title: Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches.
abstract: Covalent drugs have attracted increasing attention in recent years due to good inhibitory activity and selectivity. Targeting noncatalytic cysteines with irreversible inhibitors is a powerful approach for enhancing pharmacological potency and selectivity because cysteines can form covalent bonds with inhibitors through their nucleophilic thiol groups. However, most human kinases have multiple noncatalytic cysteines within the active site; to accurately predict which cysteine is most likely to form covalent bonds is of great importance but remains a challenge when designing irreversible inhibitors. In this work, FTMap was first applied to check its ability in predicting covalent binding site defined as the region where covalent bonds are formed between cysteines and irreversible inhibitors. Results show that it has excellent performance in detecting the hot spots within the binding pocket, and its hydrogen bond interaction frequency analysis could give us some interesting instructions for identification of covalent binding cysteines. Furthermore, we proposed a simple but useful covalent fragment probing approach and showed that it successfully predicted the covalent binding site of seven targets. By adopting a distance-based method, we observed that the closer the nucleophiles of covalent warheads are to the thiol group of a cysteine, the higher the possibility that a cysteine is prone to form a covalent bond. We believe that the combination of FTMap and our distance-based covalent fragment probing method can become a useful tool in detecting the covalent binding site of these targets.
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Yanmin
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Danfeng
authors.initials: D
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Haozhong
authors.initials: H
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jiao
authors.affiliation: State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Zhihao
authors.initials: Z
authors.lastname: Shi
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Ran
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Haichun
authors.initials: H
authors.lastname: Liu
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.|State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Lu
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Anyang
authors.initials: A
authors.lastname: Xu
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Qiao
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Pan
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Yin
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Weineng
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.|State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tongjiaxiang, Nanjing 210009, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Lu
authors.affiliation: Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University , 639 Longmian Avenue, Nanjing 211198, China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Chen
mesh_terms: D001665:Binding Sites; D003545:Cysteine / Q000737:chemistry* / Q000378:metabolism; D066246:ErbB Receptors / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D047428:Protein Kinase Inhibitors / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D013329:Structure-Activity Relationship
chemical_list: D047428:Protein Kinase Inhibitors; C512478:EGFR protein, human; D066246:ErbB Receptors; D003545:Cysteine
keywords: covalent binding sites; cysteines; fragment probing; irreversible inhibitors