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BHUSARE NILAM, KUMAR MAUSHMI. A review on potential heterocycles for the treatment of glioblastoma targeting receptor tyrosine kinases. Oncol Res 2024; 32:849-875. [PMID: 38686058 PMCID: PMC11055995 DOI: 10.32604/or.2024.047042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/10/2024] [Indexed: 05/02/2024] Open
Abstract
Glioblastoma, the most aggressive form of brain tumor, poses significant challenges in terms of treatment success and patient survival. Current treatment modalities for glioblastoma include radiation therapy, surgical intervention, and chemotherapy. Unfortunately, the median survival rate remains dishearteningly low at 12-15 months. One of the major obstacles in treating glioblastoma is the recurrence of tumors, making chemotherapy the primary approach for secondary glioma patients. However, the efficacy of drugs is hampered by the presence of the blood-brain barrier and multidrug resistance mechanisms. Consequently, considerable research efforts have been directed toward understanding the underlying signaling pathways involved in glioma and developing targeted drugs. To tackle glioma, numerous studies have examined kinase-downstream signaling pathways such as RAS-RAF-MEK-ERK-MPAK. By targeting specific signaling pathways, heterocyclic compounds have demonstrated efficacy in glioma therapeutics. Additionally, key kinases including phosphatidylinositol 3-kinase (PI3K), serine/threonine kinase, cytoplasmic tyrosine kinase (CTK), receptor tyrosine kinase (RTK) and lipid kinase (LK) have been considered for investigation. These pathways play crucial roles in drug effectiveness in glioma treatment. Heterocyclic compounds, encompassing pyrimidine, thiazole, quinazoline, imidazole, indole, acridone, triazine, and other derivatives, have shown promising results in targeting these pathways. As part of this review, we propose exploring novel structures with low toxicity and high potency for glioma treatment. The development of these compounds should strive to overcome multidrug resistance mechanisms and efficiently penetrate the blood-brain barrier. By optimizing the chemical properties and designing compounds with enhanced drug-like characteristics, we can maximize their therapeutic value and minimize adverse effects. Considering the complex nature of glioblastoma, these novel structures should be rigorously tested and evaluated for their efficacy and safety profiles.
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Affiliation(s)
- NILAM BHUSARE
- Somaiya Institute for Research & Consultancy, Somaiya Vidyavihar University, Vidyavihar (East), Mumbai, 400077, India
| | - MAUSHMI KUMAR
- Somaiya Institute for Research & Consultancy, Somaiya Vidyavihar University, Vidyavihar (East), Mumbai, 400077, India
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2
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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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3
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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4
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Zhao Z, Bourne PE. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett 2023; 14:1503-1508. [PMID: 37974950 PMCID: PMC10641887 DOI: 10.1021/acsmedchemlett.3c00212] [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: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first created a kinase structure-assay database (KSAD) containing 2705 nM ligand-bound kinase complexes. Then, using KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs.
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Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
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5
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Yan Z, Du Y, Zhang H, Zheng Y, Lv H, Dong N, He F. Research progress of anticancer drugs targeting CDK12. RSC Med Chem 2023; 14:1629-1644. [PMID: 37731700 PMCID: PMC10507796 DOI: 10.1039/d3md00004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/17/2023] [Indexed: 09/22/2023] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated CDK that plays key roles in transcription, translation, mRNA splicing, the cell cycle, and DNA damage repair. Research has identified that high expression of CDK12 in organs such as the breast, stomach, and uterus can lead to HER2-positive breast cancer, gastric cancer and cervical cancer. Inhibiting high expression of CDK12 suppresses tumor growth and proliferation, suggesting that it is both a biomarker for cancer and a potential target for cancer therapy. CDK12 inhibitors can competitively bind the CDK12 hydrophobic pocket with ATP to avoid CDK12 phosphorylation, blocking subsequent signaling pathways. The development of CDK12 inhibitors is challenging due to the high homology of CDK12 with other CDKs. This review summarizes the research progress of CDK12 inhibitors, their mechanism of action and the structure-activity relationship, providing new insights into the design of CDK12 selective inhibitors.
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Affiliation(s)
- Zhijia Yan
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yongli Du
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Haibin Zhang
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Yong Zheng
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Huiting Lv
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Ning Dong
- School of Chemistry & Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences) 3501 Da Xue Road Jinan 250353 China
| | - Fang He
- School of Water Conservancy and Environment, University of Jinan 336 Nanxinzhuang West Road Jinan 250022 China
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6
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Cirillo D, Diceglie M, Nazaré M. Isoform-selective targeting of PI3K: time to consider new opportunities? Trends Pharmacol Sci 2023; 44:601-621. [PMID: 37438206 DOI: 10.1016/j.tips.2023.06.002] [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: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/14/2023]
Abstract
Phosphoinositide-3-kinases (PI3Ks) are central to several cellular signaling pathways in human physiology and are potential pharmacological targets for many pathologies including cancer, thrombosis, and pulmonary diseases. Tremendous efforts to develop isoform-selective inhibitors have culminated in the approval of several drugs, validating PI3K as a tractable and therapeutically relevant target. Although successful therapeutic validation has focused on isoform-selective class I orthosteric inhibitors, recent clinical findings have indicated challenges regarding poor drug tolerance owing to sustained on-target inhibition. Hence, additional approaches are warranted to increase the clinical benefits of specific clinical treatment options, which may involve the employment of so far underexploited targeting modalities or the development of inhibitors for currently underexplored PI3K class II isoforms. We review recent key discoveries in the development of isoform-selective inhibitors, focusing particularly on PI3K class II isoforms, and highlight the emerging importance of developing a broader arsenal of pharmacological tools.
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Affiliation(s)
- Davide Cirillo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Marta Diceglie
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany.
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7
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [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: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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8
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Zhao Z, Bourne PE. Rigid Scaffolds Are Promising for Designing Macrocyclic Kinase Inhibitors. ACS Pharmacol Transl Sci 2023; 6:1182-1191. [PMID: 37588756 PMCID: PMC10425998 DOI: 10.1021/acsptsci.3c00078] [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: 04/12/2023] [Indexed: 08/18/2023]
Abstract
Macrocyclic kinase inhibitors (MKIs) are gaining attention due to their favorable selectivity and potential to overcome drug resistance, yet they remain challenging to design because of their novel structures. To facilitate the design and discovery of MKIs, we investigate MKI rational design starting from initial acyclic compounds by performing microsecond-scale atomistic simulations for multiple MKIs, constructing an MKI database, and analyzing MKIs using hierarchical cluster analysis. Our studies demonstrate that the binding modes of MKIs are like those of their corresponding acyclic counterparts against the same kinase targets. Importantly, within the respective binding sites, the MKI scaffolds retain the same conformations as their corresponding acyclic counterparts, demonstrating the rigidity of scaffolds before and after molecular cyclization. The MKI database includes 641 nanomole-level MKIs from 56 human kinases elucidating the features of rigid scaffolds and the core structures of MKIs. Collectively these results and resources can facilitate MKI development.
