Abstract
The early and late stages of human immunodeficiency virus (HIV) replication are orchestrated by the capsid (CA) protein, which self-assembles into a conical protein shell during viral maturation. Small molecule drugs known as capsid inhibitors (CIs) impede the highly regulated activity of CA. Intriguingly, a few CIs, such as PF-3450074 (PF74) and GS-CA1, exhibit effects at multiple stages of the viral lifecycle at effective concentrations in the pM to nM regimes, while the majority of CIs target a single stage of the viral lifecycle and are effective at nM to μM concentrations. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanisms that enable CIs to have such curious broad-spectrum activity. Our quantitatively analyzed findings show that CIs can have a profound impact on the hierarchical self-assembly of CA by perturbing populations of small CA oligomers. The self-assembly process is accelerated by the emergence of alternative assembly pathways that favor the rapid incorporation of CA pentamers, and leads to increased structural pleomorphism in mature capsids. Two relevant phenotypes are observed: (1) eccentric capsid formation that may fail to encase the viral genome and (2) rapid disassembly of the capsid, which express at late and early stages of infection, respectively. Finally, our study emphasizes the importance of adopting a dynamical perspective on inhibitory mechanisms and provides a basis for the design of future therapeutics that are effective at low stoichiometric ratios of drug to protein.
Highlights
Over the past few decades, antiretroviral therapy (ART) for human immunodeficiency virus type 1 (HIV-1) has made substantial progress.[1−3] These advances can be attributed, in part, to the identification of multiple enzymes that are critical to the HIV-1 lifecycle,[4−6] such as reverse transcriptase, integrase, and protease, as well as the development of small molecules that competitively inhibit their activities
We use CG molecular dynamics simulations and elucidate underlying mechanisms that contribute to the broadspectrum HIV-1 inhibitory effects of capsid inhibitors (CIs), such as PF74 and GS-CA1, by virtue of small perturbations to the hierarchical self-assembly of viral capsid (CA) proteins
We find that an important mode of action by CIs is to stimulate CA association and propagate anisotropic assembly pathways, which results from the stabilization of a subpopulation of trimer of dimers (TODs); this behavior is consistent in all of our CG simulations, even at the lowest accessible drug to CA stoichiometry of less than 1 mol%
Summary
Over the past few decades, antiretroviral therapy (ART) for human immunodeficiency virus type 1 (HIV-1) has made substantial progress.[1−3] These advances can be attributed, in part, to the identification of multiple enzymes that are critical to the HIV-1 lifecycle,[4−6] such as reverse transcriptase, integrase, and protease, as well as the development of small molecules that competitively inhibit their activities. An emerging class of drugs aims to disrupt the activity of the Gag (group-specific antigen) polyprotein, which is responsible for coordinating the late stages of the viral lifecycle.[8,9] The capsid domain (CA) of Gag is an attractive therapeutic target, since both the assembly and maturation of infectious viral particles are mediated by interactions between CA.[10−16] During maturation, for example, CA self-assembles into a conical capsid (i.e., the mature core), composed of more than 1000 CA monomers, that encases the viral genome.[17,18] Given the functional significance of the CA, it is important to note that its sequence is highly conserved (around 70%) among HIV-1 subtypes, thereby reducing the risk of viral polymorphism.[19,20] Drugs that target CA are known as capsid inhibitors (CIs) and have been studied for nearly a decade.[21,22] Several candidates have been identified that demonstrate the feasibility of the CI approach, such as Bevirimat and PF3450074 (PF74), which have half maximal effective concentrations (EC50), a measure of drug potencies, at nM to μM concentrations.[23,24] Most recently, GS-CA1 was introduced as a promising CI with an EC50 around 85 pM concentration, and targets the same binding pocket as PF74 during early and late stages of viral infection.[25] a clinically viable CI has yet to be discovered. A molecular understanding of the mechanism of action for CIs is currently lacking, and represents a barrier for the development of new therapeutics
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