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Instruments / Technical Area	Publication Details	Published
I04-1-Macromolecular Crystallography (fixed wavelength)	A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase Naoki Kuki , David L. Walmsley , Kazuo Kanai , Sho Takechi , Masao Yoshida , Ryo Murakami , Kohei Takano , Yuichi Tominaga , Mizuki Takahashi , Shuichiro Ito , Naoki Nakao , Hayley Angove , Lisa M. Baker , Edward Carter , Pawel Dokurno , Loic Le Strat , Alba T. Macias , Carrie-Anne Molyneaux , James B. Murray , Allan E. Surgenor , Tomoaki Hamada , Roderick E. Hubbard Rsc Medicinal Chemistry 14, 2731 - 2737 DOI: 10.1039/D3MD00439B Show Abstract ▼ Abstract: Several generations of ATP-competitive anti-cancer drugs that inhibit the activity of the intracellular kinase domain of the epidermal growth factor receptor (EGFR) have been developed over the past twenty years. The first-generation of drugs such as gefitinib bind reversibly and were followed by a second-generation such as dacomitinib that harbor an acrylamide moiety that forms a covalent bond with C797 in the ATP binding pocket. Resistance emerges through mutation of the T790 gatekeeper residue to methionine, which introduces steric hindrance to drug binding and increases the Km for ATP. A third generation of drugs, such as osimertinib were developed which were effective against T790M EGFR in which an acrylamide moiety forms a covalent bond with C797, although resistance has emerged by mutation to S797. A fragment-based screen to identify new starting points for an EGFR inhibitor serendipitously identified a fragment that reacted with C775, a previously unexploited residue in the ATP binding pocket for a covalent inhibitor to target. A number of acrylamide containing fragments were identified that selectively reacted with C775. One of these acrylamides was optimized to a highly selective inhibitor with sub-1 μM activity, that is active against T790M, C797S mutant EGFR independent of ATP concentration, providing a potential new strategy for pan-EGFR mutant inhibition.	Dec 2023
I02-Macromolecular Crystallography I04-Macromolecular Crystallography	The effect of core replacement on S64315, a selective MCL-1 inhibitor, and its analogues Szabolcs Sipos , Balázs Bálint , Zoltán B. Szabó , Levente Ondi , Márton Csékei , Zoltán Szlávik , Ágnes Proszenyák , James B. Murray , James Davidson , Ijen Chen , Pawel Dokurno , Allan E. Surgenor , Christopher Pedder , Roderick E. Hubbard , Ana-Leticia Maragno , Maia Chanrion , Frederic Colland , Olivier Geneste , András Kotschy Acs Omega 6, 22073 - 22102 DOI: 10.1021/acsomega.1c02595 Diamond Proposal Number(s): [1857] Open Access Show Abstract ▼ Abstract: Following the identification of thieno[2,3-d]pyrimidine-based selective and potent inhibitors of MCL-1, we explored the effect of core swapping at different levels of advancement. During hit-to-lead optimization, X-ray-guided S-N replacement in the core provided a new vector, whose exploration led to the opening of the so-called deep-S2 pocket of MCL-1. Unfortunately, the occupation of this region led to a plateau in affinity and had to be abandoned. As the project approached selection of a clinical candidate, a series of core swap analogues were also prepared. The affinity and cellular activity of these compounds showed a significant dependence on the core structure. In certain cases, we also observed an increased and accelerated epimerization of the atropoisomers. The most potent core replacement analogues showed considerable in vivo PD response. One compound was progressed into efficacy studies and inhibited tumor growth.	