Covalent Probes Reveal Small-Molecule Binding Pockets in Structured RNA and Enable Bioactive Compound Design

Sandra Kovachka, Jielei Wang, Amirhossein Taghavi, Yilin Jia, Taro Asaba, Karen C. Wolff, Mason Martin, Xueyi Yang, Samantha M. Meyer, Sabine Ottilie, Mina Heacock, Zhong Cheng, Case W. McNamara, Gurudutt Dubey, Arnab K. Chatterjee, Sumit Chanda, José Gallego, Jessica L. Childs-Disney, and Matthew D. Disney

Journal of the American Chemical Society 2025

DOI: 10.1021/jacs.5c11898

The SARS-CoV-2 frameshift stimulation element (FSE) is a critical RNA structure that is essential for viral replication and represents a promising target for antiviral intervention. Here, Chemical Cross-Linking and Isolation by Pull-down (Chem-CLIP) covalent target validation and binding site mapping was applied, to identify small-molecule binding pockets within the FSE and ultimately develop a ligandability map. These studies employed ∼ 190 Chem-CLIP fragments, including the fluoroquinolone merafloxacin, previously shown to interact with this element. Covalent mapping defined merafloxacin’s binding pocket at a nucleotide-level resolution and revealed interactions that, along with structure-based design, efficient one-pot on-plate synthesis and competitive displacement assays, enabled the development of bioactive compounds with antiviral activity. Complementary chemical probing with dimethyl sulfate (DMS) in the presence of a bioactive ligand, coupled to Deconvolution of RNA Alternative Conformations (DRACO), revealed that compound binding increased the reactivity of specific nucleotides with DMS, indicative of changes in local RNA folding. These results highlight the importance of combining Chem-CLIP and DMS profiling to differentiate direct ligand binding from ligand-induced changes in RNA structure. In addition, in silico pocket analysis of FSE structures derived from cryogenic-electron microscopy (cryo-EM) studies identified four recurring cavities, including the experimentally determined merafloxacin and Chem-CLIP fragments binding pockets. Altogether, the findings advance our understanding of RNA–ligand interactions and support a strategy to design and discover small molecules that bind RNA structures.

AI-assisted delivery of novel covalent WRN inhibitors from a non-covalent fragment screen

Geoffrey M.T. Smith, Laksh Aithani, Charlotte E. Barrett, Alwin O. Bucher, Christopher D.O. Cooper, Sébastien L. Degorce, Andrew S. Doré, Catherine T. Fletcher, Sophie Huber, Rosemary Huckvale, Amanda J. Kennedy,  Abigail A. Mornement, Mark Pickworth, Prakash Rucktooa, Conor C.G. Scully,  Sarah E. Skerratt

Bioorganic & Medicinal Chemistry Letters, 2025

https://doi.org/10.1016/j.bmcl.2025.130421

Werner (WRN) helicase, has emerged as a promising therapeutic target for cancers associated with microsatellite instability (MSI). This letter describes the discovery of small molecule inhibitors from a fragment screen that occupy a cryptic, allosteric site of WRN helicase. Key findings include the identification of benzimidazole and amino-indazole scaffolds, exploiting their proximity to Cys727 via covalent modification. The use of our proprietary co-folding model DragonFold assisted the identification of novel WRN helicase inhibitors. These, together with near-neighbor profiling, offer tools for furthering the understanding of WRN and BLM helicase function, and potential therapeutic avenues for MSI-associated cancers.

Sulfinyl Aziridines as Stereoselective Covalent Destabilizing Degraders of the Oncogenic Transcription Factor MYC

H. T. Rosen, K. Li, C. E. Stieger, E. L. Li, B. Currier, S. M. Brittain, F. J. Garcia, D. C. Beard, M. D. Jones, S. Haenni-Holzinger, D. Dovala, J. M. McKenna, M. Schirle, T. J. Maimone, D. K. Nomura, Angew. Chem. Int. Ed.. 2025, e202508518.

https://doi.org/10.1002/anie.202508518

Although MYC is a significant oncogenic transcription factor driver of cancer, directly targeting MYC has remained challenging due to its intrinsic disorder and poorly defined structure, deeming it “undruggable.” Whether transient pockets formed within unstructured regions of proteins can be selectively targeted with small molecules remains an outstanding challenge. Here, we developed a stereochemically paired spirocyclic oxindole aziridine covalent library and screened this library for degradation of MYC. We identified a hit covalent ligand, KL2-236, bearing a unique sulfinyl aziridine warhead, that engaged MYC as a pure MYC/MAX protein complex, and in cancer cells to destabilize MYC, inhibit MYC transcriptional activity and degrade MYC in a proteasome-dependent manner through targeting intrinsically disordered C203 and D205 residues. Notably, this reactivity was most pronounced for specific stereoisomers of KL2-236 with a diastereomer, KL4-019, that was largely inactive. Mutagenesis of both C203 and D205 completely attenuated KL2-236-mediated MYC degradation. We also optimized our KL2-236 hit compound to generate a more potent, selective, and durable MYC degrader, KL4-219A. Our results reveal a novel ligandable site within MYC and indicate that certain intrinsically disordered regions within transcription factors, such as MYC, can be interrogated by isomerically unique chiral small molecules, leading to destabilization and degradation.

Covalent Ligand Electrophiles Are Differentially Activated by Proximity Effects Which Govern Latent Protein Reactivit

 Tomas V. Frankovich, Harrison M. McCann, Kyle S. Hoffman, and Anthony F. Rullo

ACS Central Science Article ASAP

DOI: 10.1021/acscentsci.5c00699

Covalent ligands contain an electrophilic moiety that reacts with a nucleophilic residue on a target protein, following an initial reversible binding event. Covalent ligand development typically involves efforts to increase on-target selectivity by maximizing the ligand binding affinity and minimizing intrinsic electrophile reactivity. Problematically, this limits labeling kinetics and requires high affinity ligands. The concept of “latency” describes the potential for “turn-on” activation of electrophiles upon target engagement. Here, we investigate the potential intrinsic latency of covalent electrophiles and test the hypothesis that diverse electrophiles can be differentially activated by proximity effects. We develop a kinetic effective molarity (EMk) approach to quantitatively characterize kinetics associated with diverse electrophilic reaction mechanisms, both with and without binding proximity effects. We observe that different electrophiles are associated with significantly different EMk parameters, with SuFEx and acrylamide electrophiles associated with the highest intrinsic latency. Eyring transition state analysis revealed that all covalent ligands, independent of electrophile, benefit from significant transition state entropic stabilization. Strikingly, electrophiles associated with the highest latency are associated with greater relative transition state stabilization with different enthalpic and entropic contributions. These findings quantitatively describe electrophile latency and will aid the mechanism-guided development of next-generation covalent ligands associated with “turn-on” reactivity.

