Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms항체가 있는 SARS-CoV-2 스파이크 변이체 복합체에서 결합 및 알로스테리의 돌연변이 프로파일링을 위한 형태 역학 및 섭동 기반 네트워크 모델링 통합: 돌연변이 탈출 메커니즘의 로컬 및 글로벌 결정인자 균형 조정Article Published on 2022-07-102022-09-11 Journal: Biomolecules [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, [키워드] Affect allosteric communication Analysis antibodies antibody Antibody binding antibody combination antibody escape approach balancing binding binding affinity binding energy binding hotspots binding interaction change complexes conformational conformational dynamics conserved cross-reactive determinant determined by dominant dynamic network modeling Dynamics Effect Efficiency energetics escape escape mutant escape mutants Factors flexibility fluctuation host receptor identify Interaction interactions Local MD simulations mechanism modeling modulate Mutation mutational profiling mutations network neutralization neutralize omicron pattern predict Profiling Protein protein folding protein stability residue SARS-CoV-2 spike SARS-CoV-2 spike protein single antibody spike spike plasticity Spike protein stability suggested the antibody the SARS-CoV-2 ultrapotent antibodies. variant [DOI] 10.3390/biom12070964 PMC 바로가기 [Article Type] Article
Receptor binding domain of SARS-CoV-2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2우한 균주에서 Omicron B.1.1.529까지의 SARS-CoV-2 수용체 결합 도메인은 인간 ACE2의 가변 구조에 대한 증가된 친화성을 특성으로 합니다.Article Published on 2022-07-012022-09-11 Journal: Journal of infection and public health [Category] COVID19(2023년), MERS, SARS, 변종, 진단, 치료기술, [키워드] ACE2 ACE2 receptor ACE2 receptors ACE2 variant ACE2 variants ACE2-RBD affinity analysed Analysis angiotensin Angiotensin-converting enzyme attribute B.1.1.529 binding binding domain binding efficiency binding energy Care caused changes in coding region complexes contributing to COVID-19 detect determine docking dynamic Dynamic simulation enzyme Genetic variant genetic variants global pandemic help highlight homology model Homology models Human human ACE2 human host Infectious disease Interaction isolates lead management molecular molecular dynamics nucleotide omicron pathogenic polymorphism Protein docking RBD RBD complex RBDs receptor Receptor binding domain Repository retrieved risk RMSD RMSF Safe SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-COV-2 infection SARS-CoV-2 strain SARS-CoV-2 virus SARS‐CoV‐2 selected severity single nucleotide stability Structural variant structural variants Structure the RBD Total variant Variation was performed wildtype Wuhan Wuhan strain [DOI] 10.1016/j.jiph.2022.06.004 PMC 바로가기 [Article Type] Article
The naturally-derived alkaloids as a potential treatment for COVID-19: A scoping reviewCOVID-19의 잠재적 치료제로서의 천연 유래 알칼로이드: 범위 검토Review Published on 2022-07-012022-09-11 Journal: Phytotherapy research : PTR [Category] COVID19(2023년), SARS, 치료제, [키워드] activities acute respiratory syndrome coronavirus alkaloids Anti-inflammatory Antiviral applicability assessments berberine binding energy caused cephaeline clinical trial clinical trials Colchicine coronavirus coronavirus 2 coronavirus disease Coronavirus disease 2019 COVID-19 database described Effects eligible Emetine Ergotamine high mortality rate homoharringtonine in silico in vitro Inflammatory marker inflammatory markers inhibit knowledge lycorine medicinal plant narciclasine natural product new treatment strategy observational studies papaverine pharmacological plant Potential treatment Protein target protein targets Quinine reduce respiratory SARS-CoV-2 severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 target proteins Therapeutic compounds Transmissibility treating COVID-19 variety was performed [DOI] 10.1002/ptr.7442 PMC 바로가기 [Article Type] Review
