Structural and Chemical Analysis of Highly Potent ALLINI Platform - Project Summary – Kim HIV-1 integrase (IN) is one of the major antiviral targets, and multiple IN inhibitors have been developed as a key component of current antiretroviral therapy (ART). However, considering viral resistance and toxicity potentials of current INSTIs, compounds with new modes of action (MOA), improved safety profiles, high genetic barrier, and long-acting formulation potentials still remain highly in demand. Allosteric IN inhibitors (ALLINIs) are a new class of IN inhibitors that target the non-catalytic sites of HIV-1 IN. Initially, ALLINIs were originally developed to block the binding of a host factor, LEDGF/p75, to the cleft formed between two IN monomers. The binding of IN to LEDGF/p75, which is a transcription factor, facilitates the selection of viral integration sites toward actively transcribed genes, which can facilitate LTR-mediated viral transcription post integration. Also, it was later discovered that the binding of these ALLINI compounds targeting the LEDGF/p75 binding site of IN also inhibit HV-1 maturation by inducing aberrant IN multimerization that blocks the IN-viral RNA interaction essential for the proper localization of viral genomes within viral capsid during viral maturation. This new activity of IN during HIV-1 maturation further re-enforced the discovery efforts of ALLINI compounds as a potential new class of antivirals (maturation inhibitors). However, after more than a decade of efforts, no ALLINI compounds have progressed to clinical developments, due to their apparent toxicity or limited efficacy. STP0404 is a highly potent pyrrolopyridine-based ALLINI with a sub-nanomolar IC50 efficacy, outstanding PK, and safety profiles observed in both preclinical in vitro and animal investigations. This grant has been supporting various intense MOA investigations of STP0404, which, together with extensive cellular and animal PK and toxicology evaluations conducted by ST Pharm, STP0404 was recently moved to human trials. Indeed, STP0404 became the first-in-human (FIH) ALLINI compound: the phase I trial of STP0404, which was completed in 2022, demonstrated its outstanding safety and human PK profile for once-a-day oral formulations, which further supports advanced clinical evaluations for its anti-viral efficacy in HIV-1 patients. In this renewal application, we will characterize a new STP0404 derivative, EKC110, designed to have improved genetic barrier and altered resistant mutation profile, and also investigate its cellular pharmacology/safety, and synergy with other ART agents. We will also investigate novel antiviral activity and resistance MOAs of our pyrrolopyridine ALLINIs by employing a series of biochemical, structural biology, virological, and computational biology approaches. Finally, we will investigate the effect of STP0404 and EKC110 on HIV-1 integration site selection and their HIV-1 reactivation suppression activity from latently infected CD4+ T cells. Overall, we aim to deliver a new class of safe and effective anti-HIV agents that can be used potentially for treatments for both viral infection and persistence through mechanistic and chemical innovations.
