Portrait of Professor David Brown

Professor David Brown

Professor of Structural Biology

About

David joined the School of Biosciences in October 2011. He obtained his first degree in Biophysics at the University of Leeds in 1998 and then went on to study for his PhD in Structural Biology at the Institute of Cancer Research studying drug/DNA interactions. David then was awarded an SERC personal fellowship to focus on drug discovery at Kings College University of London where he worked on structural studies of complexes of inhibitors of Thymidine Kinase from Herpes Simplex Virus.
He then spent 15 years at Pfizer working on a large number of drug discovery programmes for a wide range of disease areas including Cardiovascular, Tissue Repair, Sexual Health, Allergy and Respiratory, Antifungals, Antivirals. David became Director of Structural Biology and Biophysics Group which utilised techniques such as NMR, X-ray crystallography, Mass Spectrometry, ITC and SPR to investigate protein structure and function and elucidate mode of action of ligand binding. During his time at Pfizer David solved the first structure of a Phosphodiesterase (PDE5 – the biological target of Viagra) which was a novel enzyme class to understand the function, mechanism and modes of inhibition. David is a member of the Protein Form and Function Group.
ORCID ID:0000-0003-4605-4779

Research interests

David's research is focussed on Structure, function and mechanism of protein inhibition for drug targets, in particular phosphodiesterases and kinases 

Professional

  • Fellow of the Royal Society of Chemistry 
  • British Crystallographic Association 
  • Co-Founder of CANGENX (a Structural Biology and Biophysics CRO) 
  • CCP4 Executive Committee 
  • Chair of MXWG (Macromolecular Crystallography Working Group ) for DIAMOND 

