Editorial pubs.acs.org/jmc
Journal of Medicinal Chemistry, Technological Advances: Highlights 2015−2016
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applying lead discovery techniques that were disparate and complementary in nature and hybridizing discoveries and observations in a fashion that took advantage of the strengths of the independent approaches. Subsequent lead optimization was influenced by monitoring the efficiency metrics LE and LLEAT and carefully controlling physicochemical properties (log D), providing an elegant example of the need to rely upon multiple avenues for lead discovery and optimization that uses both contemporary design practices and chemical intuition. The utility of DNA-encoded library technology for the identification of robust lead molecules remains of high interest, and many pharmaceutical houses have invested heavily in this approach to the synthesis of a large number (>1 billion) of diverse structures, either through the development of an internal effort or through external collaboration. However, as with any nascent methodology, the question that has been posed frequently is whether the technology has actually led to the identification of drug candidates. Harris and colleagues (DOI: 10.1021/acs.jmedchem.5b01898) at GlaxoSmithKline provide an answer to this query highlighted by the identification of refined receptor interacting protein 1 (RIP1) kinase inhibitors that have clear potential to be developed into clinical candidates.3 More specifically, the recent discovery of the role of RIP1 kinase in the genesis of tumor necrosis factor (TNF) mediated inflammation has led to its emergence as a highly promising target for the treatment of multiple inflammatory diseases. RIP1 kinase was screened against DNA-encoded small-molecule libraries leading to the identification of a novel and highly potent benzoxazepinone inhibitor series. It was subsequently demonstrated that this template possessed complete monokinase selectivity for RIP1 plus unique species selectivity for the primate enzyme over nonprimate homologues. This series differentiated itself from known RIP1 inhibitors by combining high potency and kinase selectivity with good pharmacokinetic profiles in rodents. The favorable developability profile of this benzoxazepinone template, as exemplified by the prototype compound GSK481, made it an excellent starting point for further optimization into a RIP1 kinase inhibitor clinical candidate. Interleukin 17 (IL-17) is a proinflammatory cytokine produced by T-helper cells and is induced by IL-23. To elicit its functions, IL-17 binds to the type I cell surface receptor IL17R. IL-17 acts as a potent mediator in delayed-type reactions by increasing chemokine production in various tissues and signaling from IL-17 recruits monocytes and neutrophils to a site of inflammation in response to invasion by pathogens, similar to interferon-γ. In promoting inflammation, IL-17 has been demonstrated to act synergistically with TNF and interleukin-1. This activity can also be redirected toward the host and result in various autoimmune disorders that involve chronic inflammation, including the skin disorder psoriasis. As a
he development and implementation of new enabling technologies in drug discovery continue to provide advances that assist in what is typically a very a difficult challenge. In collaboration with ACS Combinatorial Science and ACS Medicinal Chemistry Letters, we have assembled a virtual issue collection that highlights six articles selected from the Journal of Medicinal Chemistry that were published in 2015 and 2016 which we believe capture practical applications of techniques that are of particular interest to the medicinal chemistry community. Fragment-based drug discovery (FBDD) remains a key technology for the identification of novel lead molecules for targets of interest in the drug discovery arena including difficult-to-drug targets such as protein−protein interactions (PPIs). Recently, high throughput crystallography approaches have become popular; however, in the first of two articles selected, the authors demonstrate the utility of a combination of methods that includes a marrying of X-ray crystallography (XRC) and the standard surface plasmon resonance (SPR) technique.1 In essence, FBDD is contingent on the development of analytical methods to identify weak, noncovalent protein−fragment interactions. Woods et al. (DOI: 10.1021/ acs.jmedchem.5b01940) combine an underutilized fragment screening method, native state mass spectrometry (MS), together with the two proven and more popular fragment screening methods, SPR and XRC, in a fragment screening campaign against the enzyme human carbonic anhydrase II (CA II). In the initial screen sampling a 720-member fragment library, seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. The fragment binding results were extremely well correlated across the three methods utilized, and the findings demonstrate that there is a significant opportunity to apply native state MS as a complementary fragment screening method to accelerate drug discovery. In the second FBDD article that we highlight, Bertrand and colleagues (DOI: 10.1021/acs.jmedchem.5b01607) exploit a combination of fragment and high-throughput screening (HTS) to identify and optimize inhibitors of mitochondrial branched-chain aminotransferase (BCATm), a ubiquitous enzyme (with the notable exception of the liver) that metabolizes branched amino acids to the α-keto acid.2a BCATm inhibitors are of interest as therapeutics for the treatment of diet-induced obesity, and the authors sought molecules with pharmacokinetic (PK) properties suitable for in vivo studies that could help elucidate the potential of this mechanistic approach.2b While fragment-based screening identified several leads, it was the confluence of these structural elements with HTS hits that allowed a fuller appreciation of the chemotype (Scanlon, DOI: 10.1021/acs.jmedchem.5b01244).2b While the fragment hits identified a water molecule that could be displaced, the HTS leads surfaced an accessible pocket induced by movement of the side chain of a residue in the binding site. The success of the effort was dependent on © XXXX American Chemical Society
