Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors

ABSTRACT Hepatitis C virus (HCV) infects millions of people worldwide, causing chronic liver disease that can lead to cirrhosis, hepatocellular carcinoma, and liver transplant. In the last several years, the advent of direct-acting antivirals, including NS3/4A protease inhibitors (PIs), has remarkably improved treatment outcomes of HCV-infected patients. However, selection of resistance-associated substitutions and polymorphisms among genotypes can lead to drug resistance and in some cases treatment failure. A proactive strategy to combat resistance is to constrain PIs within evolutionarily conserved regions in the protease active site. Designing PIs using the substrate envelope is a rational strategy to decrease the susceptibility to resistance by using the constraints of substrate recognition. We successfully designed two series of HCV NS3/4A PIs to leverage unexploited areas in the substrate envelope to improve potency, specifically against resistance-associated substitutions at D168. Our design strategy achieved better resistance profiles over both the FDA-approved NS3/4A PI grazoprevir and the parent compound against the clinically relevant D168A substitution. Crystallographic structural analysis and inhibition assays confirmed that optimally filling the substrate envelope is critical to improve inhibitor potency while avoiding resistance. Specifically, inhibitors that enhanced hydrophobic packing in the S4 pocket and avoided an energetically frustrated pocket performed the best. Thus, the HCV substrate envelope proved to be a powerful tool to design robust PIs, offering a strategy that can be translated to other targets for rational design of inhibitors with improved potency and resistance profiles. IMPORTANCE Despite significant progress, hepatitis C virus (HCV) continues to be a major health problem with millions of people infected worldwide and thousands dying annually due to resulting complications. Recent antiviral combinations can achieve >95% cure, but late diagnosis, low access to treatment, and treatment failure due to drug resistance continue to be roadblocks against eradication of the virus. We report the rational design of two series of HCV NS3/4A protease inhibitors with improved resistance profiles by exploiting evolutionarily constrained regions of the active site using the substrate envelope model. Optimally filling the S4 pocket is critical to avoid resistance and improve potency. Our results provide drug design strategies to avoid resistance that are applicable to other quickly evolving viral drug targets.

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Detection and analysis of hepatitis C virus NS3 serine protease inhibitors

Journal of Hepatology ◽

10.1016/s0168-8278(01)80459-1 ◽

2001 ◽

Vol 34 (0) ◽

pp. 126-127

Author(s):

R Zemel

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Serine Protease ◽

Protease Inhibitors ◽

Serine Protease Inhibitors

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Faculty Opinions recommendation of Development of a GB virus B marmoset model and its validation with a novel series of hepatitis C virus NS3 protease inhibitors.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017920.207523 ◽

2004 ◽

Author(s):

Jeffrey Cohen

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Protease Inhibitors ◽

Ns3 Protease Inhibitors ◽

Ns3 Protease

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Macrocyclic Hepatitis C Virus NS3/4A Protease Inhibitors: An Overview of Medicinal Chemistry

Current Medicinal Chemistry ◽

10.2174/0929867323666160510122525 ◽

2016 ◽

Vol 23 (29) ◽

pp. 3404-3447 ◽

Cited By ~ 5

Author(s):

Thanigaimalai Pillaiyar ◽

Vigneshwaran Namasivayam ◽

Manoj Manickam

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Protease Inhibitors ◽

Medicinal Chemistry

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Substrate Envelope-Designed Potent HIV-1 Protease Inhibitors to Avoid Drug Resistance

Chemistry & Biology ◽

10.1016/j.chembiol.2013.07.014 ◽

2013 ◽

Vol 20 (9) ◽

pp. 1116-1124 ◽

Cited By ~ 36

Author(s):

Madhavi N.L. Nalam ◽

Akbar Ali ◽

G.S. Kiran Kumar Reddy ◽

Hong Cao ◽

Saima G. Anjum ◽

...

Keyword(s):

Drug Resistance ◽

Protease Inhibitors ◽

Hiv 1 ◽

Substrate Envelope

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Computer-aided identification of a series of novel ligands showing high potency as hepatitis C virus NS3/4A protease inhibitors

Bulletin of the National Research Centre ◽

10.1186/s42269-020-00467-w ◽

2021 ◽

Vol 45 (1) ◽

Author(s):

Stephen Ejeh ◽

Adamu Uzairu ◽

Gideon Adamu Shallangwa ◽

Stephen E. Abechi

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Binding Energy ◽

Protease Inhibitor ◽

Protease Inhibitors ◽

Antiviral Agents ◽

High Potency ◽

Direct Acting Antiviral ◽

Direct Acting ◽

Direct Acting Antiviral Agents

Abstract Background Hepatitis C virus (HCV) is a global medical condition that causes several life-threatening chronic diseases in the liver. The conventional interferon-free treatment regimens are currently in use by a blend of direct-acting antiviral agents (DAAs) aiming at the viral NS3 protease. However, major concerns may be the issue of DAA-resistant HCV strains and the limited availability to the DAAs due to their high price. Due to this crisis, the developments of a new molecule with high potency as an NS3/4A protease inhibitor of the hepatitis-C virus remain a high priority for medical research. This study aimed to use in-silico methods to identify high potent molecule as an NS3/4A protease inhibitor and investigating the binding energy of the identified molecule in comparison with approved direct-acting antiviral agents (Telaprevir, Simeprevir, and Voxilaprevir) through molecular docking. Results The model obtained by in-silico method have the following statistical records, coefficient of determination (r2) of 0.7704, cross-validation (q2LOO = 0.6914); external test set (r2(pred) = 0.7049) and Y-randomization assessment (cR2p = 0.7025). The results from the model were used to identify 12 new potential human HCV NS3/4A protease inhibitors, and it was observed that the identified molecule is well-fixed when docked with the receptor and was found to have the lowest binding energy of − 10.7, compared to approved direct-acting antiviral agents (Telaprevir, Simeprevir, and Voxilaprevir) with − 9.5, − 10.0, − 10.5 binding energy, respectively. Conclusion The binding affinity (− 10.7) of the newly identified molecule docked with 3D structures of HCV NS3/4a protease/helicase (PDB ID: 4A92) was found to be better than that of Telaprevir, Simeprevir, and Voxilaprevir (approved direct-acting antiviral agents) which are − 9.5, − 10.0, and − 10.5, respectively. Hence, a novel molecule was identified showing high potency as HCV NS3/4a protease inhibitors.

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