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Propionibacterium acnes, though generally considered part of the normal flora of human skin, is an opportunistic pathogen associated with acne vulgaris as well as other diseases, including endocarditis, endophthalmitis and prosthetic joint infections. Its virulence potential is also supported by knowledge gained from its sequenced genome. Indeed, a vaccine targeting a putative cell wall-anchored P. acnes sialidase has been shown to suppress cytotoxicity and pro-inflammatory cytokine release induced by the organism, and is proposed as an alternative treatment for P. acnes-associated diseases. Here, we report the crystal structures of the surface sialidase and its complex with the transition-state mimic Neu5Ac2en. Our structural and kinetic analyses, together with insight from a glycan array screen, which probes subtle specificities of the sialidase for α-2,3-sialosides, provide a basis for the structure-based design of novel small-molecule therapeutics against P. acnes infections.

Polysialyltransferases synthesize polysialic acid on cell surface-expressed glycoconjugates, which is crucial for developing processes and signaling pathways in eukaryotes. Recent advances in cancer research have rendered polysialyltransferases important drug targets because polysialic acid contributes to cancer cell progression, metastasis, and treatment of resistant tumors. To aid the development of high-throughput screening assays for polysialyltransferase inhibitors, we demonstrate that a previously developed class of fluorescent CMP-sialic acid mimetics for sialyltransferases has nanomolar affinities for oligo- and polysialyltransferases and can be used for the rapid screening of new polysialyltransferase inhibitors. We demonstrate that these CMP-Neu5Ac mimetics inhibit polysialylation in vitro and perform cell culture experiments, where we observe reduced polysialylation of NCAM. Furthermore, we describe the structural basis of CMP-Neu5Ac mimetics binding to the human oligosialyltransferase ST8SiaIII and extrapolate why their affinity is high for human polysialyltransferases. Our results show that this novel class of compounds is a promising tool for the development of potent and selective drugs against polysialyltransferase activity.

IL-12 is a cytokine produced by antigen-presenting cells that increases T cell proliferation, IFN gamma mediated Th1 effector functions and T and NK cell cytotoxicity. While these effects generate potent anti-tumor immunity in mouse models, the high toxicity of IL-12 in cancer patients has limited its clinical utility. Potency attenuation and intratumoral cytokine localization may improve IL-12 tolerability, but these approaches can reduce efficacy or be limited by intratumoral delivery or tumor antigen expression. To improve both tolerability and efficacy of IL-12, we engineered IL-12Fc fusions with anti-IL-12 antibodies to block IL-12 potency. Using linkers designed to be cleaved by highly active intratumoral proteases, blocking antibodies are released specifically in the tumor microenvironment, thereby increasing intratumoral IL-12 activity. Single chain IL-12 was fused to one C-termini of an Azymetric™ Fc heterodimer. To the other Fc C-termini, an anti-IL-12 scFv was fused via a protease-cleavable linker in order to block IL-12 activity. In addition to antibody blockade, modifications of IL-12Fc fusions were used to further limit IL-12Fc activity. In vitro potency was determined by CD8T cell IFN gamma release. Anti-IL-12 scFv cleavage in the presence of recombinant enzyme or human tumor material was assessed by reducing CE-SDS and LC/MS, respectively. All IL-12Fc fusions were produced with favorable biophysical characteristics. Modified IL-12Fc molecules had up to 500x reduced potency, while antibody blocked IL-12Fc molecules had up to 100,000x reduced potency compared to IL-12Fc control. In vitro cleavage of the anti-IL-12 scFv from IL-12Fc recovered potency to that of the corresponding non-masked IL-12Fc molecules. Reducing CE-SDS confirmed that anti-IL-12 scFvs were cleaved from IL-12Fc in the presence of recombinant enzyme. Cleavage of anti-IL-12 scFvs also occurred when variants were incubated in pancreatic tumor cell supernatant or human tumor tissue lysate. These results indicate that antibody blockade and re-activation by protease cleavage is a promising strategy to localize the activity of IL-12 to the tumor microenvironment while potentially limiting off-tumor toxicities. Further modifying antibody blocked IL-12 has the potential to better fine tune therapeutic index. We are pursuing tumor-specific IL-12 fusions for clinical application in tumors with high intratumoral protease activity. Citation Format: Jennifer Leah Bishop, Ryan Blackler, Gesa Volkers, Maya Poffenberger, Irene Yu, Joel Smith, Akram Khodabandehloo, Sifa Arrafi, Desmond Lau, Liz Stangle, Leisa Stenberg, Patricia Zwierzchowski, Iulia Dude, David Douda, Grant Wickman, Jeff Proctor, Gerry Rowse, Laurence Madera, Genevieve Desjardins, Nicole Afacan, Stuart Barnscher, David Mills, Thomas Spreter, Surjit Dixit. Increasing the therapeutic index of IL12 by engineering for tumor specific protease activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1788.

