Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification

Deetanya, Peerapon; Hengphasatporn, Kowit; Wilasluck, Patcharin; Shigeta, Yasuteru; Rungrotmongkol, Thanyada; Wangkanont, Kittikhun

doi:10.1016/j.csbj.2021.05.053

Cited by 31 publications

(53 citation statements)

References 39 publications

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“…As previously described, the enzyme-based assay for SARS-CoV-2 M pro was carried out [37] . SARS-CoV-2 M pro was expressed and purified using a method as previously reported for SARS-CoV M pro [38] .…”

Section: Methodsmentioning

confidence: 99%

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Nutho

Wilasluck²,

Deetanya³

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Methodsmentioning

confidence: 99%

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Nutho

Wilasluck²,

Deetanya³

et al. 2022

Computational and Structural Biotechnology Journal

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“…From molecular docking study on ~4,000 known drugs from the DrugCentral database (Br et al, 2020) and ~7,000 antiviral agents from the Asinex database (Farouk et al, 2021) on the S/ACE2 interface followed by molecular dynamic (MD) simulation of screened compounds, the glycyrrhizic acid and the compound 6,612 with the highest binding affinity from the two following databases, respectively, were suggested for further in vitro and/or in vivo tests. The molecular docking, and physicochemical, pharmacokinetic, and MD studies indicated the solanine, acetoside, and rutin from plantbased natural compounds as the S and Mpro dual inhibitors (Teli et al, 2020;Deetanya et al, 2021). Moreover, several natural herbal compounds such as luteolin, andrographolide, zhebeirine, 3-dehydroverticine, ophiopogonin D, glycyrrhizin, saikosaponin C, crocin-1, and militarine formed strong hydrogen bonds at RBD could prevent the viral binding to ACE2 receptor (Stalin et al, 2021).…”

Section: Spike Proteinmentioning

confidence: 99%

Pharmacogenetics and Precision Medicine Approaches for the Improvement of COVID-19 Therapies

et al. 2022

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Many drugs are being administered to tackle coronavirus disease 2019 (COVID-19) pandemic situations without establishing clinical effectiveness or tailoring safety. A repurposing strategy might be more effective and successful if pharmacogenetic interventions are being considered in future clinical studies/trials. Although it is very unlikely that there are almost no pharmacogenetic data for COVID-19 drugs, however, from inferring the pharmacokinetic (PK)/pharmacodynamic(PD) properties and some pharmacogenetic evidence in other diseases/clinical conditions, it is highly likely that pharmacogenetic associations are also feasible in at least some COVID-19 drugs. We strongly mandate to undertake a pharmacogenetic assessment for at least these drug–gene pairs (atazanavir–UGT1A1, ABCB1, SLCO1B1, APOA5; efavirenz–CYP2B6; nevirapine–HLA, CYP2B6, ABCB1; lopinavir–SLCO1B3, ABCC2; ribavirin–SLC28A2; tocilizumab–FCGR3A; ivermectin–ABCB1; oseltamivir–CES1, ABCB1; clopidogrel–CYP2C19, ABCB1, warfarin–CYP2C9, VKORC1; non-steroidal anti-inflammatory drugs (NSAIDs)–CYP2C9) in COVID-19 patients for advancing precision medicine. Molecular docking and computational studies are promising to achieve new therapeutics against SARS-CoV-2 infection. The current situation in the discovery of anti-SARS-CoV-2 agents at four important targets from in silico studies has been described and summarized in this review. Although natural occurring compounds from different herbs against SARS-CoV-2 infection are favorable, however, accurate experimental investigation of these compounds is warranted to provide insightful information. Moreover, clinical considerations of drug–drug interactions (DDIs) and drug–herb interactions (DHIs) of the existing repurposed drugs along with pharmacogenetic (e.g., efavirenz and CYP2B6) and herbogenetic (e.g., andrographolide and CYP2C9) interventions, collectively called multifactorial drug–gene interactions (DGIs), may further accelerate the development of precision COVID-19 therapies in the real-world clinical settings.

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“…When simulating the dimer, LB-PaCS-MD must consider the double binding sites. Since one of us has already performed the dimer simulation with a ligand in the A chain [67,68], the dimer simulation will be a next application of LB-PaCS-MD for the purpose of in silico screening of compounds.…”

Section: Elucidations Of the Ligand Binding Pathways Of Sars-cov2 Mai...mentioning

confidence: 99%

Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD

2022

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Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important configurations as conformational resampling cycles. In this study, PaCS-MD was extended to sample ligand binding pathways toward a target protein, which is referred to as LB-PaCS-MD. In a ligand-concentrated environment, where multiple ligand copies are randomly arranged around the target protein, LB-PaCS-MD allows for the frequent sampling of ligand binding pathways. To select the important configurations, we specified the center of mass (COM) distance between each ligand and the relevant binding site of the target protein, where snapshots generated by the short-time MD simulations were ranked by their COM distance values. From each cycle, snapshots with smaller COM distance values were selected as the important configurations to be resampled using the short-time MD simulations. By repeating conformational resampling cycles, the COM distance values gradually decreased and converged to constants, meaning that a set of ligand binding pathways toward the target protein was sampled by LB-PaCS-MD. To demonstrate relative efficiency, LB-PaCS-MD was applied to several proteins, and their ligand binding pathways were sampled more frequently than conventional MD simulations.

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Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification

Cited by 31 publications

References 39 publications

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Pharmacogenetics and Precision Medicine Approaches for the Improvement of COVID-19 Therapies

Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD

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