The HIV-1 Envelope (Env) in its pre-receptor “closed” conformation is targeted by broadly neutralizing antibodies (bnAbs), while its receptor-bound “open” conformation, exposes immunodominant epitopes targeted by non-neutralizing antibodies. A human immunoglobin G (IgG) monoclonal antibody (mAb), 19b, binds an Env third variable (V3) loop epitope that is only exposed in the open Env conformation. Despite widespread use of 19b to detect the open Env conformation in immunoassays, its epitope has not yet been structurally defined. Here we determine crystal structures of ligand-free and V3 peptide-bound 19b Fab to visualize details of this interaction. 19b utilizes both its heavy and light chains to interact with the V3 loop. The 5-residue heavy chain complementarity-determining region (CDR H3) facilitates a hydrophobic pocket for V3 residues to associate with. 19b adopts a cradle binding mode with its CDRH1, CDRL2 and CDRL3 mediating interactions with V3 regions that flank the conserved GPGR/Q motif, without making substantial contacts with the GPGR arch region. Our high-resolution structures by elucidating the epitope, binding mode and the structural basis for the broad reactivity of 19b, fill a gap in our knowledge of a reagent that is widely used in immunoassays.

T-cell receptors (TCRs) recognize peptides presented by MHC, enabling access to intracellular targets that are largely inaccessible to antibodies and difficult to target with small molecules. Despite this potential, their inherent cross-reactivity limits tumor specificity, while single-antigen targeting provides limited coverage of intratumoral heterogeneity. Dual-TCR therapeutics comprising two distinct TCRs could enhance tumor specificity via combinatorial recognition while broadening coverage across heterogeneous antigens. However, practical development of dual-TCR therapeutics has been limited by α/β subunit mispairing that prevents efficient production and creates undesired binding properties. Here, we develop orthogonal TCR α/β interfaces that prevent subunit mispairing. Using computational multistate design and second-site suppressor strategies implemented in Rosetta, we identified over 250 TCR variants for experimental screening to assess protein stability and pairing fidelity. The top-performing designs achieved approximately 95% correct pairing, as validated by mass spectrometry and X-ray crystallography. Focusing mutations on constant domains and conserved framework regions of variable domains enabled broad applicability across diverse TCRs while preserving antigen recognition. Using these orthogonal interfaces, we developed trispecific T-cell engagers (TriTEs) that target two cancer-testis antigens and CD3 on T cells, demonstrating enhanced potency under dual-antigen engagement (EC50 of 380 fM) while maintaining high activity when targeting cells displaying a single antigen (EC50s of 48 pM and 20 pM). This orthogonal TCR interface technology establishes a generalizable platform for engineering multi-specific immune therapeutics targeting diverse cancer antigens.

Protein-based biologic therapies, particularly antibody-like therapeutics, have emerged as a major modality to treat nearly all chronic and infectious diseases. Antagonists have dominated the first wave of antibody and antibody-like biologics, whereas agonism has generally been challenging due to systemic activation leading to issues with therapeutic index and problems with pleiotropic activity. Additionally, agonists that use native proteins such as cytokines can be challenging to produce at scale given these proteins evolved to act locally and are not designed for large scale manufacturing. To address these challenges, we generated a biologics platform comprised of stabilized human VH domains (VH-Select™) which encompass the entire human germline repertoire with the goal of building multispecific biologics denoted Tentacles™ that use avidity-based binding to achieve conditional activity directed to specific cell types or tissues. Stabilizing disulfides and point mutations were identified computationally with Rosetta, evaluated in vitro , and combined into designs with 3-5 amino acid substitutions for each of the seven germline families (VH1-VH7). Computational design was also employed to reduce dimerization from both VL and homotypic VH-VH interactions. Optimization of specific sequences improved expression by greater than 600-fold and thermostability by more than 20°C. Each of the germline variants were screened for low HLA class II binding and incorporated into a library which demonstrated significant improvements in cellular protein production, thereby increasing sequence diversity for screening campaigns. These VH-Select™ scaffolds are useful for the discovery of novel binders used to build multispecific Tentacles™ designed for cis-interactions that achieve cell- and tissue-specific activation. As an example of the utility of the platform, we generated a set of Tentacles™ that use VH-Select™ binders to conditionally agonize IL2Rγβ and 41BB on PD1+, LAG3+, or CD8+ T cells. These Tentacles™ demonstrate promising manufacturability, antibody-like exposure in vivo , and strong anti-tumor activity in a humanized tumor model. Overall, we believe the incorporation of VH-Select™ binders into multispecific Tentacles™ has the potential to create a host of conditionally active biologics to treat various chronic and acute diseases.