Aug 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Fragment-derived selective inhibitors of dual-specificity kinases DYRK1A and DYRK1B David Lee Walmsley , James B. Murray , Pawel Dokurno , Andrew J. Massey , Karen Benwell , Andrea Fiumana , Nicolas Foloppe , Stuart Ray , Julia Smith , Allan E. Surgenor , Thomas Edmonds , Didier Demarles , Mike Burbridge , Francisco Cruzalegui , Andras Kotschy , Roderick E. Hubbard Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.1c00024 Open Access Show Abstract ▼ Abstract: The serine/threonine kinase DYRK1A has been implicated in regulation of a variety of cellular processes associated with cancer progression, including cell cycle control, DNA damage repair, protection from apoptosis, cell differentiation, and metastasis. In addition, elevated-level DYRK1A activity has been associated with increased severity of symptoms in Down’s syndrome. A selective inhibitor of DYRK1A could therefore be of therapeutic benefit. We have used fragment and structure-based discovery methods to identify a highly selective, well-tolerated, brain-penetrant DYRK1A inhibitor which showed in vivo activity in a tumor model. The inhibitor provides a useful tool compound for further exploration of the effect of DYRK1A inhibition in models of disease.	Jun 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Design and synthesis of pyrrolo[2,3-d]pyrimidine-derived leucine-rich repeat kinase 2 (LRRK2) inhibitors using a checkpoint kinase 1 (CHK1)-derived crystallographic surrogate Douglas S. Williamson , Garrick P. Smith , Gitte K. Mikkelsen , Thomas Jensen , Pamela Acheson-Dossang , Lassina Badolo , Simon T. Bedford , Victoria Chell , I-Jen Chen , Pawel Dokurno , Morten Hentzer , Stephanie Newland , Stuart C. Ray , Terry Shaw , Allan E. Surgenor , Lindsey Terry , Yikang Wang , Kenneth V. Christensen Journal Of Medicinal Chemistry 56 DOI: 10.1021/acs.jmedchem.1c00720 Diamond Proposal Number(s): [27063, 2103, 5791, 6001] Open Access Show Abstract ▼ Abstract: Inhibitors of leucine-rich repeat kinase 2 (LRRK2) and mutants, such as G2019S, have potential utility in Parkinson’s disease treatment. Fragment hit-derived pyrrolo[2,3-d]pyrimidines underwent optimization using X-ray structures of LRRK2 kinase domain surrogates, based on checkpoint kinase 1 (CHK1) and a CHK1 10-point mutant. (2R)-2-Methylpyrrolidin-1-yl derivative 18 (LRRK2 G2019S cKi 0.7 nM, LE 0.66) was identified, with increased potency consistent with an X-ray structure of 18/CHK1 10-pt. mutant showing the 2-methyl substituent proximal to Ala147 (Ala2016 in LRRK2). Further structure-guided elaboration of 18 gave the 2-[(1,3-dimethyl-1H-pyrazol-4-yl)amino] derivative 32. Optimization of 32 afforded diastereomeric oxolan-3-yl derivatives 44 and 45, which demonstrated a favorable in vitro PK profile, although they displayed species disconnects in the in vivo PK profile, and a propensity for P-gp- and/or BCRP-mediated efflux in a mouse model. Compounds 44 and 45 demonstrated high potency and exquisite selectivity for LRRK2 and utility as chemical probes for the study of LRRK2 inhibition.	Jun 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Structure-guided discovery of potent and selective DYRK1A inhibitors Csaba Weber , Melinda Sipos , Attila Paczal , Balazs Balint , Vilibald Kun , Nicolas Foloppe , Pawel Dokurno , Andrew J. Massey , David Lee Walmsley , Roderick E. Hubbard , James Murray , Karen Benwell , Thomas Edmonds , Didier Demarles , Alain Bruno , Mike Burbridge , Francisco Cruzalegui , Andras Kotschy Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.1c00023 Diamond Proposal Number(s): [1857, 2103] Show Abstract ▼ Abstract: The kinase DYRK1A is an attractive target for drug discovery programs due to its implication in multiple diseases. Through a fragment screen, we identified a simple biaryl compound that is bound to the DYRK1A ATP site with very high efficiency, although with limited selectivity. Structure-guided optimization cycles enabled us to convert this fragment hit into potent and selective DYRK1A inhibitors. Exploiting the structural differences in DYRK1A and its close homologue DYRK2, we were able to fine-tune the selectivity of our inhibitors. Our best compounds potently inhibited DYRK1A in the cell culture and in vivo and demonstrated drug-like properties. The inhibition of DYRK1A in vivo translated into dose-dependent tumor growth inhibition in a model of ovarian carcinoma.	May 2021