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Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
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9
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White MEH, Gil J, Tate EW. Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics. Cell Chem Biol 2023; 30:828-838.e4. [PMID: 37451266 DOI: 10.1016/j.chembiol.2023.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/20/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Covalent drug discovery has undergone a resurgence over the past two decades and reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through on- and off-target profiling; however, the scope of this approach has not been fully explored at the whole-proteome level. We combined AlphaFold2-predicted side-chain accessibilities for >95% of the human proteome with a meta-analysis of eighteen public cysteine profiling datasets, totaling 44,187 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further showed that hit elaboration and optimization drives increased bias against buried cysteine residues. Based on these data, we suggest that current profiling approaches cover a small proportion of potential ligandable cysteine residues and propose future directions for increasing coverage, focusing on high-priority residues and depth. All analysis and produced resources are freely available and extendable to other reactive amino acids.
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Affiliation(s)
- Matthew E H White
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; The Francis Crick Institute, London NW1 1AT, UK.
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10
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Șandor A, Ionuț I, Marc G, Oniga I, Eniu D, Oniga O. Structure-Activity Relationship Studies Based on Quinazoline Derivatives as EGFR Kinase Inhibitors (2017-Present). Pharmaceuticals (Basel) 2023; 16:534. [PMID: 37111291 PMCID: PMC10141396 DOI: 10.3390/ph16040534] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) plays a critical role in the tumorigenesis of various forms of cancer. Targeting the mutant forms of EGFR has been identified as an attractive therapeutic approach and led to the approval of three generations of inhibitors. The quinazoline core has emerged as a favorable scaffold for the development of novel EGFR inhibitors due to increased affinity for the active site of EGFR kinase. Currently, there are five first-generation (gefitinib, erlotinib, lapatinib, vandetanib, and icotinib) and two second-generation (afatinib and dacomitinib) quinazoline-based EGFR inhibitors approved for the treatment of various types of cancers. The aim of this review is to outline the structural modulations favorable for the inhibitory activity toward both common mutant (del19 and L858R) and resistance-conferring mutant (T790M and C797S) EGFR forms, and provide an overview of the newly synthesized quinazoline derivatives as potentially competitive, covalent or allosteric inhibitors of EGFR.
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Affiliation(s)
- Alexandru Șandor
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (G.M.); (O.O.)
| | - Ioana Ionuț
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (G.M.); (O.O.)
| | - Gabriel Marc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (G.M.); (O.O.)
| | - Ilioara Oniga
- Department of Pharmacognosy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 12 Ion Creangă Street, 400010 Cluj-Napoca, Romania;
| | - Dan Eniu
- Department of Surgical Oncology, “Iuliu Hațieganu” University of Medicine and Pharmacy, 34-36 Republicii Street, 40015 Cluj-Napoca, Romania;
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (G.M.); (O.O.)
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11
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Zhao Z, Bohidar N, Bourne PE. Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. J Chem Inf Model 2023; 63:1362-1370. [PMID: 36780612 DOI: 10.1021/acs.jcim.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
KRAS, a common human oncogene, has been recognized as a critical drug target in treating multiple cancers. After four decades of effort, one allosteric KRAS drug (Sotorasib) has been approved, inspiring more KRAS-targeted drug research. Here, we provide the features of KRAS binding pockets and ligand-binding characteristics of KRAS complexes using a structural systems pharmacology approach. Three distinct binding sites (conserved nucleotide-binding site, shallow Switch-I/II pocket, and allosteric Switch-II/α3 pocket) are characterized. Ligand-binding features are determined based on encoded KRAS-inhibitor interaction fingerprints. Finally, the flexibility of the three distinct binding sites to accommodate different potential ligands, based on MD simulation, is discussed. Collectively, these findings are intended to facilitate rational KRAS drug design.
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Affiliation(s)
- Zheng Zhao
- School of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Niraja Bohidar
- School of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E Bourne
- School of Data Science, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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12
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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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13
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Ngo C, Ekanayake A, Zhang C. Identification of Covalent Ligands – from Single Targets to Whole Proteome. Isr J Chem 2023. [DOI: 10.1002/ijch.202200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chau Ngo
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
| | - Arunika Ekanayake
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
- Current address: Department of Chemistry University of Alberta T6G 2G2 Edmonton AB Canada
| | - Chao Zhang
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
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14
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Battisti UM, Gao C, Nilsson O, Akladios F, Lulla A, Bogucka A, Nain-Perez A, Håversen L, Kim W, Boren J, Hyvönen M, Uhlen M, Mardinoglu A, Grøtli M. Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase. Chembiochem 2023; 24:e202200339. [PMID: 36250581 PMCID: PMC10099687 DOI: 10.1002/cbic.202200339] [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: 06/14/2022] [Revised: 10/14/2022] [Indexed: 01/05/2023]
Abstract
Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC50 =0.29 μM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.
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Affiliation(s)
- Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Agnieszka Bogucka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
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15
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Sousa B, de Almeida CR, Barahona AF, Lopes R, Martins-Logrado A, Cavaco M, Neves V, Carvalho LA, Labão-Almeida C, Coelho AR, Leal Bento M, Lopes RMR, Oliveira BL, Castanho MARB, Neumeister P, Deutsch A, Vladimer GI, Krall N, João C, Corzana F, Seixas JD, Fior R, Bernardes GJL. Selective Inhibition of Bruton's Tyrosine Kinase by a Designed Covalent Ligand Leads to Potent Therapeutic Efficacy in Blood Cancers Relative to Clinically Used Inhibitors. ACS Pharmacol Transl Sci 2022; 5:1156-1168. [PMID: 36407952 PMCID: PMC9667546 DOI: 10.1021/acsptsci.2c00163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Indexed: 11/06/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a member of the TEC-family kinases and crucial for the proliferation and differentiation of B-cells. We evaluated the therapeutic potential of a covalent inhibitor (JS25) with nanomolar potency against BTK and with a more desirable selectivity and inhibitory profile compared to the FDA-approved BTK inhibitors ibrutinib and acalabrutinib. Structural prediction of the BTK/JS25 complex revealed sequestration of Tyr551 that leads to BTK's inactivation. JS25 also inhibited the proliferation of myeloid and lymphoid B-cell cancer cell lines. Its therapeutic potential was further tested against ibrutinib in preclinical models of B-cell cancers. JS25 treatment induced a more pronounced cell death in a murine xenograft model of Burkitt's lymphoma, causing a 30-40% reduction of the subcutaneous tumor and an overall reduction in the percentage of metastasis and secondary tumor formation. In a patient model of diffuse large B-cell lymphoma, the drug response of JS25 was higher than that of ibrutinib, leading to a 64% "on-target" efficacy. Finally, in zebrafish patient-derived xenografts of chronic lymphocytic leukemia, JS25 was faster and more effective in decreasing tumor burden, producing superior therapeutic effects compared to ibrutinib. We expect JS25 to become therapeutically relevant as a BTK inhibitor and to find applications in the treatment of hematological cancers and other pathologies with unmet clinical treatment.
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Affiliation(s)
- Bárbara
B. Sousa
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | | | - Ana F. Barahona
- Champalimaud
Foundation, Avenida de Brasília, 1400-038, Lisbon, Portugal
| | - Raquel Lopes
- Champalimaud
Foundation, Avenida de Brasília, 1400-038, Lisbon, Portugal
| | | | - Marco Cavaco
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Vera Neves
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Luís A.