Due to the lack of an effective vaccine or a cure, HIV-1 continues to be a major global health threat with the World Health Organization (WHO) reporting 39.0 million people living with HIV-1 and 1.3 new infections in 2022. The HIV-1 Envelope (Env) protein mediates viral entry through interactions with host cell receptors. The pre-receptor Env conformation is targeted by broadly neutralizing antibodies and is the focus of vaccine design, while its altered conformation post receptor binding exposes immunodominant epitopes that are targeted by non-neutralizing antibodies. 19b is a non-neutralizing human immunoglobin G (IgG) monoclonal antibody (mAb) isolated from an asymptomatic person infected with HIV-1 that binds the third variable region (V3) of Env. We expressed and purified 19b IgG. We characterized 19b binding using Surface Plasmon Resonance (SPR). We determined crystal structures of the unliganded 19b Fab and in complex with its V3 peptide epitope from three different HIV-1 strains. Env V3 peptide interacts with both the heavy and light chains of 19b Fab via the complementarity-determining regions (CDRs) L2 and H1. We see a novel V3-Fab binding motif when compared to previously published Env V3 - Fab structures wherein the bulk of 19b recognition occurs at the circlet and band regions of V3. These structures lack the GPGR V3 crown – Fab interaction which agrees with the cradle binding V3 epitopes seen in other non-neutralizing antibodies. 19b is a commonly used reagent in vaccine studies and is widely used to detect the exposure of non-neutralizing Env epitopes. Our high-resolution structures elucidate the epitope and binding mode of 19b, thereby filling a long-standing gap in knowledge that will aid vaccine design against HIV-1.

Biomolecules continually sample alternative conformations. Consequently, even the most energetically favored ground conformational state has a finite lifetime. Here, we show that, in addition to the 3D structure, the lifetime of a ground conformational state determines its biological activity. Using hydrogen-deuterium exchange nuclear magnetic resonance spectroscopy, we found that Zika virus exoribonuclease-resistant RNA (xrRNA) encodes a ground conformational state with a lifetime that is ~10 5 –10 7 longer than that of canonical base pairs. Mutations that shorten the apparent lifetime of the ground state without affecting its 3D structure decreased exoribonuclease resistance in vitro and impaired virus replication in cells. Additionally, we observed this exceptionally long-lived ground state in xrRNAs from diverse infectious mosquito-borne flaviviruses. These results demonstrate the biological significance of the lifetime of a preorganized ground state and further suggest that elucidating the lifetimes of dominant 3D structures of biomolecules may be crucial for understanding their behaviors and functions.

ABSTRACTHuman immunodeficiency virus type 1 typically requires a high density of CD4 for efficient entry as a mechanism to target CD4+ T cells (T-tropic), with CCR5 being used most often as the coreceptor. When target T cells are limiting, the virus can evolve to infect cells with a low density of CD4 such as macrophages (M-tropic). The entry phenotype is known to be encoded in the viral Env protein on the surface of the virus particle. Using data showing a dose response for infectivity based on CD4 surface density, we built a model consistent with T-tropic viruses requiring multiple CD4 molecules to mediate infection, whereas M-tropic viruses can infect cells using a single CD4 receptor molecule interaction. We also found that T-tropic viruses bound to the surface of cells with a low density of CD4 are released more slowly than M-tropic viruses which we modeled to be due to multiple interactions of the T-tropic virus with multiple CD4 molecules to allow the initial stable binding. Finally, we found that some M-tropic Env proteins, as the gp120 subunit, possess an enhanced affinity for CD4 compared with their T-tropic pair, indicating that the evolution of macrophage tropism can be reflected both in the closed Env trimer conformation on the virion surface and, in some cases, also in the open confirmation of gp120 Env. Collectively, these studies reveal differences in the stoichiometry of interaction of T-tropic and M-tropic viruses with CD4 and start to identify the basis of binding differences at the biochemical level.IMPORTANCEHuman immunodeficiency virus type 1 normally targets CD4+ T cells for viral replication. When T cells are limiting, the virus can evolve to infect myeloid cells. The evolutionary step involves a change from requiring a high surface density of CD4 for entry to being able to infect cells with a low density of CD4, as is found on myeloid lineage cells such as macrophage and microglia. Viruses able to infect macrophages efficiently are most often found in the CNS late in the disease course, and such viruses may contribute to neurocognitive impairment. Here, we examine the CD4 binding properties of the viral Env protein to explore these two different entry phenotypes.

