Molecular Pathways Leading to Drug Resistance in HIV-1 Integrase

About This Grant

ABSTRACT There are ~40 million people world-wide infected by the Human Immunodeficiency Virus (HIV). In the absence of a functional cure, antiretroviral therapy (ART) represents the primary treatment option against HIV. ART regimens containing the integrase strand transfer inhibitors (INSTIs) form first-line treatments for people living with HIV/AIDS (PLWH). INSTIs work by blocking the function of the viral intasome, which is the nucleoprotein complex that forms on the linear ends of the viral long-terminal repeats and mediates the insertion of viral DNA into host target DNA. Despite significant advances afforded by the inclusion of INSTIs to ART regimens, resistance to even the latest drugs is becoming a greater clinical problem. In the clinical literature, there are specific sets of drug-resistant mutations (DRMs) within the IN protein that arise most frequently to INSTI therapy, including individual mutations E138K, G140A/S, and Q148H/K/R. Eventually, the virus evolves more complex combinations of mutations, including the clinically relevant triple mutants E138K/G140A/Q148K (KAK) and E138K/G140S/Q148H (KSH). In preliminary data, models of HIV fitness landscapes built from viral sequences derived from PLWH suggest that the pathways through which combinations of complex triple mutant KAK and KSH combinations emerge can vary dramatically. However, the underlying basis for how and why distinct DRM combinations preferentially emerge remains unclear. This work will test the fundamental hypothesis that the pathways toward drug resistance evolution can be rationalized using atomic resolution structures, supported by multiple experimental measures of viral fitness. In three specific aims, this work will (i) derive drug- specific pathway orderings for KAK and KSH combinations using tools that measure prevalence-based fitness based on extensive viral sequencing data available from PLWH, (ii) determine atomic structures of HIV intasomes along KAK and KSH pathways using the latest technological advances in cryogenic electron microscopy, and (iii) gain dynamic and mechanistic insights into select DRMs along KAK and KSH pathways. Collectively, the structural snapshots will be ordered along the predicted pathway trajectories and, together with existing fitness measurements and complementary molecular dynamics-based analyses, will begin to rationalize the pathways of drug resistance evolution, as well as the associated mechanisms of drug resistance to INSTI therapy. Although the mechanistic analyses of drug resistance have been interrogated in the past, considerably less attention has been given to understanding pathways of drug resistance evolution. Dissecting both pathways and mechanisms of patient-derived clinically relevant complex DRM combinations that arise in response to treatment will build a foundation for prospectively forecasting the evolutionary trajectories leading to drug resistance. The principles can be extended to other infectious diseases, beyond HIV.