Discovery and development of Krazati (adagrasib/MRTX849), a potent, selective, orally bioavailable, covalent KRASG12C(OFF) inhibitor

Adrian L. Gill, Mathew A. Marx

RAS Drug Discovery Past, Present and Future 2025, 205-227

https://doi.org/10.1016/B978-0-443-21861-3.00017-6

Krazati (adagrasib/MRTX849) is a potent, selective, and covalent KRASG12C inhibitor, representing a significant breakthrough in directly targeting KRAS. Adagrasib demonstrates favorable drug-like properties, selectively modifying mutant cysteine 12 in GDP-bound KRASG12C, leading to the inhibition of KRAS-dependent signaling both in vitro and in vivo, and tumor regression in many KRASG12C-positive cell lines and patient-derived xenograft models across various tumor types. Objective responses have been observed in clinical trials, particularly in lung and colon adenocarcinoma patients with KRASG12C mutations. Comprehensive pharmacodynamic and pharmacogenomic profiling in both sensitive and partially resistant nonclinical models has shed light on the mechanisms limiting adagrasib antitumor activity. These resistance mechanisms include contributing factors related to KRAS nucleotide cycling, feedback reactivation pathways through activation of receptor tyrosine kinases, instances where tumors bypass KRAS dependence, and genetic dysregulation of the cell cycle. The ongoing characterization of adagrasib's activity, along with insights into response and resistance mechanisms, provides valuable understanding of KRAS dependence and opened a long-awaited opportunity to selectively target KRASG12C in patients. Furthermore, the identification of effective preclinical combinations, such as adagrasib with agents targeting RTKs, SHP2, mTOR, or the cell cycle, demonstrates enhanced responses and marked tumor regression. These findings contribute to the rational development of this class of agents, holding promise for improving therapeutic outcomes in KRASG12C-mutant human cancers.

Tuning isatoic anhydrides’ lysine ligation chemistry for bioconjugation and drug delivery

Tiwari, Sona, Senthil, Sathyapriya, Khanna, Shweta, Duraisamy, Santhosh, Vechalapu, Sai Kumari, Mallojjala, Sharath Chandra, Allimuthu, Dharmaraja,

Cell Reports Physical Science, 2024

DOI: https://doi.org/10.1016/j.xcrp.2024.102260

The discovery of new chemical entities for the selective modification of protein lysines is a recent interest in the development of unique covalent chemical probes. Isatoic anhydride (benzoxauracil), possessing aminophilic reactivity, was employed for the profiling of ligandable lysines in the cellular proteome. Our reactivity evaluation of benzoxauracil with proteins using mass spectral peptide mapping revealed a biased reactivity profile with nearly all the nucleophilic amino acids. The chemoselective reactivity of electrophilic tags is a key determinant of their idiosyncratic reactions. We applied the hard-soft-acid-base (HSAB) principle for tuning isatoic anhydride’s reactivity through systematic chemical modifications for lysine-dominant reactivity. We demonstrated the employability of ring-opening chemistry in isatoic anhydride as a drug delivery modality for the release of a small molecule and doxorubicin in cancer cells. Broadly, the tunable reactivity of isatoic anhydride could be leveraged for developing lysine-selective probes and drug delivery cargos.

CovalentInDB 2.0: an updated comprehensive database for structure-based and ligand-based covalent inhibitor design and screening

Hongyan Du, Xujun Zhang, Zhenxing Wu, Odin Zhang, Shukai Gu, Mingyang Wang, Feng Zhu, Dan Li, Tingjun Hou, Peichen Pan 

Nucleic Acids Research, 2024, gkae946

 https://doi.org/10.1093/nar/gkae946

The rational design of targeted covalent inhibitors (TCIs) has emerged as a powerful strategy in drug discovery, known for its ability to achieve strong binding affinity and prolonged target engagement. However, the development of covalent drugs is often challenged by the need to optimize both covalent warhead and non-covalent interactions, alongside the limitations of existing compound libraries. To address these challenges, we present CovalentInDB 2.0, an updated online database designed to support covalent drug discovery. This updated version includes 8303 inhibitors and 368 targets, supplemented by 3445 newly added cocrystal structures, providing detailed analyses of non-covalent interactions. Furthermore, we have employed an AI-based model to profile the ligandability of 144 864 cysteines across the human proteome. CovalentInDB 2.0 also features the largest covalent virtual screening library with 2 030 192 commercially available compounds and a natural product library with 105 901 molecules, crucial for covalent drug screening and discovery. To enhance the utility of these compounds, we performed structural similarity analysis and drug-likeness predictions. Additionally, a new user data upload feature enables efficient data contribution and continuous updates. CovalentInDB 2.0 is freely accessible at http://cadd.zju.edu.cn/cidb/.

