1
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Schnaider L, Tan S, Singh PR, Capuano F, Scott AJ, Hambley R, Lu L, Yang H, Wallace EJ, Jo H, DeGrado WF. SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex. J Am Chem Soc 2024; 146:25047-25057. [PMID: 39190920 DOI: 10.1021/jacs.4c07920] [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: 08/29/2024]
Abstract
Proximity-enhanced chemical cross-linking is an invaluable tool for probing protein-protein interactions and enhancing the potency of potential peptide and protein drugs. Here, we extend this approach to covalently stabilize large macromolecular assemblies. We used SuFEx chemistry to covalently stabilize an 18-subunit pore-forming complex, CsgG:CsgF, consisting of nine CsgG membrane protein subunits that noncovalently associate with nine CsgF peptides. Derivatives of the CsgG:CsgF pore have been used for DNA sequencing, which places high demands on the structural stability and homogeneity of the complex. To increase the robustness of the pore, we designed and synthesized derivatives of CsgF-bearing sulfonyl fluorides, which react with CsgG in very high yield to form a covalently stabilized CsgG:CsgF complex. The resulting pores formed highly homogeneous channels when added to artificial membranes. The high yield and rapid reaction rate of the SuFEx reaction prompted molecular dynamics simulations, which revealed that the SO2F groups in the initially formed complex are poised for nucleophilic reaction with a targeted Tyr. These results demonstrate the utility of SuFEx chemistry to structurally stabilize very large (here, 280 kDa) assemblies.
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Affiliation(s)
- Lee Schnaider
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Sophia Tan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | | | | | | | - Lei Lu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
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2
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Sun J, Lou L, Zhu C, Chen P, Tang G, Gu M, Xia S, Dong X, Zhang ZM, Gao L, Yao SQ, Xiao Q. Rationally designed BCR-ABL kinase inhibitors for improved leukemia treatment via covalent and pro-/dual-drug targeting strategies. J Adv Res 2024:S2090-1232(24)00392-8. [PMID: 39255927 DOI: 10.1016/j.jare.2024.09.008] [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: 06/28/2024] [Revised: 08/08/2024] [Accepted: 09/04/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Chronic Myeloid Leukemia (CML) is a blood cancer that remains challenging to cure due to drug resistance and side effects from current BCR-ABL inhibitors. There is an urgent need for novel and more effective BCR-ABL targeting inhibitors and therapeutic strategies to combat this deadly disease. METHOD We disclose an "OH-implant" strategy to improve a noncovalent BCR-ABL inhibitor, PPY-A, by adding a hydroxyl group to its scaffold. By taking advantage of this OH "hot spot", we designed a panel of irreversible covalent kinase inhibitors and hypoxia-responsive pro-/dual-drugs, and their biological activities were studied in vitro, in cellulo and in vivo. RESULT The resulting compound B1 showed enhanced solubility and biological activity. B4 achieved sustained BCR-ABL inhibition by forming a stable covalent bond with ABL kinase. Hypoxia-responsive prodrug P1 and dual-drugs D1/D2/D3 demonstrated significant anti-tumor effects under hypoxic conditions. The in vivo studies using K562-xenografted mice showed that B1 displayed superior antitumor activity than PPY-A, while P1 and D3 offered better safety profiles alongside significant tumor control. CONCLUSION We have successfully developed a chemical biology approach to convert a known noncovalent BCR-ABL inhibitor into more potent and safer inhibitors through covalent and pro-/dual-drug targeting strategies. Our "OH-implant" approach and the resulting drug design strategies have general applicability and hold promise for improvement the performance of various other reported drugs/drug candidates, thereby providing advanced medicines for disease treatment.
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Affiliation(s)
- Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Liang Lou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Mingxi Gu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Shu Xia
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China.
| | - Xiao Dong
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China.
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
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3
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Weaver J, Craven GB, Tram L, Chen H, Taunton J. Aminomethyl Salicylaldehydes Lock onto a Surface Lysine by Forming an Extended Intramolecular Hydrogen Bond Network. J Am Chem Soc 2024; 146:24233-24237. [PMID: 39177126 DOI: 10.1021/jacs.4c04314] [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: 08/24/2024]
Abstract
The development of electrophilic ligands that rapidly modify specific lysine residues remains a major challenge. Salicylaldehyde-based inhibitors have been reported to form stable imine adducts with the catalytic lysine of protein kinases. However, the targeted lysine in these examples is buried in a hydrophobic environment. A key unanswered question is whether this strategy can be applied to a lysine on the surface of a protein, where rapid hydrolysis of the resulting salicylaldimine is more likely. Here, we describe a series of aminomethyl-substituted salicylaldehydes that target a fully solvated lysine on the surface of the ATPase domain of Hsp90. By systematically varying the orientation of the salicylaldehyde, we discovered ligands with long residence times, the best of which engages Hsp90 in a quasi-irreversible manner. Crystallographic analysis revealed a daisy-chain network of intramolecular hydrogen bonds in which the salicylaldimine is locked into position by the adjacent piperidine linker. This study highlights the potential of aminomethyl salicylaldehydes to generate conformationally stabilized, hydrolysis-resistant imines, even when the targeted lysine is far from the ligand binding site and is exposed to bulk solvent.
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Affiliation(s)
- Jacqueline Weaver
- Chemistry and Chemical Biology Program, University of California─San Francisco, San Francisco, California 94143, United States
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
| | - Linh Tram
- Chemistry and Chemical Biology Program, University of California─San Francisco, San Francisco, California 94143, United States
| | - Hao Chen
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
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4
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Zhai Y, Zhang X, Chen Z, Yan D, Zhu L, Zhang Z, Wang X, Tian K, Huang Y, Yang X, Sun W, Wang D, Tsai YH, Luo T, Li G. Global profiling of functional histidines in live cells using small-molecule photosensitizer and chemical probe relay labelling. Nat Chem 2024; 16:1546-1557. [PMID: 38834725 DOI: 10.1038/s41557-024-01545-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
Recent advances in chemical proteomics have focused on developing chemical probes that react with nucleophilic amino acid residues. Although histidine is an attractive candidate due to its importance in enzymatic catalysis, metal binding and protein-protein interaction, its moderate nucleophilicity poses challenges. Its modification is frequently influenced by cysteine and lysine, which results in poor selectivity and narrow proteome coverage. Here we report a singlet oxygen and chemical probe relay labelling method that achieves high selectivity towards histidine. Libraries of small-molecule photosensitizers and chemical probes were screened to optimize histidine labelling, enabling histidine profiling in live cells with around 7,200 unique sites. Using NMR spectroscopy and X-ray crystallography, we characterized the reaction mechanism and the structures of the resulting products. We then applied this method to discover unannotated histidine sites key to enzymatic activity and metal binding in select metalloproteins. This method also revealed the accessibility change of histidine mediated by protein-protein interaction that influences select protein subcellular localization, underscoring its capability in discovering functional histidines.
