BICYCLES® - KEY PROPERTIES

Bicycles are highly constrained bicyclic peptides, typically between 9 and 15 amino acids in size. The structural constraint, delivered using a variety of proprietary molecular scaffolds, results in molecules with antibody-like target specificity and high affinity as demonstrated by the company’s generation of multiple molecules with sub-nanomolar affinity against diverse targets and target classes (including: enzymes, proteases, receptors, GPCRs, surface ligands and secreted proteins). Indeed, many target classes of high biological and commercial interest previously thought intractable to a selective small molecule approach, such as the metalloproteases, serine proteases and interleukins have been selectively drugged using Bicycles. In contrast to antibodies, Bicycles also generally exhibit cross-species activity, which allows a more precise extrapolation from efficacy and toxicology experiments. Bicycles present a large surface area for binding (500–1000 Å2) allowing them to modulate protein-protein interactions. However, in contrast to antibodies, they have a low molecular weight (1.5–2 kDa), providing rapid and deep tissue penetration, and are likely to avoid the immunogenicity that is often problematic in antibody development. Bicycles have been defined as small molecules by the regulatory authorities, are chemically synthesised and highly soluble, providing manufacturing and formulation flexibility. Finally, as Bicycles are peptidic, they have “tuneable” pharmacokinetics and are cleared by the kidney thereby avoiding gastrointestinal and liver exposure with the risk of associated toxicity.

 
 

Bicycles combine the beneficial attributes of three other drug classes into a single modality to deliver therapies with unique properties

 
 

The video above models the molecular dynamics of an amino acid sequence as a linear peptide (left), as a monocycle (centre) and as a Bicycle (right). The greater constraint of the Bicycle results in the three amino acid side chains being more frequently presented to the target in the correct orientation for binding. This constraint provides Bicycles their antibody-like affinity and specificity.

BICYCLE® SCREENING PLATFORM

The cornerstone to Bicycle Therapeutics’ value proposition is its proprietary technology that enables the systematic cyclisation of peptides on the surface of phage with variable loop sizes to generate large, diverse phage display libraries comprising more than 10 15 unique Bicycles. The platform combines the power of evolution driven biological selection with the antibody-like affinity and selectivity conferred by the constraint of a chemical scaffold. Screening can be conducted against either isolated proteins or with whole cells expressing the target of interest.

 
 

Bicycles can generate vast chemical libraries that are screened via phage display following cyclisation of the initially linear peptides. Additional diversity and differential properties can also be derived from variations in scaffolding agent and in Bicycle loop size and format.

Bicycle Therapeutics has conducted over 80 screens and has successfully identified high potency Bicycles in 80% of these against a variety of targets many of which have been intractable to a small molecule approach, including cytokines, chemokines, enzymes, proteases and a diverse collection of cell surface receptors such as GPCRs, extracellular tethered enzymes and receptor tyrosine kinases. These screens have been performed on a diverse array of different scaffolding agents, which we have shown to deliver additional desirable properties to the Bicycle, including improved physicochemical properties and differential levels of structural constraint.

BICYCLE® screening process

 
 

The Bicycle screening process consists of multiple iterative rounds of phage selection combined with identification of the Bicycle using sequencing and a parallel functional assay to determine its binding and affinity.


A hugely diverse set of cyclised peptides is initially generated using phage display and subsequently incubated as phage-bound Bicycles with soluble target proteins or alternatively transfected cells can be substituted to screen integral membrane protein. Phage that bind to the target are recovered on a matrix and identification of the encoded Bicycle is via sequencing and, unique to this platform, a parallel functional assay is performed to determine binding affinity to inform structure relationship activities. The screening process, optimized over the course of many target campaigns, is highly efficient, rapid and progresses over multiple rounds of phage selections. During these selections, a vast and diverse chemical space is sampled from numerous phage libraries that are prioritised to represent a wide variety of binding motifs and pharmacophores. Subsequently, the chemical space is narrowed using evolved-selection to identify the most promising Bicycles by sequentially affinity maturing and re-randomizing the Bicycle libraries until high affinity high selectivity molecules are identified. The use of a functional binding assay is a key activity that differentiates our platform from other cyclic peptide companies, which use only mono-cyclized peptides and select these by simple abundance in the recovered target-binding fraction. By combining functional activity with the sequence information that encodes the Bicycle, informative structure activity relationships (SAR) are generated at every stage of our screening process. This allows rational redesign of bespoke target-specific libraries and their use in iterative rounds of evolution driven phage selection. In this stepwise iterative fashion we select, expand, and qualify chemical space, allowing us to efficiently identify high affinity binders and a core pharmacophore to the designated target.