I02-Macromolecular Crystallography	Discovery of S64315, a potent and selective Mcl-1 inhibitor Zoltan Szlavik , Marton Csekei , Attila Paczal , Zoltan B. Szabo , Szabolcs Sipos , Gabor Radics , Agnes Proszenyak , Balazs Balint , James Murray , James Davidson , Ijen Chen , Pawel Dokurno , Allan E Surgenor , Zoe Marie Daniels , Roderick E. Hubbard , Gaëtane Le Toumelin-Braizat , Audrey Claperon , Gaëlle Lysiak-Auvity , Anne-Marie Girard , Alain Bruno , Maia Chanrion , Frédéric Colland , Ana-Leticia Maragno , Didier Demarles , Olivier Geneste , Andras Kotschy Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.0c01234 Diamond Proposal Number(s): [2103] Show Abstract ▼ Abstract: Myeloid cell leukemia 1 (Mcl-1) has emerged as an attractive target for cancer therapy. It is an antiapoptotic member of the Bcl-2 family of proteins, whose upregulation in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy. Here we report the discovery of our clinical candidate S64315, a selective small molecule inhibitor of Mcl-1. Starting from a fragment derived lead compound, we have conducted structure guided optimization that has led to a significant (3 log) improvement of target affinity as well as cellular potency. The presence of hindered rotation along a biaryl axis has conferred high selectivity to the compounds against other members of the Bcl-2 family. During optimization, we have also established predictive PD markers of Mcl-1 inhibition and achieved both efficient in vitro cell killing and tumor regression in Mcl-1 dependent cancer models. The preclinical candidate has drug-like properties that have enabled its development and entry into clinical trials.	Nov 2020
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Structure-guided discovery of a selective Mcl-1 inhibitor with cellular activity Zoltan Szlávik , Levente Ondi , Márton Csékei , Attila Paczal , Zoltán B. Szabó , Gábor Radics , James Murray , James Davidson , Ijen Chen , Ben Davis , Roderick E. Hubbard , Christopher Pedder , Pawel Dokurno , Allan Surgenor , Julia Smith , Alan Robertson , Gaetane Letoumelin-Braizat , Nicolas Cauquil , Marion Zarka , Didier Demarles , Francoise Perron-Sierra , Audrey Claperon , Frederic Colland , Olivier Geneste , András Kotschy Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.9b00134 Diamond Proposal Number(s): [17182, 1194, 2103] Show Abstract ▼ Abstract: Myeloid cell leukemia 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family of proteins, whose upregulation when observed in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy, has emerged as an attractive target for cancer therapy. Here, we report the discovery of selective small molecule inhibitors of Mcl-1 that inhibit cellular activity. Fragment screening identified thienopyrimidine amino acids as promising but nonselective hits that were optimized using nuclear magnetic resonance and X-ray-derived structural information. The introduction of hindered rotation along a biaryl axis has conferred high selectivity to the compounds, and cellular activity was brought on scale by offsetting the negative charge of the anchoring carboxylate group. The obtained compounds described here exhibit nanomolar binding affinity and mechanism-based cellular efficacy, caspase induction, and growth inhibition. These early research efforts illustrate drug discovery optimization from thienopyrimidine hits to a lead compound, the chemical series leading to the identification of our more advanced compounds S63845 and S64315.	Jul 2019