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Affiliation(s)
- Yansheng Zhai
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xinyu Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, China
| | - Zijing Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | | | - Lin Zhu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhe Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xianghe Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kailu Tian
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yan Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xi Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, China
| | - Dong Wang
- Shenzhen University, Shenzhen, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Tuoping Luo
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
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5
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Tang G, Wang X, Huang H, Xu M, Ma X, Miao F, Lu X, Zhang CJ, Gao L, Zhang ZM, Yao SQ. Small Molecule-Induced Post-Translational Acetylation of Catalytic Lysine of Kinases in Mammalian Cells. J Am Chem Soc 2024; 146:23978-23988. [PMID: 39162335 DOI: 10.1021/jacs.4c07181] [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: 08/21/2024]
Abstract
Reversible lysine acetylation is an important post-translational modification (PTM). This process in cells is typically carried out enzymatically by lysine acetyltransferases and deacetylases. The catalytic lysine in the human kinome is highly conserved and ligandable. Small-molecule strategies that enable post-translational acetylation of the catalytic lysine on kinases in a target-selective manner therefore provide tremendous potential in kinase biology. Herein, we report the first small molecule-induced chemical strategy capable of global acetylation of the catalytic lysine on kinases from mammalian cells. By surveying various lysine-acetylating agents installed on a promiscuous kinase-binding scaffold, Ac4 was identified and shown to effectively acetylate the catalytic lysine of >100 different protein kinases from live Jurkat/K562 cells. In order to demonstrate that this strategy was capable of target-selective and reversible chemical acetylation of protein kinases, we further developed six acetylating compounds on the basis of VX-680 (a noncovalent inhibitor of AURKA). Among them, Ac13/Ac14, while displaying excellent in vitro potency and sustained cellular activity against AURKA, showed robust acetylation of its catalytic lysine (K162) in a target-selective manner, leading to irreversible inhibition of endogenous kinase activity. The reversibility of this chemical acetylation was confirmed on Ac14-treated recombinant AURKA protein, followed by deacetylation with SIRT3 (a lysine deacetylase). Finally, the reversible Ac13-induced acetylation of endogenous AURKA was demonstrated in SIRT3-transfected HCT116 cells. By disclosing the first cell-active acetylating compounds capable of both global and target-selective post-translational acetylation of the catalytic lysine on kinases, our strategy could provide a useful chemical tool in kinase biology and drug discovery.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xuan Wang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xingyu Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fengfei Miao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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6
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Wang M, Hou J, Do H, Wang C, Zhang X, Du Y, Dong Q, Wang L, Ni K, Ren F, An J. Intramolecular chalcogen bonding activated SuFEx click chemistry for efficient organic-inorganic linking. Nat Commun 2024; 15:6849. [PMID: 39127764 DOI: 10.1038/s41467-024-50922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
SuFEx click chemistry demonstrates remarkable molecular assembly capabilities. However, the effective utilization of alkyl sulfonyl fluoride hubs in SuFEx chemistry, particularly in reactions with alcohols and primary amines, presents considerable challenges. This study pioneers an intramolecular chalcogen bonding activated SuFEx (S-SuFEx) click chemistry employing alkyl sulfonyl fluorides with γ-S as the activating group. The ChB-activated alkyl sulfonyl fluorides can react smoothly with phenols, alcohols, and amines, exhibiting enhanced reactivity compared to SO2F2. Excellent yields have been achieved with all 75 tested substrates. Pioneering the application of S-SuFEx chemistry, we highlight its immense potential in organic-inorganic linking, considering the critical role of interfacial covalent bonding in material fabrication. The S-SuFEx hub 1c, incorporating a trialkoxy silane group has been specifically designed and synthesized for organic-inorganic linking. In a simple step, 1c efficiently anchors various organic compounds onto surfaces of inorganic materials, forming functionalized surfaces with properties such as antibacterial activity, hydrophobicity, and fluorescence.
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Affiliation(s)
- Minlong Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jiaman Hou
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Chao Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaohe Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Ying Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Qixin Dong
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Lijun Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Ke Ni
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Fazheng Ren
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie An
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China.
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7
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Li H, Zhang X, Wang Z, Sun C, Huang M, Liu J, Li Y, Zou Z, Pan Y, Zhang W, Wang Y. Pyridinium-Based Fluorosulfonamide Reagents Enabled Photoredox-Catalyzed Radical Fluorosulfonamidation. Org Lett 2024; 26:6714-6719. [PMID: 39058587 DOI: 10.1021/acs.orglett.4c02344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Sulfamoyl fluorides, as a crucial building block of SuFEx, have garnered extensive research interest due to their unique properties. However, the direct radical fluorosulfonamidation process for the synthesis of sulfamoyl fluorides has been overlooked. We herein disclosed a practical procedure for constructing a redox-active fluorosulfonamide radical reagent named fluorosulfonyl-N-pyridinium tetrafluoroborate (PNSF) from SO2F2. These reagents can facilitate a range of reactions, including the N-(fluorosulfonyl) sulfonamidation of (hetero)arenes, sequential radical stereoselective fluorosulfonamidation, and 1,2-difunctionalization of alkenes.
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Affiliation(s)
- Heyin Li
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xian Zhang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Wang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chao Sun
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mengjun Huang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing Liu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yifan Li
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhenlei Zou
- Anhui Technology Research Center of Optoelectronic Technology Appliance, Biomimetic Energy Laboratory, School of Electrical Engineering, Tongling University, Tongling 244000, China
| | - Yi Pan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Weigang Zhang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi Wang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Fikry E, Orfali R, Tawfeek N, Perveen S, Ghafar S, El-Domiaty MM, El-Shafae AM. Unveiling the Bioactive Efficacy of Cupressus sempervirens 'Stricta' Essential Oil: Composition, In Vitro Activities, and In Silico Analyses. Pharmaceuticals (Basel) 2024; 17:1019. [PMID: 39204124 PMCID: PMC11357629 DOI: 10.3390/ph17081019] [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: 06/25/2024] [Revised: 07/20/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024] Open
Abstract
Prior studies have extensively investigated the essential oil derived from the Mediterranean cypress, Cupressus sempervirens. However, the 'Stricta' variety, known for its ornamental value, has received less attention in terms of its oil composition and potential health benefits. The objective of this research was to comprehensively analyze the chemical components and medicinal properties of the essential oil extracted from C. sempervirens 'Stricta' (CSSLEO) grown in Egypt. Utilizing gas chromatography-mass spectrometry (GC-MS), the investigation identified 22 compounds within CSSLEO, with α-pinene and δ-3-carene being predominant, accounting for 96.01% of the oil. In vitro assays evaluated CSSLEO's cytotoxic effects on cancer cell lines, revealing notable anticancer potential. Additionally, the oil displayed antidiabetic properties by impeding crucial enzymes involved in glucose metabolism. Complementary in silico network pharmacology and molecular docking studies provided insights into the possible interactions between CSSLEO's key compounds and essential proteins and pathways in cancer treatment. The results underscored CSSLEO's intricate composition and its promising applications in cancer prevention and diabetes management. The conclusions drawn from this research underscore the need for further investigation to validate CSSLEO's clinical effectiveness and to gain a deeper understanding of its therapeutic mechanisms, with a view to harnessing its potential in oncology and endocrinology.
