1
|
Mason M, Belvisi L, Pignataro L, Dal Corso A. A Tight Contact: The Expanding Application of Salicylaldehydes in Lysine-Targeting Covalent Drugs. Chembiochem 2024; 25:e202300743. [PMID: 37986243 DOI: 10.1002/cbic.202300743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
The installation of aldehydes into synthetic protein ligands is an efficient strategy to engage protein lysine residues in remarkably stable imine bonds and augment the compound affinity and selectivity for their biological targets. The high frequency of lysine residues in proteins and the reversibility of the covalent ligand-protein bond support the application of aldehyde-bearing ligands, holding promises for their future use as drugs. This review highlights the increasing exploitation of salicylaldehyde modules in various classes of protein binders, aimed at the reversible-covalent engagement of lysine residues.
Collapse
Affiliation(s)
- Mattia Mason
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Luca Pignataro
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| | - Alberto Dal Corso
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133, Milan, Italy
| |
Collapse
|
2
|
Kawano M, Murakawa S, Higashiguchi K, Matsuda K, Tamura T, Hamachi I. Lysine-Reactive N-Acyl- N-aryl Sulfonamide Warheads: Improved Reaction Properties and Application in the Covalent Inhibition of an Ibrutinib-Resistant BTK Mutant. J Am Chem Soc 2023; 145:26202-26212. [PMID: 37987622 DOI: 10.1021/jacs.3c08740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The covalent inhibition of a target protein has gained widespread attention in the field of drug discovery. Most of the current covalent drugs utilize the high reactivity of cysteines toward modest electrophiles. However, there is a growing need for warheads that can target lysine residues to expand the range of covalently druggable proteins and to deal with emerging proteins with mutations resistant to cysteine-targeted covalent drugs. We have recently developed an N-acyl-N-alkyl sulfonamide (NASA) as a lysine-targeted electrophile. Despite its successful application, this NASA warhead suffered from instability in physiological environments, such as serum-containing medium, because of its high intrinsic reactivity. In this study, we sought to modify the structure of the NASA warhead and found that N-acyl-N-aryl sulfonamides (ArNASAs) are promising electrophiles for use in a lysine-targeted covalent inhibition strategy. We prepared a focused library of ArNASA derivatives with diverse structures and reactivity and identified several warhead candidates with suppressed hydrolysis-mediated inactivation and reduced nonspecific reactions with off-target proteins, without sacrificing the reactivity toward the target. These reaction properties enabled the improved covalent inhibition of intracellular heat shock protein 90 (HSP90) in the presence of serum and the development of the first irreversible inhibitor for ibrutinib-resistant Bruton's tyrosine kinase (BTK) bearing the C481S mutation. This study clearly demonstrated the use of a set of ArNASA warheads to create highly potent covalent drugs and highlighted the importance of enriching the current arsenal of lysine-reactive warheads.
Collapse
Affiliation(s)
- Masaharu Kawano
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Syunsuke Murakawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Higashiguchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Matsuda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| |
Collapse
|
3
|
Sacco G, Arosio D, Paolillo M, Gloger A, Scheuermann J, Pignataro L, Belvisi L, Dal Corso A, Gennari C. RGD Cyclopeptide Equipped with a Lysine-Engaging Salicylaldehyde Showing Enhanced Integrin Affinity and Cell Detachment Potency. Chemistry 2023; 29:e202203768. [PMID: 36594507 DOI: 10.1002/chem.202203768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/04/2023]
Abstract
Salicylaldehyde (SA) derivatives are emerging as useful fragments to obtain reversible-covalent inhibitors interacting with the lysine residues of the target protein. Here the SA installation at the C terminus of an integrin-binding cyclopeptide, leading to enhanced ligand affinity for the receptor as well as stronger biological activity in cultured glioblastoma cells is reported.