4-1BB is a TNF family receptor expressed on the surface of tumor-infiltrating T cells. Activation of 4-1BB enhances the activation, metabolism and function of tumor-infiltrating T cells and promotes tumor regression. Several anti-4-1BB antibodies have entered the clinic and have suffered from liver toxicity or lack of activity. To address the clinical liabilities with 4-1BB targeting, we designed bispecific 4-1BB x tumor associated antigen (TAA) antibodies to selectively activate T cells within the tumor microenvironment. To understand the impact of antibody format on potency of T cell activation, we generated a panel of 4-1BBxTAA bispecific antibodies in different formats with the AzymetricTM and EFECTTM platforms. We compared potency and maximal activity of these constructs in co-culture assays with tumor cells and T or Jurkat reporter cells, in comparison to urelumab as a clinical benchmark. The AzymetricTM platform allowed the production and evaluation of unique antibody formats from which an extensive structure activity relationship analysis was performed. We also examined the accessible epitope space by sampling the possible paratope binding conformations of the molecule. From this we determined the geometric limits of antigen engagement. Bispecific antibody constructs utilizing monovalent 4-1BB targeting showed inferior activity than urelumab in co-culture assays with TAAhi tumor cells. Activity greater than urelumab was seen with constructs containing two 4-1BB arms with one or two TAA binding scFv on the C-terminus of the Fc. Bivalent 4-1BB antibodies with an anti-TAA scFv fused to the N-terminus of the 4-1BB Fab showed decreased activity, potentially due to reduced ability to engage 4-1BB in a bivalent manner. Critically, the activity seen was transferable across multiple TAAs. The activity of the 4-1BB bispecific constructs was dependent on the expression level of the TAA. Without the presence of tumor cells, or with constructs where the TAA scFv was replaced by an irrelevant scFv, minimal activity was seen. The modelling of the space accessible to the 4-1BB paratopes showed that the constructs with which we saw the most activity had a distance between 4-1BB and TAA binding paratopes similar to that seen between T and APC membranes as part of an immune synapse, suggesting that this may be a key characteristic for the development of conditional T cell agonist bispecifics. This work represents an investigation of 4-1BBxTAA formats which would be difficult to make without an efficient bispecific technology. We identified a series of 4-1BBxTAA bispecific agonist antibody formats which were transferable between multiple TAAs. These formats also allowed optimization of activity and selectivity to promote maximal therapeutic index and efficacy, key factors which are potentially able to contribute to improved clinical outcomes. Citation Format: Anna von Rossum, Harsh Pratap, Lisa Newhook, Elizabeth C. Halvorsen, Lee Freiburger, Renee Duan, Charles Stevens, Dimitri Tcaciuc, Gesa Volkers, Duncan Browman, Brandon Clavette, David Mills, Thomas Spreter, Daniel T. Patton. Understanding the geometry and valency of bispecific antibodies in the optimization of tumor-dependent activation of 4-1BB [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1737.

