Discovery and Characterization of a Bicyclic Peptide (Bicycle) Binder to Thymic Stromal Lymphopoietin

Thymic stromal lymphopoietin (TSLP) is an epithelial-derived pro-inflammatory cytokine involved in the development of asthma and other atopic diseases. We used Bicycle Therapeutics' proprietary phage display platform to identify bicyclic peptides (Bicycles) with high affinity for TSLP, a target that is difficult to drug with conventional small molecules due to the extended protein-protein interactions it forms with both receptors. The hit series was shown to bind to TSLP in a hotspot, that is also used by IL-7Rα. Guided by the first X-ray crystal structure of a small peptide binding to TSLP and the identification of key metabolites, we were able to improve the proteolytic stability of this series in lung S9 fractions without sacrificing binding affinity. This resulted in the potent Bicycle 46 with nanomolar affinity to TSLP (KD = 13 nM), low plasma clearance of 6.4 mL/min/kg, and an effective half-life of 46 min after intravenous dosing to rats.

Discovery of BT8009: A Nectin-4 Targeting Bicycle Toxin Conjugate for the Treatment of Cancer

Bicycle toxin conjugates (BTCs) are a promising new class of molecules for targeted delivery of toxin payloads into tumors. Herein we describe the discovery of BT8009, a Nectin-4 targeting BTC currently under clinical evaluation. Nectin-4 is overexpressed in multiple tumor types and is a clinically validated target for selective delivery of cytotoxic payloads. A Nectin-4 targeting bicyclic peptide was identified by phage display, which showed highly selective binding for Nectin-4 but suffered from low plasma stability and poor physicochemical properties. Multiparameter chemical optimization involving introduction of non-natural amino acids resulted in a lead Bicycle that demonstrated high affinity for Nectin-4, good stability in biological matrices, and a much-improved physicochemical profile. The optimized Bicycle was conjugated to the cytotoxin Monomethyl auristatin E via a cleavable linker to give the targeted drug conjugate BT8009, which demonstrates potent anticancer activity in in vivo rodent models.

An Assay for Periplasm Entry Advances the Development of Chimeric Peptide Antibiotics

The treatment of infection by Gram-negative bacteria is increasingly challenging as resistance to existing antibiotics spreads. Constrained peptides, selected for high target specificity and affinity via library display technologies, are an emerging therapeutic modality in many disease areas and may be a fertile source of new antibiotics. Currently, the utility of constrained peptides and other large molecules as antibiotics is limited by the outer membrane (OM) barrier of Gram-negative bacteria. However, the addition of certain moieties to large molecules can confer the ability to cross the OM; these moieties function as intramolecular trans-OM "vectors". Here, we present a method to systematically assess the carrying capacity of candidate trans-OM vectors using a real-time luminescence assay ("SLALOM", Split Luciferase Assay for Live monitoring of Outer Membrane transit), reporting on periplasmic entry. We demonstrate the usefulness of our tools by constructing a 3800 Da chimeric compound composed of a constrained bicyclic peptide (Bicycle) with a periplasmic target, linked to an intramolecular peptide vector; the resulting chimera is a broad-spectrum inhibitor of pathogenic Gram-negative bacterial growth.

Identification and Optimization of EphA2-Selective Bicycles for the Delivery of Cytotoxic Payloads

Bicycles are constrained bicyclic peptides that represent a promising binding modality for use in targeted drug conjugates. A phage display screen against EphA2, a receptor tyrosine kinase highly expressed in a number of solid tumors, identified a number of Bicycle families with low nanomolar affinity. A Bicycle toxin conjugate (BTC) was generated by derivatization of one of these Bicycles with the potent cytotoxin DM1 via a cleavable linker. This BTC demonstrated potent antitumor activity in vivo but was poorly tolerated, which was hypothesized to be the result of undesired liver uptake caused by poor physicochemical properties. Chemical optimization of a second Bicycle, guided by structural biology, provided a high affinity, metabolically stable Bicycle with improved physicochemical properties. A BTC incorporating this Bicycle also demonstrated potent antitumor activity and was very well tolerated when compared to the initial BTC. Phage display selection followed by chemical optimization of Bicycles can deliver potent drug conjugates with favorable pharmaceutical properties.

Abstract 3257: Activation of CD137 using multivalent and tumor targeted Bicyclic peptides

CD137 (4-1BB/TNFRSF9) is a costimulatory T-cell receptor belonging to the TNF receptor superfamily. Agonistic anti-CD137 antibodies have shown potent, often curative anti-tumor activity in preclinical models. Two human anti-CD137 antibodies, urelumab and utomilumab are currently undergoing clinical testing. Urelumab has shown several single-agent, partial responses, but its use has been hampered by hepatoxicity, while utomilumab has shown little or no single agent activity.

