligand ligands molecular molecular docking molecular dynamics platform producing Protein Protein Data Bank provide receptor Receptor flexibility Research resolved SARS-CoV-2 SARS-CoV-2 protein SARS-CoV-2 proteins shown temperature tested Virtual screening [DOI] 10.1016/j.compbiomed.2021.104943 [Article Type] Research article
E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studiesSARS-CoV-2 RBD의 E484K 돌연변이는 hACE2와의 결합 친화도를 향상시키지만 중화 항체 및 나노바디와의 상호작용을 감소시킵니다. 결합 자유 에너지 계산 연구Article Published on 2021-12-012022-09-11 Journal: Journal of molecular graphics & modelling [Category] SARS, 변종, 유전자 메커니즘, 진단, [키워드] addition All-atom molecular dynamics simulation angiotensin Angiotensin-converting enzyme antibody binding binding affinities binding affinity Burial cause caused compensating conformational contribute COVID-19 COVID-19 disease death decrease drug design E484K E484K mutation Effect effective effective vaccine Effective vaccines Effectiveness electrostatic interaction ENhance enzyme group hACE2 Human human Angiotensin-converting enzyme Human angiotensin-converting enzyme 2 hydrogen Hydrogen bond hydrogen bonds immune response Impact IMPROVE Infection information Interaction investigated leads molecular molecular dynamics Molecular mechanics molecular mechanism mutant mutate Mutation mutations nanobodies nanobody Neutralizing Neutralizing antibodies neutralizing antibody pandemic polar RBD receptor Receptor binding receptor hACE2 Receptor-binding domain Recognition reduce reduced residue SARS-CoV-2 SARS-CoV-2 RBD selected significantly surface area the binding affinity the receptor-binding domain Transmissibility Vaccine development variant variants [DOI] 10.1016/j.jmgm.2021.108035 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
Computational redesign of Fab CC12.3 with substantially better predicted binding affinity to SARS-CoV-2 than human ACE2 receptor인간 ACE2 수용체보다 SARS-COV-2에 대한 실질적으로 더 나은 예측 결합 친화력을 갖는 FAB CC12.3의 계산 재 설계Article Published on 2021-11-122022-09-01 Journal: Scientific Reports [Category] MERS, SARS, 진단, [키워드] ACE2 angiotensin Angiotensin-converting enzyme angiotensin-converting enzyme 2 Antibody fragment therapy best binding binding affinities binding affinity binding interaction candidate Candidates caused CDR comparable COVID-19 COVID-19 pandemic deaths domain effective ENhance Fab Fab fragment Fabs human ACE2 receptor human cell human cells initiate molecular molecular dynamics Neutralizing antibodies neutralizing antibody Patient predicted Prevent Previous studies previous study Protein design Receptor binding domain responsible S1 subunit SARS-CoV-2 SARS-CoV-2-RBD Spike protein therapeutic [DOI] 10.1038/s41598-021-00684-x PMC 바로가기 [Article Type] Article
Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer SimulationsImmunology Published on 2021-11-112022-11-01 Journal: Frontiers in Immunology [Category] COVID-19, SARS, [키워드] Affect affinity antibody approach assessment bind binding affinities binding affinity Biomolecule can be used cause change circulating computer Coronavirus disease 2019 COVID-19 domain Dynamics Effect experimental work expression facilitate hACE2 hACE2 receptor helping host cell membrane hotspot Human human ACE2 human Angiotensin-converting enzyme infect Infection modulate molecular dynamics mutated Mutation mutations Neutralizing Neutralizing antibodies protein-protein interaction protocol Rapid S-RBD S1 domain S2 domain SARS-CoV-2 SARS-CoV-2 genome Screening selected Simulation spike spike glycoprotein Spike protein Spike-RBD the binding affinity time-consuming vaccination variant virus [DOI] 10.3389/fimmu.2021.730099 PMC 바로가기 [Article Type] Immunology
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptorSARS-CoV-2 스파이크 단백질 및 인간 ACE2 수용체에 결합된 돌연변이체의 인 실리코(in silico) 결합 프로필 특성화Article Published on 2021-11-052022-09-11 Journal: Briefings in Bioinformatics [Category] MERS, SARS, 변종, 진단, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus affected approach binding binding affinities binding affinity binding free energies binding free energy complexes coronavirus country COVID-19 decomposition domain drug resistance free energies free energy Free energy calculation and decomposition Free energy calculations G476S hACE2 hACE2 protein hotspot Hotspot residues human ACE2 human ACE2 receptor infect interfere investigated MD simulation molecular molecular dynamics Molecular mechanics mutant nine Novel coronavirus pandemic Poisson Protein–protein interaction protocol prototype provide RBD RBD mutations RBDs receptor Receptor-binding domain respiratory SARS-CoV-2 SARS-CoV-2 spike protein SARS-CoV-2 Spike RBD severe acute respiratory syndrome Coronavirus small molecule small molecule drug small molecule drugs spike spike glycoprotein Spike RBD/hACE2. Structure structures surface area V367F V483A Vaccine virus [DOI] 10.1093/bib/bbab188 PMC 바로가기 [Article Type] Article
Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein자주 볼 수있는 SARS-COV-2 ORF3A 횡단 단백질의 노출 된 N 및 C 말단 영역을 인식하는 단일 클론 인간 항체Communication Published on 2021-11-022022-09-01 Journal: Viruses [Category] MERS, SARS, 바이오마커, 진단, [키워드] activities activity Analysis anti-ORF3a mAbs antibody antigens apoptosis induction autophagy binding affinities binding affinity C terminal calcium cellular complex conformation COVID-19 infections cytosolic diagnostic Disruption disturbance domain enzyme enzyme-linked immunosorbent assay enzyme-linked immunosorbent assays epitope Epitopes evaluate evaluated Extracellular fluorescent fluorescent microscopy full-length generate homeostasis Human infected cell infected cells inflammasome activation involved linear Microscopy modulate monoclonal antibody N Terminal naïve ORF3a ORF3a protein pathophysiological peptide peptides performed prognostic biomarker Prognostic biomarkers Protein Proteins protocols recombinant antibodies Region SARS-CoV-2 SARS-CoV-2 infected cells selected surface plasmon surface plasmon resonance terminal therapeutic potential transfected cell transmembrane transmembrane protein viroporin western blot [DOI] 10.3390/v13112201 PMC 바로가기 [Article Type] Communication
Identification of nut protein-derived peptides against SARS-CoV-2 spike protein and main proteaseSARS-CoV-2 스파이크 단백질 및 메인 프로테아제에 대한 견과류 단백질 유래 펩타이드 동정Article Published on 2021-11-012022-09-11 Journal: Computers in biology and medicine [Category] SARS, 치료제, [키워드] addition Amino acid amino acid residue amino acid residues assist binding affinities binding affinity binding site coronavirus coronavirus disease COVID-19 COVID-19 patients develop domain effective Entry inhibitor entry inhibitors evaluated exhibited identification in silico inhibitor inhibitor N3 inhibitory M pro molecular docking molecular dynamics Molecular dynamics simulation Novel coronavirus novel coronavirus disease Nut proteins outbreak pandemic peanuts peptide peptides proportions protease Protein RBD reached SARS-CoV-2 SARS-COV-2 M(pro) SARS-CoV-2 main protease SARS-CoV-2 spike protein SARS-CoV-2 Spike RBD SARS-CoV-2 spike RBD. screened Spike protein target the SARS-CoV-2 the spike protein Treatment [DOI] 10.1016/j.compbiomed.2021.104937 PMC 바로가기 [Article Type] Article