A covalent inhibitor targeting Cys16 on RhoA in colorectal cancer

Tin-Yan Koo, Jason Ying Ki Li, Nga-Sze Lee, Jintian Chen, Hillary Yui-Yan Yip, Ianto Bosheng Huang, Kai-Yu Ng, Helen H.N. Yan, Suet Yi Leung, Stephanie Ma, Jingying Zhou, Clive Yik-Sham Chung

https://www.cell.com/cell-chemical-biology/fulltext/S2451-9456%2825%2900255-7

RhoA is a key cancer driver and potential colorectal cancer (CRC) therapy target but remains undrugged clinically. Using activity-based protein profiling (ABPP) and mass spectrometry (MS), we identified CL16, a covalent inhibitor targeting the unique Cys16 on RhoA subfamily, which confers high specificity over other Rho family proteins. Cys16 is adjacent to the nucleotide-binding pocket and switch regions, which are critical for RhoA function. The binding by CL16 effectively disrupts GTP binding and inhibits RhoA activity in CRC cells, leading to cytotoxic killing of CRC cells through cell-cycle arrest and apoptosis. In mouse CRC models, CL16 exhibits strong antitumor and antimetastatic effects, promotes T cell infiltration into the tumor microenvironment, and shows no observable toxicity. Our findings suggest that covalent targeting of the druggable Cys16 on RhoA offers a promising strategy for CRC treatment, providing a foundation for developing specific RhoA inhibitors for clinical application.

Covalent Irreversible Inhibitors of Tetracycline Destructases

Ruihao Li, Yao-Peng Xue, Steven T. Le, Wai Kwan Tang, Niraj H. Tolia, Gautam Dantas, and Timothy A. Wencewicz

ACS Infectious Diseases 2025

DOI: 10.1021/acsinfecdis.5c00322

 Next-generation tetracycline antibiotics are threatened by an emerging resistance mechanism ─ enzymatic inactivation. The relevant enzymes ─ tetracycline destructases (TDases) ─ are structural homologues of class A flavin monooxygenase (FMO) that oxidize tetracycline antibiotics, leading to various inactive degradation products. Small molecule inhibitors of antibiotic-inactivating enzymes are critical clinical therapeutics used to manage bacterial resistance with combination therapy. While reversible TDase inhibitors have been reported, we sought to develop covalent inhibitors that are better aligned with clinically effective covalent β-lactamase inhibitors. Here, we report the design, chemical synthesis, and biochemical characterization of the first covalent irreversible inhibitors of TDases based on C9-derivatives of anhydrotetracycline (aTC). The reactive warheads were installed via a one-step Mannich reaction linking either an N-(1-methyl)cyclopropylamine or N-propargylamine group to the C9-position of the aTC D-ring via an amino methylene linkage. We also synthesized two nonspecific FMO inhibitors, N-(1-methyl)cyclopropylbenzylamine (1) and N-methyl-N-benzyl-propargylamine (2) as mechanistic probes to distinguish reactivity with the essential FAD cofactor in TDases via one- or two-electron transfer pathways, respectively. We evaluated the compounds as potential inhibitors of representative TDases from the two major classes─Type 1 (TetX6 and TetX7) and Type 2 (Tet50). The aTC-based compounds 3-5 inhibited both Type 1 and Type 2 TDases with notable differences in potency and inhibition mechanism. The inhibition of Type 1 TDases was more potent but reversible with no time dependence. The inhibition of Type 2 TDases was time-dependent and irreversible even after exhaustive dialysis, consistent with a covalent mechanism of inhibition. Molecular modeling of the inhibitors supports unique inhibitor binding modes for Type 1 and Type 2 TDases that are consistent with the observed differences in the inhibition modes. Blue light irradiation of the Type 2 TDase enhanced this reactivity. Treatment of Tet50 with probe molecules 1 and 2 under blue light exposure enabled the identification of covalent FAD adducts via mass spectrometry that are consistent with the expected one- and two-electron transfer reaction modes of the cyclopropylamine and propargylamine warheads with the FAD cofactor. At concentrations as low as 2 μg/mL, the aTC-based covalent inhibitors 3-5 recovered tetracycline activity against E. coli overexpressing TDases. Our findings suggest that the inhibition of TDases through covalent trapping of the FAD cofactor is a viable strategy for overcoming TDase-mediated antibiotic resistance.

Covalent chemical probes

Backus, K.M., Wilson, A.J. 

Commun Chem 8, 266 (2025). 

https://doi.org/10.1038/s42004-025-01652-6

Cell-Active, Irreversible Covalent Inhibitors Targeting a Surface-Exposed Non-Catalytic Lysine on Aurora a Kinase by Using Squarate Chemistry

Z. Wang, X. Wang, Y. Li, P. Li, S. Huang, P. Chen, G. Tang, X. Ding, Z. Zhang, Z.-M. Zhang, Y. Zhou, S. Q. Yao, X. Lu, 

Angew. Chem. Int. Ed. 2025, e202510763

https://doi.org/10.1002/anie.202510763

Targeting surface-exposed lysines in kinases through covalent modification presents a major challenge due to their high pKa and inherently low reactivity. While current research primarily targets more reactive catalytic lysines buried in the ATP-binding pocket, no systematic rational strategy has yet been developed for selectively engaging surface-exposed lysines. Herein, we present a versatile strategy for developing cell-active covalent kinase inhibitors (CKIs) by selectively targeting unique surface-exposed lysines using squarate chemistry. By using Aurora A (AURKA) as a proof-of-concept, we systematically evaluated this approach against other well-known lysine-reactive warheads (e.g., EBA, SO2F, and OSO2F) and demonstrated, for the first time, squarates’ superior efficacy in engaging these challenging low-reactivity lysines. Amongst various AURKA CKIs, AL8 emerged as the first-in-class squarate-based, cell-active inhibitor, exhibiting excellent selectivity in both biochemical and cellular assays with long-residence time in covalently engaging endogenous AURKA. Detailed investigation of effects of leaving groups on squaric esters provided valuable insights for future development of lysine-reactive CKIs. Our finding has established squarate-containing ligands as a unique and readily tunable platform for covalent modification of surface-exposed, non-catalytic lysines in targeted kinase drug discovery.

