Structural basis of HIV-1 maturation inhibitor binding and activity

Design, synthesis and structure-activity relationships of novel HIV capsid inhibitors with potent antiviral activities

The HIV capsid (CA) protein is a highly promising target for anti-HIV treatment due to its critical role in viral replication. Based on the optimization of 11L guided by PF74, a series of novel HIV CA inhibitors targeting the NTD-CTD interface were identified, demonstrating potent inhibitory effects against both HIV-1 and HIV-2. Notably, compound IC-2b4 (EC50 = 0.08 ± 0.02 μM) exhibits twice the potency of 11L and three times that of PF74 against HIV-1. For HIV-2, IC-2a4 (EC50 = 0.01 ± 0.00 μM) demonstrates twice the efficacy of 11L and 221 times that of PF74. In mechanistic studies, IC-2b4 was shown to bind directly and stably to CA, exerting robust inhibitory effects during both the early and late stages of infection-a property also observed with IC-2b3. Molecular dynamics simulations revealed that IC-2b4 forms more extensive interactions with CA compared to PF74, thereby enhancing antiviral activity. These novel antiviral compounds collectively provide valuable insights into developing anti-HIV therapies and highlight the therapeutic potential of the CA protein as a drug target.

Considerations for capsid-targeting antiretrovirals in pre-exposure prophylaxis

Antiretroviral therapy (ART) impairs viral replication in people living with HIV (PLWH) by suppressing infection or spread. However, not all treatment strategies apply to preventive applications like pre-exposure prophylaxis (PrEP) for uninfected individuals. To prevent the establishment of HIV infection, PrEP must block viral replication either before, or at the stage of integration into the host genome. A promising PrEP approach under investigation utilizes lenacapavir (LEN), which targets the HIV-1 capsid protein (CA) potently before integration. LEN, a first-in-class antiretroviral, has shown high protective efficacy in the ongoing PURPOSE trials thus far. Here, we discuss clinical investigations of LEN, theoretical suitability of preclinical CA-binding antivirals in PrEP, and other key considerations for preventing HIV-1 infection by targeting the capsid.

OPTO: Automated Optimization for Solid-State NMR Spectroscopy

NMR spectroscopy presents boundless opportunities for understanding the structure, dynamics, and function for a broad range of scientific applications. Solid-state NMR (SSNMR), in particular, provides novel insights into biological and material systems that are not amenable to other approaches. However, a major bottleneck is the extent of user training and the difficulty of obtaining reproducible, high-quality experimental results, especially for the sophisticated multidimensional pulse sequences that are essential to provide site-resolved measurements in large biomolecules. Here, we present OPTO, a software operating environment that addresses these challenges and enhances the performance of many types of commonly utilized SSNMR experiments. OPTO is compatible with Varian OpenVnmrJ and Bruker Topspin, with a front-end graphical user interface that presents the instrument operator with access to powerful underlying optimization algorithms, including simplex and grid searches of the dozens of parameter settings required for optimal performance. Therefore, OPTO efficiently leverages instrument time and enables instrument operators to find optimal experimental conditions reliably. We demonstrate examples including improvements in (1) resolution, with an automated, global search of 21 shimming parameters to achieve a 12 parts per billion line width; (2) sensitivity, with searches and refinements of several cross-polarization conditions dependent on 16 parameters in triple resonance experiments; and (3) robustness, with results from protein samples on several spectrometers operating at different magnetic field strengths and magic-angle spinning rates.

Treatment of HIV Infection in Children Across the Age Spectrum: Achievements and New Prospects

Despite advances in human immunodeficiency virus (HIV) prevention, new pediatric HIV infections continue, necessitating optimized and simplified antiretroviral treatment (ART) regimens tailored for children. Advances in treatment options have been made possible by the availability of child-friendly fixed-dose formulations with decreased dosing frequency, especially in low- and middle-income countries. Ongoing work to improve ART options for neonates and supporting the shift toward long-acting ART for children and adolescents remains a priority. Achieving the UNAIDS goal of 95:95:95 for children will require a comprehensive and holistic approach that addresses both the biomedical and social challenges of managing children with HIV.

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM

HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LEN's structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine in situ cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings offer a more accurate model of BVM engaging the Gag lattice and, importantly, demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors.