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Affiliation(s)
- Eman Fikry
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (E.F.); (M.M.E.-D.); (A.M.E.-S.)
| | - Raha Orfali
- Department of Pharmacognosy, Collage of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Nora Tawfeek
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (E.F.); (M.M.E.-D.); (A.M.E.-S.)
| | - Shagufta Perveen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Safina Ghafar
- Department of Pharmacognosy, Collage of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Maher M. El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (E.F.); (M.M.E.-D.); (A.M.E.-S.)
| | - Azza M. El-Shafae
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (E.F.); (M.M.E.-D.); (A.M.E.-S.)
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9
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Gundam SR, Bansal A, Kethamreddy M, Ghatamaneni S, Lowe VJ, Murray ME, Pandey MK. Synthesis and preliminary evaluation of novel PET probes for GSK-3 imaging. Sci Rep 2024; 14:15960. [PMID: 38987294 PMCID: PMC11237012 DOI: 10.1038/s41598-024-65943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Non-invasive imaging of GSK-3 expression in the brain will help to understand the role of GSK-3 in disease pathology and progression. Herein, we report the radiosynthesis and evaluation of two novel isonicotinamide based 18F labeled PET probes, [18F]2 and [18F]6 for noninvasive imaging of GSK3. Among the developed PET probes, the in vitro blood-brain permeability coefficient of 2 (38 ± 20 × 10-6 cm/s, n = 3) was found to be better than 6 (8.75 ± 3.90 × 10-6 cm/s, n = 5). The reference compounds 2 and 6 showed nanomolar affinity towards GSK-3α and GSK-3β. PET probe [18F]2 showed higher stability (100%) in mouse and human serums compared to [18F]6 (67.01 ± 4.93%, n = 3) in mouse serum and 66.20 ± 6.38%, n = 3) in human serum at 120 min post incubation. The in vivo imaging and blocking studies were performed in wild-type mice only with [18F]2 due to its observed stability. [18F]2 showed a SUV of 0.92 ± 0.28 (n = 6) in mice brain as early as 5 min post-injection followed by gradual clearance over time.
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Affiliation(s)
- Surendra Reddy Gundam
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Aditya Bansal
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Manasa Kethamreddy
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sujala Ghatamaneni
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Val J Lowe
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Mukesh K Pandey
- Division of Nuclear Medicine, Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA.
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10
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Ma S, Patel H, Peeples CA, Shen J. QM/MM Simulations of Afatinib-EGFR Addition: The Role of β-Dimethylaminomethyl Substitution. J Chem Theory Comput 2024; 20:5528-5538. [PMID: 38877999 DOI: 10.1021/acs.jctc.4c00290] [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: 07/10/2024]
Abstract
Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a β-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib, and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state β-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States
| | - Heeral Patel
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States
| | - Craig A Peeples
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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11
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Wang X, Sun J, Huang H, Tang G, Chen P, Xiang M, Li L, Zhang ZM, Gao L, Yao SQ. Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking. Angew Chem Int Ed Engl 2024; 63:e202404195. [PMID: 38695161 DOI: 10.1002/anie.202404195] [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: 02/29/2024] [Indexed: 07/02/2024]
Abstract
Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) have emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme's active site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.
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Affiliation(s)
- Xuan Wang
- 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
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, 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
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12
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Hansen T, Danková D, Bæk M, Grlaš L, Olsen CA. Sulfur(VI) Fluoride Exchange Chemistry in Solid-Phase Synthesis of Compound Arrays: Discovery of Histone Deacetylase Inhibitors. JACS AU 2024; 4:1854-1862. [PMID: 38818074 PMCID: PMC11134391 DOI: 10.1021/jacsau.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/01/2024]
Abstract
Multistep synthesis performed on solid support is a powerful means to generate small-molecule libraries for the discovery of chemical probes to dissect biological mechanisms as well as for drug discovery. Therefore, expansion of the collection of robust chemical transformations amenable to solid-phase synthesis is desirable for achieving chemically diverse libraries for biological testing. Here, we show that sulfur(VI) fluoride exchange (SuFEx) chemistry, exemplified by pairing phenols with aryl fluorosulfates, can be used for the solid-phase synthesis of biologically active compounds. As a case study, we designed and synthesized a library of 84 hydroxamic acid-containing small molecules, providing a rich source of inhibitors with diverse selectivity profiles across the human histone deacetylase enzyme family. Among other discoveries, we identified a scaffold that furnished inhibitors of HDAC11 with exquisite selectivity in vitro and a selective inhibitor of HDAC6 that was shown to affect the acetylation of α-tubulin over histone sites H3K18, H3K27, as well as SMC3 in cultured cells. Our results encourage the further use of SuFEx chemistry for the synthesis of diverse small-molecule libraries and provide insight for future design of selective HDAC inhibitors.
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Affiliation(s)
| | | | | | - Linda Grlaš
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
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13
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Alboreggia G, Udompholkul P, Baggio C, Muzzarelli K, Assar Z, Pellecchia M. Histidine-Covalent Stapled Alpha-Helical Peptides Targeting hMcl-1. J Med Chem 2024; 67:8172-8185. [PMID: 38695666 PMCID: PMC11129181 DOI: 10.1021/acs.jmedchem.4c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024]
Abstract
Several novel and effective cysteine targeting (Cys) covalent drugs are in clinical use. However, the target area containing a druggable Cys residue is limited. Therefore, methods for creating covalent drugs that target different residues are being looked for; examples of such ligands include those that target the residues lysine (Lys) and tyrosine (Tyr). Though the histidine (His) side chain is more frequently found in protein binding locations and has higher desirable nucleophilicity, surprisingly limited research has been done to specifically target this residue, and there are not many examples of His-targeting ligands that have been rationally designed. In the current work, we created novel stapled peptides that are intended to target hMcl-1 His 252 covalently. We describe the in vitro (biochemical, NMR, and X-ray) and cellular design and characterization of such agents. Our findings further suggest that the use of electrophiles to specifically target His residues is warranted.