Delineating cysteine-reactive compound modulation of cellular proteostasis processes

Ashley R. Julio, Flowreen Shikwana, Cindy Truong, Nikolas R. Burton, Emil R. Dominguez III, Alexandra C. Turmon, Jian Cao & Keriann M. Backus 

Nat Chem Biol 2024

https://doi.org/10.1038/s41589-024-01760-9

Covalent modulators and covalent degrader molecules have emerged as drug modalities with tremendous therapeutic potential. Toward realizing this potential, mass spectrometry-based chemoproteomic screens have generated proteome-wide maps of potential druggable cysteine residues. However, beyond these direct cysteine-target maps, the full scope of direct and indirect activities of these molecules on cellular processes and how such activities contribute to reported modes of action, such as degrader activity, remains to be fully understood. Using chemoproteomics, we identified a cysteine-reactive small molecule degrader of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nonstructural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host protein disulfide isomerases. This degrader activity was further potentiated by generalized electrophile-induced global protein ubiquitylation, proteasome activation and widespread aggregation and depletion of host proteins, including the formation of stress granules. Collectively, we delineate the wide-ranging impacts of cysteine-reactive electrophilic compounds on cellular proteostasis processes.

Expanding the Library of Covalent Cysteine Cathepsin Probes Featuring Sulfoxonium Ylide Electrophiles

Bangyan Xu, Simon J. Mountford, Philip E. Thompson, and Laura E. Edgington-Mitchell

ACS Omega 2024

DOI: 10.1021/acsomega.4c07604

Covalent activity-based probes are invaluable tools to monitor protease activity in vitro and in vivo. We recently discovered that dimethyl sulfoxonium ylides (SYs) bind selectively to cysteine cathepsin proteases in a mechanism-dependent manner. Herein, we present the synthetic routes and characterization of an expanded library of SY probes with a greater diversity in recognition sequences. The probes exhibit a range of potency and selectivity for the cathepsin family members. We also investigated the impact of fluorophore positioning on probes bearing P1 lysine. When sulfonated cyanine 5 was attached via the lysine side chain, the resulting probe was selective for cathepsin S. When attached to the α-amine, with the side chain amine either free or Boc-protected, the probes reacted with both cathepsin S and X. Bulk in the P1 position is thus well tolerated by cathepsin S but not cathepsin X. We examined the impact of Cy5 sulfonation on probe properties, demonstrating that unsulfonated probes exhibit greater cellular uptake, which affects their relative selectivity. Finally, we demonstrated that SY probes exhibit minimal labeling of cathepsin S in freshly prepared lysates, but this increases during the prolonged incubation of lysates. This work extends our understanding of SY probes and informs future probe development.

Redirecting the pioneering function of FOXA1 with covalent small molecules

Sang Joon Won, Yuxiang Zhang, Christopher J. Reinhardt,Lauren M. Hargis, Nicole S. MacRae,Kristen E. DeMeester,Evert Njomen,Jarrett R. Remsberg,Bruno Melillo, Benjamin F. Cravatt, Michael A. Erb

Molecular Cell, 2024

https://www.cell.com/molecular-cell/abstract/S1097-2765(24)00780-9

Pioneer transcription factors (TFs) bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report the chemical proteomic discovery of electrophilic compounds that stereoselectively and site-specifically bind the pioneer TF forkhead box protein A1 (FOXA1) at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the ligands relax the canonical DNA-binding preference of FOXA1 by strengthening interactions with suboptimal sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.

Potent Inhibition and Rapid Photoactivation of Endogenous Bruton’s Tyrosine Kinase Activity in Native Cells via Opto-Covalent Modulators

Weizhi Weng, Ping Zhang, and Zhengying Pan

Journal of the American Chemical Society 2024

DOI: 10.1021/jacs.4c06459

Naturally, kinases exert their activities in a highly regulated fashion. A number of ingenious approaches have been developed to artificially control kinase activity by external stimuli, such as the incorporation of unnatural amino acids or the fusion of additional protein domains; however, methods that directly modulate endogenous kinases in native cells are lacking. Herein, we present a facile and potent method that takes advantage of recent developments in targeted covalent inhibitors and rapid light-mediated uncaging chemistry. Using an important drug target, Bruton’s tyrosine kinase (BTK), as an example, these opto-covalent modulators successfully blocked the activity of endogenous BTK in native cells after simple incubation and washout steps. However, upon a few minutes of light irradiation, BTK activity was cleanly restored, and could be blocked again by conventional inhibitors. Promisingly, this photoactivation strategy easily worked in human peripheral blood mononuclear cells (hPBMCs).

