Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design

Yulan Wang, Yang Dai, Xiaowei Wu, Fei Li, Bo Liu, Chunpu Li, Qiufeng Liu, Yuanyang Zhou, Bao Wang, Mingrui Zhu, Rongrong Cui, Xiaoqin Tan, Zhaoping Xiong, Jia Liu, Minjia Tan, Yechun Xu, Meiyu Geng, Hualiang Jiang, Hong Liu, Jing Ai, and Mingyue Zheng

J. Med. Chem. 2019, 62 (16), 7473-7488

DOI: 10.1021/acs.jmedchem.9b00510

Alterations of fibroblast growth factor receptors (FGFRs) play key roles in numerous cancer progression and development, which makes FGFRs attractive targets in the cancer therapy. In the present study, based on a newly devised FGFR target-specific scoring function, a novel FGFR inhibitor hit was identified through virtual screening. Hit-to-lead optimization was then performed by integrating molecular docking and site-of-metabolism predictions with an array of in vitro evaluations and X-ray cocrystal structure determination, leading to a covalent FGFR inhibitor 15, which showed a highly selective and potent FGFR inhibition profile. Pharmacokinetic assessment, protein kinase profiling, and hERG inhibition evaluation were also conducted, and they confirmed the value of 15 as a lead for further investigation. Overall, this study exemplifies the importance of the integrative use of computational methods and experimental techniques in drug discovery.

Pd-catalyzed site-selective C(sp2)–H radical acylation of phenylalanine containing peptides with aldehydes

Marcos San Segundo  and  Arkaitz Correa

Chem. Sci., 2019
doi: 10.1039/C9SC03425K

The site-selective functionalization of C–H bonds within a peptide framework remains a challenging task of prime synthetic importance. Herein, the first Pd-catalyzed δ-C(sp2)–H acylation of Phe containing peptides with aldehydes is described. This oxidative coupling is distinguished by its site-specificity, tolerance of sensitive functional groups, scalability, and enantiospecificity and exhibits entire chemoselectivity for Phe motifs over other amino acid units. The compatibility of this dehydrogenative acylation platform with a number of oligopeptides of high structural complexity illustrates its ample opportunities for the late-stage peptide modification and bioconjugation.

Spontaneous Isomerization of Long-Lived Proteins Provides a Molecular Mechanism for the Lysosomal Failure Observed in Alzheimer’s Disease

Tyler R. Lambeth, Dylan L. Riggs, Lance E. Talbert, Jin Tang, Emily Coburn, Amrik S. Kang, Jessica Noll, Catherine Augello, Byron D. Ford, Ryan R. Julian

ACS Central Science, 2019
DOI: 10.1021/acscentsci.9b00369

Proteinaceous aggregation is a well-known observable in Alzheimer’s disease (AD), but failure and storage of lysosomal bodies within neurons is equally ubiquitous and actually precedes bulk accumulation of extracellular amyloid plaque. In fact, AD shares many similarities with certain lysosomal storage disorders though establishing a biochemical connection has proven difficult. Herein, we demonstrate that isomerization and epimerization, which are spontaneous chemical modifications that occur in long-lived proteins, prevent digestion by the proteases in the lysosome (namely, the cathepsins). For example, isomerization of aspartic acid into l-isoAsp prevents digestion of the N-terminal portion of Aβ by cathepsin L, one of the most aggressive lysosomal proteases. Similar results were obtained after examination of various target peptides with a full series of cathepsins, including endo-, amino-, and carboxy-peptidases. In all cases peptide fragments too long for transporter recognition or release from the lysosome persisted after treatment, providing a mechanism for eventual lysosomal storage and bridging the gap between AD and lysosomal storage disorders. Additional experiments with microglial cells confirmed that isomerization disrupts proteolysis in active lysosomes. These results are easily rationalized in terms of protease active sites, which are engineered to precisely orient the peptide backbone and cannot accommodate the backbone shift caused by isoaspartic acid or side chain dislocation resulting from epimerization. Although Aβ is known to be isomerized and epimerized in plaques present in AD brains, we further establish that the rates of modification for aspartic acid in positions 1 and 7 are fast and could accrue prior to plaque formation. Spontaneous chemistry can therefore provide modified substrates capable of inducing gradual lysosomal failure, which may play an important role in the cascade of events leading to the disrupted proteostasis, amyloid formation, and tauopathies associated with AD.

