Targeting the HIV-1 RNA packaging signal via small molecules
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Despite the success of highly active antiretroviral therapy (HAART), great concern remains due to rapid emergence of new HIV-1 genetic variants that help the virus escape host immunity and multidrug therapies. We propose a project with the long-term goal of finding a new anti-HIV drug that is less susceptible to evasion by resistant HIV-1 strains. Specifically, we will explore the feasibility of attacking a novel target in the HIV-1 RNA, whose sequence is nearly 100% conserved, by finding small molecules, to serve as drug leads, that bind this target. In addition to coding for viral proteins, RNA, the genetic material of HIV-1, carries many regulatory signals essential for the life of the virus. The very highly conserved regulatory signal we will explore as a feasible drug design target is in the HIV-1 RNA packaging signal. We should be able to design small molecules that bind to this target and prevent proper incorporation of RNA molecules into new infectious virus particles. A part of the HIV-1 packaging signal contains a specific sequence of RNA residues, rich in guanine (G) residues, which forms a specific structure, a so-called internal loop, when unpaired residues are sandwiched between residues forming base-pairs. The sequence of this G-rich internal loop is nearly 100% conserved among all known HIV-1 sequences. This motif is a site of binding of the nucleocapsid protein NCp7. Experimental studies modifying this site, e.g., via mutations, impair packaging of RNA and the overall infectivity of the virus. Recently, we determined the three-dimensional structure of an HIV-1 RNA fragment that includes the G-rich internal loop. We intend to use this structure as the basis to find small molecules, with the potential of being developed into drugs that will bind tightly to RNA and interfere with packing the RNA genome into a new virus particle. The rate of mutations in the G-rich internal loop is very low, so emergence of HIV-1 strains resistant to any drug that binds this site will be very slow. The procedure we will employ to find novel compounds that bind to the G-rich internal loop structure first entails computational screening of a large database of "drug-like" and biologically pertinent compounds using our recently developed program MORDOR. MORDOR is particularly well suited for this endeavor, because it can identify small molecules that bind to RNA by induced-fit. This is crucial for unique RNA sites, such as internal loops, since they are flexible; when binding occurs, the conformation of the RNA as well as the small molecule changes. The compounds that score best in the computational screening will be tested experimentally to see if and how they bind to the target using two different nuclear magnetic resonance (NMR) protocols. One, termed saturation transfer difference NMR, quickly identifies whether or not the ligand binds and the other, monitoring changes in the NMR peak positions of signals from the RNA, enables determination of the binding constant as well as an assessment of where on the RNA the ligand binds. For compounds found to bind to the G-rich internal loop, they will be tested to see if they inhibit binding of the NCp7 protein to the same site and tested for the inhibition of viral growth. In the course of this two-year project, we expect to obtain compounds that bind well to the G-rich internal loop; they will be subsequently optimized for reducing RNA packaging and viral infectivity.