Publications

Article

  • Sijm, M. et al. (2019). Phenyldihydropyrazolones as Novel Lead Compounds Against Trypanosoma cruzi. ACS Omega [Online] 4:6585-6596. Available at: https://doi.org/10.1021/acsomega.8b02847.
    As over 6 million people are infected with Chagas disease and only limited therapeutic options are available, there is an urgent need for novel drugs. The involvement of cyclic nucleotide phosphodiesterases (PDE) in the lifecycle and biological fitness of a number of protozoan parasites has been described and several of these enzymes are thought to be viable drug targets. Within this context, a PDE-focused library was screened for its ability to affect the viability of Trypanosoma cruzi parasites. 5-(3-(Benzyloxy)-4-methoxyphenyl)-2-isopropyl-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one (4), previously reported as a human PDE4 inhibitor, was identified as a hit. Upon optimization on three positions of the phenylpyrazolone scaffold, 2-isopropyl-5-(4-methoxy-3-(pyridin-3-yl)phenyl)-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one (34) proved to be the most active compound against intracellular forms of T. cruzi (pIC50 = 6.4) with a 100-fold selectivity with respect to toxicity toward human MRC-5 cells. Evaluation on different life stages and clinically relevant T. cruzi strains revealed that the phenylpyrazolones are not active against the bloodstream form of the Y strain but show submicromolar activity against the intracellular form of the Y- and Tulahuen strains as well as against the nitro-drug-resistant Colombiana strain. In vitro screening of phenylpyrazolones against TcrPDEB1, TcrPDEC, and TcrCYP51 showed that there was a poor correlation between enzyme inhibition and the observed phenotypic effect. Among the most potent compounds, both TcrCYP51 and non-TcrCYP51 inhibitors are identified, which were both equally able to inhibit T. cruzi in vitro.
  • Blaazer, A. et al. (2018). Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. Journal of Medicinal Chemistry [Online] 61:3870-3888. Available at: https://doi.org/10.1021/acs.jmedchem.7b01670.
    Several trypanosomatid cyclic nucleotide phosphodiesterases (PDEs) possess a unique, parasite-specific cavity near the ligand-binding region that is referred to as the P-pocket.
    One of these enzymes, Trypanosoma brucei PDE B1 (TbrPDEB1), is considered a drug target for the treatment of African sleeping sickness. Here, we elucidate the molecular
    determinants of inhibitor binding and reveal that the P-pocket is amenable to directed design. By iterative cycles of design, synthesis, and pharmacological evaluation and by elucidating the structures of inhibitor-bound TbrPDEB1, hPDE4B, and hPDE4D complexes, we have developed 4a,5,8,8a-tetrahydrophthalazinones as the first selective TbrPDEB1 inhibitor series. Two of these, 8 (NPD-008) and 9 (NPD-039), were potent (Ki = 100 nM) TbrPDEB1 inhibitors with antitrypanosomal effects (IC50 = 5.5 and 6.7 ?M, respectively). Treatment of parasites with 8 caused an increase in intracellular cyclic adenosine monophosphate (cAMP) levels and severe disruption of T. brucei cellular organization, chemically validating trypanosomal PDEs as therapeutic targets in trypanosomiasis.
  • Whitewood, A. et al. (2018). Chlamydial virulence factor TarP mimics talin to disrupt the talin-vinculin complex. FEBS Letters [Online] 592:1751-1760. Available at: https://doi.org/10.1002/1873-3468.13074.
    Vinculin is a central component of mechanosensitive adhesive complexes that form between cells and the extracellular matrix. A myriad of infectious agents mimic vinculin binding sites (VBS), enabling them to hijack the adhesion machinery and facilitate cellular entry. Here, we report the structural and biochemical characterisation of a VBS from the chlamydial virulence factor TarP. Whilst the affinities of isolated VBS peptides from TarP and talin for vinculin are similar, their behaviour in larger fragments is markedly different. In talin, VBS are cryptic and require mechanical activation to bind vinculin, whereas the TarP VBS are located in disordered regions, and so are constitutively active. We demonstrate that the TarP VBS can uncouple talin:vinculin complexes, which may lead to adhesion destabilisation.
  • Lawrence, A. et al. (2018). Construction of Fluorescent Analogs to Follow the Uptake and Distribution of Cobalamin (Vitamin B 12 ) in Bacteria, Worms, and Plants. Cell Chemical Biology [Online]. Available at: https://doi.org/10.1016/j.chembiol.2018.04.012.
    Vitamin B12 is made by only certain prokaryotes yet is required by a number of eukaryotes
    such as mammals, fish, birds, worms and Protista, including algae. There is still much to learn
    about how this nutrient is trafficked across the domains of life. Herein, we describe ways to
    make a number of different corrin analogues with fluorescent groups attached to the main
    tetrapyrrole-derived ring. A further range of analogues were also constructed by attaching
    similar fluorescent groups to the ribose ring of cobalamin, thereby generating a range of
    complete and incomplete corrinoids to follow uptake in bacteria, worms and plants. By using
    these fluorescent derivatives we were able to demonstrate that Mycobacterium tuberculosis
    is able to acquire both cobyric acid and cobalamin analogues, that Caenorhabditis elegans
    takes up only the complete corrinoid, and that seedlings of higher plants such as Lepidium
    sativum are also able to transport B12.
  • Skerratt, S. et al. (2016). The Discovery of a Potent, Selective, and Peripherally Restricted Pan-Trk Inhibitor (PF-06273340) for the Treatment of Pain. Journal of Medicinal Chemistry [Online] 59:10084-10099. Available at: http://doi.org/10.1021/acs.jmedchem.6b00850.
    The neurotrophin family of growth factors, comprised of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4), is implicated in the physiology of chronic pain. Given the clinical efficacy of anti-NGF monoclonal antibody (mAb) therapies, there is significant interest in the development of small molecule modulators of neurotrophin activity. Neurotrophins signal through the tropomyosin related kinase (Trk) family of tyrosine kinase receptors, hence Trk kinase inhibition represents a potentially “druggable” point of intervention. To deliver the safety profile required for chronic, nonlife threatening pain indications, highly kinase-selective Trk inhibitors with minimal brain availability are sought. Herein we describe how the use of SBDD, 2D QSAR models, and matched molecular pair data in compound design enabled the delivery of the highly potent, kinase-selective, and peripherally restricted clinical candidate PF-06273340.
