An estimated 180 million people are infected with hepatitis C virus (HCV) globally and 3-4 million are newly infected each year and is the leading cause of death from liver disease in the United States. For those aware of their positive HCV status, treatment involves a year of clinic visits with an often poorly tolerated treatment regime and even so only about 50% of treated patients are cured. New drugs targeting the viral protein, NS3/4A, which is a bifunctional protease/helicase are in clinical trials. However, drug resistance is arising quickly, likely rendering many of these promising therapeutics obsolete before their time. We are proposing a new drug design strategy to avoid drug resistance, which we have successfully applied to HIV-1 protease and developed single-digit pM inhibitors that retain affinity against a panel of drug resistant viruses. We hypothesize that this strategy works and is applicable to the protease domain of HCV NS3/4A, since at a molecular level drug resistance is a change in the balance of molecular recognition events that selectively weakens inhibitor binding but maintains substrate recognition and cleavage. To understand and reduce the likelihood of drug resistance, the atomic details of substrate recognition need to be elucidated. Thus in this proposal we are characterizing the four diverse natural substrate complexes of NS3/4A, through a combination of crystal structures, molecular dynamics simulations and enzyme kinetics. The resulting structures will likely define a substrate envelope, which defines the region necessary for substrate recognition and will be compared with the binding of inhibitors and the known patterns of drug resistance. The HCV NS3/4A substrate envelope can then be used as an added constraint in the design, synthesis and assessment of novel NS3/4A protease inhibitors that will likely be less susceptible to HCV drug resistance.)

Public Health Relevance

An estimated 180 million people are infected with hepatitis C virus (HCV) globally and 3-4 million are newly infected each year and is the leading cause of death from liver disease in the United States. For those aware of their positive HCV status, treatment involves a year of clinic visits with an often poorly tolerated treatment regime and even so only about 50% of treated patients are cured. New drugs targeting the viral protein, NS3/4a are in clinical trials, however, drug resistance is arising quickly, likely rendering many of these promising therapeutics obsolete before their time. We are proposing a new drug design strategy to avoid drug resistance. )

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI085051-03
Application #
8260858
Study Section
Drug Discovery and Mechanisms of Antimicrobial Resistance Study Section (DDR)
Program Officer
Koshy, Rajen
Project Start
2010-05-01
Project End
2015-04-30
Budget Start
2012-05-01
Budget End
2013-04-30
Support Year
3
Fiscal Year
2012
Total Cost
$407,138
Indirect Cost
$159,638
Name
University of Massachusetts Medical School Worcester
Department
Biochemistry
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
Matthew, Ashley N; Zephyr, Jacqueto; Hill, Caitlin J et al. (2017) Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants. J Med Chem 60:5699-5716
Lin, Kuan-Hung; Ali, Akbar; Rusere, Linah et al. (2017) Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side. J Virol 91:
Soumana, Djadé I; Kurt Yilmaz, Nese; Ali, Akbar et al. (2016) Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease. J Am Chem Soc 138:11850-9
Kurt Yilmaz, Nese; Swanstrom, Ronald; Schiffer, Celia A (2016) Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol 24:547-57
Soumana, Djadé I; Kurt Yilmaz, Nese; Prachanronarong, Kristina L et al. (2016) Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172. ACS Chem Biol 11:900-9
Lin, Kuan-Hung; Nalivaika, Ellen A; Prachanronarong, Kristina L et al. (2016) Dengue Protease Substrate Recognition: Binding of the Prime Side. ACS Infect Dis 2:734-743
Ndjomou, Jean; Corby, M Josie; Sweeney, Noreena L et al. (2015) Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy. ACS Chem Biol 10:1887-96
Soumana, Djadé I; Ali, Akbar; Schiffer, Celia A (2014) Structural analysis of asunaprevir resistance in HCV NS3/4A protease. ACS Chem Biol 9:2485-90
Ali, Akbar; Aydin, Cihan; Gildemeister, Reinhold et al. (2013) Evaluating the role of macrocycles in the susceptibility of hepatitis C virus NS3/4A protease inhibitors to drug resistance. ACS Chem Biol 8:1469-78
Schiffer, Celia (2013) Interview with Celia Schiffer. Future Med Chem 5:1193-7

Showing the most recent 10 out of 16 publications