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Affiliation(s)
- Giulia Alboreggia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Kendall Muzzarelli
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Zahra Assar
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Maurizio Pellecchia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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14
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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15
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Ma S, Patel H, Peeples CA, Shen J. QM/MM simulations of EFGR with afatinib reveal the role of the β-dimethylaminomethyl substitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.18.580887. [PMID: 38766221 PMCID: PMC11100610 DOI: 10.1101/2024.02.18.580887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a β-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state β-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Heeral Patel
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Craig A Peeples
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
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16
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Zheng Z, Zeng Y, Lai K, Liao B, Li P, Tan CSH. Protein painting for structural and binding site analysis via intracellular lysine reactivity profiling with o-phthalaldehyde. Chem Sci 2024; 15:6064-6075. [PMID: 38665522 PMCID: PMC11040650 DOI: 10.1039/d4sc00032c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The three-dimensional structure and the molecular interaction of proteins determine their roles in many cellular processes. Chemical protein painting with protein mass spectrometry can identify changes in structural conformations and molecular interactions of proteins including their binding sites. Nevertheless, most current protein painting techniques identify protein targets and binding sites of drugs in vitro using a cell lysate or purified protein. Here, we tested 11 membrane-permeable lysine-reactive chemical probes for intracellular covalent labeling of endogenous proteins, which reveals ortho-phthalaldehyde (OPA) as the most reactive probe in the intracellular environment. An MS workflow and a new data analysis strategy termed RAPID (Reactive Amino acid Profiling by Inverse Detection) was developed to enhance detection sensitivity. RAPID with OPA successfully identified structural changes induced by the allosteric drug TEPP-46 on its target protein PKM2 and was applied to profile the conformation change of the proteome occurring in cells during thermal denaturation. The application of RAPID-OPA on cells treated with geldanamycin, selumetinib, and staurosporine successfully revealed their binding sites on target proteins. Thus, RAPID-OPA for cellular protein painting enables the identification of ligand-binding sites and detection of protein structural changes occurring in cells.
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Affiliation(s)
- Zhenxiang Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Ya Zeng
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong PR China
| | - Kunjia Lai
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Bin Liao
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Chris Soon Heng Tan
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
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17
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Tang G, Wang W, Zhu C, Huang H, Chen P, Wang X, Xu M, Sun J, Zhang CJ, Xiao Q, Gao L, Zhang ZM, Yao SQ. Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development. Angew Chem Int Ed Engl 2024; 63:e202316394. [PMID: 38248139 DOI: 10.1002/anie.202316394] [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: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2 F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2 F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2 F-based TCIs.
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Affiliation(s)
- 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
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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18
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Veth TS, Kannegieter NM, de Graaf EL, Ruijtenbeek R, Joore J, Ressa A, Altelaar M. Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors. Drug Discov Today 2024; 29:103907. [PMID: 38301799 DOI: 10.1016/j.drudis.2024.103907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
The development of protein kinase inhibitors (PKIs) has gained significance owing to their therapeutic potential for diseases like cancer. In addition, there has been a rise in refining kinase activity assays, each possessing unique biological and analytical characteristics crucial for PKI development. However, the PKI development pipeline experiences high attrition rates and approved PKIs exhibit unexploited potential because of variable patient responses. Enhancing PKI development efficiency involves addressing challenges related to understanding the PKI mechanism of action and employing biomarkers for precision medicine. Selecting appropriate kinase activity assays for these challenges can overcome these attrition rate issues. This review delves into the current obstacles in kinase inhibitor development and elucidates kinase activity assays that can provide solutions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | | | - Erik L de Graaf
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | | | - Jos Joore
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Anna Ressa
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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19
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Yin CL, Qin RZ, Qin HL. One-Pot Three-Component Synthesis of Indolyl-4 H-chromene-3-sulfonyl Fluoride: A Class of Important Pharmacophore. J Org Chem 2024; 89:3618-3628. [PMID: 38358945 DOI: 10.1021/acs.joc.3c02706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
A one-pot, sequential three-component reaction between salicylaldehyde, indole, and 2-bromoprop-2-ene-1-sulfonyl fluoride (BPESF) has been demonstrated for the synthesis of sulfonyl fluoride substituted 4H-chromene derivatives in moderate to excellent yields (45%-94%). This one-pot sequential method features easily available starting materials, wide substrate scope, mild conditions, and great efficiency.
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Affiliation(s)
- Cheng-Lin Yin
- State Key Laboratory of Silicate Materials for Architectures; and School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Richard Zijian Qin
- State Key Laboratory of Silicate Materials for Architectures; and School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures; and School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, People's Republic of China
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20
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Leng J, Xu J, Li Y, Wang SM, Qin HL. A mild protocol for efficient preparation of functional molecules containing triazole. RSC Adv 2024; 14:7601-7608. [PMID: 38440271 PMCID: PMC10911410 DOI: 10.1039/d4ra01271b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
The construction of a class of novel triazole molecules containing sulfonyl fluoride functionalities was achieved through Cu-catalyzed click chemistry in good to excellent yields. The sulfonyl fluoride moieties were cleaved completely under base conditions to produce N-unsubstituted triazoles quantitatively, which provides a strategy to combine SuFEx click chemistry with Cu-catalyzed click chemistry ingeniously.
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Affiliation(s)
- Jing Leng
- School of Chemistry and Chemical Engineering, Yangzhou Polytechnic Institute Yangzhou Jiangsu 225127 P. R. China
| | - Jie Xu
- School of Chemistry and Chemical Engineering, Yangzhou Polytechnic Institute Yangzhou Jiangsu 225127 P. R. China
| | - Yanan Li
- School of Chemistry and Chemical Engineering, Yangzhou Polytechnic Institute Yangzhou Jiangsu 225127 P. R. China
| | - Shi-Meng Wang
- Xiangyang Public Inspection and Testing Center No. 69, Taiziwan Road Xiangyang Hubei Province 441000 P. R. China
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology 205 Luoshi Road Wuhan Hubei Province 430070 P. R. China
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21
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Zhao Y, Duan K, Fan Y, Li S, Huang L, Tu Z, Sun H, Cook GM, Yang J, Sun P, Tan Y, Ding K, Li Z. Catalyst-free late-stage functionalization to assemble α-acyloxyenamide electrophiles for selectively profiling conserved lysine residues. Commun Chem 2024; 7:31. [PMID: 38355988 PMCID: PMC10866925 DOI: 10.1038/s42004-024-01107-4] [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: 11/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Covalent probes coupled with chemical proteomics represent a powerful method for investigating small molecule and protein interactions. However, the creation of a reactive warhead within various ligands to form covalent probes has been a major obstacle. Herein, we report a convenient and robust process to assemble a unique electrophile, an α-acyloxyenamide, through a one-step late-stage coupling reaction. This procedure demonstrates remarkable tolerance towards other functional groups and facilitates ligand-directed labeling in proteins of interest. The reactive group has been successfully incorporated into a clinical drug targeting the EGFR L858R mutant, erlotinib, and a pan-kinase inhibitor. The resulting probes have been shown to be able to covalently engage a lysine residue proximal to the ATP-binding pocket of the EGFR L858R mutant. A series of active sites, and Mg2+, ATP-binding sites of kinases, such as K33 of CDK1, CDK2, CDK5 were detected. This is the first report of engaging these conserved catalytic lysine residues in kinases with covalent inhibition. Further application of this methodology to natural products has demonstrated its success in profiling ligandable conserved lysine residues in whole proteome. These findings offer insights for the development of new targeted covalent inhibitors (TCIs).
