Approaches to Mitigate the Risk of Serious Adverse Reactions in Covalent Drug Design

Thomas A. Baillie (2020) Approaches to Mitigate the Risk of Serious Adverse Reactions in Covalent Drug Design, Expert Opinion on Drug Discovery 

DOI: 10.1080/17460441.2021.1832079

A review is provided of the current status of the covalent drug approach, emphasizing the unique benefits and attendant risks associated with reversible and irreversible binders. Areas of application beyond inhibition of tyrosine kinases are presented, and design considerations to de-risk covalent inhibitors with respect to undesirable off-target effects are discussed.

KRAS G12C Inhibition with Sotorasib in Advanced Solid Tumors

David S. Hong, M.D., Marwan G. Fakih, M.D., John H. Strickler, M.D., Jayesh Desai, M.D., Gregory A. Durm, M.D., Geoffrey I. Shapiro, M.D., Ph.D., Gerald S. Falchook, M.D., Timothy J. Price, M.B., B.S., D.Hlth.Sc., Adrian Sacher, M.D., M.M.Sc., Crystal S. Denlinger, M.D., Yung-Jue Bang, M.D., Ph.D., Grace K. Dy, M.D., John C. Krauss, M.D., Yasutoshi Kuboki, M.D., James C. Kuo, M.D., Andrew L. Coveler, M.D., Keunchil Park, M.D., Ph.D., Tae Won Kim, M.D., Ph.D., Fabrice Barlesi, M.D., Ph.D., Pamela N. Munster, M.D., Suresh S. Ramalingam, M.D., Timothy F. Burns, M.D., Ph.D., Funda Meric-Bernstam, M.D., Haby Henary, M.D., Jude Ngang, Pharm.D., Gataree Ngarmchamnanrith, M.D., June Kim, Ph.D., Brett E. Houk, Ph.D., Jude Canon, Ph.D., J. Russell Lipford, Ph.D., Gregory Friberg, M.D., Piro Lito, M.D., Ph.D., Ramaswamy Govindan, M.D., and Bob T. Li, M.D., M.P.H

N. Engl. J. Med. 2020; 383:1207-1217

DOI: 10.1056/NEJMoa1917239 

Abstract

BACKGROUND

No therapies for targeting KRAS mutations in cancer have been approved. The KRASp.G12C mutation occurs in 13% of non–small-cell lung cancers (NSCLCs) and in 1 to 3% of colorectal cancers and other cancers. Sotorasib is a small molecule that selectively and irreversibly targets KRASG12C.

METHODS

We conducted a phase 1 trial of sotorasib in patients with advanced solid tumors harboring the KRAS p.G12C mutation. Patients received sotorasib orally once daily. The primary end point was safety. Key secondary end points were pharmacokinetics and objective response, as assessed according to Response Evaluation Criteria in Solid Tumors (RECIST), version 1.1.

RESULTS

A total of 129 patients (59 with NSCLC, 42 with colorectal cancer, and 28 with other tumors) were included in dose escalation and expansion cohorts. Patients had received a median of 3 (range, 0 to 11) previous lines of anticancer therapies for metastatic disease. No dose-limiting toxic effects or treatment-related deaths were observed. A total of 73 patients (56.6%) had treatment-related adverse events; 15 patients (11.6%) had grade 3 or 4 events. In the subgroup with NSCLC, 32.2% (19 patients) had a confirmed objective response (complete or partial response) and 88.1% (52 patients) had disease control (objective response or stable disease); the median progression-free survival was 6.3 months (range, 0.0+ to 14.9 [with + indicating that the value includes patient data that were censored at data cutoff]). In the subgroup with colorectal cancer, 7.1% (3 patients) had a confirmed response, and 73.8% (31 patients) had disease control; the median progression-free survival was 4.0 months (range, 0.0+ to 11.1+). Responses were also observed in patients with pancreatic, endometrial, and appendiceal cancers and melanoma.

CONCLUSIONS

Sotorasib showed encouraging anticancer activity in patients with heavily pretreated advanced solid tumors harboring the KRAS p.G12C mutation. Grade 3 or 4 treatment-related toxic effects occurred in 11.6% of the patients. (Funded by Amgen and others; CodeBreaK100 ClinicalTrials.gov number, NCT03600883. opens in new tab.)

Site-Specific Bioconjugation through Enzyme-Catalyzed Tyrosine–Cysteine Bond Formation

Marco J. Lobba, Marco J. Lobba, Christof Fellmann*, Alan M. Marmelstein, Johnathan C. Maza, Elijah N. Kissman, Stephanie A. Robinson, Brett T. Staahl, Cole Urnes, Rachel J. Lew, Casey S. Mogilevsky, Jennifer A. Doudna*, and Matthew B. Francis*

ACS Cent. Sci. 2020, 6, 9, 1564–1571

https://doi.org/10.1021/acscentsci.0c00940

The synthesis of protein–protein and protein–peptide conjugates is an important capability for producing vaccines, immunotherapeutics, and targeted delivery agents. Herein we show that the enzyme tyrosinase is capable of oxidizing exposed tyrosine residues into o-quinones that react rapidly with cysteine residues on target proteins. This coupling reaction occurs under mild aerobic conditions and has the rare ability to join full-size proteins in under 2 h. The utility of the approach is demonstrated for the attachment of cationic peptides to enhance the cellular delivery of CRISPR-Cas9 20-fold and for the coupling of reporter proteins to a cancer-targeting antibody fragment without loss of its cell-specific binding ability. The broad applicability of this technique provides a new building block approach for the synthesis of protein chimeras.

