Molecular modeling evaluation of the binding effect of five protease inhibitors to COVID-19 main protease

Liu, Jian; Zhai, You; Liang, Lijun; Zhu, Danyan; Zhao, Qiu; Qiu, Yunqing

doi:10.1016/j.chemphys.2020.111080

Cited by 7 publications

(4 citation statements)

References 35 publications

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“…141,142 The cut off energy was set at 520 eV, while 2 Â 2 Â 2 and 2 Â 3 Â 2 Monkhorst-Pack kmeshes were adopted for the geometrical optimization and electronic calculation of Cs 2 CuSbCl 6 and Cs 4 CuSb 2 Cl 12 , respectively. 143 For the structural relaxation, the maximum residual force on each atom is required to be smaller than 0.01 eV Å À1 , and the convergence criterion of total energy is less than 10 À6 eV. 143 Our calculated lattice parameters are listed in Table 3, which are consistent with the recent reported experiment.…”

Section: Thermal Stability and Optoelectronic Propertiessupporting

confidence: 81%

“…143 For the structural relaxation, the maximum residual force on each atom is required to be smaller than 0.01 eV Å À1 , and the convergence criterion of total energy is less than 10 À6 eV. 143 Our calculated lattice parameters are listed in Table 3, which are consistent with the recent reported experiment. 34,38 Moreover, the obtained bandgaps agree with previous investigations, for instance, the bandgap of 2.09 eV for Cs 4 CuSb 2 Cl 12 is close to the previously reported value (2.07 eV).…”

Section: Thermal Stability and Optoelectronic Propertiessupporting

confidence: 81%

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Lead-free all-inorganic halide double perovskite materials for optoelectronic applications: progress, performance and design

Zuo

Yam

et al. 2022

Phys. Chem. Chem. Phys.

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Section: Thermal Stability and Optoelectronic Propertiessupporting

confidence: 81%

Section: Thermal Stability and Optoelectronic Propertiessupporting

confidence: 81%

Lead-free all-inorganic halide double perovskite materials for optoelectronic applications: progress, performance and design

Zuo

Yam

et al. 2022

Phys. Chem. Chem. Phys.

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“…With the emergence of COVID‐19 pandemic, drug repurposing studies included several antiviral drugs, including a well‐known HIV‐1 protease inhibitor lopinavir 42,67–70 . Among the FDA approved antiviral drugs, it has the highest predicted activity against 3CLpro 42 .…”

Section: Resultsmentioning

confidence: 99%

“…With the emergence of COVID-19 pandemic, drug repurposing studies included several antiviral drugs, including a well-known HIV-1 protease inhibitor lopinavir. 42,[67][68][69][70] Among the FDA approved antiviral drugs, it has the highest predicted activity against 3CLpro. 42 Unfortunately, it was demonstrated by Zhang et al 71 that although it is good inhibitor of SARS-CoV-2 3CLpro in vitro, it is not effective in vivo due…”

Section: Sars-cov-2 Repurposing Studymentioning

confidence: 99%

The design of compounds with desirable properties – The anti‐HIV case study

et al. 2022

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Efficacy and safety are among the most desirable characteristics of an ideal drug. The tremendous increase in computing power and the entry of artificial intelligence into the field of computational drug design are accelerating the process of identifying, developing, and optimizing potential drugs. Here, we present novel approach to design new molecules with desired properties. We combined various neural networks and linear regression algorithms to build models for cytotoxicity and anti-HIV activity based on Continual Molecular Interior analysis (CoMIn) and Cinderella's Shoe (CiS) derived molecular descriptors. After validating the reliability of the models, a genetic algorithm was coupled with the Des-Pot Grid algorithm to generate new molecules from a predefined pool of molecular fragments and predict their bioactivity and cytotoxicity. This combination led to the proposal of 16 hit molecules with high anti-HIV activity and low cytotoxicity. The anti-SARS-CoV-2 activity of the hits was predicted.

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A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study

Novak

Потемкин

2022

Mol Divers

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Coronavirus disease 2019 (COVID-19) is caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2). Its main protease, 3C-like protease (3CLpro), is an attractive target for drug design, due to its importance in virus replication. The analysis of the radial distribution function of 159 3CLpro structures reveals a high similarity index. A study of the catalytic pocket of 3CLpro with bound inhibitors reveals that the influence of the inhibitors is local, perturbing dominantly only residues in the active pocket. A machine learning based model with high predictive ability against SARS-CoV-2 3CLpro is designed and validated. The model is used to perform a drug-repurposing study, with the main aim to identify existing drugs with the highest 3CLpro inhibition power. Among antiviral agents, lopinavir, idoxuridine, paritaprevir, and favipiravir showed the highest inhibition potential. Graphical abstract Enzyme – ligand interactions as a key ingredient for successful drug design Supplementary Information The online version contains supplementary material available at 10.1007/s11030-021-10355-8.

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Molecular modeling evaluation of the binding effect of five protease inhibitors to COVID-19 main protease

Cited by 7 publications

References 35 publications

Lead-free all-inorganic halide double perovskite materials for optoelectronic applications: progress, performance and design

Lead-free all-inorganic halide double perovskite materials for optoelectronic applications: progress, performance and design

The design of compounds with desirable properties – The anti‐HIV case study

A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study

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