R. Carvalho
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Carlos Labão-Almeida
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Ana R. Coelho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Marta Leal Bento
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
- Centro
Hospitalar Lisboa Norte, Department of Hematology and Bone Marrow
Transplantation, Avenida
Prof. Egas Moniz, 1649-035 Lisbon, Portugal
| | - Ricardo M. R.
M. Lopes
- Research
Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1600-277 Lisbon, Portugal
| | - Bruno L. Oliveira
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Miguel A. R. B. Castanho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Peter Neumeister
- Division
of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria
| | - Alexander Deutsch
- Division
of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036 Graz, Austria
| | - Gregory I. Vladimer
- Exscientia, The Schrödinger Building,
Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Nikolaus Krall
- Exscientia, The Schrödinger Building,
Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Cristina João
- Champalimaud
Foundation, Avenida de Brasília, 1400-038, Lisbon, Portugal
| | - Francisco Corzana
- Centro
de Investigación en Síntesis Química, Departamento
de Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - João D. Seixas
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
- TARGTEX
S.A., Avenida Tenente
Valadim, N°17, 2F, 2560-275 Torres Vedras, Portugal
| | - Rita Fior
- Champalimaud
Foundation, Avenida de Brasília, 1400-038, Lisbon, Portugal
| | - Gonçalo J. L. Bernardes
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina,
Universidade de Lisboa, Avenida Prof. Egas Moniz, 1649-028, Lisbon, Portugal
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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16
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Covalent Warheads Targeting Cysteine Residue: The Promising Approach in Drug Development. Molecules 2022; 27:molecules27227728. [PMID: 36431829 PMCID: PMC9694382 DOI: 10.3390/molecules27227728] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Cysteine is one of the least abundant amino acids in proteins of many organisms, which plays a crucial role in catalysis, signal transduction, and redox regulation of gene expression. The thiol group of cysteine possesses the ability to perform nucleophilic and redox-active functions that are not feasible for other natural amino acids. Cysteine is the most common covalent amino acid residue and has been shown to react with a variety of warheads, especially Michael receptors. These unique properties have led to widespread interest in this nucleophile, leading to the development of a variety of cysteine-targeting warheads with different chemical compositions. Herein, we summarized the various covalent warheads targeting cysteine residue and their application in drug development.
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17
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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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18
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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19
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Systematic Exploration of Privileged Warheads for Covalent Kinase Drug Discovery. Pharmaceuticals (Basel) 2022; 15:ph15111322. [PMID: 36355497 PMCID: PMC9695834 DOI: 10.3390/ph15111322] [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: 08/12/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Kinase-targeted drug discovery for cancer therapy has advanced significantly in the last three decades. Currently, diverse kinase inhibitors or degraders have been reported, such as allosteric inhibitors, covalent inhibitors, macrocyclic inhibitors, and PROTAC degraders. Out of these, covalent kinase inhibitors (CKIs) have been attracting attention due to their enhanced selectivity and exceptionally strong affinity. Eight covalent kinase drugs have been FDA-approved thus far. Here, we review current developments in CKIs. We explore the characteristics of the CKIs: the features of nucleophilic amino acids and the preferences of electrophilic warheads. We provide systematic insights into privileged warheads for repurposing to other kinase targets. Finally, we discuss trends in CKI development across the whole proteome.
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20
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Zhao Z, Bourne PE. Harnessing systematic protein-ligand interaction fingerprints for drug discovery. Drug Discov Today 2022; 27:103319. [PMID: 35850431 DOI: 10.1016/j.drudis.2022.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 12/15/2022]
Abstract
Determining protein-ligand interaction characteristics and mechanisms is crucial to the drug discovery process. Here, we review recent progress and successful applications of a systematic protein-ligand interaction fingerprint (IFP) approach for investigating proteome-wide protein-ligand interactions for drug development. Specifically, we review the use of this IFP approach for revealing polypharmacology across the kinome, predicting promising targets from which to design allosteric inhibitors and covalent kinase inhibitors, uncovering the binding mechanisms of drugs of interest, and demonstrating resistant mechanisms of specific drugs. Together, we demonstrate that the IFP strategy is efficient and practical for drug design research for protein kinases as targets and is extensible to other protein families.
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Affiliation(s)
- Zheng Zhao
- School of Data Science and Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- School of Data Science and Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA.
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21
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Arter C, Trask L, Ward S, Yeoh S, Bayliss R. Structural features of the protein kinase domain and targeted binding by small-molecule inhibitors. J Biol Chem 2022; 298:102247. [PMID: 35830914 PMCID: PMC9382423 DOI: 10.1016/j.jbc.2022.102247] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are key components in cellular signaling pathways as they carry out the phosphorylation of proteins, primarily on Ser, Thr, and Tyr residues. The catalytic activity of protein kinases is regulated, and they can be thought of as molecular switches that are controlled through protein-protein interactions and post-translational modifications. Protein kinases exhibit diverse structural mechanisms of regulation and have been fascinating subjects for structural biologists from the first crystal structure of a protein kinase over 30 years ago, to recent insights into kinase assemblies enabled by the breakthroughs in cryo-EM. Protein kinases are high-priority targets for drug discovery in oncology and other disease settings, and kinase inhibitors have transformed the outcomes of specific groups of patients. Most kinase inhibitors are ATP competitive, deriving potency by occupying the deep hydrophobic pocket at the heart of the kinase domain. Selectivity of inhibitors depends on exploiting differences between the amino acids that line the ATP site and exploring the surrounding pockets that are present in inactive states of the kinase. More recently, allosteric pockets outside the ATP site are being targeted to achieve high selectivity and to overcome resistance to current therapeutics. Here, we review the key regulatory features of the protein kinase family, describe the different types of kinase inhibitors, and highlight examples where the understanding of kinase regulatory mechanisms has gone hand in hand with the development of inhibitors.
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Affiliation(s)
- Chris Arter
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Luke Trask
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah Ward
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Engineering and Physical Sciences, School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Sharon Yeoh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom; Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.
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22
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Du H, Jiang D, Gao J, Zhang X, Jiang L, Zeng Y, Wu Z, Shen C, Xu L, Cao D, Hou T, Pan P. Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network. Research (Wash D C) 2022; 2022:9873564. [PMID: 35958111 PMCID: PMC9343084 DOI: 10.34133/2022/9873564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022] Open
Abstract
Covalent ligands have attracted increasing attention due to their unique advantages, such as long residence time, high selectivity, and strong binding affinity. They also show promise for targets where previous efforts to identify noncovalent small molecule inhibitors have failed. However, our limited knowledge of covalent binding sites has hindered the discovery of novel ligands. Therefore, developing in silico methods to identify covalent binding sites is highly desirable. Here, we propose DeepCoSI, the first structure-based deep graph learning model to identify ligandable covalent sites in the protein. By integrating the characterization of the binding pocket and the interactions between each cysteine and the surrounding environment, DeepCoSI achieves state-of-the-art predictive performances. The validation on two external test sets which mimic the real application scenarios shows that DeepCoSI has strong ability to distinguish ligandable sites from the others. Finally, we profiled the entire set of protein structures in the RCSB Protein Data Bank (PDB) with DeepCoSI to evaluate the ligandability of each cysteine for covalent ligand design, and made the predicted data publicly available on website.
