Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Kneller, D.W., Li, H., Phillips, G. et al. 

Nat Commun 13, 2268 (2022). 

https://doi.org/10.1038/s41467-022-29915-z

Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.

Intracellular Formation of a DNA Damage-Induced, Histone Post-Translational Modification Following Bleomycin Treatment

Marco Paolo Jacinto, Stephen D. Fried, and Marc M. Greenberg

Journal of the American Chemical Society Article ASAP

DOI: 10.1021/jacs.2c02880

Evaluating the significance of various forms of DNA damage is complicated by discoveries that some lesions inactivate repair enzymes or produce more deleterious forms of damage. Histone lysines within nucleosomes react with the commonly produced C4′-oxidized abasic site (C4-AP) to concomitantly yield an electrophilic modification (KMP) on lysine and DNA strand scission. We developed a chemoproteomic approach to identify KMP in HeLa cells. More than 60 000 KMP-modified histones are produced per cell. Using LC-MS/MS, we detected KMP at 17 of the 57 lysine residues distributed throughout the four core histone proteins. Therefore, KMP constitutes a DNA damage-induced, nonenzymatic histone post-translational modification. KMP formation suggests that downstream processes resulting from DNA damage could have ramifications on cells.

Conditional covalent lethality driven by oncometabolite accumulation

Minervo Perez, Kellie D Nance, Daniel W Bak, Supuni Thalalla Gamage, Susana S Najera, Amy N Conte, W. Marston Linehan, Eranthie Weerapana, Jordan L Meier

bioRxiv 2022.04.26.489575; 

doi: https://doi.org/10.1101/2022.04.26.489575

Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a cancer predisposition syndrome driven by mutation of the tumor suppressor fumarate hydratase (FH). Inactivation of FH causes accumulation of the electrophilic oncometabolite fumarate. In the absence of methods for reactivation, tumor suppressors can be targeted via identification of synthetic lethal interactions using genetic screens. Inspired by recent advances in chemoproteomic target identification, here we test the hypothesis that the electrophilicity of the HLRCC metabolome may produce unique susceptibilities to covalent small molecules, a phenomenon we term conditional covalent lethality. Screening a panel of chemically diverse electrophiles we identified a covalent ligand, MP-1, that exhibits FH-dependent cytotoxicity. Synthesis and structure-activity profiling identified key molecular determinants underlying the molecule's effects. Chemoproteomic profiling of cysteine reactivity together with clickable probes validated the ability of MP-1 to engage an array of functional cysteines, including one lying in the Zn-finger domain of the tRNA methyltransferase enzyme TRMT1. TRMT1 overexpression rescues tRNA methylation from inhibition by MP-1 and partially attenuates the covalent ligand's cytotoxicity. Our studies highlight the potential for covalent metabolites and small molecules to synergistically produce novel synthetic lethal interactions and raise the possibility of applying phenotypic screening with chemoproteomic target identification to identify new functional oncometabolite targets.

Cell-Active, Reversible, and Irreversible Covalent Inhibitors that Selectively Target the Catalytic Lysine of BCR-ABL Kinase

Chen, P., Sun, J., Zhu, C., Tang, G., Wang, W., Xu, M., Xiang, M., Zhang, C., Zhang, Z., Gao, L. and Yao, S..Q. 

Angew. Chem. Int. Ed. 2022

https://doi.org/10.1002/anie.202203878

Despite recent interests in developing lysine-targeting covalent inhibitors, no general approach is available to create such compounds. We report herein a general approach to develop cell-active covalent inhibitors of protein kinases by targeting the conserved catalytic lysine residue using key SuFEx and salicylaldehyde-based imine chemistries. We validated the strategy by successfully developing (irreversible and reversible) covalent inhibitors against BCR-ABL kinase. Our lead compounds showed high levels of selectivity in biochemical assays, exhibited nanomolar potency against endogenous ABL kinase in cellular assays, and were active against most drug-resistant ABL mutations. Among them, the salicylaldehyde-containing A5 is the first-ever reversible covalent ABL inhibitor that possessed time-dependent ABL inhibition with prolonged residence time and few cellular off-targets in K562 cells. Bioinformatics further suggested the generality of our strategy against the human kinome.

Discovery, Preclinical Characterization, and Early Clinical Activity of JDQ443, a Structurally Novel, Potent and Selective, Covalent Oral Inhibitor of KRASG12C

Andreas Weiss1*, Edwige Lorthiois1*, Louise Barys1, Kim S. Beyer1, Claudio Bomio-Confaglia1, Heather Burks2, Xueying Chen3, Xiaoming Cui3, Ruben de Kanter1, Lekshmi Dharmarajan1, Carmine Fedele2, Marc Gerspacher1, Daniel Alexander Guthy1, Victoria Head 1, Ashley Jaeger2, Eloísa Jiménez Núñez 1, Jeffrey D Kearns2, Catherine Leblanc1, Sauveur-Michel Maira1, Jason Murphy2, Helen Oakman2, Nils Ostermann1, Johannes Ottl1, Pascal Rigollier1, Danielle Roman1, Christian Schnell1, Richard Sedrani1, Toshio Shimizu4, Rowan Stringer1, Andrea Vaupel1, Hans Voshol1, Peter Wessels5, Toni Widmer5, Rainer Wilcken1, Kun Xu3, Frederic Zecri2, Anna F. Farago2#, Simona Cotesta1# and Saskia M. Brachmann

Cancer Discov candisc.0158.2022.

https://doi.org/10.1158/2159-8290.CD-22-0158

Covalent inhibitors of KRASG12C have shown antitumor activity against advanced/metastatic KRAS 46 G12C-mutated cancers, though resistance emerges and additional strategies are needed to improve 47 outcomes. JDQ443 is a structurally unique, covalent inhibitor of GDP-bound KRASG12C that forms 48 novel interactions with the switch II pocket. JDQ443 potently inhibits KRASG12C-driven cellular 49 signaling and demonstrates selective antiproliferative activity in KRAS G12C-mutated cell lines, 50 including those with G12C/H95 double mutations. In vivo, JDQ443 induces AUC exposure-driven 51 antitumor efficacy in KRAS G12C-mutated cell-derived (CDX) and patient-derived (PDX) tumor 52 xenografts. In PDX models, single-agent JDQ443 activity is enhanced by combination with SHP2, 53 MEK or CDK4/6 inhibitors. Notably, the benefit of JDQ443 plus the SHP2 inhibitor TNO155 is 54 maintained at reduced doses of either agent in CDX models, consistent with mechanistic synergy. 55 JDQ443 is in clinical development as monotherapy and in combination with TNO155, with both 56 strategies showing antitumor activity in patients with KRAS G12C-mutated tumors.