Bardoxolone conjugation enables targeted protein degradation of BRD4

Bingqi Tong, Mai Luo, Yi Xie, Jessica N. Spradlin, John A. Tallarico, Jeffrey M. McKenna, Markus Schirle, Thomas J. Maimone & Daniel K. Nomura

Sci Rep 10, 15543 (2020).

https://doi.org/10.1038/s41598-020-72491-9

Targeted protein degradation (TPD) has emerged as a powerful tool in drug discovery for the perturbation of protein levels using heterobifunctional small molecules. E3 ligase recruiters remain central to this process yet relatively few have been identified relative to the ~ 600 predicted human E3 ligases. While, initial recruiters have utilized non-covalent chemistry for protein binding, very recently covalent engagement to novel E3’s has proven fruitful in TPD application. Herein we demonstrate efficient proteasome-mediated degradation of BRD4 by a bifunctional small molecule linking the KEAP1-Nrf2 activator bardoxolone to a BRD4 inhibitor JQ1.

Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4

Robin A. Fairhurst, Thomas Knoepfel, Nicole Buschmann, Catherine Leblanc, Robert Mah, Milen Todorov, Pierre Nimsgern, Sebastien Ripoche, Michel Niklaus, Nicolas Warin, Van Huy Luu, Mario Madoerin, Jasmin Wirth, Diana Graus-Porta, Andreas Weiss, Michael Kiffe, Markus Wartmann, Jacqueline Kinyamu-Akunda, Dario Sterker, Christelle Stamm, Flavia Adler, Alexandra Buhles, Heiko Schadt, Philippe Couttet, Jutta Blank, Inga Galuba, Joerg Trappe, Johannes Voshol, Nils Ostermann, Chao Zou, Joerg Berghausen, Alberto Del Rio Espinola, Wolfgang Jahnke, and Pascal Furet

Journal of Medicinal Chemistry 2020

DOI: 10.1021/acs.jmedchem.0c01019

FGF19 signaling through the FGFR4/β-klotho receptor complex has been shown to be a key driver of growth and survival in a subset of hepatocellular carcinomas making selective FGFR4 inhibition an attractive treatment opportunity. A kinome-wide sequence alignment highlighted a poorly-conserved cysteine residue within the FGFR4 ATP-binding site at position 552, two positions beyond the gate-keeper residue. Several strategies for targeting this cysteine to identify FGFR4 selective inhibitor starting points are summarised which made use of both rationale and unbiased screening approaches. The optimisation of a 2-formylquinoline amide hit series is described in which the aldehyde makes a hemithioacetal reversible-covalent interaction with cysteine 552. Key challenges addressed during the optimisation are improving the FGFR4 potency, metabolic stability and solubility leading ultimately to the highly-selective first-in-class clinical candidate roblitinib.

An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases Author links open overlay panel

László Petria, Attila Egyeda, Dávid Bajusza, Tímea Imreb, Anasztázia Hetényic, Tamás Martinekc, Péter Ábrányi-Balogha, György M. Keserűa

European Journal of Medicinal Chemistry, 2020

https://doi.org/10.1016/j.ejmech.2020.112836

Targeted covalent inhibitors represent a viable strategy to block protein kinases involved in different disease pathologies. Although a number of computational protocols have been published for identifying druggable cysteines, experimental approaches are limited for mapping the reactivity and accessibility of these residues. Here, we present a ligand based approach using a toolbox of fragment-sized molecules with identical scaffold but equipped with diverse covalent warheads. Our library represents a unique opportunity for the efficient integration of warhead-optimization and target-validation into the covalent drug development process. Screening this probe kit against multiple kinases could experimentally characterize the accessibility and reactivity of the targeted cysteines and helped to identify suitable warheads for designed covalent inhibitors. The usefulness of this approach has been confirmed retrospectively on Janus kinase 3 (JAK3). Furthermore, representing a prospective validation, we identified Maternal embryonic leucine zipper kinase (MELK), as a tractable covalent target. Covalently labelling and biochemical inhibition of MELK would suggest an alternative covalent strategy for MELK inhibitor programs.

Using sulfuramidimidoyl fluorides that undergo sulfur(VI) fluoride exchange for inverse drug discovery

Gabriel J. Brighty, Rachel C. Botham, Suhua Li, Luke Nelson, David E. Mortenson, Gencheng Li, Christophe Morisseau, Hua Wang, Bruce D. Hammock, K. Barry Sharpless & Jeffery W. Kelly 

Nat. Chem., 2020) 

https://doi.org/10.1038/s41557-020-0530-4

 candidates that form covalent linkages with their target proteins have been underexplored compared with the conventional counterparts that modulate biological function by reversibly binding to proteins, in part due to concerns about off-target reactivity. However, toxicity linked to off-target reactivity can be minimized by using latent electrophiles that only become activated towards covalent bond formation on binding a specific protein. Here we study sulfuramidimidoyl fluorides, a class of weak electrophiles that undergo sulfur(VI) fluoride exchange chemistry. We show that equilibrium binding of a sulfuramidimidoyl fluoride to a protein can allow nucleophilic attack by a specific amino acid side chain, which leads to conjugate formation. We incubated small molecules, each bearing a sulfuramidimidoyl fluoride electrophile, with human cell lysate, and the protein conjugates formed were identified by affinity chromatography–mass spectrometry. This inverse drug discovery approach identified a compound that covalently binds to and irreversibly inhibits the activity of poly(ADP-ribose) polymerase 1, an important anticancer target in living cells.