  • Adams, P. et al. (2016). Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure [Online] 24:502-508. Available at: http://dx.doi.org/10.1016/j.str.2016.02.017.
    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent
    an important source of information concerning drug-target interactions, providing atomic level insights
    into the physical chemistry of complex formation between macromolecules and ligands. Of the
    more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ~75% include at least one non-polymeric
    ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug
    discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across
    the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic
    Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop
    held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015.
    Experts in protein crystallography from academe and industry came together with non-profit and for-profit
    software providers for crystallography and with experts in computational chemistry and data archiving to
    discuss and make recommendations on best practices, as framed by a series of questions central to structural
    studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived
    in the PDB? How should the ligands be best represented? How should structural models of macromoleculeligand
    complexes be validated? What supplementary information should accompany publications of structural
    studies of biological macromolecules? Consensus recommendations on best practices developed in
    response to each of these questions are provided, together with some details regarding implementation.
    Important issues addressed but not resolved at the workshop are also enumerated.
  • Jones, P. et al. (2016). Design and Synthesis of a Pan-Janus Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin. Journal of Medicinal Chemistry [Online] 60:767-786. Available at: http://dx.doi.org/10.1021/acs.jmedchem.6b01634.
    By use of a structure-based computational method for identification of structurally novel Janus kinase (JAK)
    inhibitors predicted to bind beyond the ATP binding site, a potent series of indazoles was identified as selective pan-JAK
    inhibitors with a type 1.5 binding mode. Optimization of the series for potency and increased duration of action commensurate
    with inhaled or topical delivery resulted in potent pan-JAK inhibitor 2 (PF-06263276), which was advanced into clinical studies
  • Palmer, D. et al. (2014). The structure, function and properties of sirohaem decarboxylase - an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Molecular Microbiology [Online] 93:247-261. Available at: http://dx.doi.org/10.1111/mmi.12656.
  • Deery, E. et al. (2012). An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nature Chemical Biology [Online] 8:933-940. Available at: http://dx.doi.org/10.1038/nchembio.1086.
    The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B 12) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.
  • Hughes, S. et al. (2011). Fragment based discovery of a novel and selective PI3 kinase inhibitor. Bioorganic & Medicinal Chemistry Letters [Online] 21:6586-6590. Available at: http://dx.doi.org/10.1016/j.bmcl.2011.07.117.
    We report the use of fragment screening and fragment based drug design to develop a PI3? kinase fragment hit into a lead. Initial fragment hits were discovered by high concentration biochemical screening, followed by a round of virtual screening to identify additional ligand efficient fragments. These were developed into potent and ligand efficient lead compounds using structure guided fragment growing and merging strategies. This led to a potent, selective, and cell permeable PI3? kinase inhibitor with good metabolic stability that was useful as a preclinical tool compound.
  • Phillips, C. et al. (2011). Design and Structure of Stapled Peptides Binding to Estrogen Receptors. Journal of the American Chemical Society [Online] 133:9696-9699. Available at: http://dx.doi.org/10.1021/ja202946k.
    Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor–stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.
  • Luban, J. et al. (2010). HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention. PLoS Pathogens [Online] 6:e1001220. Available at: http://dx.doi.org/10.1371/journal.ppat.1001220.
    Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We report a new class of small molecule antiretroviral compounds that directly target HIV-1 capsid (CA) via a novel mechanism of action. The compounds exhibit potent antiviral activity against HIV-1 laboratory strains, clinical isolates, and HIV-2, and inhibit both early and late events in the viral replication cycle. We present mechanistic studies indicating that these early and late activities result from the compound affecting viral uncoating and assembly, respectively. We show that amino acid substitutions in the N-terminal domain of HIV-1 CA are sufficient to confer resistance to this class of compounds, identifying CA as the target in infected cells. A high-resolution co-crystal structure of the compound bound to HIV-1 CA reveals a novel binding pocket in the N-terminal domain of the protein. Our data demonstrate that broad-spectrum antiviral activity can be achieved by targeting this new binding site and reveal HIV CA as a tractable drug target for HIV therapy.
  • Owen, D. et al. (2009). Identification, synthesis and SAR of amino substituted pyrido[3,2b]pyrazinones as potent and selective PDE5 inhibitors. Bioorganic & Medicinal Chemistry Letters [Online] 19:4088-4091. Available at: http://dx.doi.org/10.1016/j.bmcl.2009.06.012.
  • Palmer, M. et al. (2007). Design of second generation phosphodiesterase 5 inhibitors. Current Topics in Medicinal Chemistry [Online] 7:405-419. Available at: http://dx.doi.org/10.2174/156802607779941288.
