Covalent inhibitors of the RAS binding domain of PI3Ka impair tumor growth driven by RAS and HER2

Joseph E Klebba, Nilotpal Roy, Steffen M Bernard, Stephanie Grabow, Melissa A. Hoffman, Hui Miao, Junko Tamiya, Jinwei Wang, Cynthia Berry, Antonio Esparza-Oros, Richard Lin, Yongsheng Liu, Marie Pariollaud, Holly Parker, Igor Mochalkin, Sareena Rana, Aaron N. Snead, Eric J. Walton, Taylor E. Wyrick, Erick Aitichson, Karl Bedke, Jacyln C. Brannon, Joel M. Chick, Kenneth Hee, Benjamin D. Horning, Mohamed Ismail, Kelsey N. Lamb, Wei Lin, Justine Metzger, Martha K. Pastuszka, Jonathan Pollock, John J. Sigler, Mona Tomaschko, Eileen Tran, Todd M. Kinsella, Miriam Molina-Arcas, Gabriel M. Simon, David S. Weinstein, Julian Downward, Matthew P. Patricelli

bioRxiv 2024.12.17.629001; 

doi: https://doi.org/10.1101/2024.12.17.629001

Genetic disruption of the RAS binding domain (RBD) of PI 3-kinase (PI3K) prevents the growth of mutant RAS driven tumors in mice and does not impact PI3Ks role in insulin mediated control of glucose homeostasis. Selectively blocking the RAS-PI3K interaction may represent an attractive strategy for treating RAS-dependent cancers as it would avoid the toxicity associated with inhibitors of PI3K lipid kinase activity such as alpelisib. Here we report compounds that bind covalently to cysteine 242 in the RBD of PI3K p110a and block the ability of RAS to activate PI3K activity. These inhibitors have a profound impact on the growth of RAS mutant and also HER2 over-expressing tumors, particularly when combined with other inhibitors of the RAS/MAPK pathway, without causing hyperglycemia.

Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors

Zheng Zhao and Philip E. Bourne

Journal of Chemical Information and Modeling 2024

DOI: 10.1021/acs.jcim.4c00890

In designing covalent kinase inhibitors (CKIs), the inclusion of electrophiles as attacking warheads demands careful choreography, ensuring not only their presence on the scaffold moiety but also their precise interaction with nucleophiles in the binding sites. Given the limited number of known electrophiles, exploring adjacent chemical space to broaden the palette of available electrophiles capable of covalent inhibition is desirable. Here, we systematically analyze the characteristics of warheads and the corresponding adjacent fragments for use in CKI design. We first collect all the released cysteine-targeted CKIs from multiple databases and create one CKI data set containing 16,961 kinase-inhibitor data points from 12,381 unique CKIs covering 146 kinases with accessible cysteines in their binding pockets. Then, we analyze this data set, focusing on the extended warheads (i.e., warheads + adjacent fragments)─including 30 common warheads and 1344 unique adjacent fragments. In so doing, we provide structural insights and delineate chemical properties and patterns in these extended warheads. Notably, we highlight the popular patterns observed within reversible CKIs for the popular warheads cyanoacrylamide and aldehyde. This study provides medicinal chemists with novel insights into extended warheads and a comprehensive source of adjacent fragments, thus guiding the design, synthesis, and optimization of CKIs.

Structure-Based Discovery of a Series of Covalent, Orally Bioavailable, and Selective BFL1 Inhibitors

Adeline Palisse, Tony Cheung, Aileen Blokhuis, Thomas Cogswell, Bruna S. Martins, Rick Riemens, Rick Schellekens, Giovanni Battocchio, Chimed Jansen, Matthew A. Cottee, Kimberly Ornell, Claudia Sacchetto, Leonardo Leon, Maaike van Hoek- Emmelot, Mark Bostock, Brooke Leann Brauer, Kevin Beaumont, Simon C. C. Lucas, Samiyah Ahmed, J. Henry Blackwell, Ulf Börjesson, Andrea Gohlke, Iva Monique T. Gramatikov, David Hargreaves, Vera van Hoeven, Vasudev Kantae, Lea Kupcova, Alexander G. Milbradt, Uthpala Seneviratne, Nancy Su, John Vales, Haiyun Wang, Michael J. White, and Olaf Kinzel

Journal of Medicinal Chemistry 2024

DOI: 10.1021/acs.jmedchem.4c01995

BFL1, a member of the antiapoptotic BCL2 family, has been relatively understudied compared to its counterparts despite evidence of its overexpression in various hematological malignancies. Across two articles, we describe the development of BFL1 in vivo tools. The first article describes the hit identification from a covalent fragment library and the subsequent evolution from the hit to compound 6.22 This work reports the structure-based optimization of compound 6 into a series of BFL1 inhibitors selective over the other BCL2 family members, with low nanomolar cellular activity when combined with AZD5991, exemplified by compound 20. Compound 20 demonstrated a cell death phenotype in SUDHL1 and OCILY10 cell lines and in the in vivo study, BFL1 stabilization and cleaved caspase 3 activation were observed in a dose-dependent manner. In addition, the enzymatic turnover studies with the BFL1 protein showed that compound 20 stabilized the protein, extending the half-life to 10.8 h.

