Design and Synthesis of HIV Integrase as Potential Anti-AIDS Drugs

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

FDA-approved inhibitors of HIV-1 IN belong to a class of drugs called integrase strand transfer inhibitors (INSTIs), due to their ability to preferentially block the enzyme's strand transfer (ST) reaction as compared to the enzymes 3'-processing (3'-P) reaction. The current recommended front-line therapy for HIV-1 infected patients is an INSTI, either Dolutegravir (DTG) or Bictegravir (BIC), in combination with two nucleoside analog reverse transcriptase inhibitors. Both DTG and BIC potently inhibit most of the first generation INSTI-resistant IN mutants. Although little resistance has been selected by either BIC or DTG in treatment-naive patients, some patients who had preexisting first-generation INSTI-resistant mutants and switched to a salvage therapy did not respond to DTG-based therapy, emphasizing the importance of developing new and improved IN inhibitors. This adds impetus to a continuing need to develop next-generation agents that have the ability to retain high antiviral efficacy against emerging strains of INSTI-resistant virus. Utilizing my laboratory's design and synthetic capabilities, we have teamed with pharmacologists (Dr. Yves Pommier, NCI) and virologists (Dr. Hughes, NCI) to develop a new genre of INSTIs. We have examined our best inhibitors side by side with the clinically relevant INSTIs using a single round infection assay against panel of new IN-resistant mutants that were selected in vitro with DTG, BIC, and CAB. Of these three INSTIs, BIC and our compounds had the broadest efficacy and were superior to DTG. In further collaborations with structural biologists (Dr. Robert Craigie, NIDDK, Dr. Dmitry Lyumkis, the Salk Institute, Dr. Cherepanov, the Francis Crick Institute, UK and Dr. Goedele Maertens, Imperial College London) we have performed studies to better understand the interactions of INSTIs with intasomes (multimeric integrase with DNA substrate and metal cofactor) and to clarify the roles that mutations play in down-regulating these interactions. Cryo-electron microscopy (Cryo-EM) has played a key role in these efforts. Cryo-EM structures of our best INSTIs bound to HIV-1 intasomes revealed a complex and dynamic network of water molecules surrounding bound INSTIs, with many of these waters appearing to be conserved and occupying similar positions in the unliganded and INSTI-bound structures. However, some waters are displaced or shifted as a consequence of binding of the INSTI; others are found only when INSTIs are bound, suggesting that the conformational changes induced by the binding stabilize their position. We concluded that within the substrate envelope (the region defined by the binding of host and viral DNA), differences in geometry of the catalytic pockets, their overall volume, the nearby patterns of hydration, among other features, all matter for understanding INSTI interactions. In order to generate key pharmacokinetic (PK) data on our best INSTIs, we have partnered with the NCI Invention Development Program (IDP) to obtain early-stage PK data and formulation studies, including studies in rodents. Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this deltaretrovirus. In a collaboration with Drs. Peter Cherepanov and Goedele Maertens we have examined a diverse selection of our IN inhibitors against HTLV-1. A number of our synthetic constructs show significant potency against this target. Using single-particle Cryo-EM, we have visualized one of our most effective INSTIs as well as the clinical HIV-1 INSTIs RAL and BIC bound to the active site of the deltaretroviral intasome. The structures reveal subtle differences in the coordination environment of the Mg2+ ion pair involved in the interaction with the INSTIs. Our results elucidate the binding of INSTIs to the HTLV-1 intasome and support their use for pre-exposure prophylaxis and possibly future treatment of HTLV-1 infection.