Computational Approaches to Study Peptidomimetic and Macrocyclic Hepatitis C Virus NS3 Protease Inhibitors

Ezat, Ahmed A.; Mostafa, Hamdy I.A.; Elbialy, Nihal Saad; Saleh, Noha A.; Ibrahim, Medhat

doi:10.1166/jctn.2015.3697

Cited by 7 publications

(2 citation statements)

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“…Peptidomimetic inhibitors are capable of interacting with biological targets and producing the same therapeutic effects as native peptides. Using peptidomimetic inhibitors can eliminate some of the drawbacks of using native peptides, including proteolysis and low bioavailability (Vankadara et al 2021 ; Paul et al 2021 ; Somboon et al 2021 ; Wang et al 2022 ; Phoo et al 2018 ; Colarusso et al 2022 ; Ezat et al 2015 ; Mostafa et al 2014 ; Ibrahim et al 2013 ; Saleh and Elshemey 2017 ; Calugi et al 2014 ; Frecer et al 2008 ).…”

Section: Introductionmentioning

confidence: 99%

In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

Saleh

2023

3 Biotech

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COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, has become a global pandemic resulting in significant morbidity and mortality. This study presents 12 new peptidomimetic fullerene-based derivatives in three groups that are investigated theoretically as SARS-CoV-2 M pro inhibitors to increase the chance of treating COVID-19. Studied compounds are designed and optimized at B88-LYP/DZVP method. Molecular descriptors results show the stability and reactivity of the compounds with M pro , especially in the 3rd group (Ser compounds). However, Lipinski's Rule of Five values indicates that the compounds are not suitable as oral drugs. Furthermore, molecular docking simulations are carried out to investigate the binding affinity and interaction modes of the top five compounds (compounds 1, 9, 11, 2, and 10) with the M pro protein, which have the lowest binding energy. Molecular dynamics simulations are also performed to evaluate the stability of the protein–ligand complexes with compounds 1 and 9 and compare them with natural substrate interaction. The analysis of RMSD, H-bonds, Rg, and SASA indicates that both compounds 1 (Gly-α acid) and 9 (Ser-α acid) have good stability and strong binding affinity with the M pro protein. However, compound 9 shows slightly better stability and binding affinity compared to compound 1.

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Section: Introductionmentioning

confidence: 99%

In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

Saleh

2023

3 Biotech

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“…HCV proteins include both structural and non-structural proteins [11,27]. The protease NS3 and the RNA-dependent RNA polymerase NS5B are the most targeted nonstructural proteins [10,13,20]. Viral proteases are essential proteins that regulate the life cycles of many viruses, including HCV.…”

Section: Introductionmentioning

confidence: 99%

Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study

et al. 2019

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In 2011, the FDA approved boceprevir as a hepatitis C virus (HCV) NS3 serine protease inhibitor. The sustained virological response rate for treatment with this approved compound is considerably low. Patients have not responded as much as expected to boceprevir therapy. In this in silico study, modified boceprevir compounds are suggested and tested on wild-type HCV NS3 protease and 19 mutated HCV NS3 proteases using molecular docking. Results reveal the superiority of two of the proposed modified compounds to boceprevir. One of which appears to be more potent than boceprevir itself concerning activity against wild-type NS3 and most of the examined mutated NS3 proteases.

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Design and Development of Some Viral Protease Inhibitors by QSAR and Molecular Modeling Studies

Saleh

Elhaes

Ibrahim

2017

Viral Proteases and Their Inhibitors

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Computational Approaches to Study Peptidomimetic and Macrocyclic Hepatitis C Virus NS3 Protease Inhibitors

Cited by 7 publications

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In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 Mpro

Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study

Design and Development of Some Viral Protease Inhibitors by QSAR and Molecular Modeling Studies

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