Collapse
Affiliation(s)
- Giovanni Sacco
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, I-20133, Milan, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) "Giulio Natta", Consiglio Nazionale delle Ricerche, Via Golgi 19, I-20133, Milan, Italy
| | - Mayra Paolillo
- Dipartimento di Scienze del Farmaco, Università degli Studi di Pavia, Viale Taramelli 6, 27100, Pavia, Italy
| | - Andreas Gloger
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Luca Pignataro
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, I-20133, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, I-20133, Milan, Italy
| | - Alberto Dal Corso
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, I-20133, Milan, Italy
| | - Cesare Gennari
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, I-20133, Milan, Italy
| |
Collapse
|
4
|
Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang CJ, Zhang ZM, Gao L, Yao SQ. Cell-Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR-ABL Kinase. Angew Chem Int Ed Engl 2022; 61:e202203878. [PMID: 35438229 DOI: 10.1002/anie.202203878] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/16/2022]
Abstract
Despite recent interests in developing lysine-targeting covalent inhibitors, no general approach is available to create such compounds. We report herein a general approach to develop cell-active covalent inhibitors of protein kinases by targeting the conserved catalytic lysine residue using key SuFEx and salicylaldehyde-based imine chemistries. We validated the strategy by successfully developing (irreversible and reversible) covalent inhibitors against BCR-ABL kinase. Our lead compounds showed high levels of selectivity in biochemical assays, exhibited nanomolar potency against endogenous ABL kinase in cellular assays, and were active against most drug-resistant ABL mutations. Among them, the salicylaldehyde-containing A5 is the first-ever reversible covalent ABL inhibitor that possessed time-dependent ABL inhibition with prolonged residence time and few cellular off-targets in K562 cells. Bioinformatics further suggested the generality of our strategy against the human kinome.
Collapse
Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| |
Collapse
|
5
|
Dal Corso A, Frigoli M, Prevosti M, Mason M, Bucci R, Belvisi L, Pignataro L, Gennari C. Advanced Pyrrolidine-Carbamate Self-Immolative Spacer with Tertiary Amine Handle Induces Superfast Cyclative Drug Release. ChemMedChem 2022; 17:e202200279. [PMID: 35620983 PMCID: PMC9544318 DOI: 10.1002/cmdc.202200279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 11/07/2022]
Abstract
Amine-carbamate self-immolative (SI) spacers represent practical and versatile tools in targeted prodrugs, but their slow degradation mechanism limits drug activation at the site of disease. We engineered a pyrrolidine-carbamate SI spacer with a tertiary amine handle which strongly accelerates the spacer cyclization to give a bicyclic urea and the free hydroxy groups of either cytotoxic (Camptothecin) or immunostimulatory (Resiquimod) drugs. In silico conformational analysis and p K a calculations suggest a plausible mechanism for the superior efficacy of the advanced SI spacer compared to state-of-art analogues.
Collapse
Affiliation(s)
- Alberto Dal Corso
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, ITALY
| | - Margaux Frigoli
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, 20133, Milano, ITALY
| | - Martina Prevosti
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, 20133, Milano, ITALY
| | - Mattia Mason
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, 20133, Milano, ITALY
| | - Raffaella Bucci
- Università degli Studi di Milano: Universita degli Studi di Milano, Pharmaceutical Sciences, Via Venezian 21, 20133, Milano, ITALY
| | - Laura Belvisi
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, Via Golgi 19, 20133, Milano, ITALY
| | - Luca Pignataro
- Università degli Studi di Milano: Universita degli Studi di Milano, Chemistry, Via Golgi 19, 20133, Milano, ITALY
| | - Cesare Gennari
- Universita degli Studi di Milano, Chemistry Department, via C. Golgi 19, 20133, Milan, ITALY
| |
Collapse
|
6
|
Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang C, Zhang Z, Gao L, Yao SQ. Cell‐Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR‐ABL Kinase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chengjun Zhu
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Zhi‐Min Zhang
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| |
Collapse
|
7
|
Fan S, Yue L, Wan W, Zhang Y, Zhang B, Otomo C, Li Q, Lin T, Hu J, Xu P, Zhu M, Tao H, Chen Z, Li L, Ding H, Yao Z, Lu J, Wen Y, Zhang N, Tan M, Chen K, Xie Y, Otomo T, Zhou B, Jiang H, Dang Y, Luo C. Inhibition of Autophagy by a Small Molecule through Covalent Modification of the LC3 Protein. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shijie Fan
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Liyan Yue
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Wei Wan
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Yuanyuan Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Bidong Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Chinatsu Otomo
- Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA 92037 USA
| | - Quanfu Li
- Key Laboratory of Metabolism and Molecular Medicine the Ministry of Education Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Fudan University Shanghai 200032 China
| | - Tingting Lin
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- School of Life Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
| | - Junchi Hu
- Center for Novel Target and Therapeutic Intervention Institute of Life Sciences Chongqing Medical University No. 1, Yixueyuan Road, Yuzhong District Chongqing China
| | - Pan Xu
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Mingrui Zhu
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Hongru Tao
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Zhifeng Chen
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Lianchun Li
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Hong Ding
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Zhiyi Yao
- Suzhou Autopharm 108 Yuxin Road Jiangsu 215123 China
| | - Junyan Lu
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Yi Wen
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Naixia Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Minjia Tan
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
| | - Kaixian Chen