Small-Molecule Covalent Stabilization and Inhibition of the TEAD·YAP1 Transcription Factor in Cancer Cells

I-Ju Yeh, Khuchtumur Bum-Erdene, Mona K. Ghozayel, Giovanni Gonzalez-Gutierrez, and Samy O. Meroueh

ACS Chemical Biology 2025

https://pubs.acs.org/doi/10.1021/acschembio.5c00283

Transcriptional enhanced associate domain transcription factors (TEAD1 to TEAD4) bind to transcriptional coactivator Yes-Associated Protein (YAP1) or its paralog transcriptional coactivator with PDZ-binding motif (TAZ) to regulate Hippo pathway target genes. The Hippo pathway is a conserved signaling pathway that regulates organ size and cell fate by controlling cell proliferation and apoptosis. Here we report small acrylamide molecules that form a covalent bond with a conserved cysteine at the TEAD palmitate pocket. Binding studies showed profound stabilization of TEADs by the small molecules, and cocrystal structures reveal that the compounds mimic the binding mode of palmitate. The small molecules achieved submicromolar binding constants and subhour reaction half-lives for all four TEADs. In mammalian cells, the compounds stabilize the TEAD•YAP1 interaction yet inhibit the TEAD transcription factor activity. Unexpectedly, several compounds degraded TEAD and YAP1 proteins and inhibited cancer cell viability. This work suggests that degradation of TEAD and YAP1 may amplify the antitumor effects of small molecules targeting the TEAD palmitate pocket, with implications for other cancer targets featuring allosteric lipid-binding sites.

Chemoselective Installation of Electrophilic Warheads onto C-Terminal Peptide Hydrazides for Covalent Protease Inhibitor Synthesis

Shaun O’Hare, Kateryna A. Tolmachova, and Jeffrey W. Bode

ACS Chemical Biology 2025

DOI: 10.1021/acschembio.5c00281

Covalent binders to protein targets offer a powerful approach to the generation of tool compounds and an increasingly common strategy for therapeutic development. The installation of electrophiles onto peptide binders, however, is often precluded by standard conditions for peptide synthesis, which involve strong nucleophiles, bases, and acids. The introduction of C-terminal electrophiles is further complicated by the C → N directionality of standard solid-phase peptide synthesis. Here, we employ chemoselective, site-specific functionalization of C-terminal peptide acyl hydrazides to install strong electrophiles on unprotected peptides. Using automated, high-throughput liquid handling and solid-phase extraction techniques, we have established a combinatorial workflow for the synthesis of peptide-derived covalent protease inhibitors. This methodology enables the synthesis and initial screening of inhibitor libraries in a 96-well plate format without the need for chromatographic purification prior to enzyme inhibition studies, leading to the identification of covalent Cathepsin S inhibitors active in the nanomolar range. When tested in cells, the covalent probes revealed strong off-target interactions with the protein disulfide isomerase PDIA1. These findings both underscore the role of chemoselective chemistries for covalent probe synthesis and highlight the utility of the platform for both the rapid identification of potent inhibitors and the detection of potential off-target interactions.

Structure-based rational design of covalent probes

Holcomb, M., Llanos, M., Hansel-Harris, A. et al. 

Commun Chem 8, 242 (2025). 

https://doi.org/10.1038/s42004-025-01606-y

Covalent probes are becoming increasingly important to both fundamental biology and drug design, as what was once an idiosyncrasy at best and a source of toxicity at worst has transitioned to a paradigm for drug discovery. However, these covalent probes offer different challenges for the incorporation of structural data into the design process than do non-covalent probes, whose activity may be captured by very few bound states. In this review, we discuss the role of structure-based design in the discovery and optimization of covalent probes, with a special emphasis on computational methods to leverage structural data.

Potent Inducers of Paraptosis through Electronic Tuning of Hemicyanine Electrophiles

uan F. Tamez-Fernández, Craig F. Steven, Jade Nguyen, and Pablo Rivera-Fuentes

Journal of the American Chemical Society 2025

DOI: 10.1021/jacs.5c07109

Paraptosis is a distinct form of programmed cell death characterized by cytoplasmic vacuolization, mitochondrial swelling, and endoplasmic reticulum (ER) dilation, offering an alternative to apoptosis for therapeutic applications. In this study, we identified a hemicyanine derivative that is a potent paraptosis inducer in two cancer cell lines. This compound triggers hallmark paraptotic features, including ER swelling, mitochondrial morphological changes, increased superoxide production, and caspase-independent cell death. This activity is dependent on the ability of the probe to modify thiols covalently. Proteomic analysis using a biotinylated, activity-based probe revealed Sec23 homologue A and GDP-dissociation inhibitor alpha as potential targets implicated in paraptosis activation. This lead compound already displayed some degree of selectivity, exemplified by its minimal interaction with well-known nucleophilic protein targets such as protein disulfide isomerases. These findings establish the hemicyanine chemical family as a promising scaffold for paraptosis research and suggest potential as a therapeutic lead for diseases where traditional apoptosis pathways are dysregulated.

Profiling the proteome-wide selectivity of diverse electrophiles

Zanon, P. R. A.; Yu, F.; Musacchio, P.; Lewald, L.; Zollo, M.; Krauskopf, K.; Mrdović, D.; Raunft, P.; Maher, T. E.; Cigler, M.; Chang, C.; Lang, K.; Toste, F. D.; Nesvizhskii, A. I.; Hacker, S. M. 

ChemRxiv 2021.  

https://doi.org/10.26434/chemrxiv-2021-w7rss-v2

Targeted covalent inhibitors are powerful entities in drug discovery, but their application has so far mainly been limited to addressing cysteine residues. The development of cysteine-directed covalent inhibitors has largely profited from determining their proteome-wide selectivity using competitive residue-specific proteomics. Several probes have recently been described to monitor other amino acids using this technology and many more electrophiles exist to modify proteins. Nevertheless, a direct, proteome-wide comparison of the selectivity of diverse probes is still entirely missing. Here, we developed a completely unbiased workflow to analyse electrophile selectivity proteome-wide and applied it to directly compare 54 alkyne probes containing diverse reactive groups. In this way, we verified and newly identified probes to monitor a total of nine different amino acids as well as the N-terminus proteome-wide. This selection includes the first probes to globally monitor tryptophans, histidines and arginines as well as novel tailored probes for methionines, aspartates and glutamates.

Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 Mpro Inhibitor with Pan-Coronavirus Activity

Qian Wen Tan, Subramanyam Vankadara, Jia Yi Fong, Yi Yang See, Nithya Baburajendran, Pearly Shuyi Ng, Weijun Xu, Yee Khoon Yeo, Weiling Wang, Choon Heng Low, Li Hong Tan, Eileen Gui Ju Tay, Yun Xuan Wong, Chuhui Huang, Sandra Sim, Shi Hua Ang, Hannah Hui Min Toh, Juliana Mohammad, Gang Wang, Boping Liu, Shu Ting Tan, Perlyn Zekui Kwek, Monique Danielle Dawson, Qin Yao Oh, Xiaoying Koh, Joma Joy, May Ann Lee, Walter Stunkel, Vishal Pendharkar, Hannes Hentze, Siew Pheng Lim, Kantharaj Ethirajulu, C. S. Brian Chia, and Joseph Cherian

J. Med. Chem. 2025

https://doi.org/10.1021/acs.jmedchem.5c00581

Resulting in several million deaths globally, the COVID-19 pandemic has highlighted the criticality of antiviral drugs during a viral pandemic. Herein, we describe our efforts toward targeting SARS-CoV-2 Mpro, a key viral protease, which led to the discovery of compound 18, a reversible covalent inhibitor with potent antiviral activity against several clinical variants of SARS-CoV-2. Compound 18 demonstrated dose-dependent efficacy in a mouse-adapted SARS-CoV-2 infection model, with favorable pharmacokinetic profiles in mice, rats, dogs, and monkeys.

 

A twist in the tale: shifting from covalent targeting of a tyrosine in JAK3 to a lysine in MK2

Laura Hillebrand, Guiqun Wang, Alexander Rasch, Benedikt Masberg, Apirat Chaikuad, Thales Kronenberger, Ellen Günther, Michael Forster, Antti Poso, Michael Lämmerhofer, Stefan A. Laufer, Stefan Knapp, Matthias Gehringer

RSC Med. Chem., 2025

https://doi.org/10.1039/D5MD00440C

While cysteine targeting in kinases is well established and widely used, covalent interactions with other amino acids remain much less explored. We aimed to develop covalent inhibitors targeting tyrosine residues in the protein kinases JAK3 and MK2 using structure-based design principles to generate small sets of ligands containing tyrosine-reactive sulfonyl fluoride and the less-explored fluorosulfate warheads. While the JAK3 inhibitors failed to achieve covalent binding, the fluorosulfate-bearing MK2 inhibitor 42, which had been designed as an allosteric binder, unexpectedly formed a bond with the “catalytic” lysine, additionally uncovering a unique interaction at the hinge region. This highlights the untapped potential of fluorosulfates and provides a rare example of the use of this electrophile for lysine targeting in kinases. Our results highlight the limitations of traditional design methods and support the integration of fragment/lead-like covalent library screening to discover unanticipated interactions.

AGPAT4 targeted covalent inhibitor potentiates targeted therapy to overcome cancer cell plasticity in hepatocellular carcinoma mouse models

Ng, K.-Y.; Koo, T.-Y.; Huang, I. B.; Lee, T. K.-W.; Fong, T.-L.; Gao, Y.; Wong, T.-L.; Gao, Y.; Yun, J.-P.; Guan, X.-Y.; Liu, M.; Chung, C. Y.-S.; Ma, S.

Sci. Transl. Med.17,eadn9472(2025).

DOI:10.1126/scitranslmed.adn9472

The development of cancerous cells leads to considerable changes in metabolic processes to meet the demands of tumor growth. Tumor lineage plasticity has been identified as a key factor in therapy resistance and tumor recurrence. Herein, we showed one aspect of this plasticity to be abnormal glycerophospholipid metabolism, specifically the presence of a metabolic protein called 1-acylglycerol-3-phosphate o-acyltransferase 4 (AGPAT4). We identified AGPAT4 as an oncofetal protein that is abundant in embryonic stem cells and hepatocellular carcinoma (HCC) tumor cells but is low or absent in most normal tissues. We demonstrated that AGPAT4 is a functional regulator of tumor lineage plasticity, which correlates with enhanced metastasis and resistance to sorafenib. Heightened plasticity was induced as a result of increased AGPAT4-mediated conversion of LPA (lysophosphatidic acid) to phosphatidic acid (PA), which then acts on its downstream mTOR/S6K/S6 signaling pathway. Inhibition of Agpat4 by the AAV8-mediated liver-directed strategy in an immunocompetent HCC mouse model reduced tumorigenicity and stemness and sensitized tumors to sorafenib. Through a chemical biology approach, a cysteine-reacting compound that specifically targets AGPAT4 at the Cys228 residue and therefore hinders its acyltransferase activity was identified and found to work synergistically with sorafenib in suppressing HCC in tumor xenograft models derived from patients with preclinical HCC and sorafenib-resistant HCC. Toxicological analysis revealed minimal side effects associated with the covalent inhibitor. In conclusion, the plasticity of tumor lineages induced by AGPAT4 represents a potential target for HCC treatment and could expand the effectiveness of sorafenib treatment, offering new possibilities for HCC therapy.

A Covalent Self-Reporting Peptide Degrader Enables Real-Time Monitoring of Targeted Protein Degradation In Vivo

Wei Zhang, Lizhen Yuan, Rui Liu, Yanbo Jing, Shijun Lin, Hao Fang, Yuxuan Li, Xiaohui Zhang, Jun Dai, Tao Liu, Fan Xia, and Xiaoding Lou

Journal of the American Chemical Society 2025

DOI: 10.1021/jacs.5c07041

Peptides have demonstrated great potential in drug development. However, their broader application in modalities such as proteolysis-targeting chimeras (PROTACs) remains limited by the lack of real-time efficacy feedback and poor pharmacokinetic stability. Herein, we develop a covalent self-reporting peptide degrader (Co-SPeD) by integrating a fluorine-substituted aryl fluorosulfate warhead and a rotor fluorophore derived from stilbene derivatives, which allows for covalent binding to target proteins via sulfur(VI) fluoride exchange chemistry and emitting activatable fluorescence. Co-SPeD is found to covalently bind to the K51 residue of the MDM2 protein, enabling real-time monitoring of targeted MDM2 degradation. By swapping the targeting peptide and screening rotor fluorophores, the Co-SPeD platform is successfully extended to other oncogenic proteins, including BCL-xL, GRP78, and KRAS (G12D). Additionally, Co-SPeD demonstrates significant antitumor efficacy in preclinical tumor models. More importantly, real-time in vivo monitoring of MDM2 degradation using Co-SPeD plays a crucial role in guiding cisplatin combination administration, leading to a 50% increase in tumor growth inhibition compared to nonguided treatment groups. This approach provides a targeted endogenous protein degradation strategy with real-time monitoring, offering a powerful and generalizable platform for next-generation PROTAC design, the advancement of peptide-based therapeutics, and the rational optimization of cancer therapy.