Bicycles® are a new class of drugs - fully synthetic, constrained bicyclic peptides that combine the attributes of antibodies, small molecules, and peptides by delivering high affinity, selectivity, and rapid clearance. Their small size (1.5-2 kDa) delivers advantages in tumor penetration, and renal elimination may avoid the liver and GI toxicity often associated with other drug modalities, including certain antibodies. We hypothesized that fully synthetic Bicycle CD137 agonists with rapid clearance, minimal liver exposure and no Fc receptor interaction may induce CD137 mediated anti-tumor activity while avoiding liver toxicity.

A high affinity lead BCY3814 (KD ~30 nM) that binds to the CD137 ligand-binding site was identified. CD137 activation requires receptor crosslinking, thus multivalent binding would be expected to recapitulate the action of the natural trimeric ligand. We envisioned that CD137 agonism could be achieved directly by using multimeric CD137 Bicycles or in a tumor targeted fashion with bispecific or “heterotandem” Bicycles. The synthetic simplicity and highly modular nature of the Bicycle® platform enabled us to rapidly explore both formats.

To generate a “pure” CD137 agonist we synthesized >50 different multimeric variants of BCY3814 with chemical linkers of various lengths and rigidity and using different sites of attachments, while maintaining a compact size (<15 kDa). Tumor targeted CD137 agonists were generated as heterotandems, whereby BCY3814 is conjugated to a tumor antigen targeting Bicycle. In this design, the CD137 Bicycle only induces CD137 agonism after the molecule binds to a tumor cell with high receptor expression.

We discovered Bicycle multimers that exhibit a range of potencies in a cell-based CD137-dependent reporter assay, activate human T cells in vitro as indicated by increased cytokine release, and show biological activity in vivo. Bicycle heterotandems targeting Nectin-4 and EphA2 exhibited highly potent and tumor cell specific activity in both the cell-based reporter assay and the human T cell assay. Selected CD137 multimers and heterotandems are being tested further in humanized mouse models for T cell activation, anti-tumor activity, and liver safety. These molecules are promising, novel cancer immunotherapy candidates and importantly, they pave the way for development of synthetic agonists of other TNF receptors that can be targeted to the local tumor microenvironment.

Citation Format: Kristen E. Hurov, Punit Upadhyaya, Jessica Kublin, Xueyuan Zhou, Julia Kristensson, Rachid Lani, Gemma Mudd, Katerine van Rietschoten, Frank An, Johanna Lahdenranta, Liuhong Chen, Gavin Bennett, Kevin McDonnell, Peter Park, Nicholas Keen. Activation of CD137 using multivalent and tumor targeted Bicyclic peptides [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3257.

Abstract 5855: Bicycle Drug Conjugates targeting EphA2 for the treatment of solid tumors: Discovery and selection of BT5528

Ephrin receptor A2 (EphA2) is a member of the Ephrin receptor family of cell-cell junction proteins and is both highly overexpressed in several solid tumors and associated with poor prognosis in patients. Bicycles® are novel therapeutic agents: bicyclic peptides constrained via a chemical scaffold, which confer structural stability leading to high affinity and selectivity usually associated with antibodies. Bicycles can be elaborated to carry payloads to a specific target and their relatively small size (1.5-3 kDa) allows rapid tissue penetration and extravasation. Bicycle binders for EphA2 were identified using a proprietary phage display peptide technology consisting of highly diverse phage libraries of Bicycles. Initial screening identified Bicycle binders with high affinity for EphA2. EphA2 binding Bicycles were conjugated to cytotoxic payload via a cleavable linker to form a Bicycle Toxin Conjugate (BTC) and evaluated for EphA2 dependent cytotoxicity in vitro and in vivo. Efficacy was seen in EphA2-expressing xenograft models, but toxicity was seen at higher doses. These Bicycles were highly plasma protein bound, and relatively lipophilic. Visualization of Bicycle distribution by microPET showed localization to tumor, but with significant distribution to liver. Subsequent screening with a wider range of phage libraries and scaffolds identified Bicycle binders with alternate structures, lower PPB and lipophilicity. Crystal structures of these Bicycles bound to EphA2 enabled rational design to enhance potency and drug-like properties. Visualization of bio-distribution of these optimised Bicycles by microPET showed localization to tumor, with negligible localization to liver and renal clearance. A range of Bicycle Toxin Conjugates were produced by linking bicycle binders to cleavable linkers and toxin payloads. A series of BTCs were developed with DM1 payload, with linkers ranging from uncleavable to unhindered disulfide. Similarly, a series of BTCs were developed with MMAE payload, using uncleavable linker and a variety of cleavable peptidic linkers with different enzyme sensitivity. Binding affinity is maintained to EphA2 protein and cells expressing EphA2. BTC efficacy was evaluated in EphA2-expressing xenograft models, initially the HT-1080 fibrosarcoma model, but also MDA-MB-231 triple-negative breast cancer and NCI-H1975 lung cancer models. Efficacy was seen from 1mg/kg qw and complete regression of tumors from 2 weeks dosing at 2mg/kg qw. No efficacy was seen in xenograft models without EphA2 expression (eg MOLP-8).From >75 BTCs evaluated, BT5528 was chosen as a candidate molecule to progress to in-depth preclinical profiling. The development of Bicycle Toxin Conjugates against EphA2 allows fast and efficient targeting of solid tumors while sparing non-tumor tissues.

