SELECTBIO

Discovery Chemistry Congress 2015

The Translational Drug Discovery Group was established in 2011 at the University of Sussex to deliver both drug candidates into clinical development and novel chemical probes to enable validation of new therapeutic targets.  Our philosophy is to combine expertise in clinical and biological disease understanding with our pharma track record in drug discovery and development.  This presentation will exemplify our strategy and research in the areas of DNA damage repair pathways for oncology and ion channel modulators for neuroscience indications.  The approach will highlight both our use of structure-based drug design in both lead optimisation and identification and also our approach to hit finding for novel, challenging protein classes.

A Structured Approach to Academic Drug Discovery

The goal of performing bio-independent syntheses in biological environs, so called bioorthogonal chemistry, has inspired the search for novel biocompatible organic reactions for more than a decade and found a niche application as a labelling strategy to study biomolecules in their native state . While metal-free bioorthogonal reactions are considered optimal for living systems due to their biocompatibility, significant progress has been made in recent years by our group and others in the development of cell-tolerated bioorthogonal organometallic (BOOM) reactions, opening up new avenues for the exploitation of the bioorthogonal paradigm. However, the potential of such selective processes in medicine is yet to be determined. Based on the biocompatibility of metallic palladium (widely used, e.g., in dental restoration and jewelry) and its remarkable catalytic properties, our group investigates the use of heterogeneous palladium catalysis to enable site-specific conversion of cytotoxic prodrugs into its active form. As opposed to biolabile prodrugs, whose activation process relies on metabolic pathways, an efficient Pd0-activated prodrug therapy would be entirely dependent on the distinct catalytic properties of this metal and therefore the prodrug would remain intact in the absence of a Pd0 source. In this talk I will present the discovery of two palladium-mediated deprotections that take place under biocompatible conditions and their application as masking methods to suppress the activity of chemotherapeutic drugs, while enabling the bioorthogonal rescue of the drugs’ pharmacological properties by heterogeneous palladium chemistry in cancer cell culture.

Bioorthogonal Palladium-Labile Prodrugs for Site-Specific Anticancer Therapy

There is often a debate about just how useful fragments are for well-established conventional targets such as protein kinases. Fragment screening however can be extremely valuable, providing critical ideas that lead to novelty, demonstrating how to achieve selectivity, helping dissect and make the most of HTS and literature compounds, alongside maximising ligand efficiency.Finding fragments that bind to such targets is straight-forward. For most kinases, a screen of our 1350 member fragment library results in between 40 to 170 validated and chemically distinct hits. In addition, crystal structures for these hits bound to the kinase can usually be obtained quite rapidly. The real challenge is how to digest all this information and decide how and which fragments to progress in order to identify the highest quality leads. My presentation will illustrate the approach taken at Vernalis in some recent projects which led to the discovery of novel lead series for a number of different kinases. The main messages are that: fragments always tell you something new about the binding site; careful triage and exploration of fragment SAR can give indications of how to achieve selectivity, novelty and affinity;it is important to optimise the fragment before investing large chemistry resources and that with patience, a fragment derived series will often supersede an HTS derived series and deliver a better quality of compound for lead optimisation.

Choosing & Using Fragments in the Generation of Selective Kinase Inhibitors

The importance of synthesis of peptides warranted by the need for peptide-based medicines, the roles of peptides and foldamers in drug discovery, etc. Since its introduction by Merrifield, peptide synthesis was performed almost exclusively on solid supports. It has been applied for the synthesis of foldamers as well. However, still a general property of these methodologies are the high number of amino acid equivalents required for total coupling. Continuous-flow (CF) approaches have recently gained in significance among synthetic techniques. We show here that the number of amino acid equivalents used for SPPS can be lowered drastically to around 1.5 equivalents through the application of a CF technique and by complete reaction parameter optimization. Under the optimized conditions the couplings of all 20 proteinogenic amino acids with 1.5 amino acid equivalents proceeded with excellent conversions. To demonstrate the efficiency of the CF-SPPS methodology, known difficult sequences were synthetized in automated way. As further evidence of the effectiveness, ß-peptide foldamers with alicyclic side-chains were synthetized in excellent yields. Importantly, exotic and expensive artificial amino acids were incorporated into sequences by an automated way through the use of exceptionally low numbers of amino acid equivalents at low costs.