Inhibition of SARS-CoV-2 pathogenesis by potent peptides designed by the mutation of ACE2 binding regionACE2 결합 영역의 돌연변이에 의해 설계된 강력한 펩티드에 의한 SARS-CoV-2 발병 억제Article Published on 2022-07-012022-09-11 Journal: Computers in biology and medicine [Category] COVID19(2023년), SARS, 변종, [키워드] ACE2 ACE2 binding allergenicity angiotensin Angiotensin-converting enzyme antiviral peptide binding energy complex Computational approaches COVID-19 COVID-19 treatment criteria deaths determined by Diagnosis docked domain Drug development effective inhibitor entry inhibitors Final host receptor identify information inhibition inhibitor inhibitory action initial Interaction mechanism molecular docking molecular dynamics Molecular dynamics simulation molecular dynamics simulations Mutation OSPREY outbreak pandemic peptide Peptide design Peptide inhibitor Peptide Inhibitors peptides provided RBD RBD binding RBD residue RBD residues RBD-ACE2 Receptor-binding domain residue residues SARS-CoV-2 SARS-CoV-2 entry SARS-CoV-2 pathogenesis screened Spike protein spread of COVID-19 targeting Template the RBD Therapeutics Treatment vaccination variant Viral entry inhibitors. viral infection virus was determined [DOI] 10.1016/j.compbiomed.2022.105625 PMC 바로가기 [Article Type] Article
Computational investigation of benzalacetophenone derivatives against SARS-CoV-2 as potential multi-target bioactive compoundsSARS-CoV-2에 대한 벤잘아세토페논 유도체의 잠재적 다중 표적 생리활성 화합물의 전산 조사Article Published on 2022-07-012022-09-11 Journal: Computers in biology and medicine [Category] COVID19(2023년), SARS, 치료제, [키워드] 3CL pro 3CL(pro) addition Anti-SARS-CoV-2 Activity Antiviral antiviral activities Antiviral agents AutoDock Benzalacetophenones binding affinity binding energy binding free energy biological processes Candidates cellular components Compound COVID-19 derivative develop Diseases domain down-regulated enrichment analysis evaluated FIVE flavonoids free energy highest highest binding affinity identify Immune boost immune system Immunity immunostimulant Interaction lab modulated modulation molecular molecular docking molecular dynamics Molecular dynamics simulation molecular functions Molecular mechanics multiple pathway multiple pathways network network pharmacology nine non-infectious Papain Papain-like protease pathway Pathways Patient pharmacological PL(pro) precursor precursors protease Protein recorded reflected regulated retrieved SARS-CoV-2 scored screened Simulation spike Spike protein surface area target upregulated was performed [DOI] 10.1016/j.compbiomed.2022.105668 PMC 바로가기 [Article Type] Article
Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern우려되는 SARS-CoV-2 변이체의 차동 역학에 대한 분자적 통찰력Article Published on 2022-07-012022-09-11 Journal: Journal of molecular graphics & modelling [Category] COVID19(2023년), SARS, 변종, [키워드] ACE2 ACE2 complexes acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 affected Alpha angiotensin Angiotensin-converting enzyme angiotensin-converting enzyme 2 attribute attributes Beta binding binding affinity binding energy changes in complexes coronavirus 2 Delta delta variant effective electrostatic interaction electrostatic interactions enzyme Gamma increase in individual information Interaction molecular dynamics mutated Mutation Orientation RBD Receptor binding domain reported residue respiratory Result SARS-CoV-2 SARS-CoV-2 variant Severe acute respiratory syndrome severe acute respiratory syndrome Coronavirus therapeutic strategy therapy Vaccine variant variants variants of SARS-CoV-2 Viral transmission virus VoC VOCs wild-type [DOI] 10.1016/j.jmgm.2022.108194 PMC 바로가기 [Article Type] Article
