A multicenter, open-label, first-in-human study of TYRA-200 in advanced intrahepatic cholangiocarcinoma and other solid tumors with activating FGFR2 gene alterations (SURF201).

Jordi Rodon Ahnert, Sameek Roychowdhury, Haley Ellis, Fernando F. Blanco, Timothy Burn, Jennifer Michelle Davis, Alex Balcer, Alena Zalutskaya

Journal of Clinical Oncology 2025

Volume 43, Number 4_suppl

https://doi.org/10.1200/JCO.2025.43.4_suppl.TPS646

Background: Approved Fibroblast Growth Factor Receptor (FGFR) inhibitors have demonstrated clinical benefit in locally advanced or metastatic cholangiocarcinoma harboring oncogenic FGFR2 fusions or other rearrangements. However, the emergence of acquired resistance mutations limits the clinical activity and duration of responses to currently available inhibitors. TYRA-200 is an orally bioavailable FGFR1/2/3 inhibitor designed to specifically address these clinically observed acquired resistance alterations in FGFR2. Methods: SURF201 is a single arm, multicenter, open-label, first-in-human, dose escalation and expansion study designed to investigate TYRA-200 in patients (pts) with advanced intrahepatic cholangiocarcinoma and other solid tumors with primary activating FGFR2 gene alterations and on-target acquired known FGFR2 resistance mutations. The study is being conducted in two parts. Part A dose escalation uses an i3+3 design and is evaluating the safety, tolerability, and the pharmacokinetic profile of TYRA-200. Part B dose expansion will further characterize the safety profile and evaluate the preliminary anti-tumor activity of TYRA-200 by RECIST v1.1 in pts with unresectable locally advanced/metastatic intrahepatic cholangiocarcinoma who have previously received an FGFR inhibitor(s) and have developed acquired FGFR2 kinase domain resistance mutations. The study is currently planned for approximately four centers in the US and is actively enrolling (NCT06160752). Clinical trial information: NCT06160752.

Discovery of Fulzerasib (GFH925) for the Treatment of KRAS G12C-Mutated Solid Tumors

Tao Jiang, Chonglan Lin, Siyuan Le, Leitao Zhang, Tao Liang, Lijian Cai, Xiaoling Lan, Mei Ge, Zhubo Liu, Wan He, Ling Peng, Yanhui Zhao, Jinmin Ren, Feng Yan, Qiang Lu, Jiong Lan, and Fusheng Zhou

J. Med. Chem. 2025, 68, 15, 15386–15402

DOI: 10.1021/acs.jmedchem.4c03183

RAS mutations are the most prevalent genetic alterations in human tumors, accounting for 30% of all cases. Among these mutations, KRAS G12C emerged as the first druggable target through covalent attachment, which locks the protein in its inactive state. Employing a structure-based drug design strategy, we identified fulzerasib (GFH925), which features a novel lactam-based tetracyclic naphthyridinone scaffold. This molecule demonstrates high in vitro potency and selectivity, favorable pharmacokinetic profiles across species, and significant in vivo antitumor efficacy in various cancer-related xenograft models, including intracranial tumors. Fulzerasib has recently received accelerated approval in China for adult NSCLC patients with the KRAS G12C mutation after prior systemic therapy.

Discovery of an Internal Alkyne Warhead Scaffold for Irreversible hTG2 Inhibition

Lavleen K. Mader, Namita Maunick, Jessica E. Borean, Jeffrey W. Keillor

RSC Med. Chem., 2025

https://doi.org/10.1039/D5MD00777A

Human tissue transglutaminase (hTG2) is a multifunctional enzyme with both protein cross-linking and G-protein activity. Dysregulation of these functions has been implicated in diseases such as celiac disease and cancer, prompting the development of hTG2 inhibitors, many of which act covalently via a pendant electrophilic warhead. Most small molecule hTG2 inhibitors to date feature terminal, sterically minimal warheads, based on the assumption that bulkier electrophiles impair binding and reactivity. Here, we report structure–activity relationships (SAR) of a novel internal alkynyl warhead scaffold for irreversible inhibition of hTG2. This series includes one of the most potent non-peptidic hTG2 inhibitors reported to date. We demonstrate that this scaffold not only inhibits transamidase activity but also abolishes GTP binding, while exhibiting excellent isozyme selectivity. In addition, we investigate the tunability and stability of this warhead, providing insights into its broader applicability. Through detailed kinetic analysis, this study establishes a new scaffold for irreversible hTG2 inhibition and expands the design principles for covalent warheads beyond traditional terminal systems.

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.