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Affiliation(s)
- Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lingxiao Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Yundian Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410004 Hunan, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
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23
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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24
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Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang CJ, Zhang ZM, Gao L, Yao SQ. Cell-Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR-ABL Kinase. Angew Chem Int Ed Engl 2022; 61:e202203878. [PMID: 35438229 DOI: 10.1002/anie.202203878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/16/2022]
Abstract
Despite recent interests in developing lysine-targeting covalent inhibitors, no general approach is available to create such compounds. We report herein a general approach to develop cell-active covalent inhibitors of protein kinases by targeting the conserved catalytic lysine residue using key SuFEx and salicylaldehyde-based imine chemistries. We validated the strategy by successfully developing (irreversible and reversible) covalent inhibitors against BCR-ABL kinase. Our lead compounds showed high levels of selectivity in biochemical assays, exhibited nanomolar potency against endogenous ABL kinase in cellular assays, and were active against most drug-resistant ABL mutations. Among them, the salicylaldehyde-containing A5 is the first-ever reversible covalent ABL inhibitor that possessed time-dependent ABL inhibition with prolonged residence time and few cellular off-targets in K562 cells. Bioinformatics further suggested the generality of our strategy against the human kinome.
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Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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25
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Hall A, Abendroth J, Bolejack MJ, Ceska T, Dell’Aiera S, Ellis V, Fox D, François C, Muruthi MM, Prével C, Poullennec K, Romanov S, Valade A, Vanbellinghen A, Yano J, Geraerts M. Discovery and Characterization of a Novel Series of Chloropyrimidines as Covalent Inhibitors of the Kinase MSK1. ACS Med Chem Lett 2022; 13:1099-1108. [PMID: 35859861 PMCID: PMC9290008 DOI: 10.1021/acsmedchemlett.2c00134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
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We describe the identification and
characterization of a series
of covalent inhibitors of the C-terminal kinase domain (CTKD) of MSK1.
The initial hit was identified via a high-throughput screening and
represents a rare example of a covalent inhibitor which acts via an
SNAr reaction of a 2,5-dichloropyrimidine with a
cysteine residue (Cys440). The covalent mechanism of action was supported
by in vitro biochemical experiments and was confirmed
by mass spectrometry. Ultimately, the displacement of the 2-chloro
moiety was confirmed by crystallization of an inhibitor with the CTKD.
We also disclose the crystal structures of three compounds from this
series bound to the CTKD of MSK1, in addition to the crystal structures
of two unrelated RSK2 covalent inhibitors bound to the CTKD of MSK1.
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Affiliation(s)
- Adrian Hall
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | - Jan Abendroth
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Madison J. Bolejack
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Tom Ceska
- UCB, 216 Bath Road, Slough SL1 3WE, U.K
| | | | | | - David Fox
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Cyril François
- NovAliX, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | - Muigai M. Muruthi
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Camille Prével
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | | | - Sergei Romanov
- NANOSYN, 3100 Central Expressway, Santa Clara, California 95051, United States
| | - Anne Valade
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | | | - Jason Yano
- UCB Boston, 87 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
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26
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Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang C, Zhang Z, Gao L, Yao SQ. Cell‐Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR‐ABL Kinase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chengjun Zhu
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Zhi‐Min Zhang
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
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27
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Atz K, Isert C, Böcker MNA, Jiménez-Luna J, Schneider G. Δ-Quantum machine-learning for medicinal chemistry. Phys Chem Chem Phys 2022; 24:10775-10783. [PMID: 35470831 PMCID: PMC9093086 DOI: 10.1039/d2cp00834c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many molecular design tasks benefit from fast and accurate calculations of quantum-mechanical (QM) properties. However, the computational cost of QM methods applied to drug-like molecules currently renders large-scale applications of quantum chemistry challenging. Aiming to mitigate this problem, we developed DelFTa, an open-source toolbox for the prediction of electronic properties of drug-like molecules at the density functional (DFT) level of theory, using Δ-machine-learning. Δ-Learning corrects the prediction error (Δ) of a fast but inaccurate property calculation. DelFTa employs state-of-the-art three-dimensional message-passing neural networks trained on a large dataset of QM properties. It provides access to a wide array of quantum observables on the molecular, atomic and bond levels by predicting approximations to DFT values from a low-cost semiempirical baseline. Δ-Learning outperformed its direct-learning counterpart for most of the considered QM endpoints. The results suggest that predictions for non-covalent intra- and intermolecular interactions can be extrapolated to larger biomolecular systems. The software is fully open-sourced and features documented command-line and Python APIs.
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Affiliation(s)
- Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Markus N A Böcker
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - José Jiménez-Luna
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland. .,Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riss, Germany
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland. .,ETH Singapore SEC Ltd., 1 CREATE Way, #06-01 CREATE Tower, Singapore 138602, Singapore
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28
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Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. J Am Chem Soc 2022; 144:6326-6342. [PMID: 35353516 PMCID: PMC9011356 DOI: 10.1021/jacs.1c13568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Covalent protein
kinase inhibitors exploit currently noncatalytic
cysteines in the adenosine 5′-triphosphate (ATP)-binding site
via electrophiles directly appended to a reversible-inhibitor scaffold.
Here, we delineate a path to target solvent-exposed cysteines at a
distance >10 Å from an ATP-site-directed core module and produce
potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors.
First, reactive warheads are used to reach out to Cys862 on PI3Kα,
and second, enones are replaced with druglike warheads while linkers
are optimized. The systematic investigation of intrinsic warhead reactivity
(kchem), rate of covalent bond formation
and proximity (kinact and reaction space
volume Vr), and integration of structure
data, kinetic and structural modeling, led to the guided identification
of high-quality, covalent chemical probes. A novel stochastic approach
provided direct access to the calculation of overall reaction rates
as a function of kchem, kinact, Ki, and Vr, which was validated with compounds with varied linker
lengths. X-ray crystallography, protein mass spectrometry (MS), and
NanoBRET assays confirmed covalent bond formation of the acrylamide
warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351,
the only known PI3Kα irreversible inhibitor. Washout experiments
in cancer cell lines with mutated, constitutively activated PI3Kα
showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds 19 and 22 revealed PI3Kβ-dependent signaling,
which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kα-selective
signaling branches. The proposed approach is generally suited to develop
covalent tools targeting distal, unexplored Cys residues in biologically
active enzymes.
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Affiliation(s)
- Chiara Borsari
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Erhan Keles
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexander Schaefer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rohitha Sriramaratnam
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Goch
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Thorsten Schaefer
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Martina De Pascale
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Matthias P Wymann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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29
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Shao M, Chen X, Yang F, Song X, Zhou Y, Lin Q, Fu Y, Ortega R, Lin X, Tu Z, Patterson AV, Smaill JB, Chen Y, Lu X. Design, Synthesis, and Biological Evaluation of Aminoindazole Derivatives as Highly Selective Covalent Inhibitors of Wild-Type and Gatekeeper Mutant FGFR4. J Med Chem 2022; 65:5113-5133. [PMID: 35271262 DOI: 10.1021/acs.jmedchem.2c00096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aberrant FGF19/FGFR4 signaling has been shown to be an oncogenic driver of growth and survival in human hepatocellular carcinoma (HCC) with several pan-FGFR inhibitors and FGFR4-selective inhibitors currently being evaluated in the clinic. However, FGFR4 gatekeeper mutation induced acquired resistance remains an unmet clinical challenge for HCC treatment. Thus, a series of aminoindazole derivatives were designed and synthesized as new irreversible inhibitors of wild-type and gatekeeper mutant FGFR4. One representative compound (7v) exhibited excellent potency against FGFR4, FGFR4V550L, and FGFR4V550M with nanomolar activity in both the biochemical and cellular assays while sparing FGFR1/2/3. While compound 7v demonstrated modest in vivo antitumor efficacy in nude mice bearing the Huh-7 xenograft model consistent with its unfavorable pharmacokinetic properties, it provides a promising new starting point for future drug discovery combating FGFR4 gatekeeper mediated resistance in HCC patients.