Sirtuin-2 (SIRT2) is an NAD+-dependent deacylase that removes acetyl and fatty acyl modifications from lysine residues. Here, we used chemical crosslinking, size exclusion chromatography, and crystallographic analyses to demonstrate that SIRT2 efficiently dimerizes in solution at concentrations greater than ∼100 nM. We also used a split-GFP system to show that SIRT2 dimerizes in cells. SIRT2 undergoes a dimer to monomer transition when bound to long fatty acyl groups such as myristoyl-lysine, but SIRT2 remains a dimer in the presence of acetyl-lysine.

Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that is impaired in its ability to dimerize, which was confirmed with chemical cross-linking and in cells with a split-GFP approach. In enzyme assays, the SIRT2(Q142A/E340A) mutant had normal defatty-acylase activity and impaired deacetylase activity compared with the wild-type protein. These results indicate that dimerization is essential for optimal SIRT2 function as a deacetylase. Moreover, we show that SIRT2 dimers can be dissociated by a deacetylase and defatty-acylase inhibitor, ascorbyl palmitate. Our finding that its oligomeric state can affect the acyl substrate selectivity of SIRT2 is a novel mode of activity regulation by the enzyme that can be altered genetically or pharmacologically.

The androgen receptor (AR) is a crucial coactivator of ELK1 for prostate cancer (PCa) growth, associating with ELK1 through two peptide segments (358-457 and 514-557) within the amino-terminal domain (NTD) of AR. The small-molecule antagonist 5-hydroxy-2-(3-hydroxyphenyl)chromen-4-one (KCI807) binds to AR, blocking ELK1 binding and inhibiting PCa growth. We investigated the mode of interaction of KCI807 with AR using systematic mutagenesis coupled with ELK1 coactivation assays, testing polypeptide binding and Raman spectroscopy. In full-length AR, deletion of neither ELK1 binding segment affected sensitivity of residual ELK1 coactivation to KCI807. Although the NTD is sufficient for association of AR with ELK1, interaction of the isolated NTD with ELK1 was insensitive to KCI807. In contrast, coactivation of ELK1 by the AR-V7 splice variant, comprising the NTD and the DNA binding domain (DBD), was sensitive to KCI807. Deletions and point mutations within DBD segment 558-595, adjacent to the NTD, interfered with coactivation of ELK1, and residual ELK1 coactivation by the mutants was insensitive to KCI807. In a glutathione S-transferase pull-down assay, KCI807 inhibited ELK1 binding to an AR polypeptide that included the two ELK1 binding segments and the DBD but did not affect ELK1 binding to a similar AR segment that lacked the sequence downstream of residue 566. Raman spectroscopy detected KCI807-induced conformational change in the DBD. The data point to a putative KCI807 binding pocket within the crystal structure of the DBD and indicate that either mutations or binding of KCI807 at this site will induce conformational changes that disrupt ELK1 binding to the NTD. SIGNIFICANCE STATEMENT The small-molecule antagonist KCI807 disrupts association of the androgen receptor (AR) with ELK1, serving as a prototype for the development of small molecules for a novel type of therapeutic intervention in drug-resistant prostate cancer. This study provides basic information needed for rational KCI807-based drug design by identifying a putative binding pocket in the DNA binding domain of AR through which KCI807 modulates the amino-terminal domain to inhibit ELK1 binding.

Many different viruses modulate the protein machinery required for ubiquitination to enhance viral fitness. Specifically, several viruses hijack the cullin-RING ligase CRL4 DDB1 to degrade host resistance factors.

