A comparative study of the efficiency of HCV NS3/4A protease drugs against different HCV genotypes using in silico approaches

Ezat, Ahmed A.; Elshemey, Wael M.

doi:10.1016/j.lfs.2018.12.004

Cited by 8 publications

(6 citation statements)

References 54 publications

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“…Grazoprevir has the best IC50 value against HCV (4-7 pM) [19,26], while Telaprevir and Boceprevir have slightly higher values against HCV (50 and 80 pM) [22,40]. GRL-0667, GRL-0617, and…”

Section: Discussionmentioning

confidence: 99%

“…MERS CoV PL pro is a multifunctional cysteine protease that processes both viral polyprotein and some host-cell proteins by hydrolyzing the peptide and isopeptide bonds in the substrates [38]. In order to perform this function, a conserved active site triad is required [20,23,39,40]. C111, H278, and D293 are reported to be the active site triad residues in MERS CoV PL pro [1,2].…”

Section: Discussionmentioning

confidence: 99%

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Drug repurposing against MERS CoV and SARS-COV-2 PLpro in silico

Elfiky

Ibrahim

Elshemey

2020

Preprint

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Aim: The Middle East Respiratory Syndrome coronavirus (MERS-CoV) and COVID-19 cause severe acute, deadly, pneumonia. Papain-like protease (PLpro), is HCoV cysteine protease encoded within the Non-Structural protein 3. Materials and Methods: Molecular docking is performed to test the binding performance of six protease inhibitors against MERS CoV and SARS-CoV-2 PLpro. Results: The compound, GRL-0667, shows the highest binding affinity to MERS CoV PLpro, while Grazoprevir shows the highest binding affinity against HCV NS3. Moreover, the interaction pattern in the case of HCV NS3 is the same as in the case of coronaviruses. Conclusion: The present study shows the ability of some anti-SARS CoV and anti-HCV NS3 drugs to inhibit MERS CoV PLpro, interestingly, including the newly emerged SARS-COV-2 PLpro.

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“…Grazoprevir has the best IC50 value against HCV (4-7 pM) [19,26], while Telaprevir and Boceprevir have slightly higher values against HCV (50 and 80 pM) [22,40]. GRL-0667, GRL-0617, and…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Drug repurposing against MERS CoV and SARS-COV-2 PLpro in silico

Elfiky

Ibrahim

Elshemey

2020

Preprint

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“…For further evaluation, the binding energy of these selected hits were identified. The binding affinity showed the polar interaction of the hits with the binding site of receptor, and the value observed between 5 and 15 kcal/mol is considered a strong interaction among the ligands and the receptor [107,108]. The molecular docking was also carried out using AutoDock and AutoDock Vina [109,110].…”

Section: Biomed Research Internationalmentioning

confidence: 99%

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Waqas

Ali

Rehman

et al. 2021

BioMed Research International

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Background. Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. Methods. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. Results. The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. Conclusion. Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.

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“…Furthermore, biomolecular simulations solved different human-related health problems as the algorithms and hardware developed rapidly during the last two decades [ 1 , 2 ]. For example, the human immunodeficiency virus (HIV) and hepatitis C virus (HCV) were successful case studies that heavily relied on computer simulations to find potential inhibitors [ [3] , [4] , [5] , [6] , [7] ]. The pandemic SARS-CoV-2 represents the best recent example of utilizing molecular simulations to investigate human-health-related problems saving time, effort, money, and life [ 8 ].…”

Section: Introductionmentioning

confidence: 99%