 
Helix forming Bicycle with its peptide backbone shown as a ribbon and its core scaffold shown as sticks, bound to the ligand binding domain of a receptor tyrosine kinase, shown as a surface hydrophobicity plot.

Helix forming Bicycle with its peptide backbone shown as a ribbon and its core scaffold shown as sticks, bound to the ligand binding domain of a receptor tyrosine kinase, shown as a surface hydrophobicity plot.

 
Summary of Bicycle screening process

Summary of Bicycle screening process

Applications

Bicycles® can be developed to modulate single targets as stand-alone therapeutics (Bicycles), bind two targets where two Bicycles are coupled together (bispecific Bicycles), or deliver other molecular cargos (Bicycle Drug Conjugates® or BDCs, Bicycle Therapeutics’ initial focus). These cargos can include toxins, small molecules, biologics, radio-labelled ligands or nucleic acids.  

One advantage of identifying Bicycles attached to a large phage particle, is that this “molecular bulk” can be removed and replaced without changing the binding affinity of the Bicycle. Some of these applications of the Bicycle technology are illustrated below.

 

BICYCLES® CAN BE USED AS SIMPLE UNELABORATED STRUCTURES AS A NEW CLASS OF THERAPEUTICS

 
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BICYCLES® CAN ALSO BE USED TO GENERATE MORE COMPLEX MOLECULES

 
 
 
 
 
 
 
 

BICYCLES® CAN BE USED IN COMBINATION, OR WITH OTHER MOLECULAR CARGOES, TO DELIVER ADDITIONAL FUNCTIONALITY

 
 
 
 

Bicycle Therapeutics’ initial focus is on BDCs that selectively deliver payloads to tumours. The company is looking to explore its technology outside of oncology through partnerships, as exemplified by its existing collaborations with AstraZeneca in respiratory, cardiovascular and metabolic diseases and with ThromboGenics in ophthalmology.   

Publications

Phage-encoded combinatorial chemical libraries based on bicyclic peptides Nature Chemical Biology vol. 5, pp 502–507, 2009

Bicyclic peptides with optimized ring size inhibit human plasma kallikrein and its orthologues while sparing paralogous proteases ChemMedChem vol. 7, pp 1173–1176, 2012

 

PRESENTATIONS AT PREVIOUS MEETINGS


November 2016
28th EORTC-NCI-AACR MOLECULAR TARGETS AND CANCER THERAPEUTICS SYMPOSIUM, Munich Germany

-Development of BT1718, a Bicycle Drug Conjugate® (BDC) targeting MT1-MMP for treatment of solid tumours

-Design and characterization of a high affinity and selective bicyclic peptide binder to MT1-MMP for development of a treatment for solid tumours

 

July 2016
SMi’s 3rd annual Peptides event

-Development of cytotoxic bicyclic peptide drug conjugates and applications in molecular targeted cancer therapy

 

April 2016
3rd Annual Peptides Congress

-Development of Cytotoxic Bicyclic Peptide Drug Conjugates and Applications in Molecular Targeted Cancer Therapy

 

January 2016
Future of Healthcare Investor Forum

-Bicycle Therapeutics

 

Intellectual Property

The Bicycle patent estate covers many aspects of the screening platform, initially assigned from the U.K.’s Medical Research Council, plus many additional patents covering composition of matter and key concepts and applications of the Bicycle technology. Currently we have over 50 patents filed, granted or in preparation that covers various aspects of the platform and products.

 
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Summary of Bicycle technology and attributes of the platform covered by Bicycle IP estate.