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Affiliation(s)
- Yuanyuan Zhao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Kang Duan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Youlong Fan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shengrong Li
- Guangdong Second Provincial General Hospital, Postdoctoral Station of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, China
| | - Liyan Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengchao Tu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 TatChee Avenue, Kowloon, Hong Kong, 999077, China
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Jing Yang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, China
| | - Pinghua Sun
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
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22
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Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [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: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
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Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
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23
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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24
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Chowdhury SR, Chuong P, Mgbemena VE, Statsyuk A. Development of a PROTAC Targeting Chk1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573733. [PMID: 38260247 PMCID: PMC10802242 DOI: 10.1101/2023.12.30.573733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
A series of Chk1 degraders were designed and synthesized. The degraders were developed through the conjugation of a promiscuous kinase binder and thalidomide. One of the degraders PROTAC-2 was able to decrease Chk1 levels in a concentration-dependent manner in A375 cells. The developed probes can be useful for the development of selective and more potent Chk1 degraders.
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Affiliation(s)
- Sandipan Roy Chowdhury
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
| | - Patrick Chuong
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
| | - Victoria E Mgbemena
- Department of Biology, MD and S Brailsford College of Arts and Sciences, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Alexander Statsyuk
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Health 2, 4349 Martin Luther King Boulevard, Houston, Texas, 77204
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25
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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26
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Gabizon R, Tivon B, Reddi RN, van den Oetelaar MCM, Amartely H, Cossar PJ, Ottmann C, London N. A simple method for developing lysine targeted covalent protein reagents. Nat Commun 2023; 14:7933. [PMID: 38040731 PMCID: PMC10692228 DOI: 10.1038/s41467-023-42632-5] [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: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters-electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.
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Affiliation(s)
- Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maxime C M van den Oetelaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Hadar Amartely
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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27
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Cosgrove B, Grant EK, Bertrand S, Down KD, Somers DO, P Evans J, Tomkinson NCO, Barker MD. Covalent targeting of non-cysteine residues in PI4KIIIβ. RSC Chem Biol 2023; 4:1111-1122. [PMID: 38033723 PMCID: PMC10685791 DOI: 10.1039/d3cb00142c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/02/2023] Open
Abstract
The synthesis and characterisation of fluorosulfate covalent inhibitors of the lipid kinase PI4KIIIβ is described. The conserved lysine residue located within the ATP binding site was targeted, and optimised compounds based upon reversible inhibitors with good activity and physicochemical profile showed strong reversible interactions and slow onset times for the covalent inhibition, resulting in an excellent selectivity profile for the lipid kinase target. X-Ray crystallography demonstrated a distal tyrosine residue could also be targeted using a fluorosulfate strategy. Combination of this knowledge showed that a dual covalent inhibitor could be developed which reveals potential in addressing the challenges associated with drug resistant mutations.
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Affiliation(s)
- Brett Cosgrove
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow G1 1XL UK
| | - Emma K Grant
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Sophie Bertrand
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Kenneth D Down
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Don O Somers
- Structural and Biophysical Science, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - John P Evans
- Screening, Profiling and Mechanistic Biology, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | | | - Michael D Barker
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
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28
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Tang G, Wang W, Wang X, Ding K, Ngan SC, Chen JY, Sze SK, Gao L, Yuan P, Lu X, Yao SQ. Cell-active, irreversible covalent inhibitors that selectively target the catalytic lysine of EGFR by using fluorosulfate-based SuFEx chemistry. Eur J Med Chem 2023; 259:115671. [PMID: 37499291 DOI: 10.1016/j.ejmech.2023.115671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
EGFR signaling is involved in multiple cellular processes including cell proliferation, differentiation and development, making this protein kinase one of the most valuable drug targets for the treatment of non-small cell lung carcinomas (NSCLC). Herein, we describe the design and synthesis of a series of potential covalent inhibitors targeting the catalytically conserved lysine (K745) of EGFR on the basis of Erlotinib, an FDA-approved first-generation EGFR drug. Different amine-reactive electrophiles were introduced at positions on the Erlotinib scaffold proximal to K745 in EGFR. The optimized compound 26 (as well as its close analog 30), possessing a novel arylfluorosulfate group (ArOSO2F), showed excellent in vitro potency (as low as 0.19 nM in independent IC50 determination) and selectivity against EGFR and many of its drug-resistant mutants. Both intact protein mass spectrometry (MS) and site-mapping analysis revealed that compound 26 covalently bound to EGFR at K745 through the formation of a sulfamate. In addition, compound 26 displayed good anti-proliferative potency against EGFR-overexpressing HCC827 cells by inhibiting endogenous EGFR autophosphorylation. The pharmacokinetic studies of compound 26 demonstrated the druggable potential of other ArOSO2F-containing compounds. Finally, competitive activity-based protein profiling (ABPP), cellular thermal shift assay (CETSA), as well as cellular wash-out experiments, all showed compound 26 to be the first cell-active, fluorosulfate-based targeted covalent inhibitor (TCI) of protein kinases capable of covalently engaging the catalytically conserved lysine of its target in live mammalian cells.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China; State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Jiao-Yu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China.
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
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29
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Leung CON, Yang Y, Leung RWH, So KKH, Guo HJ, Lei MML, Muliawan GK, Gao Y, Yu QQ, Yun JP, Ma S, Zhao Q, Lee TKW. Broad-spectrum kinome profiling identifies CDK6 upregulation as a driver of lenvatinib resistance in hepatocellular carcinoma. Nat Commun 2023; 14:6699. [PMID: 37872167 PMCID: PMC10593849 DOI: 10.1038/s41467-023-42360-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
Increasing evidence has demonstrated that drug resistance can be acquired in cancer cells by kinase rewiring, which is an obstacle for efficient cancer therapy. However, it is technically challenging to measure the expression of protein kinases on large scale due to their dynamic range in human proteome. We employ a lysine-targeted sulfonyl fluoride probe, named XO44, which binds to 133 endogenous kinases in intact lenvatinib-resistant hepatocellular carcinoma (HCC) cells. This analysis reveals cyclin-dependent kinase 6 (CDK6) upregulation, which is mediated by ERK/YAP1 signaling cascade. Functional analyses show that CDK6 is crucial in regulation of acquired lenvatinib resistance in HCC via augmentation of liver cancer stem cells with clinical significance. We identify a noncanonical pathway of CDK6 in which it binds and regulates the activity of GSK3β, leading to activation of Wnt/β-catenin signaling. Consistently, CDK6 inhibition by palbociclib or degradation by proteolysis targeting chimeras (PROTACs) is highly synergistic with lenvatinib in vitro. Interestingly, palbociclib not only exerts maximal growth suppressive effect with lenvatinib in lenvatinib-resistant HCC models but also reshapes the tumor immune microenvironment. Together, we unveil CDK6 as a druggable target in lenvatinib-resistant HCC and highlight the use of a chemical biology approach to understand nongenetic resistance mechanisms in cancer.