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Affiliation(s)
- Min Shao
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Fang Yang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Xiaojuan Song
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Yang Zhou
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Qianmeng Lin
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ying Fu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Raquel Ortega
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Xiaojing Lin
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag, Auckland 92019, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag, Auckland 92019, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 92019, New Zealand
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China
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30
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Gianferrara T, Cescon E, Grieco I, Spalluto G, Federico S. Glycogen Synthase Kinase 3β Involvement in Neuroinflammation and Neurodegenerative Diseases. Curr Med Chem 2022; 29:4631-4697. [PMID: 35170406 DOI: 10.2174/0929867329666220216113517] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/24/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND GSK-3β activity has been strictly related to neuroinflammation and neurodegeneration. Alzheimer's disease is the most studied neurodegenerative disease, but GSK-3β seems to be involved in almost all neurodegenerative diseases including Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease and the autoimmune disease multiple sclerosis. OBJECTIVE The aim of this review is to help researchers both working on this research topic or not to have a comprehensive overview on GSK-3β in the context of neuroinflammation and neurodegeneration. METHOD Literature has been searched using PubMed and SciFinder databases by inserting specific keywords. A total of more than 500 articles have been discussed. RESULTS First of all, the structure and regulation of the kinase were briefly discussed and then, specific GSK-3β implications in neuroinflammation and neurodegenerative diseases were illustrated also with the help of figures, to conclude with a comprehensive overview on the most important GSK-3β and multitarget inhibitors. For all discussed compounds, the structure and IC50 values at the target kinase have been reported. CONCLUSION GSK-3β is involved in several signaling pathways both in neurons as well as in glial cells and immune cells. The fine regulation and interconnection of all these pathways are at the base of the rationale use of GSK-3β inhibitors in neuroinflammation and neurodegeneration. In fact, some compounds are now under clinical trials. Despite this, pharmacodynamic and ADME/Tox profiles of the compounds were often not fully characterized and this is deleterious in such a complex system.
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Affiliation(s)
- Teresa Gianferrara
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Eleonora Cescon
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Ilenia Grieco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
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31
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Islam MS, Junod SL, Zhang S, Buuh ZY, Guan Y, Zhao M, Kaneria KH, Kafley P, Cohen C, Maloney R, Lyu Z, Voelz VA, Yang W, Wang RE. Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction. Nat Commun 2022; 13:350. [PMID: 35039490 PMCID: PMC8763920 DOI: 10.1038/s41467-022-27995-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/19/2021] [Indexed: 12/31/2022] Open
Abstract
We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in unprotected peptides in the presence of intrinsic cysteines. The identified benzenedimethanethiol linker greatly promoted the alpha helicity of a variety of peptide substrates, as corroborated by molecular dynamics simulations. The cellular uptake of benzenedimethanethiol stapled peptides appeared to be universally enhanced compared to the classic ring-closing metathesis (RCM) stapled peptides. Pilot mechanism studies suggested that the uptake of FTDR-stapled peptides may involve multiple endocytosis pathways in a distinct pattern in comparison to peptides stapled by RCM. Consistent with the improved cell permeability, the FTDR-stapled lead Axin and p53 peptide analogues demonstrated enhanced inhibition of cancer cells over the RCM-stapled analogues and the unstapled peptides. Strategies capable of stapling unprotected peptides in a straightforward, chemoselective, and clean manner, as well as promoting cellular uptake are of great interest. Here the authors report a peptide macrocyclization and stapling strategy which satisfies those criteria, based on a fluorine thiol displacement reaction.
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Affiliation(s)
- Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Yifu Guan
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Mi Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Kishan H Kaneria
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Carson Cohen
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Robert Maloney
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, PA, 19122, USA.
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32
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Lu X, Smaill JB, Patterson AV, Ding K. Discovery of Cysteine-targeting Covalent Protein Kinase Inhibitors. J Med Chem 2021; 65:58-83. [PMID: 34962782 DOI: 10.1021/acs.jmedchem.1c01719] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule covalent kinase inhibitors (CKIs) have entered a new era in drug discovery, which have the advantage for sustained target inhibition and high selectivity. An increased understanding of binding kinetics of CKIs and discovery of additional irreversible and reversible-covalent cysteine-targeted warheads has inspired the development of this area. Herein, we summarize the major medicinal chemistry strategies employed in the discovery of these representative CKIs, which are categorized by the location of the target cysteine within seven main regions of the kinase: the front region, the glycine rich loop (P-loop), the hinge region, the DFG region, the activation loop (A-loop), the catalytic loop (C-loop), and the remote loop. The emphasis is placed on the design and optimization strategies of CKIs that are generated by addition of a warhead to a reversible lead/inhibitor scaffold. In addition, we address the challenges facing this area of drug discovery.
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Affiliation(s)
- Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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33
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- 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.,Tübingen Center for Academic Drug Discovery, 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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34
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Zhang P, Min Z, Gao Y, Bian J, Lin X, He J, Ye D, Li Y, Peng C, Cheng Y, Chu Y. Discovery of Novel Benzothiazepinones as Irreversible Covalent Glycogen Synthase Kinase 3β Inhibitors for the Treatment of Acute Promyelocytic Leukemia. J Med Chem 2021; 64:7341-7358. [PMID: 34027661 DOI: 10.1021/acs.jmedchem.0c02254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recently, irreversible inhibitors have attracted great interest in antitumors due to their advantages of forming covalent bonds to target proteins. Herein, some benzothiazepinone compounds (BTZs) have been designed and synthesized as novel covalent GSK-3β inhibitors with high selectivity for the kinase panel. The irreversible covalent binding mode was identified by kinetics and mass spectrometry, and the main labeled residue was confirmed to be the unique Cys14 that exists only in GSK-3β. The candidate 4-3 (IC50 = 6.6 μM) showed good proliferation inhibition and apoptosis-inducing ability to leukemia cell lines, low cytotoxicity on normal cell lines, and no hERG inhibition, which hinted the potential efficacy and safety. Furthermore, 4-3 exhibited decent pharmacokinetic properties in vivo and remarkably inhibited tumor growth in the acute promyelocytic leukemia (APL) mouse model. All the results suggest that these newly irreversible BTZ compounds might be useful in the treatment of cancer such as APL.