 

New electrophiles targeting thiols in a reversible covalent manner

Xingyu Ma,   Manyi Xu,   Fengge Wang,  Tingting Hu,  Xinyuan Chena  and  Chong-Jing Zhang

Chem. Commun., 2024

DOI

https://doi.org/10.1039/D4CC04612A

Reversible covalent electrophiles with the advantages of both reversible and covalent interactions receive much attention in the fields of chemical biology and medicinal chemistry. Here, we report two electron-deficient olefins activated by amide and ester, amide-substituted acrylamide and methyl ester-substituted acrylamide, targeting thiols in a reversible covalent manner.

Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach

Eric M. Merten  and John D. Sears  and Tina M. Leisner  and P. Brian Hardy  and Anirban Ghoshal  and Mohammad Anwar Hossain  and Kesatebrhan Haile Asressu  and Peter J. Brown  and Edwin G. Tse  and Michael A. Stashko  and Kelin Li  and Jacqueline L. Norris-Drouin  and Laura E. Herring  and Angie L. Mordant  and Thomas S. Webb  and Christine A. Mills  and Natalie K. Barker  and Zachary J. Streblow  and Sumera Perveen  and Cheryl H. Arrowsmith  and Rafael Miguez Couñago  and Jamie J. Arnold  and Craig E. Cameron  and Daniel N. Streblow  and Nathaniel J. Moorman  and Mark T. Heise  and Timothy M. Willson  and Konstantin I. Popov  and Kenneth H. Pearce 

Proc. Natl. Acad. Sci. U.S.A. 2024 121 (42) e2409166121

https://doi.org/10.1073/pnas.2409166121

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV nonstructural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose–response follow-up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC50 of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a kinact /KI of 6.4 × 103 M−1s−1. LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity in proteomic experiments or against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the identification and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic.

Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads

Bálint, D., Póti, Á.L., Alexa, A. et al. 

Nat Commun 15, 8606 (2024). 

https://doi.org/10.1038/s41467-024-52573-2

There has been a surge of interest in covalent inhibitors for protein kinases in recent years. Despite success in oncology, the off-target reactivity of these molecules is still hampering the use of covalent warhead-based strategies. Herein, we disclose the development of precision-guided warheads to mitigate the off-target challenge. These reversible warheads have a complex and cyclic structure with optional chirality center and tailored steric and electronic properties. To validate our proof-of-concept, we modified acrylamide-based covalent inhibitors of c-Jun N-terminal kinases (JNKs). We show that the cyclic warheads have high resilience against off-target thiols. Additionally, the binding affinity, residence time, and even JNK isoform specificity can be fine-tuned by adjusting the substitution pattern or using divergent and orthogonal synthetic elaboration of the warhead. Taken together, the cyclic warheads presented in this study will be a useful tool for medicinal chemists for the deliberate design of safer and functionally fine-tuned covalent inhibitors.

Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold

Póti, Á.L., Bálint, D., Alexa, A. et al. 

Nat Commun 15, 8607 (2024). 

https://doi.org/10.1038/s41467-024-52574-1

For mitogen-activated protein kinases (MAPKs) a shallow surface—distinct from the substrate binding pocket—called the D(ocking)-groove governs partner protein binding. Screening of broad range of Michael acceptor compounds identified a double-activated, sterically crowded cyclohexenone moiety as a promising scaffold. We show that compounds bearing this structurally complex chiral warhead are able to target the conserved MAPK D-groove cysteine via reversible covalent modification and interfere with the protein-protein interactions of MAPKs. The electronic and steric properties of the Michael acceptor can be tailored via different substitution patterns. The inversion of the chiral center of the warhead can reroute chemical bond formation with the targeted cysteine towards the neighboring, but less nucleophilic histidine. Compounds bind to the shallow MAPK D-groove with low micromolar affinity in vitro and perturb MAPK signaling networks in the cell. This class of chiral, cyclic and enhanced 3D shaped Michael acceptor scaffolds offers an alternative to conventional ATP-competitive drugs modulating MAPK signaling pathways.

