Chemogenomics for Drug Discovery: Clinical Molecules from Open Access Chemical Probes Cite This: RSC Chem
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RSC Chemical Biology View Article Online REVIEW View Journal | View Issue Chemogenomics for drug discovery: clinical molecules from open access chemical probes Cite this: RSC Chem. Biol., 2021, 2, 759 Robert B. A. Quinlan a and Paul E. Brennan *ab In recent years chemical probes have proved valuable tools for the validation of disease-modifying targets, facilitating investigation of target function, safety, and translation. Whilst probes and drugs often differ in their properties, there is a belief that chemical probes are useful for translational studies and can Received 27th January 2021, accelerate the drug discovery process by providing a starting point for small molecule drugs. This review Accepted 25th March 2021 seeks to describe clinical candidates that have been inspired by, or derived from, chemical probes, and DOI: 10.1039/d1cb00016k the process behind their development. By focusing primarily on examples of probes developed by the Structural Genomics Consortium, we examine a variety of epigenetic modulators along with other rsc.li/rsc-chembio classes of probe. Creative Commons Attribution 3.0 Unported Licence. Introduction catalysis.1–5 We have begun to better characterise the extra- catalytic roles of proteins and how these contribute to disease Progress in the understanding of cellular and disease biology pathology, whether as readers of epigenetic marks, as molecular has advanced our knowledge of protein function beyond solely chaperones, or scaffolding proteins. To that end, non-destructive means of target validation and investigation are useful to examine the precise role of a protein in a cellular process. a Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Where the use of RNA inhibition (RNAi) or CRISPR gene editing Old Road Campus, Oxford OX3 7FZ, UK. E-mail: [email protected] b Alzheimer’s Research (UK) Oxford Drug Discovery Institute, Nuffield Department of precludes this, chemical probes are an invaluable tool for rapid This article is licensed under a 6–8 Medicine, University of Oxford, Oxford, OX3 7FZ, UK onset, reversible, and domain specific protein inhibition. Open Access Article. Published on 26 March 2021. Downloaded 10/4/2021 1:16:57 PM. Robert Quinlan completed his Paul Brennan received his PhD MChem in Medicinal and Bio- in organic chemistry from the logical Chemistry (2016) at the University of California, Berkeley University of Edinburgh, during under the mentorship of Paul whichhespenttimeinthelabsof Bartlett working on synthetic Dr Nicolas Blanchard (Universite´ methodology for combinatorial de Strasbourg) and Professor Guy chemistry and synthesizing Lloyd-Jones FRS FRSE. He then inhibitors for new anti-bacterial joined the Synthesis for Biology targets. Following post-doctoral and Medicine Centre for Doctoral research with Steve Ley at Cam- Training (SBM CDT) at the bridge University, Paul returned University of Oxford. He began his to California to take a position at Robert B. A. Quinlan DPhil studies under the supervision Paul E. Brennan Amgen. After two years at Amgen, of Professor Paul Brennan in 2017, Paul accepted a position as working on the development of small molecule epigenetic modulators medicinal chemistry design lead at Pfizer in Sandwich, UK. In for the treatment of neurodegenerative diseases. 2011 Paul joined the Structural Genomics Consortium at the University of Oxford, before becoming Professor of Medicinal Chemistry for the Centre for Medicines Discovery and head of chemistry of the Alzheimer’s Research UK Oxford Drug Discovery Institute. His research is focused on drug discovery for dementia and on finding small molecule chemical probes for unexplored protein families. © 2021 The Author(s). Published by the Royal Society of Chemistry RSC Chem. Biol., 2021, 2, 759–795 | 759 View Article Online Review RSC Chemical Biology They permit the evaluation of a particular role a protein plays, drug-likeness with drugs distributed around a score of one, and whilst leaving other interactions intact. In combination with non-drugs at zero.14 techniques such as RNAi, they paint a complete picture of a protein’s role within a cell.7 Chemical probes are defined by four main criteria:6,9,10 BET bromodomains 1. A minimal in vitro potency of less than 100 nM. 2. Greater than 30-fold selectivity over sequence-related proteins. Bromodomains (BRDs) are a class of epigenetic reader domains 15 3. Profiled against an industry standard selection of pharmaco- that recognise acetylated lysine (KAc) residues, a reversible logically relevant targets. post-translational modification with a key role in regulating 16 4. On-target cellular effects at greater than 1 mM. transcription. A subset