Many novel immune-oncology biologics are limited in clinical utility by narrow therapeutic windows. One strategy to overcome this limitation relies on the engineering of ‘masks' that block antibody paratopes outside of the tumor microenvironment (TME). The PROTECT (PROgrammed Tumor Engagement & Checkpoint/Costimulation Targeting) platform is designed to employ the orthogonal mechanistic features of a multispecific design to increase the therapeutic window by limiting exposure and activity in peripheral tissues while focusing activities to the tumor. In particular, we aim to bring TME-specific activity and enhanced immune modulation in a single transferable, conditionally active design. To achieve this, we engineered the N-termini of antibody heavy and light chains with the fusion of IgV domains of commonly targeted immunomodulatory pairs, such as PD-1 and PD-L1, to sterically preclude binding of the antibody paratopes to their target tumor antigens. We demonstrate that this approach can effectively mask the antibody binding and activity for targets by 10-1000 fold, with recovery of binding and anti-tumor activity upon release of the immunomodulatory mask once proteolytically cleaved by a tumor-specific protease such as urokinase plasminogen activator (uPA). In addition, we also demonstrate that we can selectively cleave and remove one half of the immunomodulatory pair (e.g. PD-L1) from the antibody thereby creating an antibody fused to only PD-1. The resulting bispecific antibody can now co-engage both the tumor antigen (TA) and its counterpart checkpoint inhibitor (PD-L1) to confer additional antitumor activities. As a proof of concept, we showed that for an engineered anti-CD3/HER2 bispecific T-cell engager (TCE), incorporation of the PD-L1/PD-1 PROTECT design creates a conditionally activated anti-CD3/PD-L1/HER2 tri-specific TCE that has (i) masked CD3 engagement with a reduction of the EC50 by 2 orders of magnitude, and (ii) enhanced T-cell dependent cytotoxicity over the parent anti-CD3/HER2 TCE by an order of magnitude once activated by uPA. Importantly, the enhanced activity of the tri-specific TCE is greater than the combination of the parental TCE with the anti-PD-L1 monoclonal antibody atezolizumab. We have also demonstrated that the PROTECT platform can be combined with anti-TA antibody to introduce a masking effect while increasing antibody-dependent cell cytotoxicity (ADCC) activity upon co-engagement of TA and PD-L1, again synergistic relative to the combination of anti-TA antibody and atezolizumab. Taken together, the PROTECT platform represents a novel approach to integrate immune modulation while limiting off-tumor activities for the development of conditional multispecific antibodies with potentially enhanced therapeutic window and activity. Citation Format: Surjit Dixit, Florian Heinkel, Anna Von Rossum, Harsh Pratap, Sifa Arrafi, Javairia Rahim, Purva Bhojane, Liz Stangle, Leisa Stenberg, Gesa Volkers, Eric Escobar-Cabrera, Thomas Spreter. PROTECT, a novel antibody platform for integrating tumor-specific immune modulation and enhancing the therapeutic window of targeted multispecific biologics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 924.

Sialyltransferases of the mammalian ST8Sia family catalyze oligo- and polysialylation of surface-localized glycoproteins and glycolipids through transfer of sialic acids from CMP-sialic acid to the nonreducing ends of sialic acid acceptors. The crystal structure of human ST8SiaIII at 1.85-Å resolution presented here is, to our knowledge, the first solved structure of a polysialyltransferase from any species, and it reveals a cluster of polysialyltransferase-specific structural motifs that collectively provide an extended electropositive surface groove for binding of oligo-polysialic acid chain products. The ternary complex of ST8SiaIII with a donor sugar analog and a sulfated glycan acceptor identified with a sialyltransferase glycan array provides insight into the residues involved in substrate binding, specificity and sialyl transfer.

Polysialic acid (polySia) is a homopolymeric saccharide that is associated with some neuroinvasive pathogens and is found on selective cell types in their eukaryotic host. The presence of a polySia capsule on these bacterial pathogens helps with resistance to phagocytosis, cationic microbial peptides and bactericidal antibody production. The biosynthesis of bacterial polySia is catalysed by a single polysialyltransferase (PST) transferring sialic acid from a nucleotide-activated donor to a lipid-linked acceptor oligosaccharide. Here we present the X-ray structure of the bacterial PST from Mannheimia haemolytica serotype A2, thereby defining the architecture of this class of enzymes representing the GT38 family. The structure reveals a prominent electropositive groove between the two Rossmann-like domains forming the GT-B fold that is suitable for binding of polySia chain products. Complex structures of PST with a sugar donor analogue and an acceptor mimetic combined with kinetic studies of PST active site mutants provide insight into the principles of substrate binding and catalysis. Our results are the basis for a molecular understanding of polySia biosynthesis in bacteria and might assist the production of polysialylated therapeutic reagents and the development of novel antibiotics.

Tetracycline antibiotics and their degradation products appear in medically treated tissues, food, soil, and manure sludge in the environment. In the context of protein interactions with various tetracyclines we performed crystal structure analyses of the tetracycline repressor in complex with weak or noninducing tetracycline derivatives. Isotetracyclines are degradation products of tetracyclines, which occur under physiological conditions. The typical framework of the antibiotic is irreversibly broken at the BC-ring connection, leading to a modified orientation of the AB to the new C*D ring fragments. The shape of the zwitterionic AB-ring fragment is unchanged and still binds to the TetR recognition site in a manner comparable to the intact antibiotic but without typical Mg(2+) chelation. This work is an example that drug degradation products can still bind to specific targets and should be discussed in light of potential and critical side effects.

