Inositol phosphates are assembly co-factors for HIV-1

Dick, Robert A.; Zadrozny, Kaneil K.; Xu, Chaoyi; Schur, F.K.M.; Lyddon, Terri D.; Ricana, C.L.; Wagner, Jonathan M.; Perilla, Juan R.; Ganser‐Pornillos, Barbie K.; Johnson, Marc C.; Pornillos, Owen; Vogt, Volker M.

doi:10.1038/s41586-018-0396-4

Cited by 196 publications

(393 citation statements)

References 44 publications

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“…Inositol phosphates (IPs) are abundant cellular metabolites that play crucial roles in fundamental cellular processes 13 . Interestingly, ions and small molecules like inositol hexakisphosphate (IP6) and benzenehexacarboxylic acid (BHC, or mellitic acid) have been reported to bind to HIV-1 Gag and CA hexamers and impact virion assembly and reverse transcription 4,[14][15][16][17][18] . Here, using a multi-pronged approach combining all-atom molecular dynamics (MD) simulations, atomic force microscopy (AFM), transmission electron microscopy (TEM), confocal microscopy, and virus infectivity assays, we have analyzed the effect of IP6 on HIV-1 capsid stability and reverse transcription.…”

Section: Introductionmentioning

confidence: 99%

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Fisher

Rankovic

et al. 2020

Preprint

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Reverse transcription, an essential event in the HIV-1 lifecycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral core.The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically-favorable conditions for passive translocation of dNTPs into the HIV-1 capsid.Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import and reverse transcription.

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Section: Introductionmentioning

confidence: 99%

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Fisher

Rankovic

et al. 2020

Preprint

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“…It is also notable that self-assembly is predicted to proceed even in the absence of viral RNA, which is consistent with recent experiments that have demonstrated mature capsid formation when co-assembled with inositol phosphate, a small-molecule co-factor. 39 The conditions used in previous simulations implicitly include the putative effects of these co-factors, and the simulations presented hereafter similarly assume that RNA is not essential for core formation.…”

Section: Resultsmentioning

confidence: 99%

Supercharged Assembly: A Broad-Spectrum Mechanism of Action for Drugs that Undermine Controlled HIV-1 Viral Capsid Formation

Pak

Grime

et al. 2019

Preprint

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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 (CG) 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 the population 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 of 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.

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“…A third possibility is that CA dissociates from the core during our lysis and fractionation processes. Of note, inclusion of 10 μM IP 6 , which impacts capsid assembly and stability in vitro [10, 11], throughout the fractionation process had no observable impact on the migration behavior of CA and other core components in sucrose gradients (compare Fig. S7 and Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Inter-hexamer connections forming the hexagonal lattice are mediated through CTD-CTD interactions. In addition, recent studies revealed that a small molecule, inositol hexakisphosphate (IP 6 ), can facilitate the assembly of the CA lattice [10] and regulate its stability [11]. Mutations or compounds that target the critical interactions between individual CA subunits disrupt processes ranging from particle assembly, virion morphogenesis, reverse transcription, and nuclear entry in target cells, underscoring a wide range of functional requirements for the CA protein and/or capsid lattice in multiple steps of the viral life cycle [12–17].…”

Section: Introductionmentioning

confidence: 99%

Capsid lattice destabilization leads to premature loss of the viral genome and integrase enzyme during HIV-1 infection

Eschbach

Elliott

et al. 2020

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The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral ribonucleoprotein complex (vRNP) consisting of a dimeric viral genome and associated proteins, together constituting the viral core. Upon entry into target cells, the viral core undergoes a process termed uncoating, during which CA molecules are shed from the lattice. Although the timing and degree of uncoating are important for reverse transcription and integration, the molecular basis of this phenomenon remains unclear. Using complementary approaches, we assessed the impact of core destabilization on the intrinsic stability of the CA lattice in vitro and fates of viral core components in infected cells. We found that substitutions in CA can impact the intrinsic stability of the CA lattice in vitro in the absence of vRNPs, which mirrored findings from assessment of CA stability in virions. Altering CA stability tended to increase the propensity to form morphologically aberrant particles, in which the vRNPs were mislocalized between the CA lattice and the viral lipid envelope. Importantly, destabilization of the CA lattice led to premature dissociation of CA from vRNPs in target cells, which was accompanied by proteasomal-independent losses of the viral genome and integrase enzyme. Overall, our studies show that the CA lattice protects the vRNP from untimely degradation in target cells and provide the mechanistic basis of how CA stability influences reverse transcription.AUTHOR SUMMARYThe human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral RNA genome and the associated viral enzymes and proteins, together constituting the viral core. Upon infection of a new cell, viral cores are released into the cytoplasm where they undergo a process termed “uncoating”, i.e. shedding of CA molecules from the conical lattice. Although proper and timely uncoating has been shown to be important for reverse transcription, the molecular mechanisms that link these two events remain poorly understood. In this study, we show that destabilization of the CA lattice leads to premature dissociation of CA from viral cores, which exposes the viral genome and the integrase enzyme for degradation in target cells. Thus, our studies demonstrate that the CA lattice protects the viral ribonucleoprotein complexes from untimely degradation in target cells and provide the first causal link between how CA stability affects reverse transcription.

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Inositol phosphates are assembly co-factors for HIV-1

Cited by 196 publications

References 44 publications

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Supercharged Assembly: A Broad-Spectrum Mechanism of Action for Drugs that Undermine Controlled HIV-1 Viral Capsid Formation

Capsid lattice destabilization leads to premature loss of the viral genome and integrase enzyme during HIV-1 infection

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