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Affiliation(s)
- Peng Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China.,State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Zhihui Min
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yang Gao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jiang Bian
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xin Lin
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jie He
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yilin Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Yunfeng Cheng
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yong Chu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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35
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Costa AM, Bosch L, Petit E, Vilarrasa J. Computational Study of the Addition of Methanethiol to 40+ Michael Acceptors as a Model for the Bioconjugation of Cysteines. J Org Chem 2021; 86:7107-7118. [PMID: 33914532 PMCID: PMC8631706 DOI: 10.1021/acs.joc.1c00349] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 12/17/2022]
Abstract
A long series of Michael acceptors are studied computationally as potential alternatives to the maleimides that are used in most antibody-drug conjugates to link Cys of mAbs with cytotoxic drugs. The products of the reaction of methanethiol (CH3SH/MeSH, as a simple model of Cys) with N-methylated ethynesulfonamide, 2-ethynylpyridinium ion, propynamide, and methyl ethynephosphonamidate (that is, with HC≡C-EWG) are predicted by the M06-2X/6-311+G(d,p) method to be thermodynamically more stable, in relation to their precursors, than that of MeSH with N-methylmaleimide and, in general, with H2C═CH-EWG; calculations with AcCysOMe and tBuSH are also included. However, for the addition of the anion (MeS-), which is the reactive species, the order changes and N-methylated 2-vinylpyridinium ion, 2,3-butadienamide, and maleimide may give more easily the anionic adducts than several activated triple bonds; moreover, the calculated ΔG⧧ values increase following the order HC≡C-SO2NHMe, N-methylmaleimide, HC≡C-PO(OMe)NHMe, and HC≡C-CONHMe. In other words, MeS- is predicted to react more rapidly with maleimides than with ethynephosphonamidates and with propynamides, in agreement with the experimental results. New mechanistic details are disclosed regarding the advantageous use of some amides, especially of ethynesulfonamides, which, however, are more prone to double additions and exchange reactions.
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Affiliation(s)
- Anna M. Costa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Lluís Bosch
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Elena Petit
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Jaume Vilarrasa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
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36
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Toviwek B, Gleeson D, Gleeson MP. QM/MM and molecular dynamics investigation of the mechanism of covalent inhibition of TAK1 kinase. Org Biomol Chem 2021; 19:1412-1425. [PMID: 33501482 DOI: 10.1039/d0ob02273j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TAK1 is a serine/threonine kinase which is involved in the moderation of cell survival and death via the TNFα signalling pathway. It is also implicated in a range of cancer and anti-inflammatory diseases. Drug discovery efforts on this target have focused on both traditional reversible ATP-binding site inhibitors and increasingly popular irreversible covalent binding inhibitors. Irreversible inhibitors can offer benefits in terms of potency, selectivity and PK/PD meaning they are increasingly pursued where the strategy exists. TAK1 kinase differs from the better-known kinase EGFR in that the reactive cysteine nucleophile targeted by electrophilic inhibitors is located towards the back of the ATP binding site, not at its mouth. While a wealth of structural and computational effort has been spent exploring EGFR, only limited studies on TAK1 have been reported. In this work we report the first QM/MM study on TAK1 aiming to better understand aspects of covalent adduct formation. Our goal is to identify the general base in the catalytic reaction, whether the process proceeds via a stepwise or concerted pathway, and how the highly flexible G-loop and A-loop affect the catalytic cysteine located nearby.
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Affiliation(s)
- Borvornwat Toviwek
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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37
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Du H, Gao J, Weng G, Ding J, Chai X, Pang J, Kang Y, Li D, Cao D, Hou T. CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. Nucleic Acids Res 2021; 49:D1122-D1129. [PMID: 33068433 PMCID: PMC7778999 DOI: 10.1093/nar/gkaa876] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Inhibitors that form covalent bonds with their targets have traditionally been considered highly adventurous due to their potential off-target effects and toxicity concerns. However, with the clinical validation and approval of many covalent inhibitors during the past decade, design and discovery of novel covalent inhibitors have attracted increasing attention. A large amount of scattered experimental data for covalent inhibitors have been reported, but a resource by integrating the experimental information for covalent inhibitor discovery is still lacking. In this study, we presented Covalent Inhibitor Database (CovalentInDB), the largest online database that provides the structural information and experimental data for covalent inhibitors. CovalentInDB contains 4511 covalent inhibitors (including 68 approved drugs) with 57 different reactive warheads for 280 protein targets. The crystal structures of some of the proteins bound with a covalent inhibitor are provided to visualize the protein–ligand interactions around the binding site. Each covalent inhibitor is annotated with the structure, warhead, experimental bioactivity, physicochemical properties, etc. Moreover, CovalentInDB provides the covalent reaction mechanism and the corresponding experimental verification methods for each inhibitor towards its target. High-quality datasets are downloadable for users to evaluate and develop computational methods for covalent drug design. CovalentInDB is freely accessible at http://cadd.zju.edu.cn/cidb/.
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Affiliation(s)
- Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Gaoqi Weng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Junjie Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, China
| | - Xin Chai
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058, Zhejiang, China
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38
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Modeling Covalent Protein-Ligand Interactions. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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39
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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40
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Ceramella J, Iacopetta D, Barbarossa A, Caruso A, Grande F, Bonomo MG, Mariconda A, Longo P, Carmela S, Sinicropi MS. Carbazole Derivatives as Kinase-Targeting Inhibitors for Cancer Treatment. Mini Rev Med Chem 2020; 20:444-465. [PMID: 31951166 DOI: 10.2174/1389557520666200117144701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/19/2019] [Indexed: 12/11/2022]
Abstract
Protein Kinases (PKs) are a heterogeneous family of enzymes that modulate several biological pathways, including cell division, cytoskeletal rearrangement, differentiation and apoptosis. In particular, due to their crucial role during human tumorigenesis and cancer progression, PKs are ideal targets for the design and development of effective and low toxic chemotherapeutics and represent the second group of drug targets after G-protein-coupled receptors. Nowadays, several compounds have been claimed to be PKs inhibitors, and some of them, such as imatinib, erlotinib and gefitinib, have already been approved for clinical use, whereas more than 30 others are in various phases of clinical trials. Among them, some natural or synthetic carbazole-based molecules represent promising PKs inhibitors due to their capability to interfere with PK activity by different mechanisms of action including the ability to act as DNA intercalating agents, interfere with the activity of enzymes involved in DNA duplication, such as topoisomerases and telomerases, and inhibit other proteins such as cyclindependent kinases or antagonize estrogen receptors. Thus, carbazoles can be considered a promising this class of compounds to be adopted in targeted therapy of different types of cancer.
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Affiliation(s)
- Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Alexia Barbarossa
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Anna Caruso
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | - Fedora Grande
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
| | | | | | - Pasquale Longo
- Department of Biology and Chemistry, University of Salerno, 84084 Fisciano, Italy
| | - Saturnino Carmela
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, (CS), Italy
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41
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Bianco G, Goodsell DS, Forli S. Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors. Trends Pharmacol Sci 2020; 41:1038-1049. [PMID: 33153778 PMCID: PMC7669701 DOI: 10.1016/j.tips.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors are currently showing great promise for systems that are normally difficult to target with small molecule therapies. This renewed interest has spurred the refinement of existing computational methods as well as the designof new ones, expanding the toolbox for discovery and optimization of selectiveand effective covalent inhibitors. Commonly applied approaches are covalentdocking methods that predict the conformation of the covalent complex with known residues. More recently, a new predictive method, reactive docking, was developed, building on the growing corpus of data generated by large proteomics experiments. This method was successfully used in several 'inverse drug discovery' programs that use high-throughput techniques to isolate effective compounds based on screening of entire compound libraries based on desired phenotypes.