The flavin-dependent monooxygenase TetX2 from Bacteroides thetaiotaomicron confers resistance against tetracyclines in aerobically grown Escherichia coli. TetX2 modifies several tetracycline antibiotics by regioselective hydroxylation of the substrates to 11a-hydroxy-tetracyclines. X-ray diffraction data were collected from a native TetX2 crystal and a TetX2 crystal with incorporated selenomethionine to resolutions of 2.5 and 3.0 A, respectively. The native crystal belonged to the triclinic space group P1, with unit-cell parameters a = 68.55, b = 80.88, c = 87.53 A, alpha = 111.09, beta = 98.98, gamma = 93.38 degrees , whereas the selenomethionine-labelled TetX2 crystal belonged to the monoclinic space group P2(1), with unit-cell parameters a = 87.34, b = 68.66, c = 152.48 A, beta = 101.08 degrees .

Expression of the aromatic hydroxylase TetX under aerobic conditions confers bacterial resistance against tetracycline antibiotics. Hydroxylation inactivates and degrades tetra­cyclines, preventing inhibition of the prokaryotic ribosome. X-­ray crystal structure analyses of TetX in complex with the second-generation and third-generation tetracyclines mino­cycline and tigecycline at 2.18 and 2.30 A resolution, respectively, explain why both clinically potent antibiotics are suitable substrates. Both tetracyclines bind in a large tunnel-shaped active site in close contact to the cofactor FAD, pre-oriented for regioselective hydroxylation to 11a-hydroxy­tetracyclines. The characteristic bulky 9-tert-butylglycylamido substituent of tigecycline is solvent-exposed and does not interfere with TetX binding. In the TetX–minocycline complex a second binding site for a minocycline dimer is observed close to the active-site entrance. The pocket is formed by the crystal packing arrangement on the surface of two neighbouring TetX monomers. Crystal structure analysis at 2.73 A resolution of xenon-pressurized TetX identified two adjacent Xe-binding sites. These putative dioxygen-binding cavities are located in the substrate-binding domain next to the active site. Molecular-dynamics simulations were performed in order to characterize dioxygen-diffusion pathways to FADH2 at the active site.

The flavin-dependent monooxygenase TetX confers resistance to all clinically relevant tetracyclines, including the recently approved, broad-spectrum antibiotic tigecycline (Tygacil®) which is a critical last-ditch defense against multidrug-resistant pathogens. TetX represents the first resistance mechanism against tigecycline, which circumvents both the tet-gene encoded resistances, relying on active efflux of tetracyclines, and ribosomal protection proteins. The alternative enzyme-based mechanism of TetX depends on regioselective hydroxylation of tetracycline antibiotics to 11a-hydroxy-tetracyclines. Here, we report the X-ray crystallographic structure determinations at 2.1Å resolution of native TetX from Bacteroides thetaiotaomicron and its complexes with tetracyclines. Our crystal structures explain the extremely versatile substrate diversity of the enzyme and provide a first step towards the rational design of novel tetracycline derivatives to counter TetX-based resistance prior to emerging clinical observations.

Sialic acids are a unique posttranslational modification at the terminus of glycoproteins and -lipids. Proteins modified with oligomers of sialic acid add a repellent charge to cell surfaces, which is a crucial feature in cell migration and axonal growth during early brain development. Varied expression levels of sialic acid are linked to tumor malignancy in neuroblastoma, schizophrenia, autism and bipolar disorder but the lack thereof is linked to impaired neuronal development. On the other hand, overexpression of sialic acid oligomers in Schwann cells promotes the peripheral regeneration of lesioned nerves and improves the ability of Schwann cells to migrate into damaged tissue and to remyelinate central nervous system axons. In order to understand the molecular mechanisms of sialylation, our project focuses on the structural characterization of enzymes of the mammalian and bacterial glycosyltransferase families 29 and 42. The proteins of interest were expressed in insect cells and structural studies were undertaken by x-ray crystallography. Kinetics, SEC MALS and glycan array data will shed light on mechanism of catalysis and acceptor specificity. Altogether, the results of this study will promote further understanding of the structure-function relationship of sialyltransferases.