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Affiliation(s)
- Carmen Oi Ning Leung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yang Yang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Rainbow Wing Hei Leung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Karl Kam Hei So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hai Jun Guo
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Martina Mang Leng Lei
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Gregory Kenneth Muliawan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yuan Gao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'An, China
| | - Qian Qian Yu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Ping Yun
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China.
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hong Kong, China.
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30
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Aatkar A, Vuorinen A, Longfield OE, Gilbert K, Peltier-Heap R, Wagner CD, Zappacosta F, Rittinger K, Chung CW, House D, Tomkinson NCO, Bush JT. Efficient Ligand Discovery Using Sulfur(VI) Fluoride Reactive Fragments. ACS Chem Biol 2023; 18:1926-1937. [PMID: 37084287 PMCID: PMC10510102 DOI: 10.1021/acschembio.3c00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Sulfur(VI) fluorides (SFs) have emerged as valuable electrophiles for the design of "beyond-cysteine" covalent inhibitors and offer potential for expansion of the liganded proteome. Since SFs target a broad range of nucleophilic amino acids, they deliver an approach for the covalent modification of proteins without requirement for a proximal cysteine residue. Further to this, libraries of reactive fragments present an innovative approach for the discovery of ligands and tools for proteins of interest by leveraging a breadth of mass spectrometry analytical approaches. Herein, we report a screening approach that exploits the unique properties of SFs for this purpose. Libraries of SF-containing reactive fragments were synthesized, and a direct-to-biology workflow was taken to efficiently identify hit compounds for CAII and BCL6. The most promising hits were further characterized to establish the site(s) of covalent modification, modification kinetics, and target engagement in cells. Crystallography was used to gain a detailed molecular understanding of how these reactive fragments bind to their target. It is anticipated that this screening protocol can be used for the accelerated discovery of "beyond-cysteine" covalent inhibitors.
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Affiliation(s)
- Arron Aatkar
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Aini Vuorinen
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Oliver E. Longfield
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Katharine Gilbert
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Rachel Peltier-Heap
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Craig D. Wagner
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | | | - Chun-wa Chung
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - David House
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Nicholas C. O. Tomkinson
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Jacob T. Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
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31
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Wang W, Wang X, Tang G, Zhu C, Xiang M, Xiao Q, Zhang ZM, Gao L, Yao SQ. Multitarget inhibitors/probes that target LRRK2 and AURORA A kinases noncovalently and covalently. Chem Commun (Camb) 2023; 59:10789-10792. [PMID: 37594149 DOI: 10.1039/d3cc03530a] [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: 08/19/2023]
Abstract
Herein, we report a salicylaldehyde-based, reversible covalent inhibitor (A2) that possesses moderate cellular activity against AURKA with a prolonged residence time and shows significant non-covalent inhibition towards LRRK2. Our results indicated that this multitarget kinase inhibitor may be used as the starting point for future development of more potent, selective and dual-targeting covalent kinase inhibitors against AURKA and LRRK2 for mitophagy.
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Affiliation(s)
- Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
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32
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Porta EO, Steel PG. Activity-based protein profiling: A graphical review. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2023; 5:100164. [PMID: 37692766 PMCID: PMC10484978 DOI: 10.1016/j.crphar.2023.100164] [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: 04/17/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023] Open
Abstract
Activity-based protein profiling (ABPP) is a chemoproteomic technology that employs small chemical probes to directly interrogate protein function within complex proteomes. Since its initial application almost 25 years ago, ABPP has proven to be a powerful and versatile tool for addressing numerous challenges in drug discovery, including the development of highly selective small-molecule inhibitors, the discovery of new therapeutic targets, and the illumination of target proteins in tissues and organisms. This graphical review provides an overview of the rapid evolution of ABPP strategies, highlighting the versatility of the approach with selected examples of its successful application.
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Affiliation(s)
| | - Patrick G. Steel
- Department of Chemistry, Durham University, Durham, DH1 3LE, United Kingdom
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33
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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34
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Homer JA, Xu L, Kayambu N, Zheng Q, Choi EJ, Kim BM, Sharpless KB, Zuilhof H, Dong J, Moses JE. Sulfur fluoride exchange. NATURE REVIEWS. METHODS PRIMERS 2023; 3:58. [PMID: 38873592 PMCID: PMC11171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Sulfur Fluoride Exchange (SuFEx) is a click reaction par excellence that has revolutionized multiple research fields. In this Primer, we delve into the essential elements of SuFEx operation, catalysis, and SuFExable connective hubs. We also explore the cutting-edge applications of SuFEx in drug development, polymer science, and biochemistry. Additionally, we examine the potential limitations and promising prospects for this versatile click reaction.
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Affiliation(s)
- Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
| | - Long Xu
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Namitharan Kayambu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Current affiliation: Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Eun Joung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- School of Pharmaceutical Science & Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
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35
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Yu B, Cao L, Li S, Klauser PC, Wang L. The proximity-enabled sulfur fluoride exchange reaction in the protein context. Chem Sci 2023; 14:7913-7921. [PMID: 37502323 PMCID: PMC10370592 DOI: 10.1039/d3sc01921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023] Open
Abstract
The proximity-enabled sulfur(vi) fluoride exchange (SuFEx) reaction generates specific covalent linkages between proteins in cells and in vivo, which opens innovative avenues for studying elusive protein-protein interactions and developing potent covalent protein drugs. To exploit the power and expand the applications of covalent proteins, covalent linkage formation between proteins is the critical step, for which fundamental kinetic and essential properties remain unexplored. Herein, we systematically studied SuFEx kinetics in different proteins and conditions. In contrast to in small molecules, SuFEx in interacting proteins conformed with a two-step mechanism involving noncovalent binding, followed by covalent bond formation, exhibiting nonlinear rate dependence on protein concentration. The protein SuFEx rate consistently changed with protein binding affinity as well as chemical reactivity of the functional group and was impacted by target residue identity and solution pH. In addition, kinetic analyses of nanobody SR4 binding with SARS-CoV-2 spike protein revealed that viral target mutations did not abolish covalent binding but decreased the SuFEx rate with affinity decrease. Moreover, off-target cross-linking of a SuFEx-capable nanobody in human serum was not detected, and the SuFEx-generated protein linkage was stable at cellular acidic pHs, suggesting SuFEx suitability for in vivo usage. These results advanced our understanding of SuFEx reactivity and kinetics in proteins, which is invaluable for ongoing exploration of SuFEx-enabled covalent proteins for basic biological research and creative biotherapeutics.
