2026-10-14T13:12:05Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33980455 2026-09-24T07:05:03Z category_1 category_4 category_7 category_14 category_19 category_21 category_873 category_734 category_64 portal_63 item_type_3 month_year_09_2026

Targeting the “Undruggable” STAT3 DBD: Free-Energy Perturbation-Guided Design of Covalent Micheliolide Derivatives Targeting Cysteine 367 Yangping Deng (11926700) Hengwei Bian (13030365) Fengyuan Zhang (1424125) Jianping Lin (501681) Hongbo Li (130443) Yue Chen (73753) Jing Li (10611) Jianshuang Guo (5152619) Haohao Fu (1351521) Biophysics Biochemistry Medicine Molecular Biology Pharmacology Biotechnology Chemical Sciences not elsewhere classified Biological Sciences not elsewhere classified Cancer upstream kinase blockade upstream jak phosphorylation transcriptional activity prior study establishes c367 stage candidate act001 highly lethal malignancy exhibited limited selectivity electrostatic interactions predominate drives therapeutic resistance conserved sh2 domain druggable covalent site persistent stat3 signaling 16 </ b conventional inhibitors targeting relative binding free covalent inhibitors binding domain dependent binding covalent docking validates fep targeting stat3 superior drug stat3 inhibition residue unique promising next primarily driven optimized lipophilicity nuclear translocation mcl analogs mcl ), major contributions like profile largely due key residues inhibits stat3 ile368 ). identifies compound group enumeration generation lead findings provide fep ), energy perturbation detectable inhibition dependent cancers dbd )– active metabolite Pancreatic cancer remains a highly lethal malignancy, largely due to persistent STAT3 signaling that sustains cancer stem cells (CSCs) and drives therapeutic resistance. Conventional inhibitors targeting the conserved SH2 domain of STAT3 have exhibited limited selectivity and efficacy. Here, we report that micheliolide (MCL), the active metabolite of the clinical-stage candidate ACT001, inhibits STAT3 through Cys367 (C367)-dependent covalent engagement within the DNA-binding domain (DBD)–a residue unique to STAT3 among STAT family members. This specific modification disrupts STAT3 phosphorylation at Tyr705, nuclear translocation, and transcriptional activity prior to any detectable inhibition of upstream JAK phosphorylation, a finding that suggests that STAT3 inhibition is not primarily driven by upstream kinase blockade. Guided by covalent docking, R-group enumeration, and relative binding free-energy calculations via free-energy perturbation (FEP), we have designed and synthesized a series of MCL analogs. These derivatives retain comparable antiproliferative potency but exhibit markedly improved physicochemical properties, including enhanced kinetic aqueous solubility and optimized lipophilicity. Microscale thermophoresis confirms C367-dependent binding, while microsecond-scale molecular dynamics simulations and pair-interaction energy analyses highlight stable complexes in which electrostatic interactions predominate, with major contributions from key residues (Lys365, Val366, and Ile368). This study establishes C367 as a druggable covalent site in the historically challenging STAT3 DBD, validates FEP-guided optimization of covalent inhibitors, and identifies compound <b>16</b> as a promising next-generation lead with a superior drug-like profile for targeting STAT3-dependent cancers. All in all, these findings provide a foundation for advancing selective STAT3 DBD inhibitors toward clinical translation. 2026-09-24T00:00:00Z Dataset Dataset 10.1021/acs.jcim.6c03067.s002 https://figshare.com/articles/dataset/Targeting_the_Undruggable_STAT3_DBD_Free-Energy_Perturbation-Guided_Design_of_Covalent_Micheliolide_Derivatives_Targeting_Cysteine_367/33980455 CC BY-NC 4.0