    The clinical significance of phosphodiesterase 5 (PDE5) inhibition is increasingly understood following the pioneering work with sildenafil, and the continuing development programmes for both sildenafil and other marketed inhibitors. Since the initial launch of sildenafil for male erectile dysfunction (MED), approval has now been granted for treatment of pulmonary hypertension, whilst ongoing studies have indicated the potential of PDE5 inhibition for the treatment of a range of additional indications including cardioprotection, memory retention and diabetes. Many of these additional indications are best suited to chronic oral dosing and emphasise the need for highly selective inhibitors with extended duration of action. This article will focus on a research programme aimed at the discovery of improved second-generation PDE5 inhibitors. Essential features of these new PDE5 inhibitors would be enhanced selectivity across the whole PDE family and pharmacokinetics compatible with once daily dosing. Key elements used in this programme are high throughput screening (HTS), exploitation of co-crystal structural information for bound inhibitor in the PDE5 active site, and employment of parallel chemistry to speed progress. Under the guidance of co-crystal structural information, a non-selective HTS hit with poor physicochemistry was initially modified using parallel chemistry to give a lead compound (3) that established a new PDE5 inhibitor series. Notably, (3) displayed physicochemistry compatible with a long plasma half-life, and wide chemical scope. Subsequent optimisation of (3) using crystal structure information to guide design, led rapidly to highly potent and selective PDE5 inhibitors (47, 50). Continued focus on physical properties through ligand efficiency evaluation and lipophilicity (cLogP), maintained the inherently desirable physicochemistry of the initial lead.
  • Fish, P. et al. (2007). Selective Urokinase-Type Plasminogen Activator Inhibitors. 4. 1-(7-sulfonamidoisoquinolinyl)guanidines. Journal of Medicinal Chemistry [Online] 50:2341-51. Available at: http://dx.doi.org/10.1021/jm061066t.
    1-isoquinolinylguanidines were previously disclosed as potent and selective inhibitors of urokinase-type plasminogen activator (uPA). Further investigation of this template has revealed that incorporation of a 7-sulfonamide group furnishes a new series of potent and highly selective uPA inhibitors. Potency and selectivity can be achieved with sulfonamides derived from a variety of amines and is further enhanced by the incorporation of sulfonamides derived from amino acids. The binding mode of these 1-isoquinolinylguanidines has been investigated by X-ray cocrystallization studies. uPA inhibitor 26 was selected for further evaluation based on its excellent enzyme potency (Ki 10 nM) and selectivity profile (4000-fold versus tPA and 2700-fold versus plasmin). In vitro, compound 26 is able to inhibit exogenous uPA in human chronic wound fluid (IC50=0.89 microM). In vivo, in a porcine acute excisional wound model, following topical delivery, compound 26 is able to penetrate into pig wounds and inhibit exogenous uPA activity with no adverse effect on wound healing parameters. On the basis of this profile, compound 26 (UK-371,804) was selected as a candidate for further preclinical evaluation for the treatment of chronic dermal ulcers.
  • Bunnage, M. et al. (2007). Discovery of potent & selective inhibitors of activated thrombin-activatable fibrinolysis inhibitor for the treatment of thrombosis. Journal of Medicinal Chemistry [Online] 50:6095-6103. Available at: http://dx.doi.org/10.1021/jm0702433.
    Thrombin-activatable fibrinolysis inhibitor (TAFI) has emerged as a key link between the coagulation and fibrinolysis cascades and represents a promising new target for the treatment of thrombosis. A novel series of imidazolepropionic acids has been designed that exhibit high potency against activated TAFI (TAFIa) and excellent selectivity over plasma carboxypeptidase N (CPN). Structure activity relationships suggest that the imidazole moiety plays a key role in binding to the catalytic zinc of TAFIa, and this has been supported by crystallographic studies using porcine pancreatic carboxypeptidase B as a surrogate for TAFIa. The SAR program led to the identification of 21 (TAFIa Ki = 10 nM, selectivity TAFIa/CPN > 1000) as a candidate for clinical development. Compound 21 exhibited antithrombotic efficacy in a rabbit model of venous thrombosis, yet had no effect on surgical bleeding in the rabbit. In addition, 21 exhibited an excellent preclinical and clinical pharmacokinetic profile, characterized by paracellular absorption, low clearance, and a low volume of distribution, fully consistent with its physicochemical properties of low molecular weight (MW = 239) and high hydrophilicity (log D = -2.8). These data indicate 21 (UK-396,082) has potential as a novel TAFIa inhibitor for the treatment of thrombosis and other fibrin-dependent diseases in humans.
  • O'Brien, S. et al. (2005). Computational Tools for the Analysis and Visualization of Multiple Protein-Ligand Complexes. Journal of Molecular Graphics and Modelling [Online] 24:186-194. Available at: http://dx.doi.org/10.1016/j.jmgm.2005.08.003.
    Modern methods in genomics and high-throughput crystallography have ensured that we have access to a large and rapidly increasing, number of X-ray structures of protein-ligand complexes. A structure-based approach to drug design aims to exploit this information, but current methods are not suited to the examination of the large numbers of complexes available. We present computational tools that analyse and display multiple protein-ligand interactions and their properties in a simplified way. We illustrate how a novel binding-mode similarity metric is able to cluster 20 ligands complexed to HIV-1 reverse transcriptase into distinct groups. The properties of each cluster are then projected onto a group surface as a series of color gradients. Analysis of these surfaces reveals fundamental similarities and differences in the binding modes of these diverse compounds. In addition, the simplicity of the surface representations facilitates the transfer of information between the crystallographer, computational chemist and the chemist. We also show how two- and three-dimensional (2- and 3-D) similarities can be combined to provide enhanced understanding of 33 factor Xa inhibitor complexes. This methodology has enabled us to identify pharmaceutically relevant relationships between ligands and their binding modes that had previously been hidden in a wealth of data.
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