Open Access

Show Abstract ▼

Abstract: Constrained bicyclic peptides (Bicycle molecules) with high affinity for biological targets have emerged as potentially powerful therapeutic agents, particularly for the in vivo targeting of cancer receptors. However, their antibody-mimetic properties have yet to be explored for use in diagnostic immunoassays. These synthetically derived compounds serve as biorecognition scaffolds that allow for facile site-selective modification and large-scale production. A phage display screen against various constructs of the SARS-CoV-2 nucleocapsid (N) protein identified several Bicycle molecules with binding affinities ranging from the micromolar to the low nanomolar range. These Bicycle molecules were validated in the development of enzyme- and nanozyme-linked immunosorbent assays, as well as enzymatic and colorimetric nanoparticle-based lateral flow immunoassays (LFIA) for the detection of ultralow concentrations of the SARS-CoV-2 N protein. We envision that these moieties enable robust, cost-effective, and large-scale development of ultrasensitive biosensors for a diverse range of biomarkers by leveraging their high binding affinity, minimalistic scaffold, and synthetic accessibility.

Open Access

Show Abstract ▼

Abstract: Fragment-based drug design offers multiple routes to advance from fragments. One approach is to build structure-activity relationships (SAR) from analogue series in direct-to-biology workflows. Analogues can be prepared by automated chemistry and tested as crude reaction mixtures (CRMs) without purification, but assay noise often leads to hit resynthesis, potentially discarding false negatives and reducing SAR dataset size. High-throughput (HT) X-ray crystallography has the potential to address these issues by resolving hits directly from 100s–1000s of CRMs. However, no systematic analytics exist for extracting SAR models from HT crystallographic evaluation of CRMs. Here, we demonstrate that crystallographic SAR (xSAR) can be extracted from CRMs evaluated via HT X-ray crystallography. We developed a simple rule-based ligand scoring scheme that identifies conserved chemical features associated with crystallographic binding and non-binding. Applied to a crystallographic dataset of 957 fragment elaborations in CRMs targeting PHIP(2), a therapeutically relevant bromodomain, our xSAR model demonstrated effectiveness in two proof-of-concept experiments. First, it recovered 26 missed binders in the initial dataset (false negatives), doubling the hit rate and denoising the dataset. Second, it enabled a prospective virtual screen that identified novel hits with informative chemistries and measurable binding affinities. This work establishes a proof-of-concept that xSAR models can be directly extracted from large-scale crystallographic readouts of CRMs, offering a valuable methodology to build SAR models and accelerate design-make-test iterations without requiring CRM hit resynthesis and confirmation. This invites future work to utilise advanced analytics and modelling techniques to further strengthen purification-agnostic workflows.

Open Access

Show Abstract ▼

Abstract: TRF1 is a subunit of the shelterin complex that binds to and protects the linear ends of chromosomes known as telomeres. Both genetic deletion and chemical inhibition of TRF1 have been shown to block the growth of lung carcinoma, glioblastoma, and renal cell carcinoma in mice without affecting mouse survival or tissue function, making TRF1 a potential therapeutic target in cancer1,2,3. Here, we report the discovery of a series of fragment hits that bind at the interface between the TRFH domain of TRF1 (TRF1TRFH) and a peptide of TIN2 (TIN2TBM), an interaction essential for the recruitment of TRF1 to shelterin, using X-ray crystallography (XChem) and ligand-observed NMR (LO-NMR) fragment screening. We discovered a first-in-class inhibitor of the TRF1:TIN2 interaction (compound 40) that binds to TRF1TRFH with a KD of 29 µM (95% CI: 20–41 µM), displaces a TIN2 probe with an IC50 of 67 µM (95% CI: 10–120 µM), and expels TRF1 from purified shelterin. Aided by a novel crystal system of TRF1TRFH, we characterised fragments binding in a hotspot at the TRF1:TIN2 interface; these will serve as a starting point for the structure-guided development of potent inhibitors of TRF1 protein:protein interactions to disrupt shelterin complex assembly.

Open Access

Show Abstract ▼

Abstract: The hydrophobic effect is a central force in molecular recognition, typically attributed to the ordering of water molecules around apolar groups. Hydrophobic interaction sites on proteins are therefore readily predicted based on surface polarity. Yet, in the bromodomain-containing protein 4 (BRD4), a well-known hydrophobic hot spot is paradoxically lined by a network of water molecules. Here we combine binding assays, structural data, molecular dynamics, and free-energy calculations to resolve this apparent contradiction. We show that the water network functions as a hydrophobic recognition motif that cannot accommodate polar groups without disruption. Instead, as the protein pre-organizes the water network, apolar groups can bind with minimal entropic cost. In turn, they reinforce the surrounding hydrogen-bond network, limiting the mobility of the entire protein–water assembly. With this perspective, we identify water networks potentially functioning as hydrophobic motifs in other pharmacological targets, revealing a general but overlooked recognition element with broad implications in drug discovery and protein design.

Show Abstract ▼

Abstract: Werner (WRN) helicase, has emerged as a promising therapeutic target for cancers associated with microsatellite instability (MSI). This letter describes the discovery of small molecule inhibitors from a fragment screen that occupy a cryptic, allosteric site of WRN helicase. Key findings include the identification of benzimidazole and amino-indazole scaffolds, exploiting their proximity to Cys727 via covalent modification. The use of our proprietary co-folding model DragonFold assisted the identification of novel WRN helicase inhibitors. These, together with near-neighbor profiling, offer tools for furthering the understanding of WRN and BLM helicase function, and potential therapeutic avenues for MSI-associated cancers.