Development of a Packed Bed Reactor for the Synthesis of Peptides and Foldamers

Effective small molecule PPI blocker discovery using high fidelity DNA-encoded libraries and a low-noise homogeneous screening assay. The screen employs a unique principle of trapping small molecule binders together with the protein target in miniscule droplets.

Discovery of a Single Digit Nanomolar Small Molecule Blocker of a Protein-protein Interaction Target

The protein kinase MPS1 is a crucial component of the spindle assembly checkpoint signal and is aberrantly overexpressed in many human cancers. MPS1 is one of the top 25 genes overexpressed in tumours with chromosomal instability and aneuploidy; PTEN-deficient breast tumour cells are particularly dependent upon MPS1 for their survival making it a target of significant interest in oncology. In this talk I will present the discovery and optimization of potent and selective MPS1 inhibitors based on the 1H-pyrrolo[3,2-c]pyridine scaffold, guided by structure-based design and cellular characterization of MPS1 inhibition. Our research yielded the potent and selective chemical tool compound CCT251455, which stabilizes an inactive conformation of MPS1 with the activation loop ordered in a manner incompatible with ATP- and substrate peptide-binding. CCT251455 displays a favorable oral pharmacokinetic profile and shows dose-dependent inhibition of MPS1 in an HCT116 human tumor xenograft model. It is therefore an attractive tool compound to further elucidate the therapeutic potential of MPS1 inhibition.

Discovery of Potent and Selective Inhibitors of Monopolar Spindle 1 (MPS1) Kinase

The presented work deals with the development of a fragment based strategy for dual-target drug discovery. Here, we applied a modified self-organizing map algorithm for in silico recognition of molecular fragments binding two targets: 5-lipoxygenase and soluble epoxide hydrolase. The predicted properties were confirmed by complementary screening techniques: STD-NMR and enzyme assay. A variety of dual fragments active in both complementary assays could be obtained using self-organizing maps, which was optimized towards nanomolar inhibitory activity against both targets.

Fragment-based Approach to Multi-target Compounds

Protein-protein interaction surfaces are attractive yet challenging targets for disease intervention. We present strategies to combine rational design with in-vivo and in-vitro selection systems and implementing competitive and negative design aspects to simultaneously select for affinity and specificity. Using such a semi-rational evolutionary approach, we generated interfering peptides (iPEP) specifically directed against the coiled-coil interaction motif as found in transcription factors such as Jun, Fos, AF10 and MITF. Modifications such as photo-switchable iPEPs for external control of inhibitor activity and D-peptides for protease resistance will be discussed as well. Specific targeting of tumor cells and efficient cellular delivery has been implemented by a modular virus system based on the adeno-associated virus. 

Interfering Peptides Targeting Protein-Protein Interactions

The design and generation of peptides capable of mimicking the binding and/or functional sites of proteins, represents a promising strategy for the exploration and modulation of protein function through controlled interference with the underlying protein-ligand interactions.  We have recently designed a soluble synthetic peptide that functionally mimics the HIV-1 coreceptor CXCR4, which belongs to the family of seven-transmembrane GPCRs. This CXCR4 mimetic peptide, termed CX4-M1, presents the three extracellular loops (ECLs) of the receptor. In binding assays involving recombinant proteins, as well as in cellular infection assays, CX4-M1 was found to selectively recognize gp120 from HIV-1 strains that use CXCR4 for cellular entry (X4 tropic HIV-1). Furthermore, anti-HIV-1 antibodies modulate this interaction in a molecular mechanism related to that of their impact on the gp120-CXCR4 interaction. We could now show that the selectivity of CX4-M1 pertains not only to gp120 from X4 tropic HIV-1, but also to synthetic peptides presenting the V3 loops of these gp120 proteins. The V3 loop is thought to be an essential part of the coreceptor binding site of gp120 that contacts the second ECL of the coreceptor. We were able to experimentally confirm this notion in binding assays using substitution analogs of CX4-M1 and the V3 loop peptides, respectively, as well as in cellular infection assays.  These results demonstrate the feasibility of mimicking protein-protein interactions through peptide-peptide interactions, as well as the utility of these mimetic peptides to explore protein-protein interactions at the molecular level.

A Structured Approach to Academic Drug Discovery

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March 17, 2015

Discovery Chemistry Congress 2015

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