Preclinical Profile of the HIV-1 Maturation Inhibitor VH3739937

The HIV-1 maturation inhibitor (MI) VH3739937 (VH-937) inhibits cleavage between capsid and spacer peptide 1 and exhibits an oral half-life in humans compatible with once-weekly dosing. Here, the antiviral properties of VH-937 are described. VH-937 exhibited potent antiviral activity against all HIV-1 laboratory strains, clinical isolates, and recombinant viruses examined, with half-maximal effective concentration (EC50) values ≤ 5.0 nM. In multiple-cycle assays, viruses less susceptible to other MIs, including A364V, were inhibited at EC50 values ≤ 8.0 nM and maximal percent inhibition (MPI) values ≥ 92%. However, VH-937 was less potent against A364V in single-cycle assays (EC50, 32.0 nM; MPI, 57%) and A364V emerged in one of four resistance selection cultures. Other substitutions were selected by VH-937, although re-engineered viruses with these sequences were non-functional in multiple-cycle assays. Measured dissociation rates from wild-type and A364V-containing VLPs help explain resistance to the A364V mutation. Overall, the in vitro antiviral activity of VH-937 supports its continued development as a treatment for HIV-1.

Exploring HIV-1 Maturation: A New Frontier in Antiviral Development

HIV-1 virion maturation is an essential step in the viral replication cycle to produce infectious virus particles. Gag and Gag-Pol polyproteins are assembled at the plasma membrane of the virus-producer cells and bud from it to the extracellular compartment. The newly released progeny virions are initially immature and noninfectious. However, once the Gag polyprotein is cleaved by the viral protease in progeny virions, the mature capsid proteins assemble to form the fullerene core. This core, harboring two copies of viral genomic RNA, transforms the virion morphology into infectious virus particles. This morphological transformation is referred to as maturation. Virion maturation influences the distribution of the Env glycoprotein on the virion surface and induces conformational changes necessary for the subsequent interaction with the CD4 receptor. Several host factors, including proteins like cyclophilin A, metabolites such as IP6, and lipid rafts containing sphingomyelins, have been demonstrated to have an influence on virion maturation. This review article delves into the processes of virus maturation and Env glycoprotein recruitment, with an emphasis on the role of host cell factors and environmental conditions. Additionally, we discuss microscopic technologies for assessing virion maturation and the development of current antivirals specifically targeting this critical step in viral replication, offering long-acting therapeutic options.

Low power supercycled TPPM decoupling

Improving the spectral sensitivity and resolution of biological solids is one of the long-standing problems in nuclear magnetic resonance (NMR) spectroscopy. In this report, we introduce low-power supercycled variants of two-pulse phase-modulated (TPPM) sequence for heteronuclear decoupling. The utility of the sequence is shown by improvements in the transverse relaxation time of observed nuclei (with 1H decoupling) with its application to different samples (uniformly 13C, 15N, 2H-labeled GB1 back-exchanged with 25% H2O and 75% D2O, uniformly 13C, 15N, 2H-labeled human derived Asyn fibril back-exchanged with 100% H2O and uniformly 13C, 15N -labeled human derived Asyn fibril) at fast MAS using low radiofrequency (RF) fields. To understand the effect of spinning speed, the transverse relaxation time is monitored under different spinning frequencies. In comparison to existing heteronuclear decoupling sequences, the supercycled TPPM (sTPPM) sequence significantly improves the spectral sensitivity and resolution and is robust towards B1 inhomogeneity and decoupler offset.

Solid-State NMR 13C sensitivity at high magnetic field

Sensitivity is the foundation of every NMR experiment, and the signal-to-noise ratio (SNR) should increase with static (B0) magnetic field, by a proportionality that primarily depends on the design of the NMR probe and receiver. In the low B0 field limit, where the coil geometry is much smaller than the wavelength of the NMR frequency, SNR can increase in proportion to B0 to the power 7/4. For modern magic-angle spinning (MAS) probes, this approximation holds for rotor sizes up to 3.2 mm at 14.1 Tesla (T), corresponding to 600 MHz 1H and 151 MHz 13C Larmor frequencies. To obtain the anticipated benefit of larger coils and/or higher B0 fields requires a quantitative understanding of the contributions to SNR, utilizing standard samples and protocols that reproduce SNR measurements with high accuracy and precision. Here, we present such a systematic and comprehensive study of 13C SNR under MAS over the range of 14.1 to 21.1 T. We evaluate a range of probe designs utilizing 1.6, 2.5 and 3.2 mm rotors, including 24 different sets of measurements on 17 probe configurations using five spectrometers. We utilize N-acetyl valine as the primary standard and compare and contrast with other commonly used standard samples (adamantane, glycine, hexamethylbenzene, and 3-methylglutaric acid). These robust approaches and standard operating procedures provide an improved understanding of the contributions from probe efficiency, receiver noise figure, and B0 dependence in a range of custom-designed and commercially available probes. We find that the optimal raw SNR is obtained with balanced 3.2 mm design at 17.6 T, that the best mass-limited SNR is achieved with a balanced 1.6 mm design at 21.1 T, and that the raw SNR at 21.1 T reaches diminishing returns with rotors larger than 2.5 mm.