Prostate cancer (PC) is generally dependent on the androgen signaling axis for growth. Advanced PC is managed by androgen deprivation therapy (ADT). However, the tumors frequently progress by restoring AR signaling that is either androgen-independent or hypersensitive to androgen, leading to castration resistant prostate cancer (CRPC). CRPC is also supported by hormone-independent actions of AR splice variants which lack the ligand binding domain. Additionally, ADT has many undesirable side effects on a variety of normal tissues that depend on androgen for non-growth related functions, including effects on the cardiovascular system, central nervous system (cognitive effects), bone and muscle. Therefore, a more strategic therapy approach would be to disrupt a functional arm of AR-signaling that is critical for PC/CRPC growth but not for the essential physiological roles of AR in normal tissues. Previous studies in this laboratory have identified ELK1 as an AR tethering protein essential for activation of a critical set of androgen/AR growth genes in various PC model cell line models, both in vitro and in vivo, including those resistant to castration and enzalutamide. It was also established that the N-terminal A/B domain of AR binds to ELK1 by co-opting the two ERK docking sites on ELK1 to constitutively activate genes enriched for cell growth functions in PC cells. A platform antagonist (KCI807) was discovered that bound to AR (Kd = 7x10-8 M), blocking its association with ELK1 and inhibiting PC/CRPC tumor growth. KCI807 has a limited target gene set (a subset of AR target genes) that is primarily and highly enriched for functions in cell cycle progression and mitosis. To further drug development, we must identify the ELK1 docking site recognition sites in AR and the KCI807 binding site. Using a variety of complimentary approaches, we have now mapped and validated the ELK1 docking site recognition sites in the AR A/B domain and also the binding site of KCI807 in AR. The two docking site recognition sites in the AR A/B domain for the two docking sites in ELK1 span amino acids 358-456 and amino acids 514-557. We have also developed a working model in which KCI807 binds in a cleft adjacent to the downstream ELK1-binding site, within the DBD, displacing an alpha helix which in turn disrupts ELK1 binding. Further structural and functional studies based on this knowledge will directly aid in design of next-generation antagonists to selectively target ELK1-dependent growth signaling by AR in PC/CRPC tumors. Citation Format: Claire L. Soave, Charles Ducker, Nathan Nicely, Yanfang Huang, Luke Pardy, Peter Shaw, Manohar Ratnam. New insights into interactions of the androgen receptor with ELK1 and the platform antagonist KCI807 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2923.

Human sirtuins are a family of nicotinamide adenine dinucleotide (NAD+)‐dependent enzymes that are responsible for removing acyl modifications from lysine residues. The deacylase activity of sirtuin isoform‐2 (SIRT2) is involved in the formation and proliferation of cancers and is thought to regulate the progression of neurodegenerative diseases. The acyl substrates of SIRT2 are chemically diverse and range from small acetyl modifications to much larger, fatty acyl groups such as myristoyl. Here, we show that recombinant SIRT2 self‐associates to form dimers in a substrate‐dependent manner that regulates its deacylase activities. SIRT2’s Kd for self‐association was determined to be 98 nM, which is within range of its cellular concentration. SIRT2 alone readily forms dimers, but the enzyme undergoes a transition to monomer when bound to myristoyl substrate. SIRT2’s oligomeric transition from dimer to monomer upon myristoyl substrate binding slows its demyristoylase reaction by adding an additional step to its reaction mechanism. In contrast, SIRT2 appears to remain dimerized when performing its deacetylase reaction which enhances its activity. We propose that SIRT2 abundance in cells may regulate its oligomeric state and deacylation kinetics, and additionally, its oligomeric states may be pharmacologically targeted to modulate acyl substrate selectivity. Finally, sirtuin isoforms 3 and 6 (SIRT3 and SIRT6) do not oligomerize at concentrations relevant to cellular activity, indicating that this mode of regulation is not inherent to all human sirtuins.