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Yuli Xie
- Suzhou Autopharm 108 Yuxin Road Jiangsu 215123 China
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA 92037 USA
| | - Bing Zhou
- Department of Medicinal Chemistry State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 China
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine the Ministry of Education Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Fudan University Shanghai 200032 China
- Center for Novel Target and Therapeutic Intervention Institute of Life Sciences Chongqing Medical University No. 1, Yixueyuan Road, Yuzhong District Chongqing China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
- School of Life Science and Technology ShanghaiTech University 100 Haike Road Shanghai 201210 China
- School of Pharmacy Fudan University Shanghai 201203 China
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 China
| |
Collapse
|
8
|
Fan S, Yue L, Wan W, Zhang Y, Zhang B, Otomo C, Li Q, Lin T, Hu J, Xu P, Zhu M, Tao H, Chen Z, Li L, Ding H, Yao Z, Lu J, Wen Y, Zhang N, Tan M, Chen K, Xie Y, Otomo T, Zhou B, Jiang H, Dang Y, Luo C. Inhibition of Autophagy by a Small Molecule through Covalent Modification of the LC3 Protein. Angew Chem Int Ed Engl 2021; 60:26105-26114. [PMID: 34590387 DOI: 10.1002/anie.202109464] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/29/2021] [Indexed: 01/10/2023]
Abstract
The autophagic ubiquitin-like protein LC3 functions through interactions with LC3-interaction regions (LIRs) of other autophagy proteins, including autophagy receptors, which stands out as a promising protein-protein interaction (PPI) target for the intervention of autophagy. Post-translational modifications like acetylation of Lys49 on the LIR-interacting surface could disrupt the interaction, offering an opportunity to design covalent small molecules interfering with the interface. Through screening covalent compounds, we discovered a small molecule modulator of LC3A/B that covalently modifies LC3A/B protein at Lys49. Activity-based protein profiling (ABPP) based evaluations reveal that a derivative molecule DC-LC3in-D5 exhibits a potent covalent reactivity and selectivity to LC3A/B in HeLa cells. DC-LC3in-D5 compromises LC3B lipidation in vitro and in HeLa cells, leading to deficiency in the formation of autophagic structures and autophagic substrate degradation. DC-LC3in-D5 could serve as a powerful tool for autophagy research as well as for therapeutic interventions.
Collapse
Affiliation(s)
- Shijie Fan
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Liyan Yue
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wei Wan
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yuanyuan Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Bidong Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chinatsu Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Quanfu Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Tingting Lin
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Junchi Hu
- Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong District, Chongqing, China
| | - Pan Xu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mingrui Zhu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hongru Tao
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhifeng Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lianchun Li
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hong Ding
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhiyi Yao
- Suzhou Autopharm, 108 Yuxin Road, Jiangsu, 215123, China
| | - Junyan Lu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Wen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Naixia Zhang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Kaixian Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yuli Xie
- Suzhou Autopharm, 108 Yuxin Road, Jiangsu, 215123, China
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Bing Zhou
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.,Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University, No. 1, Yixueyuan Road, Yuzhong District, Chongqing, China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China.,School of Pharmacy, Fudan University, Shanghai, 201203, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| |
Collapse
|
9
|
Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang W, Zhang C, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine‐Targeting Reversible Covalent BCR‐ABL Inhibitors**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - John L. K. Wee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Priya Retna
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Rong Li
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Boping Liu
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Doris H. Y. Tee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Perlyn Z. Kwek
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Joma K. Joy
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Wan‐Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Klement Foo
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Thomas H. Keller
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Shao Q. Yao
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| |
Collapse
|
10
|
Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang WQ, Zhang CJ, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine-Targeting Reversible Covalent BCR-ABL Inhibitors*. Angew Chem Int Ed Engl 2021; 60:17131-17137. [PMID: 34008286 DOI: 10.1002/anie.202105383] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors have re-emerged as validated drugs to overcome acquired resistance in cancer treatment. Herein, by using a carbonyl boronic acid (CBA) warhead, we report the structure-based design of BCR-ABL inhibitors via reversible covalent targeting of the catalytic lysine with improved potency against both wild-type and mutant ABL kinases, especially ABLT315I bearing the gatekeeper residue mutation. We show the evolutionarily conserved lysine can be targeted selectively, and the selectivity depends largely on molecular recognition of the non-covalent pharmacophore in this class of inhibitors, probably due to the moderate reactivity of the warhead. We report the first co-crystal structures of covalent inhibitor-ABL kinase domain complexes, providing insights into the interaction of this warhead with the catalytic lysine. We also employed label-free mass spectrometry to evaluate off-targets of our compounds at proteome-wide level in different mammalian cells.