Research progress on covalent inhibitors targeting alkaline amino acids

Bing Zhao, Sha Xu, Shiqing Zhou, Xiangru Jiang, Ailin Jiang, Hongrui Lei, Xin Zhai

Bioorganic Chemistry, 163, 2025, 108800,

https://doi.org/10.1016/j.bioorg.2025.108800

https://doi.org/10.1016/j.bioorg.2025.108800.Over the past two decades, covalent inhibitors have undergone a remarkable resurgence in drug discovery. Currently, targeting non-catalytic cysteine residues with acrylamide and other α,β-unsaturated carbonyl compounds is a predominate strategy, especially in the protein kinase field. Several cysteine-targeting covalent inhibitors (e.g. Ibrutinib, Afatinib) have demonstrated significant clinical efficacy. Covalent inhibitors have also enabled targeting of traditionally undruggable targets, highlighting the unique advantages of covalent strategies over non-covalent ligands. The rapid recent development of covalent strategies has prompted researchers to make significant efforts to develop novel reversible and irreversible covalent binding warheads targeting non-cysteine residues, thereby opening up new chemical space for covalent strategies. This article reviews the research advancements in specific and promiscuous warheads, as well as their covalent ligands, targeting three alkaline amino acids (lysine, arginine, and histidine), which will provide more opportunities for covalent fragment approaches targeting residues beyond cysteine.

Orelabrutinib, an irreversible inhibitor of Bruton’s tyrosine kinase, for the treatment of systemic lupus erythematosus: a randomised, double-blind, placebo-controlled, phase Ib/IIa study

Xue Li, Ru Li, Xiaoxia Zhu et al.

Research Square Preprint, 23 July 2025,

https://doi.org/10.21203/rs.3.rs-7058001/v1

Orelabrutinib is a highly selective, irreversible inhibitor of Bruton’s tyrosine kinase (BTK). It has shown promising results in animal models, indicating potential for treating systemic lupus erythematosus (SLE). A multicentre, double-blind, randomised, placebo-controlled, phase Ib/IIa trial (NCT04305197) was conducted. Sixty SLE patients were randomised 1:1:1:1 to receive oral orelabrutinib (50, 80, 100 mg) or placebo once daily for 12 weeks. A total of 55 patients completed the trial. In all evaluable patients, the SRI-4 rates at week 12 were 50%, 62%, and 64% for orelabrutinib at 50 mg, 80 mg, and 100 mg, respectively, compared with 36% for placebo. Among patients with baseline SLEDAI-2K > 8, significantly higher SRI-4 responses were noted with orelabrutinib at 50 mg (80%, p = 0·048), 80 mg (83%, p = 0·048), and 100 mg (100%, p = 0·029) compared to placebo (0%). Adverse events were mostly mild or moderate in the study. In summary, orelabrutinib was effective and well-tolerated in SLE patients.

State-of-the-art covalent virtual screening with AlphaFold3

Yoav Shamir, Nir London

bioRxiv 2025.03.19.642201

doi: https://doi.org/10.1101/2025.03.19.642201

Recent years have seen an explosion in the prominence of covalent inhibitors as research and therapeutic tools. However, a lag in application of computational methods for covalent docking slows progress in this field. AI models such as AlphaFold3 have shown accuracy in ligand pose prediction but were never assessed for virtual screening. We show that AlphaFold3 reaches near-perfect classification (average AUC=98.3%) of covalent active binders over property-matched decoys, dramatically outperforming classical covalent docking tools. We identify a predicted metric that allows to reliably assign a probability of binding and demonstrate it also improves non-covalent virtual screening.

The structure of KRASG12C bound to divarasib highlights features of potent switch-II pocket engagement

Fernando, M. C., Craven, G. B., & Shokat, K. M. 

Small GTPases, 2024 15(1), 1–7. 

https://doi.org/10.1080/21541248.2025.2505441

KRAS is the most frequently mutated oncogene in human cancer. In multiple types of cancer, a missense mutation at codon 12 substitutes a glycine for a cysteine, causing hyperactivation of the GTPase and enhanced MAPK signalling. Recent drug discovery efforts culminating from work during the past decade have resulted in two FDA-approved inhibitors, sotorasib and adagrasib, which target the KRASG12C mutant allele. Ongoing medicinal chemistry efforts across academia and industry have continued developing more potent and efficacious KRASG12C inhibitors. One agent in late-stage clinical trials, divarasib, has demonstrated robust overall response rates, in some cases greater than currently approved agents. Divarasib also exhibits enhanced covalent target engagement in vitro and significant specificity for KRASG12C, yet the structural details of its binding have not been published. Here we report a high-resolution crystal structure of cysteine-light KRAS-4BG12C in complex with divarasib. Though it binds in the same allosteric pocket as sotorasib and adagrasib, the switch-II loop in each crystal structure takes on a distinct conformation differing as much as 5.6 Å between the Cα atom of residue 65 with sotorasib. Additionally, we highlight structural features of the drug complex that may guide future medicinal chemistry efforts targeting various KRAS alleles.

Rational Design of CDK12/13 and BRD4 Molecular Glue Degraders

Nathanael Schiander Gray, Zhe Zhuang, Woong Sub Byun, Zuzanna Kozicka, Katherine Donovan, Brendan Dwyer, Abby Thornhill, Hannah Jones, Zixuan Jiang, Xijun Zhu, Eric Fischer, Nicolas Thomä, 

Angew. Chem. Int. Ed. 2025, e202508427.

https://doi.org/10.1002/anie.202508427

Targeted protein degradation (TPD) is an emerging therapeutic approach for the selective elimination of disease-related proteins. While molecular glue degraders exhibit drug-like properties, their discovery has traditionally been serendipitous and often requires post-hoc rationalization. In this study, we demonstrate the rational, mechanism-guided design of molecular glue degraders using gluing moieties. Building on established principles, by appending a chemical gluing moiety to several small molecule inhibitors, we successfully transformed them into degraders, obviating the need for a specific E3 ubiquitin ligase recruiter. Specifically, we found that incorporating a hydrophobic aromatic ring or a double bond into a cyclin-dependent kinase 12 and 13 (CDK12/13) dual inhibitor enabled the recruitment of DNA damage-binding protein 1 (DDB1), thereby transforming a high-molecular-weight bivalent CDK12 degrader into a potent monovalent CDK12/13 molecular glue degrader. We also showcase that attaching a cysteine-reactive warhead to a bromodomain-containing protein 4 (BRD4) inhibitor converts it into a degrader by recruiting the DDB1 and CUL4 associated factor 16 (DCAF16) E3 ligase.