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Affiliation(s)
- Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Research Collaboratory for Structure Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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42
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Petri L, Ábrányi-Balogh P, Tímea I, Pálfy G, Perczel A, Knez D, Hrast M, Gobec M, Sosič I, Nyíri K, Vértessy BG, Jänsch N, Desczyk C, Meyer-Almes FJ, Ogris I, Golič Grdadolnik S, Iacovino LG, Binda C, Gobec S, Keserű GM. Assessment of Tractable Cysteines for Covalent Targeting by Screening Covalent Fragments. Chembiochem 2020; 22:743-753. [PMID: 33030752 DOI: 10.1002/cbic.202000700] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibition and the use of irreversible chemical probes are important strategies in chemical biology and drug discovery. To date, the availability and reactivity of cysteine residues amenable for covalent targeting have been evaluated by proteomic and computational tools. Herein, we present a toolbox of fragments containing a 3,5-bis(trifluoromethyl)phenyl core that was equipped with chemically diverse electrophilic warheads showing a range of reactivities. We characterized the library members for their reactivity, aqueous stability and specificity for nucleophilic amino acids. By screening this library against a set of enzymes amenable for covalent inhibition, we showed that this approach experimentally characterized the accessibility and reactivity of targeted cysteines. Interesting covalent fragment hits were obtained for all investigated cysteine-containing enzymes.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Imre Tímea
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Kinga Nyíri
- Genome Metabolism Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
| | - Beáta G Vértessy
- Genome Metabolism Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary.,Department of Applied Biotechnology, Budapest University of Technology and Economics, Szt Gellért tér 4, 1111, Budapest, Hungary
| | - Niklas Jänsch
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Schnittspahnstraße 12, 64287, Darmstadt, Germany
| | - Charlotte Desczyk
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Schnittspahnstraße 12, 64287, Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Schnittspahnstraße 12, 64287, Darmstadt, Germany
| | - Iza Ogris
- Laboratory for Molecular Structural Dynamics, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Luca Giacinto Iacovino
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, 27100, Pavia, Italy
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, 27100, Pavia, Italy
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, 1117, Budapest, Hungary
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43
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Baillache DJ, Unciti-Broceta A. Recent developments in anticancer kinase inhibitors based on the pyrazolo[3,4- d]pyrimidine scaffold. RSC Med Chem 2020; 11:1112-1135. [PMID: 33479617 PMCID: PMC7652001 DOI: 10.1039/d0md00227e] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/01/2020] [Indexed: 12/24/2022] Open
Abstract
Pyrazolo[3,4-d]pyrimidines have become of significant interest for the medicinal chemistry community as a privileged scaffold for the development of kinase inhibitors to treat a range of diseases, including cancer. This fused nitrogen-containing heterocycle is an isostere of the adenine ring of ATP, allowing the molecules to mimic hinge region binding interactions in kinase active sites. Similarities in kinase ATP sites can be exploited to direct the activity and selectivity of pyrazolo[3,4-d]pyrimidines to multiple oncogenic targets through focussed chemical modification. As a result, pharma and academic efforts have succeeded in progressing several pyrazolo[3,4-d]pyrimidines to clinical trials, including the BTK inhibitor ibrutinib, which has been approved for the treatment of several B-cell cancers. In this review, we examine the pyrazolo[3,4-d]pyrimidines currently in clinical trials for oncology patients, as well as those published in the literature during the last 5 years for different anticancer indications.
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Affiliation(s)
- Daniel J Baillache
- Cancer Research UK Edinburgh Centre , Institute of Genetics and Molecular Medicine , University of Edinburgh , Crewe Road South , Edinburgh EH4 2XR , UK .
| | - Asier Unciti-Broceta
- Cancer Research UK Edinburgh Centre , Institute of Genetics and Molecular Medicine , University of Edinburgh , Crewe Road South , Edinburgh EH4 2XR , UK .
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44
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Seixas JD, Sousa BB, Marques MC, Guerreiro A, Traquete R, Rodrigues T, Albuquerque IS, Sousa MFQ, Lemos AR, Sousa PMF, Bandeiras TM, Wu D, Doyle SK, Robinson CV, Koehler AN, Corzana F, Matias PM, Bernardes GJL. Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors. RSC Chem Biol 2020; 1:251-262. [PMID: 34458764 PMCID: PMC8341910 DOI: 10.1039/d0cb00033g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
The bone marrow tyrosine kinase in chromosome X (BMX) is pursued as a drug target because of its role in various pathophysiological processes. We designed BMX covalent inhibitors with single-digit nanomolar potency with unexploited topological pharmacophore patterns. Importantly, we reveal the first X-ray crystal structure of covalently inhibited BMX at Cys496, which displays key interactions with Lys445, responsible for hampering ATP catalysis and the DFG-out-like motif, typical of an inactive conformation. Molecular dynamic simulations also showed this interaction for two ligand/BMX complexes. Kinome selectivity profiling showed that the most potent compound is the strongest binder, displays intracellular target engagement in BMX-transfected cells with two-digit nanomolar inhibitory potency, and leads to BMX degradation PC3 in cells. The new inhibitors displayed anti-proliferative effects in androgen-receptor positive prostate cancer cells that where further increased when combined with known inhibitors of related signaling pathways, such as PI3K, AKT and Androgen Receptor. We expect these findings to guide development of new selective BMX therapeutic approaches.
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Affiliation(s)
- João D Seixas
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Bárbara B Sousa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
| | - Marta C Marques
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Ana Guerreiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Rui Traquete
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Inês S Albuquerque
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Marcos F Q Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
- IBET - Instituto de Biologia Experimental e Tecnológica Av. da República EAN 2780-157 Oeiras Portugal
| | - Ana R Lemos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
- IBET - Instituto de Biologia Experimental e Tecnológica Av. da República EAN 2780-157 Oeiras Portugal
| | - Pedro M F Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
- IBET - Instituto de Biologia Experimental e Tecnológica Av. da República EAN 2780-157 Oeiras Portugal
| | - Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
- IBET - Instituto de Biologia Experimental e Tecnológica Av. da República EAN 2780-157 Oeiras Portugal
| | - Di Wu
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Shelby K Doyle
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge MA 02142 USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Cambridge MA 02142 USA
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química 26006 Logroño Spain
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Av. da República EAN 2780-157 Oeiras Portugal
- IBET - Instituto de Biologia Experimental e Tecnológica Av. da República EAN 2780-157 Oeiras Portugal
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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45
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Petri L, Egyed A, Bajusz D, Imre T, Hetényi A, Martinek T, Ábrányi-Balogh P, Keserű GM. An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases. Eur J Med Chem 2020; 207:112836. [PMID: 32971426 DOI: 10.1016/j.ejmech.2020.112836] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
Targeted covalent inhibitors represent a viable strategy to block protein kinases involved in different disease pathologies. Although a number of computational protocols have been published for identifying druggable cysteines, experimental approaches are limited for mapping the reactivity and accessibility of these residues. Here, we present a ligand based approach using a toolbox of fragment-sized molecules with identical scaffold but equipped with diverse covalent warheads. Our library represents a unique opportunity for the efficient integration of warhead-optimization and target-validation into the covalent drug development process. Screening this probe kit against multiple kinases could experimentally characterize the accessibility and reactivity of the targeted cysteines and helped to identify suitable warheads for designed covalent inhibitors. The usefulness of this approach has been confirmed retrospectively on Janus kinase 3 (JAK3). Furthermore, representing a prospective validation, we identified Maternal embryonic leucine zipper kinase (MELK), as a tractable covalent target. Covalently labelling and biochemical inhibition of MELK would suggest an alternative covalent strategy for MELK inhibitor programs.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Attila Egyed
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - Anasztázia Hetényi
- Department of Medicinal Chemistry, University of Szeged, Dóm Tér 8, H-6720, Szeged, Hungary
| | - Tamás Martinek
- Department of Medicinal Chemistry, University of Szeged, Dóm Tér 8, H-6720, Szeged, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt 2, H-1117, Budapest, Hungary.