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DOI: 10.1021/acs.jmedchem.6b01600 J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
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aryl methyl-based probe and for which binding was not competed by entecapone. HIBCH is located in mitochondria, with preferred expression in the liver although it is also expressed in heart, kidney, and muscle, and there are four reported incidents of deficiency associated with an autosomal recessive disorder. While the first of these cases was reported in 1982, biochemical profiles have not been elucidated although reduced HIBCH activity in the liver has been associated with liver cirrhosis and hepatocellular carcinoma, attributed to the accumulation of the toxic methacrylyl-CoA. HIBCH removes the CoA moiety from 3-hydroxyisobutyryl-CoA, an intermediate in the valine catabolic pathway, and the results of this study implicate this enzyme in the hepatotoxicity associated with tolcapone. Additional studies confirmed the association of tolcapone cytotoxicity with HIBCH inhibition and allowed screening of a focused library of catechol derivatives that identified molecules with or without this off target effect.
result, pharmaceutical industry interest has been directed toward the identification of modulators of IL-17 function, including small molecules (IL-17 antagonists and ROR-γ regulators) and biologics, e.g., Cosentyx/secukinumab. Espada et al. (DOI: 10.1021/acs.jmedchem.5b01693) focus on the identification of small molecule binding sites on IL-17A using the highly attractive but relatively underutilized hydrogen− deuterium exchange MS (HDX-MS) technology.4 Specifically, computational assessment of the IL-17A structure identified two distinct binding sites designated as the β-hairpin and the αhelix pockets. The β-hairpin pocket was hypothesized to be the site of binding for peptide macrocycles, and support for this hypothesis was obtained using HDX-MS. The experiments revealed protection to exchange only within the β-hairpin pocket, and these data represent the first direct structural evidence of a small molecule binding site on IL-17A that functions to disrupt the interaction with its receptor. Zhang and colleagues (DOI: 10.1021/acs.jmedchem.5b01293) provide a compelling example of the combination of two independent techniques that were used to identify new avenues of structure−activity relationship (SAR) development in a series of factor IXa (FIXa) inhibitors.5 Incubation of lead compounds in liver microsomes generated metabolites that were prioritized for subsequent study by using an automated ligand identification system (ALIS) based process for assessing the affinity of compounds for FIXa. Those metabolites of greatest interest based on their affinity for the enzyme were obtained in sufficient (microgram) quantities to allow characterization via MicroCryoProbe nuclear magnetic resonance (NMR) techniques, with the samples subsequently assessed in a FIXa enzymatic assay. The IC50 values obtained correlated well with the affinity data generated by the ALIS assay, and the hydroxylated products that were isolated and characterized provided unique insights into SARs. In the final article selected, von Kleist et al. (DOI: 10.1021/ acs.jmedchem.5b01970) describe the design and exploitation of a differential competition capture compound mass spectrometric (dCCCMS) assay to differentiate the promiscuity profiles of catechol-O-methyltransferase (COMT) inhibitors two of which, tolcapone and etecapone, are used in the treatment of Parkinson’s disease.6 Clinical use of tolcapone is associated with hepatotoxicity while the more potent entecapone does not exhibit this side effect and this study sought to exploit dCCCMS to identify a possible source of the liver problem with tolcapone. The dCCCMS technique requires that a prosthetic element combining an aryl azide as a photoaffinity label and biotin be appended to a molecule and after incubation with cell lysate (the human hepatoma HepG2 liver cell line was used in the experiments) and photoactivation of the azide for 10 min, the lysate is passed over magnetic beads coated with streptavidin allowing isolation of covalently attached proteins by selection. The captured proteins are digested with trypsin, and the fragments, and hence the protein, are identified using high resolution LTQ Orbitrap hybrid MS. Tolcapone was derivatized at one of the catechol hydroxyls to give a compound that failed to bind to COMT, while the prosthetic element of the second probe molecule was appended to an aryl methyl substituent remote from the pharmacophore that preserved COMT affinity. By conducting a series of competitive binding experiments using tolcapone, entecapone, and two catechol-based analogues and focusing on proteins with differential behavior, 3-hydroxyisobutryl-CoA hydrolase (HIBCH) was identified as a protein that bound the tolcapone
Stevan W. Djuric†
AbbVie, R467, AP10-2, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
Nicholas A. Meanwell‡
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Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
AUTHOR INFORMATION
Notes
Views expressed in this editorial are those of the authors and not necessarily the views of the ACS. † S.W.D.: e-mail,
[email protected]. ‡ N.A.M.: e-mail,
[email protected].