Discovery of the Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19

Yuto Unoh, Keiichiro Hirai, Shota Uehara, Sho Kawashima, Haruaki Nobori, Jun Satom, Hiromitsu Shibayama, Akihiro Hori, Kenji Nakahara, Kana Kurahashi, Masayuki Takamatsu, Shiho Yamamoto, Qianhui Zhang, Miki Tanimura, Reiko Dodo, Yuki Maruyama, Hirofumi Sawa, Ryosuke Watari, Tetsuya Miyano, Teruhisa Kato, Takafumi Sato,Yuki Tachibana

J. Med. Chem. 2025

https://doi.org/10.1021/acs.jmedchem.5c00754

The coronavirus disease 2019 (COVID-19) pandemic crisis has been mitigated by worldwide efforts to develop vaccines and therapeutic drugs. However, there remains concern regarding public health and an unmet need for therapeutic options. Herein, we report the discovery of S-892216, a second-generation SARS-CoV-2 3C-like protease (3CLpro) inhibitor, to treat COVID-19. S-892216 is a reversible covalent 3CLpro inhibitor with highly potent antiviral activity and an EC50 value of 2.48 nM against SARS-CoV-2 infected cells. Structure-based design of a covalent modifier for compound 1 revealed that introducing a nitrile warhead increased 3CLpro inhibition activity by 180-fold. Subsequent optimization efforts yielded S-892216, which combined a favorable pharmacokinetic profile and high off-target selectivity. S-892216 exhibited antiviral activity against diverse SARS-CoV-2 variants, including major mutations reducing antiviral activities of nirmatrelvir and ensitrelvir. In SARS-CoV-2-infected mice, S-892216 inhibited viral replication in the lungs similar to ensitrelvir, although at a 30-fold lower dose.

Introduction of Reactive Thiol Handles into Tyrosine-Tagged Proteins through Enzymatic Oxidative Coupling

Paul Huang, Wendy Cao, Jennifer L. Fetzer, Nicholas S. Dolan, Matthew B. Francis

J. Am. Chem. Soc. 2025

https://doi.org/10.1021/jacs.5c06195

Site-specific protein bioconjugation methods have enabled the development of new therapeutics and materials, and further development of existing techniques has expanded the compatible library of protein substrates for bioconjugation. Among these techniques, the enzyme tyrosinase has demonstrated a promising ability to form protein–protein conjugates between exposed tyrosine and cysteine residues. In this work, we observed that the tyrosinase variant from Bacillus megaterium, termed megaTYR, has an increased tolerance for small-molecule thiol substrates, which can inhibit the activity of other tyrosinases. Among the breadth of thiol substrates that could be reliably coupled to tyrosine-tagged proteins was dithiothreitol (DTT), which effectively introduces a free thiol handle and provides a convenient method to bypass the genetic incorporation of cysteine residues for bioconjugation. Accordingly, these thiolated proteins could undergo additional coupling to commercially available maleimide probes as well as other tyrosine-tagged proteins. This was demonstrated by the conjugation of targeting proteins to drugs, fluorescent probes, and therapeutic enzymes. Of particular note and building on a previous report of a tyrosinase-sensitive tyrosine residue on the Fc region of antibodies, commercially available monoclonal antibodies (mAbs) treated with PNGase F were conjugated to DTT to produce THIOMAB equivalents. These intermediates were subsequently used to make functional antibody–drug and antibody–toxin protein conjugates. This facile method to convert accessible tyrosine residues on proteins to thiol tags extends the use of tyrosinase-mediated oxidative coupling to a broader range of protein substrates.

Diethenyl Sulfoximine (DESI) as an Irreversible Lysine-Targeting Warhead Enables the Design of Covalent Allosteric EGFR Inhibitor

Huiqi Xu, Hongjin Zhang, Suyun Jia, Yanxin Tao, Quanpeng Wei, Yingao Wang, Xuechen Liu, Yuqing Zhang, Xinpeng Ning, Yuyan Shi, Can Jin, Ke Ding, Dawei Ma, Shan Li, Mengyang Fan

Chem. Euro. J. 2025 e202501389

https://doi.org/10.1002/chem.202501389

Targeting lysine residues with covalent inhibitors is challenging due to their abundance in the proteome and the protonation of lysine's ε-amino group, which diminishes its reactivity. This study introduces diethenyl sulfoximine (DESI) as a novel bio-orthogonal aminophilic electrophile which can react with lysine via double conjugate addition to form a cyclic adduct. The second addition promotes the entire and efficient electrophilic attack by the ε-amino of lysine on the ethenyl groups. DESI exhibits superior aqueous stability, overcoming the hydrolysis issue encountered by most reported lysine-targeting covalent agents. Incorporation of DESI in the allosteric pocket binder EAI045 of oncoprotein epidermal growth factor receptor (EGFR) yields compound 4, which specifically reacts to the catalytic lysine (Lys745). Compound 4 showed potent inhibition of EGFR-driven cell proliferation with IC50 values of 0.789 µM and 1.22 µM in engineered BaF3-EGFRL858R/T790M/C797S and NCI-H1975 cells, respectively, overcoming EAI045's limitation of lack in cellular potency as a single agent. Tyrosine kinases panel profiling confirmed selectivity toward mutant EGFR while sparing the wild type with minimal off-targets. These findings highlight DESI's potential as a versatile strategy for targeting lysine residues irreversibly, offering solutions to overcome drug resistance in cancer therapy and advance next-generation precision medicines.