of BRDs have also been shown to recognise 17,18 Their utility in interrogating the function of a protein and propionylated, butyrylated, and crotonylated lysines, demon- thus its relevance11 as a drug target has led a consortium of strating the importance of these domains in interpreting the industrial and academic researchers to establish a collaboration chromatin landscape. Evolutionarily conserved, they form part 19 for the development of probes for the entire proteome.12 Target of diverse nuclear proteins and complexes. The bromo- and 2035 aims to translate the advances made in genomics13 to extra C-terminal (BET) subfamily of bromodomains is perhaps 4,20,21 advances in the clinic, specifically new small-molecules for the the best studied and validated in a disease context. Its treatment of disease. One advantage of chemical probes often members (BRD2, BRD3, BRD4, and BRDT) have been implicated touted is that they are more likely to mimic the pharmacology of in a variety of disease processes, including cancer, viral infection, 22–25 a drug.7 Whilst not designed with drug-like characteristics in and inflammation. mind (for example absorption, distribution, metabolism, and excretion (ADME) properties),7 there is nevertheless a belief that The probe: (+)-JQ1 probes can provide a small-molecule starting point to accelerate Disclosed just months apart, the first pan-BET inhibitors (+)-JQ126 27 Creative Commons Attribution 3.0 Unported Licence. the drug discovery process. In this review, we highlight some and I-BET762 (Fig. 1) represented key milestones in the targeting small-molecule chemical probes that have both inspired and of BET proteins. Inspired by a triazolothienodiazepine scaffold mirrored clinical candidates, with a focus on epigenetic modulators. patented in 2009,28 (+)-JQ1 was developed following molecular We describe the target and development of the probe itself, the modelling of potential ligands against the bromodomain of BRD4. medicinal chemistry optimisation that led to the eventual clinical It was a potent inhibitor of both bromodomains of BRD4 candidate. We also include an estimate of the relative drug-likeness (KD(BRD4(1)) = 50 nM, KD(BRD4(2)) = 90 nM by isothermal of each compound calculated using the Molsoft drug-likness and titration calorimetry (ITC)), with similar potency against both molecular property prediction tool. A higher score indicates greater bromodomains of BRD3. It showed approximately three-fold This article is licensed under a Open Access Article. Published on 26 March 2021. Downloaded 10/4/2021 1:16:57 PM. Fig. 1 Chemical probe (+)-JQ1 and structurally derived clinical candidates: I-BET762, OTX015,andCPI-0610. Their potency against relevant BET bromodomains is presented, along with pharmacokinetic (PK) data where available, and their clinical status. Also included is a relative drug-likeness score to highlight the changes in drug-likeness moving from probe to drug. a PO = per os, by mouth. b QD = quaque die, once daily. c Assume 70 kg bodyweight for humans. 760 | RSC Chem. Biol., 2021, 2, 759–795 © 2021 The Author(s). Published by the Royal Society of Chemistry View Article Online RSC Chemical Biology Review weaker binding against BRD2 and BRDT. Pan-BET inhibition assays and was selective against other representative bromo- using (+)-JQ1 has shown anti-proliferative effects against a domains. It induced growth inhibition in in vivo models of multitude of haematological and solid malignancies, including nuclear protein in testis (NUT) midline carcinoma,44 MM,45 and breast,29,30 colorectal,31 and brain cancers,32,33 as well as multiple prostate cancer.46 In 2012, I-BET762 was advanced to the clinic myeloma (MM),34,35 leukaemia,36–38 and lymphoma.35,38,39 (+)-JQ1 for the treatment of NUT carcinoma and other solid tumours.44 was key to establishing the mechanistic significance of BET Target engagement was observed with once-daily dosing, with inhibition, however was unsuitable for clinical progression due several patients experiencing clinical benefit. Despite that, I-BET762 26 to its short half-life and thus its required dose concentrations showed rapid elimination (t1/2 = 3–7 hours) and transient responses, being above tolerable levels in vivo.40 thought to be due to the activation of resistance mechanisms to I-BET762/GSK525762/molibresib. I-BET762 was identified BET inhibition. Nevertheless, it is currently under clinical inves- following a screen of compounds that upregulated the Apoli- tigation for the treatment of acute myeloid leukaemia (AML) poprotein A1 (ApoA1) gene as a proxy for BET inhibition,27 (NCT01943851), with manageable adverse events and some objective leading to the identification of an initial hit (Fig. 2, 1) with an responses observed.47 It is also being evaluated as part of a 41 EC50 of 440 nM for the induction of