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Affiliation(s)
- Bingchen Yu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
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36
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Udompholkul P, Garza-Granados A, Alboreggia G, Baggio C, McGuire J, Pegan SD, Pellecchia M. Characterization of a Potent and Orally Bioavailable Lys-Covalent Inhibitor of Apoptosis Protein (IAP) Antagonist. J Med Chem 2023. [PMID: 37262387 DOI: 10.1021/acs.jmedchem.3c00467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have recently reported on the use of aryl-fluorosulfates in designing water- and plasma-stable agents that covalently target Lys, Tyr, or His residues in the BIR3 domain of the inhibitor of the apoptosis protein (IAP) family. Here, we report further structural, cellular, and pharmacological characterizations of this agent, including the high-resolution structure of the complex between the Lys-covalent agent and its target, the BIR3 domain of X-linked IAP (XIAP). We also compared the cellular efficacy of the agent in two-dimensional (2D) and three-dimensional (3D) cell cultures, side by side with the clinical candidate reversible IAP inhibitor LCL161. Finally, in vivo pharmacokinetic studies indicated that the agent was long-lived and orally bioavailable. Collectively our data further corroborate that aryl-fluorosulfates, when incorporated correctly in a ligand, can result in Lys-covalent agents with pharmacodynamic and pharmacokinetic properties that warrant their use in the design of pharmacological probes or even therapeutics.
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Affiliation(s)
- Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Ana Garza-Granados
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Giulia Alboreggia
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Jack McGuire
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Scott D Pegan
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
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37
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Huang H, Jones LH. Covalent drug discovery using sulfur(VI) fluoride exchange warheads. Expert Opin Drug Discov 2023:1-11. [PMID: 37243622 DOI: 10.1080/17460441.2023.2218642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Covalent drug discovery has traditionally focused on targeting cysteine, but the amino acid is often absent in protein binding sites. This review makes the case to move beyond cysteine labeling using sulfur (VI) fluoride exchange (SuFEx) chemistry to expand the druggable proteome. AREAS COVERED Recent advances in SuFEx medicinal chemistry and chemical biology are described, which have enabled the development of covalent chemical probes that site-selectively engage amino acid residues (including tyrosine, lysine, histidine, serine, and threonine) in binding pockets. Areas covered include chemoproteomic mapping of the targetable proteome, structure-based design of covalent inhibitors and molecular glues, metabolic stability profiling, and synthetic methodologies that have expedited the delivery of SuFEx modulators. EXPERT OPINION Despite recent innovations in SuFEx medicinal chemistry, focused preclinical research is required to ensure the field moves from early chemical probe discovery to the delivery of transformational covalent drug candidates. The authors believe that covalent drug candidates designed to engage residues beyond cysteine using sulfonyl exchange warheads will likely enter clinical trials in the coming years.
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Affiliation(s)
- Huang Huang
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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38
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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39
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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40
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Lee SB, Yu J, Kim H, Kim KW, Jeong JW, Kim YL, Park SJ, Koo TS, Lee C, Hong KB, Choi S. Novel Strategy To Inhibit Transthyretin Amyloidosis via the Synergetic Effect of Chemoselective Acylation and Noncovalent Inhibitor Release. J Med Chem 2023; 66:2893-2903. [PMID: 36749109 DOI: 10.1021/acs.jmedchem.2c01926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strategies for developing targeted covalent inhibitors (TCIs), which have the advantages of a prolonged duration of action and selectivity toward a drug target, have attracted great interest in drug discovery. Herein, we report chemoselective covalent inhibitors that specifically target lysine ε-amine groups that conjugate with an endogenous protein to prevent disease-causing protein misfolding and aggregation. These TCIs are unique because the benzoyl group is preferentially conjugated to Lys15 at the top of the T4 binding site within transthyretin (TTR) while simultaneously releasing a potent noncovalent TTR kinetic stabilizer. The potency of these covalent inhibitors is superior to tafamidis, the only FDA-approved drug for the treatment of hereditary TTR amyloidosis. In addition to investigations into the covalent modification of TTR via reverse-phase high-performance liquid chromatography, direct methods are performed to confirm and visualize the presumed covalent interaction via mass spectrometry and X-ray crystallography.
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Affiliation(s)
- Seok Beom Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jaeni Yu
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Hyunwoo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kun Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jong Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Yun Lan Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Sungwook Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
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41
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Gilbert K, Vuorinen A, Aatkar A, Pogány P, Pettinger J, Grant EK, Kirkpatrick JM, Rittinger K, House D, Burley GA, Bush JT. Profiling Sulfur(VI) Fluorides as Reactive Functionalities for Chemical Biology Tools and Expansion of the Ligandable Proteome. ACS Chem Biol 2023; 18:285-295. [PMID: 36649130 PMCID: PMC9942091 DOI: 10.1021/acschembio.2c00633] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
Here, we report a comprehensive profiling of sulfur(VI) fluorides (SVI-Fs) as reactive groups for chemical biology applications. SVI-Fs are reactive functionalities that modify lysine, tyrosine, histidine, and serine sidechains. A panel of SVI-Fs were studied with respect to hydrolytic stability and reactivity with nucleophilic amino acid sidechains. The use of SVI-Fs to covalently modify carbonic anhydrase II (CAII) and a range of kinases was then investigated. Finally, the SVI-F panel was used in live cell chemoproteomic workflows, identifying novel protein targets based on the type of SVI-F used. This work highlights how SVI-F reactivity can be used as a tool to expand the liganded proteome.
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Affiliation(s)
- Katharine
E. Gilbert
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Aini Vuorinen
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Arron Aatkar
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Peter Pogány
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | - Jonathan Pettinger
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | | | - Katrin Rittinger
- The
Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, United Kingdom
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Glenn A. Burley
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
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42
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Carneiro SN, Khasnavis SR, Lee J, Butler TW, Majmudar JD, Am Ende CW, Ball ND. Sulfur(VI) fluorides as tools in biomolecular and medicinal chemistry. Org Biomol Chem 2023; 21:1356-1372. [PMID: 36662157 PMCID: PMC9929716 DOI: 10.1039/d2ob01891h] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023]
Abstract
Recent advances in the synthesis of sulfur(VI)-fluorides has enabled incredible growth in their application in biomolecular chemistry. This review aims to serve as a primer highlighting synthetic strategies toward a diversity of S(VI) fluorides and their application in chemical biology, bioconjugation, and medicinal chemistry.
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Affiliation(s)
- Sabrina N Carneiro
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Samuel R Khasnavis
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Jisun Lee
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Todd W Butler
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Jaimeen D Majmudar
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | | | - Nicholas D Ball
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
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43
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Chen P, Tang G, Zhu C, Sun J, Wang X, Xiang M, Huang H, Wang W, Li L, Zhang ZM, Gao L, Yao SQ. 2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases. J Am Chem Soc 2023; 145:3844-3849. [PMID: 36774655 DOI: 10.1021/jacs.2c11595] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Lysine-targeting irreversible covalent inhibitors have attracted growing interests in recent years, especially in the fields of kinase research. Despite encouraging progress, few chemistries are available to develop inhibitors that are exclusively lysine-targeting, selective, and cell-active. We report herein a 2-ethynylbenzaldehyde (EBA)-based, lysine-targeting strategy to generate potent and selective small-molecule inhibitors of ABL kinase by selectively targeting the conserved catalytic lysine in the enzyme. We showed the resulting compounds were cell-active, capable of covalently engaging endogenous ABL kinase in K562 cells with long-residence time and few off-targets. We further validated the generality of this strategy by developing EBA-based irreversible inhibitors against EGFR (a kinase) and Mcl-1 (a nonkinase) that covalently reacted with the catalytic and noncatalytic lysine within each target.