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46
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Hassaan E, Hohn C, Ehrmann FR, Goetzke FW, Movsisyan L, Hüfner-Wulsdorf T, Sebastiani M, Härtsch A, Reuter K, Diederich F, Klebe G. Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT. J Med Chem 2020; 63:6802-6820. [PMID: 32515955 DOI: 10.1021/acs.jmedchem.0c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1-recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1-recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Christoph Hohn
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Frederik R Ehrmann
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - F Wieland Goetzke
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Levon Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tobias Hüfner-Wulsdorf
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Maurice Sebastiani
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Adrian Härtsch
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Klaus Reuter
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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47
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Byrne DP, Shrestha S, Galler M, Cao M, Daly LA, Campbell AE, Eyers CE, Veal EA, Kannan N, Eyers PA. Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity. Sci Signal 2020; 13:eaax2713. [PMID: 32636306 DOI: 10.1126/scisignal.aax2713] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Reactive oxygen species (ROS) are physiological mediators of cellular signaling and play potentially damaging roles in human diseases. In this study, we found that the catalytic activity of the Ser/Thr kinase Aurora A was inhibited by the oxidation of a conserved cysteine residue (Cys290) that lies adjacent to Thr288, a critical phosphorylation site in the activation segment. Cys is present at the equivalent position in ~100 human Ser/Thr kinases, a residue that we found was important not only for the activity of human Aurora A but also for that of fission yeast MAPK-activated kinase (Srk1) and PKA (Pka1). Moreover, the presence of this conserved Cys predicted biochemical redox sensitivity among a cohort of human CAMK, AGC, and AGC-like kinases. Thus, we predict that redox modulation of the conserved Cys290 of Aurora A may be an underappreciated regulatory mechanism that is widespread in eukaryotic Ser/Thr kinases. Given the key biological roles of these enzymes, these findings have implications for understanding physiological and pathological responses to ROS and highlight the importance of protein kinase regulation through multivalent modification of the activation segment.
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Affiliation(s)
- Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Martin Galler
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Min Cao
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Leonard A Daly
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Amy E Campbell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Elizabeth A Veal
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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48
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Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis. Nat Commun 2020; 11:3216. [PMID: 32587248 PMCID: PMC7316778 DOI: 10.1038/s41467-020-17027-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine residue into cysteine at the DFG-1 position in the ATP-binding pocket, we sensitize the non-receptor tyrosine kinase FES towards covalent labeling by a complementary fluorescent chemical probe. This mutation is introduced in the endogenous FES gene of HL-60 cells using CRISPR/Cas9 gene editing. Leveraging the temporal and acute control offered by our strategy, we show that FES activity is dispensable for differentiation of HL-60 cells towards macrophages. Instead, FES plays a key role in neutrophil phagocytosis via SYK kinase activation. This chemical genetics strategy holds promise as a target validation method for kinases.
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49
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McAulay K, Hoyt EA, Thomas M, Schimpl M, Bodnarchuk MS, Lewis HJ, Barratt D, Bhavsar D, Robinson DM, Deery MJ, Ogg DJ, Bernardes GJL, Ward RA, Waring MJ, Kettle JG. Alkynyl Benzoxazines and Dihydroquinazolines as Cysteine Targeting Covalent Warheads and Their Application in Identification of Selective Irreversible Kinase Inhibitors. J Am Chem Soc 2020; 142:10358-10372. [PMID: 32412754 DOI: 10.1021/jacs.9b13391] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
With a resurgence in interest in covalent drugs, there is a need to identify new moieties capable of cysteine bond formation that are differentiated from commonly employed systems such as acrylamide. Herein, we report on the discovery of new alkynyl benzoxazine and dihydroquinazoline moieties capable of covalent reaction with cysteine. Their utility as alternative electrophilic warheads for chemical biological probes and drug molecules is demonstrated through site-selective protein modification and incorporation into kinase drug scaffolds. A potent covalent inhibitor of JAK3 kinase was identified with superior selectivity across the kinome and improvements in in vitro pharmacokinetic profile relative to the related acrylamide-based inhibitor. In addition, the use of a novel heterocycle as a cysteine reactive warhead is employed to target Cys788 in c-KIT, where acrylamide has previously failed to form covalent interactions. These new reactive and selective heterocyclic warheads supplement the current repertoire for cysteine covalent modification while avoiding some of the limitations generally associated with established moieties.
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Affiliation(s)
| | - Emily A Hoyt
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | | | - Marianne Schimpl
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Derek Barratt
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Deepa Bhavsar
- Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K
| | - Derek J Ogg
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,Instituto de Medicina Molecular, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | | | - Michael J Waring
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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50
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Zhao Z, Bourne PE. Revealing Acquired Resistance Mechanisms of Kinase-Targeted Drugs Using an on-the-Fly, Function-Site Interaction Fingerprint Approach. J Chem Theory Comput 2020; 16:3152-3161. [PMID: 32283024 DOI: 10.1021/acs.jctc.9b01134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although kinase-targeted drugs have achieved significant clinical success, they are frequently subject to the limitations of drug resistance, which has become a primary vulnerability to targeted drug therapy. Therefore, deciphering resistance mechanisms is an important step in designing more efficacious, antiresistant drugs. Here we studied two FDA-approved kinase drugs: Crizotinib and Ceritinib, which are first- and second-generation anaplastic lymphoma kinase (ALK) targeted inhibitors, to unravel drug-resistance mechanisms. We used an on-the-fly, function-site interaction fingerprint (on-the-fly Fs-IFP) approach, combining binding free-energy surface calculations with the Fs-IFPs. Establishing the potentials of mean force and monitoring the atomic-scale protein-ligand interactions, before and after L1196M-induced drug resistance, revealed insights into drug-resistance/antiresistant mechanisms. Crizotinib prefers to bind the wild-type ALK kinase domain, whereas Ceritinib binds more favorably to the mutated ALK kinase domain, in agreement with experimental results. We determined that ALK kinase-drug interactions in the region of the front pocket are associated with drug resistance. Additionally, we find that the L1196M mutation does not simply alter the binding modes of inhibitors but also affects the flexibility of the entire ALK kinase domain. Our work provides an understanding of the mechanisms of ALK drug resistance, confirms the usefulness of the on-the-fly Fs-IFP approach, and provides a practical paradigm to study drug-resistance mechanisms in prospective drug discovery.
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