Citation Format: Gavin Bennett, Philip Huxley, Amy Brown, Gemma Mudd, Katerine van Rietschoten, Silvia Pavan, Liuhong Chen, Sophie M. Watcham, Peter U. Park, Nicholas Keen. Bicycle Drug Conjugates targeting EphA2 for the treatment of solid tumors: Discovery and selection of BT5528 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5855.

Abstract 5144: BT1718, a novel bicyclic peptide-maytansinoid conjugate targeting MT1-MMP for the treatment of solid tumors: Design of bicyclic peptide and linker selection

Bicycles® are novel binding agents comprising small bicyclic peptides (1.5-3 KDa) constrained via a chemical scaffold, selected for high affinity and selectivity to targets of interest. MT1 (MMP14/MT1-MMP) is a membrane-associated metalloprotease overexpressed in many solid tumours and is implicated in tumor invasion and metastasis. MT1 expression positively correlates with poor prognosis.

Phage libraries containing 1015 unique peptide sequences were post-translationally cyclized with thiol-reactive scaffold and used in an optimized, high-throughput selection process to identify Bicycles® to the hemopexin domain of MT1. Additional iterative rounds of directed phage based screening were used to optimize affinity and off-phage non-natural amino acids were introduced at select positions to improve plasma stability to generate the lead Bicycle binder. The lead anti-MT1 Bicycle was further modified with a sarcosyl spacer to form N241. N241 binds specifically to the hemopexin domain of MT1 with a Kd of approximately 2 nM with no binding observed to the catalytic domain of the protease nor to any of the related MMP family members tested. Importantly and in contrast to most antibodies, N241 binds with similar affinity to MT1 from multiple species including rodent, dog and non-human primate.

Since the expected rapid tumor penetration and specific binding of these small peptidyl-binders makes them ideal for use in targeted delivery approaches, a series of Bicycle drug conjugates (BDCs) were prepared; N241 was conjugated to potent maytansinoid cytotoxics via linkers which varied in their cleavability. Though all the BDCs maintained high affinity for MT1, efficacy toward MT1-positive human tumor mouse xenografts varied with linker stability. BDCs with the most stable linkers were the least active suggesting that optimal tumor activation was obtained with linkers that could be cleaved more rapidly. Due to the rapid clearance and limited systemic exposure of these small-targeting BDCs, only the most labile linker showed toxicity in the mouse studies. Of the BDCs tested, BT1718, composed of N241 and DM1 conjugated via the SPP linker, demonstrated an optimal therapeutic index. Potent anti-tumor efficacy with BT1718 was observed across a panel of MT1-positive xenografts with complete tumor regressions observed in most models at doses that were well tolerated. In one example, HT-1080 fibrosarcoma subcutaneous xenografts were intraveneously treated with BT1718 when the tumor size had reached approximately 180 mm3. BT1718 given at 3 mg/kg once a week resulted in tumor stasis while BT1718 given at 10 mg/kg once a week or 3 mg/kg twice a week induced complete regression.

In summary, BT1718, a highly active, targeted drug conjugate with unique pharmacological properties is a promising therapeutic candidate for the treatment of MT1-MMP-positive solid tumors.

Citation Format: Helen Harrison, Gavin Bennett, Diane Blakeley, Amy Brown, Spencer Campbell, Liuhong Chen, Robert J. Lutz, Silvia Pavan, Katerine van Rietschoten, Daniel Teufel, Peter U. Park, Kevin Lee. BT1718, a novel bicyclic peptide-maytansinoid conjugate targeting MT1-MMP for the treatment of solid tumors: Design of bicyclic peptide and linker selection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5144. doi:10.1158/1538-7445.AM2017-5144