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Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, 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
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44
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Arafet K, Scalvini L, Galvani F, Martí S, Moliner V, Mor M, Lodola A. Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents. J Chem Inf Model 2023; 63:1301-1312. [PMID: 36762429 PMCID: PMC9976278 DOI: 10.1021/acs.jcim.2c01586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Targeted covalent inhibitors hold promise for drug discovery, particularly for kinases. Targeting the catalytic lysine of epidermal growth factor receptor (EGFR) has attracted attention as a new strategy to overcome resistance due to the emergence of C797S mutation. Sulfonyl fluoride derivatives able to inhibit EGFRL858R/T790M/C797S by sulfonylation of Lys745 have been reported. However, atomistic details of this process are still poorly understood. Here, we describe the mechanism of inhibition of an innovative class of compounds that covalently engage the catalytic lysine of EGFR, through a sulfur(VI) fluoride exchange (SuFEx) process, with the help of hybrid quantum mechanics/molecular mechanics (QM/MM) and path collective variables (PCVs) approaches. Our simulations identify the chemical determinants accounting for the irreversible activity of agents targeting Lys745 and provide hints for the further optimization of sulfonyl fluoride agents.
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Affiliation(s)
- Kemel Arafet
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Laura Scalvini
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Francesca Galvani
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Sergio Martí
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,Microbiome
Research Hub, University of Parma, Parco Area delle Scienze 11/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,. Phone: +39 0521 905062. Fax: +39 0521 905006
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45
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Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
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46
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Steffek M, Helgason E, Popovych N, Rougé L, Bruning JM, Li KS, Burdick DJ, Cai J, Crawford T, Xue J, Decurtins W, Fang C, Grubers F, Holliday MJ, Langley A, Petersen A, Satz AL, Song A, Stoffler D, Strebel Q, Tom JYK, Skelton N, Staben ST, Wichert M, Mulvihill MM, Dueber EC. A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands. Biochemistry 2023; 62:633-644. [PMID: 34985287 DOI: 10.1021/acs.biochem.1c00682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.
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Affiliation(s)
- Micah Steffek
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lionel Rougé
- Structure Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John M Bruning
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Terry Crawford
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Xue
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Willy Decurtins
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chunlin Fang
- WuXi AppTec (Wuhan) Company, Ltd., No. 666 GaoXin Road, WuHan East Lake High-tech Development Zone, Hubei 430075, China
| | - Felix Grubers
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael J Holliday
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Allyson Langley
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ann Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexander Lee Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Aimin Song
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Quentin Strebel
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jeffrey Y K Tom
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Skelton
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin C Dueber
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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47
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Liu M, Tang W, Qin HL. Discovery of ( E)-2-Methoxyethene-1-sulfonyl Fluoride for the Construction of Enaminyl Sulfonyl Fluoride. J Org Chem 2023; 88:1909-1917. [PMID: 36649643 DOI: 10.1021/acs.joc.2c02836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new sulfonyl fluoride reagent (E)-2-methoxyethene-1-sulfonyl fluoride (MeO-ESF) was developed and successfully applied for the construction of enaminyl sulfonyl fluoride (N-ESF). This protocol provides highly atom-economical access to diverse N-ESF and produces CH3OH as the sole byproduct under mild and environmentally benign conditions.
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Affiliation(s)
- Min Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
| | - Wenjian Tang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Hua-Li Qin
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China
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48
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Chen W, Ji G, Wu R, Fang C, Lu H. Mass spectrometry-based candidate substrate and site identification of PTM enzymes. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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49
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Zaia J. The 2022 Nobel Prize in Chemistry for the development of click chemistry and bioorthogonal chemistry. Anal Bioanal Chem 2023; 415:527-532. [PMID: 36602567 PMCID: PMC10848669 DOI: 10.1007/s00216-022-04483-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The 2022 Nobel Prize in Chemistry recognized the development of biorthogonal chemical ligation reactions known as click chemistry in biomedicine. This concept has catalyzed significant progress in sensing and diagnosis, chemical biology, materials chemistry, and drug discovery and delivery. In proteomics, the ability to incorporate a click tag into proteins has propelled development of powerful new methods for selective enrichment of protein complexes that inform understanding of protein networks. It also has had a strong influence on the ability to enrich for protein post-translational modifications. This feature article summarizes the impacts of biorthogonal click chemistry on proteomics.
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Affiliation(s)
- Joseph Zaia
- Dept. of Biochemistry, Boston University, 670 Albany St. Rm. 509, Boston, MA, 02118, USA.
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50
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Erchinger JE, Hoogesteger R, Laskar R, Dutta S, Hümpel C, Rana D, Daniliuc CG, Glorius F. EnT-Mediated N-S Bond Homolysis of a Bifunctional Reagent Leading to Aliphatic Sulfonyl Fluorides. J Am Chem Soc 2023; 145:2364-2374. [PMID: 36652725 DOI: 10.1021/jacs.2c11295] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sulfur(VI) fluoride exchange (SuFEx) gives rise to a plethora of high-valent sulfur linkages; however, the availability of (aliphatic) sulfonyl fluoride manifolds lag behind, owing to the limited sources of introducing the SO2F moiety via a classical two-electron approach. Recently, radical-based methodologies have emerged as a complementary strategy to increase the diversity of accessible click partners. In this work, synthesis of a bench-stable sulfamoyl fluoride reagent is presented, which may undergo sigma-bond homolysis upon visible-light-induced sensitization to form protected β-amino sulfonyl fluorides from alkene feedstocks. Notably, this offers an appealing strategy to access various building blocks for peptido sulfonyl fluorides, relevant in a medicinal chemistry context, as well as an intriguing entry to β-ammonium sulfonates and β-sultams, from alkenes. Densely functionalized 1,3-sultones were obtained by employing allyl alcohols as substrates. Surprisingly, allyl chloride-derived β-imino sulfonyl fluoride underwent S-O bond formation and ring closure to yield rigid cyclopropyl β-imino sulfonate ester under SuFEx conditions. Furthermore, by engaging a thiol-based hydrogen atom donor in the reaction, the reactivity of the same reagent can be tuned toward the direct synthesis of aliphatic sulfonyl fluorides. Mechanistic experiments indicate an energy transfer (EnT)-mediated process. The transient sulfonyl fluoride radical adds to the alkene and product formation occurs upon either radical-radical coupling or hydrogen atom transfer (HAT), respectively.
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Affiliation(s)
- Johannes E Erchinger
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Reece Hoogesteger
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Ranjini Laskar
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Subhabrata Dutta
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Carla Hümpel
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Debanjan Rana
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
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