Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics

Manish, Manish; Mishra, Shailendra; Anand, Ayush; Subbarao, Naidu

doi:10.1016/j.compbiomed.2022.106125

Cited by 13 publications

(7 citation statements)

References 63 publications

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“…However, further research is needed on the mechanism of inhibiting LSDV replication. Thea avin mainly come from black and yellow tea and can inhibit the replication of various viruses, such as the novel Zika virus (ZIKV) [34], in uenza A virus [35], HSV-1 [36], SARS-COV-2 ( [37], ASFV [38], feline calicivirus (FCV) [39]. Our study found that thea avin have a strong ability to inhibit LSDV replication with an IC50 of 10.05 µM.…”

Section: Discussionmentioning

confidence: 86%

Construction of recombinant LSDV fluorescent virus for high-throughput screening of antiviral drugs

Wang,

Ji,

zhong

et al. 2023

Preprint

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Lumpy skin disease virus (LSDV) infection is a major socio-economic issue that can cause serious threat to the global cattle farming industry. Here, a recombinant virus LSDV-ΔTK/EGFP of expressing EGFP was constructed using a homologous recombination system and applied to high-throughput screening of antiviral drugs. LSDV-ΔTK/EGFP can replicate in various kidney cell lines to consistent with wild-type LSDV. At the same time, the cytopathic effects, virus particle morphology, and growth performance caused by LSDV-ΔTK/EGFP are consistent with those of wild LSDV. High-throughput screening found that emodin (for LSDV-ΔTK/EGFP, IC50 = 10.86 µM), aloe emodin (for LSDV-ΔTK/EGFP, IC50 = 10.13 µM), theaflavin (for LSDV-ΔTK/EGFP, IC50 = 10.05 µM), 4-ethylphenol (for LSDV-ΔTK/EGFP, IC50 = 32.17 µM), tulipalin (for LSDV-ΔTK/EGFP, IC50 = 28.58 µM) and anemoside B4 (for LSDV-ΔTK/EGFP, IC50 = 845.65 µM) inhibited LSDV replication. Theaflavin strong inhibitory effect on LSDV was identified from 100 antiviral drugs in vitro. In addition, the addition time measurement shown that theaflavins play a role in the entry of LSDV into cells and subsequent viral replication stages. The development of this recombinant virus contributes to the development of LSDV antiviral drugs and the subsequent study of virus replication and mechanism of action.

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Section: Discussionmentioning

confidence: 86%

Construction of recombinant LSDV fluorescent virus for high-throughput screening of antiviral drugs

Wang,

Ji,

zhong

et al. 2023

Preprint

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“…This calculation was based on the solvent accessibility approach, the generalized Born solvation model, and the force field derived from molecular mechanics, which were used to determine the binding free energy of each snapshot from the MD trajectory. 38 The total free energy binding was calculated using eqn (2) Δ G bind = Δ G complex − (Δ G protein + Δ G ligand ) where, Δ G bind = binding free energy, Δ G complex = free energy of the complex, Δ G protein = free energy of the protein, and Δ G ligand = free energy of the ligand. 39 …”

Section: Methodsmentioning

confidence: 99%

“…This calculation was based on the solvent accessibility approach, the generalized Born solvation model, and the force eld derived from molecular mechanics, which were used to determine the binding free energy of each snapshot from the MD trajectory. 38 The total free energy binding was calculated using eqn (2)…”

Section: Molecular Dynamics Simulation (Mds)mentioning

confidence: 99%

Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancervianetwork pharmacology, molecular docking and molecular dynamics simulation

Duan,

Zhang,

Yuan

et al. 2023

RSC Adv.

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“…Root-mean-square fluctuation (RMSF). The data from the RMSF investigation, which examined residual fluctuations 49 in 3BPF and 3BWK both before and after binding with the ligands HR5, HR15, HR16, and E64, is depicted in Fig. 7(c) and (f).…”

Section: Rsc Medicinal Chemistry Articlementioning

confidence: 99%

Reinvestigation of diphenylmethylpiperazine analogues of pyrazine as new class of Plasmodial cysteine protease inhibitors for the treatment of malaria

Madhav,

Reddy,

Rizvi

et al. 2024

RSC Med. Chem.

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Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics

Cited by 13 publications

References 63 publications

Construction of recombinant LSDV fluorescent virus for high-throughput screening of antiviral drugs

Construction of recombinant LSDV fluorescent virus for high-throughput screening of antiviral drugs

Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancervianetwork pharmacology, molecular docking and molecular dynamics simulation

Reinvestigation of diphenylmethylpiperazine analogues of pyrazine as new class of Plasmodial cysteine protease inhibitors for the treatment of malaria

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