Access Type

Open Access Thesis

Date of Award

January 2015

Degree Type

Thesis

Degree Name

M.S.

Department

Biochemistry and Molecular Biology

First Advisor

Dr. Ladislau Kovari

Abstract

ABSTRACT

HIV INTEGRASE MECHANISMS OF RESISTANCE TO RALTEGRAVIR, ELVITEGRAVIR, AND DOLUTEGRAVIR

by

KYLA ROSS

December 2015

Advisor: Dr. Ladislau Kovari

Major: Biochemistry and Molecular Biology

Degree: Master of Science

HIV-1 integrase (HIV-1 IN or IN) is a multimeric enzyme that integrates the HIV-1 genome into the chromosomes of infected CD4+ T-cells. Currently there are three FDA approved HIV-1 IN strand transfer inhibitors (INSTIs) used in clinical practice: raltegravir (RAL), elvitegravir (ELV), and dolutegravir (DTG). The [Q148H], [Q148H, G140S], [Q148R], [Q148R, G140A] and [N155H, E92Q] mutations decrease IN susceptibility to RAL and ELV and may result in therapeutic failure. As an indicator of protein flexibility, the root mean square deviation (RMSD) of each HIV-1 IN residue in the last 5 ns of a 40 ns molecular dynamics simulation was calculated for HIV-1 IN catalytic core domain as an apoprotein and in complex with RAL, ELV, and DTG to study how the mutations affect HIV-1 IN flexibility. In addition, we studied the relationship between HIV-1 IN flexibility and resistance. We found that the mutants reduced overall HIV-1 IN flexibility relative to the WT IN apoprotein. We also observed that the catalytic 140s loop in the HIV-1 IN-INSTI complexes were more flexible in mutants that displayed higher reported EC50 FC (fold change) values. To further investigate the mutations effect on the more complexed full length HIV-1 IN structure, we used molecular dynamics simulations to study the impact of the mutants on binary (IN-viral DNA complex) and ternary (IN-viral DNA- INSTI) IN flexibility. RMSD analyses revealed that that the mutants have a rigid structure relative to the WT IN. Furthermore, mutant IN showed transient changes in the secondary structure of the 140s loop compared to the WT. In addition to these reduced flexibility and structural changes, resistance mutations alter the binding mode of RAL, ELV, and DTG to IN and viral DNA. This study is the first to identify a structural basis of IN mechanism of resistance to INSTIs that develops under treatment pressure in HIV-1 IN.

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