Development of an orally bioavailable covalent STING inhibitor

NIU, G.-H., Hsiao, W.-C., Lee, P.-H., Zheng, L.-G., Yang, Y.-S., Huang, W.-C., Hsieh, C.-C., Chiu, T.-Y., Wang, J.-Y., Chen, C.-P., Huang, C.-L., You, M.-S., Kuo, Y.-P., Wang, C.-M., Wen, Z.-H., Yu, G.-Y., Chen, C.-T., Chi, Y.-H., Tung, C.-W., Hsu, S.-C., Yeh, T.-K., Sung, P.-J., Zhang, M. M., and Tsou, L. K. 

ChemRxiv, 2024

https://doi.org/10.26434/chemrxiv-2024-62g35

Pharmacological inhibition of cGAS-STING-controlled innate immune pathway is an emerging therapeutic strategy for a myriad of inflammatory diseases, including autoimmune disease, ulcerative colitis, non-alcoholic fatty liver disease and aging-related neurodegeneration. Here we report GHN105 as an orally bioavailable covalent STING inhibitor. Late-stage diversification of the briarane-type diterpenoid excavatolide B allowed the installation of solubility-enhancing functional groups while enhancing its activity as a covalent STING inhibitor against multiple human STING variants, including the S154 variant responsible for a genetic autoimmune disease. Selectively engaging the membrane-proximal Cys91 residue of STING, GHN105 dose-dependently inhibited cGAS-STING signaling and type I interferon responses in cells and in vivo. Orally administered GHN105 exerted marked therapeutic efficacy and reversed key pathological features in a delayed-treatment acute colitis mouse model. Notably, we also showed that GHN105 covalently engaged STING in the colon tissues. Our study provided proof of concept that synthetic briarane analog GHN105 serves as a safe and orally active covalent STING inhibitor. With a growing number of chronic inflammatory diseases linked to aberrant STING activation, orally bioavailable STING inhibitors would benefit patients by lowering the infection risk from frequent injections while allowing long-term systemic administration.

Discovery of electrophilic degraders that exploit SNAr chemistry

Zhe Zhuang, Woong Sub Byun, Zuzanna Kozicka, Brendan G. Dwyer, Katherine A. Donovan, Zixuan Jiang, Hannah M. Jones, Dinah M. Abeja, Meredith N. Nix, Jianing Zhong, Mikołaj Słabicki, Eric S. Fischer, Benjamin L. Ebert, Nathanael S. Gray

bioRxiv 2024.09.25.615094; 

doi: https://doi.org/10.1101/2024.09.25.615094

Targeted covalent inhibition (TCI) and targeted protein degradation (TPD) have proven effective in pharmacologically addressing formerly ‘undruggable’ targets. Integration of both methodologies has resulted in the development of electrophilic degraders where recruitment of a suitable E3 ubiquitin ligase is achieved through formation of a covalent bond with a cysteine nucleophile. Expanding the scope of electrophilic degraders requires the development of electrophiles with tempered reactivity that enable selective ligase recruitment and reduce cross-reactivity with other cellular nucleophiles. In this study, we report the use of chemical moieties that enable nucleophilic aromatic substitution (SNAr) reactions in the rational design of electrophilic protein degraders. Appending an SNAr covalent warhead to several preexisting small molecule inhibitors transformed them into degraders, obviating the need for a defined E3 ligase recruiter. The SNAr covalent warhead is versatile; it can recruit various E3 ligases, including DDB1 and CUL4 associated factor 11 (DCAF11), DDB1 and CUL4 associated factor 16 (DCAF16), and possibly others. The incorporation of an SNAr covalent warhead into the BRD4 inhibitor led to the discovery of degraders with low picomolar degradation potency. Furthermore, we demonstrate the broad applicability of this approach through rational functional switching from kinase inhibitors into potent degraders.

Multi-tiered chemical proteomic maps of tryptoline acrylamide–protein interactions in cancer cells

Njomen, E., Hayward, R.E., DeMeester, K.E. et al. Multi-tiered chemical proteomic maps of tryptoline acrylamide–protein interactions in cancer cells. Nat. Chem. (2024). 

https://doi.org/10.1038/s41557-024-01601-1

Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds—termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.