title: Structural Insights into the Pharmacophore of Vinca Domain Inhibitors of Microtubules.
abstract: Antibody-drug conjugates (ADCs) have achieved great success in cancer therapy in recent years. Some peptidyl microtubule inhibitors consisting of natural and unnatural amino acids, such as monomethyl auristatin E (MMAE) and F (MMAF), are extremely cytotoxic and have been used as a payload in ADCs. However, their precise molecular interaction with tubulin and microtubules remains unclear. We determined the crystal structures of tubulin in complex with three ultra-potent peptidyl microtubule inhibitors [MMAE, taltobulin (HTI- 286), and tubulysin M] at 2.5 Å. Our data showed that the three peptides bound to the vinca domain and shared a common and key pharmacophore containing two consecutive hydrophobic groups (Val, Ile-like side chain). These groups protruded in opposite directions into hydrophobic pockets on the tubulin β and α subunits. Nitrogen and oxygen atoms from the same backbone formed hydrogen bonds with Asn329 from the α subunit and Asp179 from the β subunit in a direction normal to the surface formed by the aforementioned hydrophobic groups. In addition, our crystal structure data indicated that tubulysin M bound to the β subunit alone, providing a structural explanation for its higher affinity. We also compared the conformations of two representative structurally different vinca domain compounds, ustiloxin D and vinblastine, with those of the aforementioned peptidyl ligands, and found that they shared a similar pharmacophore. Our findings lay a foundation for the rational design of novel vinca domain ligands and may facilitate the development of microtubule inhibitors with high specificity, affinity, and efficiency as payloads for ADCs in cancer therapy.
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Yuxi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Frederick W
authors.initials: FW
authors.lastname: Benz
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Yangping
authors.initials: Y
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Qisheng
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Xiangzheng
authors.initials: X
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Huiyan
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.).
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.) jinliangyang@scu.edu.cn rundongzhang@scu.edu.cn.
authors.forename: Rundong
authors.initials: R
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.) jinliangyang@scu.edu.cn rundongzhang@scu.edu.cn.
authors.forename: Jinliang
authors.initials: J
authors.lastname: Yang
mesh_terms: D000818:Animals; D008870:Microtubules / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism*; D008968:Molecular Conformation; D011485:Protein Binding / Q000502:physiology; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary / Q000187:drug effects / Q000502:physiology; D013552:Swine; D050257:Tubulin Modulators / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D014961:X-Ray Diffraction
chemical_list: D050257:Tubulin Modulators