High-efficiency low-power 13C-15N cross polarization in MAS NMR

Biomolecular solid-state magic angle spinning (MAS) NMR spectroscopy frequently relies on selective 13C-15N magnetization transfers, for various kinds of correlation experiments. Introduced in 1998, spectrally induced filtering in combination with cross polarization (SPECIFIC-CP) is a selective heteronuclear magnetization transfer experiment widely used for biological applications. At MAS frequencies below 20 kHz, commonly used for 13C-detected MAS NMR experiments, SPECIFIC-CP transfer between amide 15N and 13Cα atoms (NCA) is typically performed with radiofrequency (rf) fields set higher than the MAS frequency for both 13C and 15N channels, and high-power 1H decoupling rf field is simultaneously applied. Here, we experimentally explore a broad range of NCA zero-quantum (ZQ) SPECIFIC-CP matching conditions at the MAS frequency of 14 kHz and compare the best high- and low-power matching conditions with respect to selectivity, robustness, and sensitivity at lower 1H decoupling rf fields. We show that low-power NCA SPECIFIC-CP matching condition gives rise to 20% sensitivity enhancement compared to high-power conditions, in 2D NCA spectra of microcrystalline assemblies of HIV-1 CACTD-SP1 protein with inositol hexakis-phosphate (IP6).

Integrative approaches for characterizing protein dynamics: NMR, CryoEM, and computer simulations

Proteins are inherently dynamic and their internal motions are essential for biological function. Protein motions cover a broad range of timescales: 10-14-10 s, spanning from sub-picosecond vibrational motions of atoms via microsecond loop conformational rearrangements to millisecond large amplitude domain reorientations. Observing protein dynamics over all timescales and connecting motions and structure to biological mechanisms requires integration of multiple experimental and computational techniques. This review reports on state-of-the-art approaches for assessing dynamics in biological systems using recent examples of virus assemblies, enzymes, and molecular machines. By integrating NMR spectroscopy in solution and the solid state, cryo electron microscopy, and molecular dynamics simulations, atomistic pictures of protein motions are obtained, not accessible from any single method in isolation. This information provides fundamental insights into protein behavior that can guide the development of future therapeutics.

Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding

During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.

Selected Plant Triterpenoids and Their Derivatives as Antiviral Agents

The results of the most recent investigation of triterpenoid-based antiviral agents namely in the HIV-1 and HSV-1 treatment were reviewed and summarized. Several key historical achievements are included to stress consequences and continuity in this research. Most of the agents studied belong to a series of compounds derived from betulin or betulinic acid, and their synthetic derivative is called bevirimat. A termination of clinical trials of bevirimat in Phase IIb initiated a search for more successful compounds partly derived from bevirimat or designed independently of bevirimat structure. Surprisingly, a majority of bevirimat mimics are derivatives of betulinic acid, while other plant triterpenoids, such as ursolic acid, oleanolic acid, glycyrrhetinic acid, or other miscellaneous triterpenoids, are relatively rarely involved in a search for a novel antiviral agent. Therefore, this review article is divided into three parts based on the leading triterpenoid core structure.

Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding

During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-gRNA interactions play a crucial role in the multimerization process, which is yet to be fully understood. We have performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model (hENM) applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to impact mainly the SP1 domain of the 18-mer and the MA-CA linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the NC domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, as well as regulates the dynamic organization of the local membrane region itself.

Significance

Gag(Pr 55 Gag ) polyprotein orchestrates many essential events in HIV-1 assembly, including packaging of the genomic RNA (gRNA) in the immature virion. Although various experimental techniques, such as cryo-ET, X-ray, and NMR, have revealed structural properties of individual domains in the immature Gag clusters, structural and biophysical characterization of a full-length Gag molecule remains a challenge for existing experimental techniques. Using atomistic molecular dynamics simulations of the different model systems of Gag polyprotein, we present here a detailed structural characterization of Gag molecules in different multimerization states and interrogate the synergy between Gag-Gag, Gag-membrane, and Gag-gRNA interactions during the viral assembly process.

Sub-stoichiometric Modulation of Viral Targets-Potent Antiviral Agents That Exploit Target Vulnerability

The modulation of oligomeric viral targets at sub-stoichiometric ratios of drug to target has been advocated for its efficacy and potency, but there are only a limited number of documented examples. In this Viewpoint, we summarize the invention of the HIV-1 maturation inhibitor fipravirimat and discuss the emerging details around the mode of action of this class of drug that reflects inhibition of a protein composed of 1,300-1,600 monomers that interact in a cooperative fashion. Similarly, the HCV NS5A inhibitor daclatasvir has been shown to act in a highly sub-stoichiometric fashion, inhibiting viral replication at concentrations that are ∼23,500 lower than that of the protein target.

HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.