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Establishing drug discovery and identification of hit series for the anti-apoptotic proteins, Bcl-2 and Mcl-1 James B. Murray , James Davidson , Ijen Chen , Ben Davis , Pawel Dokurno , Christopher J. Graham , Richard Harris , Allan Jordan , Natalia Matassova , Christopher Pedder , Stuart Ray , Stephen D. Roughley , Julia Smith , Claire Walmsley , Yikang Wang , Neil Whitehead , Douglas S. Williamson , Patrick Casara , Thierry Le Diguarher , John Hickman , Jerome Stark , András Kotschy , Olivier Geneste , Roderick E. Hubbard Acs Omega 4, 8892 - 8906 DOI: 10.1021/acsomega.9b00611 Diamond Proposal Number(s): [671, 1194, 17182] Open Access Show Abstract ▼ Abstract: We describe our work to establish structure- and fragment-based drug discovery to identify small molecules that inhibit the anti-apoptotic activity of the proteins Mcl-1 and Bcl-2. This identified hit series of compounds, some of which were subsequently optimized to clinical candidates in trials for treating various cancers. Many protein constructs were designed to identify protein with suitable properties for different biophysical assays and structural methods. Fragment screening using ligand-observed NMR experiments identified several series of compounds for each protein. The series were assessed for their potential for subsequent optimization using 1H and 15N heteronuclear single-quantum correlation NMR, surface plasmon resonance, and isothermal titration calorimetry measurements to characterize and validate binding. Crystal structures could not be determined for the early hits, so NMR methods were developed to provide models of compound binding to guide compound optimization. For Mcl-1, a benzodioxane/benzoxazine series was optimized to a Kd of 40 μM before a thienopyrimidine hit series was identified which subsequently led to the lead series from which the clinical candidate S 64315 (MIK 665) was identified. For Bcl-2, the fragment-derived series were difficult to progress, and a compound derived from a published tetrahydroquinone compound was taken forward as the hit from which the clinical candidate (S 55746) was obtained. For both the proteins, the work to establish a portfolio of assays gave confidence for identification of compounds suitable for optimization.	May 2019
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Design of leucine-rich repeat kinase 2 (LRRK2) inhibitors using a crystallographic surrogate derived from checkpoint kinase 1 (CHK1) Douglas S. Williamson , Garrick P. Smith , Pamela Acheson-Dossang , Simon T. Bedford , Victoria Chell , I-Jen Chen , Justus C. A. Daechsel , Zoe Daniels , Laurent David , Pawel Dokurno , Morten Hentzer , Martin C. Herzig , Roderick E. Hubbard , Jonathan D. Moore , James B. Murray , Samantha Newland , Stuart C. Ray , Terry Shaw , Allan E. Surgenor , Lindsey Terry , Kenneth Thirstrup , Yikang Wang , Kenneth V. Christensen Journal Of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.7b01186 Diamond Proposal Number(s): [5791, 12428, 2103, 14641, 5067] Show Abstract ▼ Abstract: Mutations in leucine-rich repeat kinase 2 (LRRK2), such as G2019S, are associated with an increased risk of developing Parkinson’s disease. Surrogates for the LRRK2 kinase domain based on checkpoint kinase 1 (CHK1) mutants were designed, expressed in insect cells infected with baculovirus, purified and crystallized. X-ray structures of the surrogates complexed with known LRRK2 inhibitors rationalized compound potency and selectivity. The CHK1 10-point mutant was preferred, following assessment of surrogate binding affinity with LRRK2 inhibitors. Fragment hit-derived arylpyrrolo[2,3-b]-pyridine LRRK2 inhibitors underwent structure-guided optimization using this crystallographic surrogate. LRRK2-pSer935 HEK293 IC50 data for 22 were consistent with binding to Ala2016 in LRRK2 (equivalent to Ala147 in CHK1 10-pt. mut. structure). Compound 22 was shown to be potent, moderately selective, orally available and brain-penetrant in wild-type mice, and confirmation of target engagement was demonstrated, with LRRK2-pSer935 IC50 values for 22 in mouse brain and kidney being 1.3 nM and 5 nM, respectively.	Oct 2017

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