Tracking the evolution of drug resistance for highly potent HIV protease inhibitors Project 2 - Swanstrom, UNC, Chapel Hill HIV-1 protease inhibitors are unique among all HIV-1 inhibitors in that they are transition state analogs which allows for binding constants that are orders of magnitude greater than any other type of inhibitor. Resistance to any inhibitor reflects the sequential addition of single amino acid changes that allow sufficient replication and resistance to the inhibitor to favor replication over the wild type virus in the presence of the inhibitor. However, if the resistance contribution of the mutation is too low to confer a growth advantage at the given level of drug compared to the wild type then resistance will not evolve. Also, potent inhibitors can restrict replication to such an extent that the evolution of resistance is slowed or even stopped. Protease inhibitors, because of their tight binding properties, offer the only possible inhibitor that can be envisioned to be able to avoid resistance and to drive (or maintain) the population at levels of negligible replication as a single agent. For this reason we propose this proof-of-concept study to explore the nature of resistance to these very tight-binding inhibitors using three approaches to identifying resistance mutations: selection of virus for resistance in expanded cell culture conditions;selection of virus for resistance in a humanized mouse model;and screening of large, genetically complex populations of protease expressed in yeast in the presence of protease inhibitors. We will also determine if these very tight binding inhibitors are able to suppress viral replication in the humanized mouse model as single agents. Finally, we will examine the role of mutations outside of the protease, in Gag, RT/IN, and gp41 to determine if there are mutations that affect fitness beyond the known mutations in the protease cleavage site.

Public Health Relevance

Tracking the evolution of drug resistance for highly potent HIV protease inhibitors Project 2 - Swanstrom, UNC, Chapel Hill Project 2 Subcontract - Bolon, UMASS Medical School Project 2 Subcontract - Luban, UMASS Medical School The selection for drug resistance is highly informative as to the pathways and mechanisms of resistance. We will examine the evolution of patterns of resistance to potent HIV-1 protease inhibitors to shed light on the underlying resistance mechanisms.

National Institute of Health (NIH)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
United States
Zip Code
Kurt Yilmaz, Nese; Swanstrom, Ronald; Schiffer, Celia A (2016) Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol 24:547-57
Özer, Nevra; Özen, Ayşegül; Schiffer, Celia A et al. (2015) Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution. Evol Appl 8:185-98
Potempa, Marc; Nalivaika, Ellen; Ragland, Debra et al. (2015) A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro. J Mol Biol 427:2360-78
Zhou, Hao; Li, Shangyang; Badger, John et al. (2015) Modulation of HIV protease flexibility by the T80N mutation. Proteins 83:1929-39
Ishima, Rieko (2015) Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression. Concepts Magn Reson Part A Bridg Educ Res 44A:252-262
Cai, Yufeng; Myint, Wazo; Paulsen, Janet L et al. (2014) Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 10:3438-3448
Ragland, Debra A; Nalivaika, Ellen A; Nalam, Madhavi N L et al. (2014) Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. J Am Chem Soc 136:11956-63
Kolli, Madhavi; Ozen, Ayşegül; Kurt-Yilmaz, Nese et al. (2014) HIV-1 protease-substrate coevolution in nelfinavir resistance. J Virol 88:7145-54
Özen, Ayşegül; Lin, Kuan-Hung; Kurt Yilmaz, Nese et al. (2014) Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proc Natl Acad Sci U S A 111:15993-8