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REFERENCES
(1) Woods, L. A.; Dolezal, O.; Ren, B.; Ryan, J. H.; Peat, T. S.; Poulsen, S.-A. Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination. J. Med. Chem. 2016, 59, 2192− 2204. (2) (a) Bertrand, S. M.; Ancellin, N.; Beaufils, B.; Bingham, R. P.; Borthwick, J. A.; Boullay, A.-B.; Boursier, E.; Carter, P. S.; Chung, C.w.; Churcher, I.; Dodic, N.; Fouchet, M.-H.; Fournier, C.; Francis, P. L.; Gummer, L. A.; Herry, K.; Hobbs, A.; Hobbs, C. I.; Homes, P.; Jamieson, C.; Nicodeme, E.; Pickett, S. D.; Reid, I. H.; Simpson, G. L.; Sloan, L. A.; Smith, S. E.; Somers, D. O’N.; Spitzfaden, C.; Suckling, C. J.; Valko, K.; Washio, Y.; Young, R.J. The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits. J. Med. Chem. 2015, 58, 7140−7163. (b) Scanlon, M. Inhibitors of BCATm: A Tough Nut To Crack. J. Med. Chem. 2015, 58, 7138−7139. (3) Harris, P. A.; King, B. W.; Bandyopadhyay, D.; Berger, S.; Campobasso, N.; Capriotti, C. A.; Cox, J. A.; Dare, L.; Dong, X.; Finger, J. N.; Grady, L. C.; Hoffman, S. J.; Jeong, J. U.; Kang, J.; Kasparcova, V.; Ami, S.; Lakdawala, A. S.; Lehr, R.; McNulty, D. E.; Nagilla, R.; Ouellette, M. T.; Pao, C. S.; Rendina, A. R.; Schaeffer, M. C.; Summerfield, J. D.; Swift, B. A.; Totoritis, R. D.; Ward, P.; Zhang, A.; Zhang, D.; Marquis, R. W.; Bertin, J.; Gough, P. J. DNA-Encoded Library Screening Identifies Benzo[b][1,4]oxazepin-4-ones as Highly Potent and Monoselective Receptor Interacting Protein 1 Kinase Inhibitors. J. Med. Chem. 2016, 59, 2163−2178. (4) Espada, A.; Broughton, H.; Jones, S.; Chalmers, M. J.; Dodge, J. A. A Binding Site on IL-17A for Inhibitory Macrocycles Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry. J. Med. Chem. 2016, 59, 2255−2260. (5) Zhang, T.; Liu, Y.; Yang, X.; Martin, G. E.; Yao, H.; Shang, J.; Bugianesi, R. M.; Ellsworth, K. P.; Sonatore, L. M.; Nizner, P.; Sherer,
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E. C.; Hill, S. E.; Knemeyer, I. W.; Geissler, W. M.; Dandliker, P. J.; Helmy, R.; Wood, H. B. Definitive Metabolite Identification Coupled with Automated Ligand Identification System (ALIS) Technology: A Novel Approach to Uncover Structure-Activity Relationships and Guide Drug Design in a Factor IXa Inhibitor Program. J. Med. Chem. 2016, 59, 1818−1829. (6) von Kleist, L.; Michaelis, S.; Bartho, K.; Graebner, O.; Schlief, M.; Dreger, M.; Schrey, A. K.; Sefkow, M.; Kroll, F.; Koester, H.; Luo, Y. Identification of Potential Off-target Toxicity Liabilities of Catechol-Omethyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry. J. Med. Chem. 2016, 59, 4664−4675.
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DOI: 10.1021/acs.jmedchem.6b01600 J. Med. Chem. XXXX, XXX, XXX−XXX