Collapse
Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - John L K Wee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Priya Retna
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Rong Li
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Boping Liu
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Doris H Y Tee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Perlyn Z Kwek
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Joma K Joy
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Wan-Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Klement Foo
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Thomas H Keller
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Shao Q Yao
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| |
Collapse
|
11
|
Sacco G, Stammwitz S, Belvisi L, Pignataro L, Dal Corso A, Gennari C. Functionalized 2‐Hydroxybenzaldehyde‐PEG Modules as Portable Tags for the Engagement of Protein Lysine ϵ‐Amino Groups. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Giovanni Sacco
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| | - Simon Stammwitz
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| | - Laura Belvisi
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| | - Luca Pignataro
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| | - Alberto Dal Corso
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| | - Cesare Gennari
- Dipartimento di Chimica Università degli Studi di Milano Via C. Golgi, 19 20133 Milan Italy
| |
Collapse
|
12
|
Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering. Angew Chem Int Ed Engl 2020; 59:21520-21524. [PMID: 32816380 PMCID: PMC7756862 DOI: 10.1002/anie.202008585] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues.
Collapse
Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| |
Collapse
|
13
|
Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Peter J. Cossar
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Laura M. Levy
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Chemistry University of Duisburg-Essen Universitätsstrasse 7 45117 Essen Germany
| |
Collapse
|
14
|
Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| |
Collapse
|
15
|
Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
| |
Collapse
|
16
|
Grygorenko OO, Volochnyuk DM, Ryabukhin SV, Judd DB. The Symbiotic Relationship Between Drug Discovery and Organic Chemistry. Chemistry 2019; 26:1196-1237. [PMID: 31429510 DOI: 10.1002/chem.201903232] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Indexed: 12/20/2022]
Abstract
All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.
Collapse
Affiliation(s)
- Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kiev, 02660, Ukraine
| | - Sergey V Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Duncan B Judd
- Awridian Ltd., Stevenage Bioscience Catalyst, Gunnelswood Road, Stevenage, Herts, SG1 2FX, UK
| |
Collapse
|
17
|
Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Alberto Dal Corso
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anja Schmid
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| |
Collapse
|
18
|
Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues. Angew Chem Int Ed Engl 2018; 57:17178-17182. [DOI: 10.1002/anie.201811650] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Alberto Dal Corso
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anja Schmid
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| |
Collapse
|
19
|
Martín‐Gago P, Olsen CA. Arylfluorosulfate-Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal. Angew Chem Int Ed Engl 2018; 58:957-966. [PMID: 30024079 PMCID: PMC6518939 DOI: 10.1002/anie.201806037] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Indexed: 01/15/2023]
Abstract
Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.
Collapse
Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| |
Collapse
|
20
|
Martín‐Gago P, Olsen CA. Arylfluorsulfat‐basierte Elektrophile für die kovalente Proteinmarkierung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806037] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
| |
Collapse
|
21
|
Jones LH. Reactive Chemical Probes: Beyond the Kinase Cysteinome. Angew Chem Int Ed Engl 2018; 57:9220-9223. [DOI: 10.1002/anie.201802693] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Lyn H. Jones
- Jnana Therapeutics; 50 Northern Avenue Boston 02210 USA
| |
Collapse
|
22
|
Affiliation(s)
- Lyn H. Jones
- Jnana Therapeutics; 50 Northern Avenue Boston 02210 USA
| |
Collapse
|