The widespread pre-existing αAAV-Abs in humans pose a critical challenge in translation of AAV gene therapy. The IgG degrading enzyme of Streptococci (IdeS) is demonstrated to specifically cleave IgG of humans and other species (not mouse). This study developed a modified new modified IdeS protein product (IdeSop). When incubated in vitro, IdeSop was shown to completely cleave human and rabbit IgGs within 6 h. To test IdeSop in a disease setting, we established a rabbitized αAAV9-Ab+ mouse by an IV infusion of purified acute αAAV9-Ab+ rabbit IgG into MPS IIIA mice, resulting in serum αAAV9-IgG at 1:6,400 and αAAV9-nAbs at 1:800. IdeSop-Ab-cleavage was shown to be dose-dependent. An IV IdeSop infusion at the effective doses resulted in rapid IgG depletion and clearance of pre-existing αAAV9-IgG and αAAV9-nAbs in rabbitized αAAV9-Abs+ MPS IIIA mice. Importantly, an IV injection of a high dose AAV9-hSGSHop vector (5 × 1013vg/kg) at 24 h post IdeSop treatment led to transduction as effective in αAAV9-Abs+ MPS IIIA mice, as in αAAV9-Abs-negative controls. We believe that transient IdeSop administration may offer a great tool to address the pre-existing-αAAV-Abs for the translation of rAAV gene therapy to treat diseases in humans, making effective rAAV gene therapy available to all patients in need.

A stabilized dimer of the surface protein from dengue virus has been engineered to elicit antibodies that neutralize the virus.

Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM(+) IgD(+)CD27(+), thus suggesting that they originated from a pool of antigen-experienced IgM(+) or marginal zone B cells.

SummaryThe HIV-1 envelope (Env) is comprised by mass of over 50% glycans. A goal of HIV-1 vaccine development is the induction of Env glycan-reactive broadly neutralizing antibodies (bnAbs). The 2G12 bnAb recognizes an Env glycan cluster using a unique variable heavy (VH) domain-swapped conformation that results in fragment antigen-binding (Fab) dimerization. Here we describe Fab-dimerized glycan (FDG)-reactive antibodies without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques that neutralized heterologous HIV-1 isolates. FDG precursors were boosted by vaccination in macaques, and were present in HIV-1-naïve humans with an average estimated frequency of one per 340,000 B cells. These data demonstrate frequent HIV-1 Env glycan-reactive bnAb B cell precursors in macaques and humans and reveal a novel strategy for their induction by vaccination.HighlightsDiscovery of Fab-dimerized HIV-1 glycan-reactive antibodies with a non-domain-swapped architectureFab-dimerized antibodies neutralize heterologous HIV-1 isolates.Antibodies with this architecture can be elicited by vaccination in macaques.Fab-dimerized antibodies are found in HIV-1 naïve humans.

Each year, >180,000 infants become infected via mother-to-child transmission (MTCT) of HIV despite the availability of effective maternal antiretroviral treatments, underlining the need for a maternal HIV vaccine. We characterized 224 maternal HIV envelope (Env)-specific IgG monoclonal antibodies (MAbs) from seven nontransmitting and transmitting HIV-infected U.S. and Malawian mothers and examined their neutralization activities against nontransmitted autologous circulating viruses and infant-transmitted founder (infant-T/F) viruses. Only a small subset of maternal viruses, 3 of 72 (4%), were weakly neutralized by maternal linear V3 epitope-specific IgG MAbs, whereas 6 out of 6 (100%) infant-T/F viruses were neutralization resistant to these V3-specific IgG MAbs. We also show that maternal-plasma broadly neutralizing antibody (bNAb) responses targeting the V3 glycan supersite in a transmitting woman may have selected for an N332 V3 glycan neutralization-resistant infant-T/F virus. These data have important implications for bNAb-eliciting vaccines and passively administered bNAbs in the setting of MTCT.IMPORTANCE Efforts to eliminate MTCT of HIV with antiretroviral therapy (ART) have met little success, with >180,000 infant infections each year worldwide. It is therefore likely that additional immunologic strategies that can synergize with ART will be required to eliminate MTCT of HIV. To this end, understanding the role of maternal HIV Env-specific IgG antibodies in the setting of MTCT is crucial. In this study, we found that maternal-plasma broadly neutralizing antibody (bNAb) responses can select for T/F viruses that initiate infection in infants. We propose that clinical trials testing the efficacy of single bNAb specificities should not include HIV-infected pregnant women, as a single bNAb might select for neutralization-resistant infant-T/F viruses.

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.