Molecular modelling identification of phytocompounds from selected African botanicals as promising therapeutics against druggable human host cell targets of SARS-CoV-2SARS-CoV-2의 약물 가능한 인간 숙주 세포 표적에 대한 유망한 치료제로서 선택된 아프리카 식물의 식물 화합물의 분자 모델링 식별Article Published on 2022-07-012022-09-11 Journal: Journal of molecular graphics & modelling [Category] COVID19(2023년), SARS, 치료제, [키워드] active site acute respiratory syndrome coronavirus African Amino acid amino acid residue angiotensin Angiotensin converting enzyme-2 bafilomycin binding binding energy candidate drug cathepsin cathepsin L caused Cell clinical evaluation clinical evaluations Compound compounds Computational methods coronavirus 2 coronavirus disease Coronavirus disease 2019 COVID-19 Critical enzyme galactoside hACE2 highly pathogenic host cell Host cell targets human cell human cells human host in vitro inhibitor inhibitors of TMPRSS2 inhibitory inhibitory action investigated kaempferol mechanism MLN-4760 Modification modifications modulate molecular dynamics Molecular dynamics simulation myricetin nafamostat Phytocompounds Protein Proteins Replication Research respiratory Respiratory disease respiratory diseases rutinoside SARS-CoV-2 selected Serine severe acute respiratory syndrome Coronavirus severe acute respiratory syndrome coronavirus 2 Structural analysis subjects subsequent target Therapeutic benefit these compound these compounds TMPRSS2 transmembrane serine protease Verbascoside viral entry viral spike protein viral spike proteins while [DOI] 10.1016/j.jmgm.2022.108185 PMC 바로가기 [Article Type] Article
Computational studies evidenced the potential of steroidal lactone to disrupt surface interaction of SARS-CoV-2 spike protein and hACE2Article Published on 2022-07-012023-07-09 Journal: Computers in biology and medicine [Category] COVID19(2023년), [키워드] binding energy Hydrogen bond occupancy protein-protein interaction Spike-receptor binding domain Withalongolide A. [DOI] 10.1016/j.compbiomed.2022.105598 PMC 바로가기
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal3d-qsar.com 포털을 통해 SARS-CoV-2 주요 프로테아제 억제제에 대한 예측 모델을 개발하기 위한 리간드 기반 및 구조 기반 연구Article Published on 2022-07-012022-09-11 Journal: Journal of computer-aided molecular design [Category] COVID19(2023년), SARS, 치료제, [키워드] 3-D QSAR Analysis applicability approach binding binding energy build calculation Candidates cleavage site co-crystallized Combination COMBINE Compound conservation coronavirus COVID-19 infected patients develop domain drug design Emergency use authorization enzyme EUA feature Final functional protein implicated in viral inhibitor inhibitors joint Ligand ligand-based drug design M pro maturation Metrics Mild-to-moderate Model molecular Nirmatrelvir outcome performed portal Predictive Predictive model promote protease Quantitative reached Replication reported resources robust robustness safety profile SARS-CoV-2 SARS-CoV-2 main protease statistical Structure-activity relationships Structure-based drug design tolerable training set Transcription Treatment U.S. FDA viral replication Virtual screening [DOI] 10.1007/s10822-022-00460-7 PMC 바로가기 [Article Type] Article
Anisotine and amarogentin as promising inhibitory candidates against SARS-CoV-2 proteins: a computational investigationSARS-CoV-2 단백질에 대한 유망한 억제 후보로서의 아니소틴 및 아마로젠틴: 전산 조사Article Published on 2022-07-012022-09-11 Journal: Journal of biomolecular structure & dynamics [Category] COVID19(2023년), SARS, 치료제, [키워드] acute respiratory syndrome acute respiratory syndrome coronavirus acute respiratory syndrome coronavirus 2 amarogentin Analysis antiviral activities antiviral activity approach binding energy binding pocket binding pockets candidate Candidates caused Compound coronavirus coronavirus disease Coronavirus disease 2019 COVID-19 drug effective enzyme Extensive feature followed by global public health Host in silico in vitro in vivo inhibitor inhibitors inhibitory Justicia adhatoda limit M pro molecular molecular docking molecular dynamics Molecular dynamics simulation molecular dynamics simulations Ocimum Ocimum sanctum pandemic physicochemical Phytocompounds plant present protease Protein RdRP reported Research research finding researcher RNA-dependent RNA polymerase robust SARS-CoV-2 SARS-CoV-2 protein SARS-CoV-2 proteins SARS-CoV-2 RdRp SARS-CoV-2 spike significantly higher Spike protein Spread Swertia Swertia chirata target therapeutic therapeutic candidates. these compound these compounds Toxicity Viral protein Viral proteins viral replication virus [DOI] 10.1080/07391102.2020.1860133 PMC 바로가기 [Article Type] Article