Open-source Electrophilic Fragment Screening Platform to Identify Chemical Starting Points for UCHL1 Covalent Inhibitors

Scott B. Ficarro, Zachary H. Marto, Nicholas M. Girardi, Dingyu Deng, Isabella Jaen Maisonet, Guillaume Adelmant, Laura E. Fleming, Mona Sharafi, Isidoro Tavares, Andrew Zhao, HyoJeon Kim, Hyuk-Soo Seo, Sirano Dhe-Paganon, Sara J. Buhrlage, Jarrod A. Marto

SLAS Discovery, 2024

https://doi.org/10.1016/j.slasd.2024.100198

Target-based screening of covalent fragment libraries with mass spectrometry has emerged as a powerful strategy to identify chemical starting points for small molecule inhibitors or find new binding pockets on proteins of interest. These libraries span diverse chemical space with a modest number of compounds. Screening covalent fragments against purified protein targets reduces the demands on the mass spectrometer with respect to absolute throughput, detection limit, and dynamic range. Given these relaxed analytical requirements, we sought to develop an open-source, medium-throughput mass spectrometry system for target-based covalent fragment screening. Our platform comprises automated, dual LC desalting columns integrated with electrospray ionization for rapid sample introduction and mass spectrometry detection. The system is operated through a simple python graphical user interface running on commodity microcontroller boards which allow integration with diverse liquid chromatography and mass spectrometry instruments. We provide scripts for fragment pooling, construction of sample batches, along with routines for data processing and visualization. The system enables primary screening of ∼10,000 covalent fragments per day in pooled format. In a proof-of-concept study we executed primary and secondary screens to identify 27 hit fragments against UCHL1, a deubiquitinating enzyme that is emerging as a drug target of interest across multiple clinical indications. We validated and triaged these covalent compounds through a series of orthogonal biochemical and chemoproteomic assays. The most promising chloroacetamide covalent fragment inhibited UCHL1 activity in vitro (IC50 <5 µM) and exhibited dose-dependent binding along with good selectivity against 57 cellular DUBs as quantified by activity-based protein profiling.

Identification of a covalent NEK7 inhibitor to alleviate NLRP3 inflammasome-driven metainflammation

Jin, X., Yang, Y., Liu, D. et al.

 Cell Commun Signal 22, 565 (2024). 

https://doi.org/10.1186/s12964-024-01919-w

Aberrant activation of NLRP3 inflammasome is associated with a variety of inflammatory diseases. Advances in understanding the molecular mechanisms of NLRP3 inflammasome have revealed that NEK7 is an essential component for its activation, but the development of drugs specifically targeting NEK7 remains challenging. Here we identify rociletinib (ROC), an anticancer drug in phase III clinical trial with high safety profile, as a highly potent and specific small-molecule antagonists of NEK7. Mechanistically, ROC covalent binds to the cysteine 79 of NEK7 through its reactive α, β-unsaturated carbonyl group, thereby inhibiting the interaction between NLRP3 and NEK7, and the subsequent assembly and activation of NLRP3 inflammasome. Furthermore, ROC alleviates the pathological features of metainflammation on the mouse model of type 2 diabetes (T2D). In summary, our results identify ROC as a covalent inhibitor of NEK7 and demonstrates that targeting NEK7 provides a potential and promising strategy for the treatment of NLRP3 inflammasome-driven T2D.

4-Oxo-β-lactams as Covalent Inhibitors of the Mitochondrial Intramembrane Protease PARL

Shanping Ji, Kathrin Bach, Vijay Madhav Miriyala, Jan Dohnálek, Miguel Riopedre-Fernandez, Martin Lepšík, Merel van de Plassche, Roeland Vanhoutte, Marta Barniol-Xicota, Rui Moreira, Kvido Strisovsky, and Steven H. L. Verhelst

ACS Medicinal Chemistry Letters 2024

DOI: 10.1021/acsmedchemlett.4c00384

Rhomboid proteases play a variety of physiological roles, but rhomboid protease inhibitors have been mostly developed for the E. coli model rhomboid GlpG. In this work, we screened different electrophilic scaffolds against the human mitochondrial rhomboid PARL and found 4-oxo-β-lactams as submicromolar inhibitors. Multifaceted computations suggest explanations for the activity at the molecular scale and provide models of covalently bound complexes. Together with the straightforward synthesis of the 4-oxo-β-lactam scaffold, this may pave the way toward selective, nonpeptidic PARL inhibitors.

Lysine-Targeted Covalent Inhibitors of PI3Kδ Synthesis and Screening by In Situ Interaction Upgradation

Bo Yuan, Yifan Feng, Mengyan Ma, Weiming Duan, Yujie Wu, Jiaxin Liu, Hong-Yi Zhao, Zhe Yang, San-Qi Zhang, and Minhang Xin

Journal of Medicinal Chemistry 2024

DOI: 10.1021/acs.jmedchem.4c01284

Targeting the lysine residue of protein kinases to develop covalent inhibitors is an emerging hotspot. Herein, we have reported an approach to develop lysine-targeted covalent inhibitors of PI3Kδ by in situ interaction upgradation of the H-bonding to covalent bonding. Several warhead groups were introduced and screened in situ, leading to lysine-targeted covalent inhibitors bearing aromatic esters with high bioactivity and PI3Kδ selectivity. Compound A11 bearing phenolic ester was finally optimized to show a long duration of action in SU-DHL-6 cells by multiple assays. Docking simulation and further protein mass spectrometry confirmed that A11 bound to PI3Kδ by covalent-bonding interactions with Lys779. Furthermore, A11 exhibited potently antitumor efficacy without obvious toxicity in the SU-DHL-6 and Pfeiffer xenograft mouse models. This study identified A11 to be a much more effective antitumor agent in vitro and in vivo as a lysine-targeted covalent inhibitor, and it also provided a practical approach for the development of lysine-targeted covalent inhibitors.