Discovery of Evobrutinib: An Oral, Potent and Highly Selective, Covalent Bruton’s Tyrosine Kinase (BTK) Inhibitor for the Treatment of Immunological Diseases

Richard Caldwell, Hui Qiu, Ben C Askew, Andrew T Bender, Nadia Brugger, Montserrat Camps, Mohanraj Dhanabal, Vikram Dutt, Thomas Eichhorn, Anna S Gardberg, Andreas Goutopoulos, Roland Grenningloh, Jared Head, Brian Healey, Brian L Hodous, Bayard R Huck, Theresa L Johnson, Christopher Jones, Reinaldo C Jones, Igor Mochalkin, Federica Morandi, Ngan Nguyen, Michael Meyring, Justin R Potnick, Dusica Cvetinovic Santos, Ralf Schmidt, Brian Sherer, Adam Shutes, Klaus Urbahns, Ariele Viacava Follis, Ansgar A Wegener, Simone C. Zimmerli, and Lesley Liu-Bujalski

J. Med. Chem., 2019
DOI: 10.1021/acs.jmedchem.9b00794 

Bruton’s tyrosine kinase (BTK) inhibitors such as ibrutinib hold a prominent role in the treatment of B cell malignancies. However, further refinement is needed to this class of agents, particularly in terms of adverse events (potentially driven by kinase promiscuity) which preclude their evaluation in non-oncology indications. Here, we report the discovery and preclinical characterization of evobrutinib, a potent, obligate covalent inhibitor with high kinase selectivity. Evobrutinib displayed sufficient preclinical pharmacokinetic and pharmacodynamic characteristics which allowed for in vivo evaluation in efficacy models. Moreover, the high selectivity of evobrutinib for BTK over epidermal growth factor receptor and other Tec family kinases suggested a low potential for off-target related adverse effects. Clinical investigation of evobrutinib is ongoing in several autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus.

Small molecule degraders of the hepatitis C virus protease reduce susceptibility to resistance mutations

Mélissanne de Wispelaere, Guangyan Du, Katherine A. Donovan, Tinghu Zhang, Nicholas A. Eleuteri, Jingting C. Yuan, Joann Kalabathula, Radosław P. Nowak, Eric S. Fischer, Nathanael S. Gray & Priscilla L. Yang

Nature Communications, 2019, 10, 3468
doi: 10.1038/s41467-019-11429-w

Targeted protein degradation is a promising drug development paradigm. Here we leverage this strategy to develop a new class of small molecule antivirals that induce proteasomal degradation of viral proteins. Telaprevir, a reversible-covalent inhibitor that binds to the hepatitis C virus (HCV) protease active site is conjugated to ligands that recruit the CRL4CRBN ligase complex, yielding compounds that can both inhibit and induce the degradation of the HCV NS3/4A protease. An optimized degrader, DGY-08-097, potently inhibits HCV in a cellular infection model, and we demonstrate that protein degradation contributes to its antiviral activity. Finally, we show that this new class of antiviral agents can overcome viral variants that confer resistance to traditional enzymatic inhibitors such as telaprevir. Overall, our work provides proof-of-concept that targeted protein degradation may provide a new paradigm for the development of antivirals with superior resistance profiles.

Integrative x-ray structure and molecular modeling for the rationalization of procaspase-8 inhibitor potency and selectivity

Janice H. Xu, Jerome Eberhardt, Brianna Hill-Payne, Gonzalo E. González-Páez, José Omar Castellón, Benjamin F. Cravatt, Stefano Forli, Dennis W. Wolan, Keriann M. Backus 

bioRxiv, 2019 
doi: 10.1101/721951

Caspases are a critical class of proteases involved in regulating programmed cell death and other biological processes. Selective inhibitors of individual caspases, however, are lacking, due in large part to the high structural similarity found in the active sites of these enzymes. We recently discovered a small-molecule inhibitor, 63-R, that covalently binds the zymogen, or inactive precursor (pro-form), of caspase-8, but not other caspases, pointing to an untapped potential of procaspases as targets for chemical probes. Realizing this goal would benefit from a structural understanding of how small molecules bind to and inhibit caspase zymogens. There have, however, been very few reported procaspase structures. Here, we employ x-ray crystallography to elucidate a procaspase-8 crystal structure in complex with 63-R, which reveals large conformational changes in active-site loops that accommodate the intramolecular cleavage events required for protease activation. Combining these structural insights with molecular modeling and mutagenesis-based biochemical assays, we elucidate key interactions required for 63-R inhibition of procaspase-8. Our findings inform the mechanism of caspase activation and its disruption by small molecules, and, more generally, have implications for the development of small molecule inhibitors and/or activators that target alternative (e.g., inactive precursor) protein states to ultimately expand the druggable proteome.