Diffusion Limit and the Reactivity/Affinity Conundrum: Implications for Optimization and Hit Finding for Irreversible Modulators

Bharath Srinivasan

J. Med. Chem. 2025

https://doi.org/10.1021/acs.jmedchem.4c02863

Irreversible inhibition as a therapeutic modality has come of age over the previous decade. With minimal theoretical guidance for the design of an irreversible modulator, empirical optimization efforts often involve increasing the affinity of the small molecule while reducing the reactivity of the electrophile. The latter, as per prevalent opinion, is to ensure that binding dictates engagement and the reactive electrophile does not pose a safety liability arising from off-target reactivity. Here I argue that, like the second-order kinetic rate constant kcat/Km, the parameter kinact/KI is limited by the upper physical limit imposed by the rate of diffusion. This capping ensures that any attempt to improve the affinity of the electrophile-containing small-molecule at the limit will come with an equivalent trade-off in their reactivity. This has implications for both hit finding and lead optimization within targeted irreversible inhibition, especially for intractable targets with shallow pockets where the interactions are collision-induced second-order processes.

Covalent Recruitment of NEDD4 for Targeted Protein Degradation: Rational Design of Small Molecular Degraders

Xiaoqiang He, Shihan Zeng, Yalei Wen, Tao Yang, Chaoming Huang, Yifang Li, Zhang Zhang, Ke Ding, Tongzheng Liu, Yi Tan, and Zhengqiu Li

J. Am. Chem. Soc. 2025, 147, 25, 21512–21525

https://doi.org/10.1021/jacs.4c18083

Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy for treating various diseases. However, current small molecule degraders predominantly rely on a limited set of E3 ubiquitin ligases, such as CRBN and VHL, which restricts their applications. Here, we report that incorporation of the 2H-azirine chemical handle into the EGFRL858R/T790M/C797S inhibitor induced remarkable degradation of the targeted protein. Proteomic profiling and functional validation confirmed that the NEDD4 E3 ligase was covalently recruited by 2H-azirine through engagement of C1286 residue, facilitating target degradation. Furthermore, the 2H-azirine moiety demonstrated versatility by acting as a small molecular degrader when conjugated to various ligands, effectively mediating the degradation of CDK4, PDE5, BTK and Brd4. More importantly, using the identical protein ligand scaffold, we demonstrated that the 2H-azirine based probe can degrade proteins resistant to degradation by CRBN or VHL recruitment. This approach provides a rational strategy for developing novel small molecular degraders that target alternative E3 ubiquitin ligases. Notably, these degraders significantly outperformed their parent kinase inhibitor in suppressing cancer cell growth.

Discovery of IHMT-15130 as a Highly Potent Irreversible BMX Inhibitor for the Treatment of Myocardial Hypertrophy and Remodeling

Shuang Qi, Jiangyan Cao, Ting Wu, Chenliang Shi, Junjie Wang, Beilei Wang, Ziping Qi, Hong Wu, Yun Wu, Aoli Wang, Jing Liu, Wenchao Wang, and Qingsong Liu

ACS Chem. Biol. 2025, 20, 6, 1181–1194

https://doi.org/10.1021/acschembio.4c00875

Cardiac hypertrophy is usually accompanied by many forms of heart disease, including hypertension, vascular disease, ischemic disease, and heart failure, and thus effectively predicts the increased cardiovascular morbidity and mortality. Bone marrow kinase in chromosome X (BMX) has been reported to be the major signaling transduction protein in cardiac arterial endothelial cells and is thought to be involved in the pathology of cardiac hypertrophy. We report here the discovery of a potent irreversible BMX kinase inhibitor, IHMT-15130, which covalently targets cysteine 496 of BMX and exhibits potent inhibitory activity against BMX kinase (IC50: 1.47 ± 0.07 nM). Compared to recently approved BTK/BMX dual inhibitor Ibrutinib, IHMT-15130 displayed selectivity over CSK kinase (IC50 > 25,000 nM), targeting of which may cause severe atrial fibrillation and bleeding. IHMT-15130 effectively reduced the secretion of inflammatory cytokines, inhibited the inflammatory signaling pathway in vitro and in vivo, and alleviated angiotensin II (Ang II)-induced myocardial hypertrophy in a murine model. This study provides further experimental evidence for the application of BMX kinase inhibitors in the treatment of cardiac hypertrophy.

Synthesis and functionalization of vinyl sulfonimidamides and their potential as electrophilic warheads

Yu Tung Wong,  Charles Bell, and  Michael C. Willis

Chem. Sci., 2025

DOI

https://doi.org/10.1039/D5SC02420J

Covalent inhibitor design is dominated by the use of electrophilic acrylamide warheads. One limitation of acrylamides is that there are limited opportunities to modify their electrophilicity, and hence reactivity, by simple structural changes. Here we show that vinyl sulfonimidamides are effective electophilic groups for reaction with both sulfur- and nitrogen-based biologically relevant nucleophiles. The parent N–H vinyl sulfonimidamides are prepared in a single step from an aryl-ONSO reagent, a vinyl organometallic, and an appropriate amine. Imidic N-functionalisation is straightforward, providing a collection of electrophilic fragments of varied reactivity. We demonstrate that the electrophilicity of these new reagents can be modulated by choice of the imidic N-substituent, and when this is used in combination with alkene substituents, allows for a reactivity range both above and below that of the parent acrylamide.

BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3Kα interaction

Dhirendra K. Simanshu, Rui Xu, James P. Stice, Daniel J. Czyzyk, Siyu Feng, John-Paul Denson, Erin Riegler, Yue Yang, Cathy Zhang, Sofia Donovan, Brian P. Smith, Maria Abreu-Blanco, Ming Chen, Cindy Feng, Lijuan Fu, Dana Rabara, Lucy C Young, Marcin Dyba, Wupeng Yan, Ken Lin, Samar Ghorbanpoorvalukolaie, Erik K. Larsen, Wafa Malik, Allison Champagne, Katie Parker, Jin Hyun Ju, Stevan Jeknic, Dominic Esposito, David M. Turner, Felice C. Lightstone, Bin Wang, Paul M. Wehn, Keshi Wang, Andrew G. Stephen, Anna E. Maciag, Aaron N. Hata, Kerstin W. Sinkevicius, Dwight V. Nissley, Eli M. Wallace, Frank McCormick, Pedro J. Beltran

Science, eadq2004

DOI:10.1126/science.adq2004

BBO-10203 is an orally available drug that covalently and specifically binds to the RAS-binding domain of phosphoinositide 3-kinase α (PI3Kα), preventing its activation by HRAS, NRAS, and KRAS. It inhibited PI3Kα activation in tumors with oncogenic mutations in KRAS or PIK3CA, and in tumors with human epidermal growth factor receptor 2 (HER2) amplification or overexpression. In preclinical models, BBO-10203 caused significant tumor growth inhibition across multiple tumor types and showed enhanced efficacy in combination with inhibitors of cyclin-dependent kinase 4/6 (CDK4/6), estrogen receptor (ER), HER2 and KRAS-G12C mutant, including in tumors harboring mutations in Kelch-like ECH-associated protein 1 (KEAP1) and Serine/Threonine Kinase 11 (STK11). Notably, these antitumor effects occurred without inducing hyperglycemia, as insulin signaling does not depend on RAS-mediated PI3Kα activation to promote glucose uptake.

Allosteric Covalent Inhibitors of the STAT3 Transcription Factor from Virtual Screening

Tibor Viktor Szalai, Vincenzo di Lorenzo, Nikolett Péczka, Levente M. Mihalovits, László Petri, Qirat F. Ashraf, Elvin D. de Araujo, Viktor Honti, Dávid Bajusz, and György M. Keserű

ACS Medicinal Chemistry Letters 2025 16 (6), 991-997

DOI: 10.1021/acsmedchemlett.4c00622

The STAT family of transcription factors are important signaling hubs, with several of them, particularly STAT3, being emerging oncotargets already investigated in clinical trials. The modular structure of STAT3 nominates several of its protein domains as possible drug targets, but their exploitation with potential small-molecule inhibitors has been unevenly distributed so far, with past efforts highly favoring the conserved SH2 domain. Here, we have targeted a sparsely studied binding site at the junction of the coiled-coil and DNA-binding domains and discovered several new lead-like covalent inhibitors by virtual screening. The most favorable hit compound has been explored via structure-guided hit expansion and optimized into a low micromolar inhibitor. This compound can serve as a chemical biology tool against this site in future exploratory studies or form the basis of a more advanced stage of lead optimization.

Covalent Destabilizing Degrader of AR and AR-V7 in Androgen-Independent Prostate Cancer Cells

Charlotte M. Zammit, Cory M. Nadel, Ying Lin, Sajjan Koirala, Elnaz Ahani, Patrick Ryan Potts, and Daniel K. Nomura

Journal of the American Chemical Society 2025

DOI: 10.1021/jacs.5c02801

Androgen-independent prostate cancers, correlated with heightened aggressiveness and poor prognosis, are caused by mutations or deletions in the androgen receptor (AR) or the expression of truncated variants of AR that are constitutively activated. Currently, drugs and drug candidates against AR target the steroid-binding domain to antagonize or degrade AR. However, these compounds cannot therapeutically access largely intrinsically disordered truncated splice variants of AR, such as AR-V7, which only possess the N-terminal transactivation domain and DNA-binding domain and are missing the ligand-binding domain. Targeting intrinsically disordered regions within transcription factors has remained challenging and is considered “undruggable”. Herein, we leverage a cysteine-reactive covalent ligand library in a cellular screen to identify the degraders of AR and AR-V7 in androgen-independent prostate cancer cells. We identified a covalent compound, EN1441, that selectively degrades AR and AR-V7 in a proteasome-dependent manner through direct covalent targeting of intrinsically disordered cysteine C125 in the N-terminal transactivation domain of AR and AR-V7. EN1441 causes significant and selective destabilization of AR and AR-V7, leading to the aggregation of AR/AR-V7 and subsequent proteasome-mediated degradation. Consistent with targeting both AR and AR-V7, we find that EN1441 completely inhibits total AR transcriptional activity in androgen-independent prostate cancer cells expressing both AR and AR-V7 compared with AR antagonists or degraders that only target the ligand-binding domain of full-length AR, such as enzalutamide and ARV-110. Our results put forth a pathfinder molecule EN1441 that targets an intrinsically disordered cysteine within AR to destabilize, degrade, and inhibit both AR and AR-V7 in androgen-independent prostate cancer cells and highlights the utility of covalent ligand discovery approaches in directly targeting, destabilizing, inhibiting, and degrading classically undruggable transcription factor targets.

Advancing Covalent Ligand and Drug Discovery beyond Cysteine

Gibae Kim, R. Justin Grams, and Ku-Lung Hsu

Chemical Reviews 2025

DOI: 10.1021/acs.chemrev.5c00001

Targeting intractable proteins remains a key challenge in drug discovery, as these proteins often lack well-defined binding pockets or possess shallow surfaces not readily addressed by traditional drug design. Covalent chemistry has emerged as a powerful solution for accessing protein sites in difficult to ligand regions. By leveraging activity-based protein profiling (ABPP) and LC-MS/MS technologies, academic groups and industry have identified cysteine-reactive ligands that enable selective targeting of challenging protein sites to modulate previously inaccessible biological pathways. Cysteines within a protein are rare, however, and developing covalent ligands that target additional residues hold great promise for further expanding the ligandable proteome. This review highlights recent advancements in targeting amino acids beyond cysteine binding with an emphasis on tyrosine- and lysine-directed covalent ligands and their applications in chemical biology and therapeutic development. We outline the process of developing covalent ligands using chemical proteomic methodology, highlighting recent successful examples and discuss considerations for future expansion to additional amino acid sites on proteins.

Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States

Kyle Ghaby, Benoît Roux

bioRxiv 2025.05.28.656658; 

doi: https://doi.org/10.1101/2025.05.28.656658

There is increasing interest in the discovery of small-molecule inhibitors that form covalent bonds with their targets for therapeutic applications. Nevertheless, identifying clear rational design principles remains challenging because the action of these molecules cannot be understood as common noncovalent inhibitors. Conventional kinetic models often reduce the binding of covalent inhibitors to a two-step irreversible process, overlooking rapid complex dynamics of the associated unlinked inhibitor before the formation of the covalent bond with its target. In the present analysis, we expand the intermediate state into two conformations—reactive (E·I) and nonreactive (E··I). To illustrate the consequences of such simplification, the expanded kinetic model can be reduced to an effective two-step scheme expressed in terms of the equilibrium probability of the unlinked inhibitor to form either conformation. A mass-action-based numerical workflow is implemented to simulate time-dependent kinetics, overcoming the common limitations of empirical models. The numerical workflow helps relate microscopic states observed in molecular dynamics simulations to macroscopic observables like EC50 and the apparent rate of covalent inhibition, showing the impact of transient intermediates on dissociation rates and potency. The proposed framework refines the interpretation of dose-response data, aiding medicinal chemists in optimizing covalent inhibitors and provides a quantitative platform for relating molecular conformational distributions to empirical parameters.