1
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Bergman MT, Zhang W, Liu Y, Jang H, Nussinov R. Binding Modalities and Phase-Specific Regulation of Cyclin/Cyclin-Dependent Kinase Complexes in the Cell Cycle. J Phys Chem B 2024. [PMID: 39314090 DOI: 10.1021/acs.jpcb.4c03243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Cyclin-dependent kinases (CDKs) are activated upon cyclin-binding to enable progression through the cell cycle. Dominant CDKs and cyclins in mammalian cells include CDK1, CDK2, CDK4, and CDK6 and corresponding cyclins A, B, D, and E. While only certain, "typical" cyclin/CDK complexes are primarily responsible for cell cycle progression, "atypical" cyclin/CDK complexes can form and sometimes perform the same roles as typical complexes. We asked what structural features of cyclins and CDKs favor the formation of typical complexes, a vital yet not fully explored question. We use computational docking and biophysical analyses to exhaustively evaluate the structure and stability of all CDK and cyclin complexes listed above. We find that binding of the complexes is generally stronger for typical than for atypical complexes, especially when the CDK is in an active conformation. Typical complexes have denser clusters, indicating that they have more defined cyclin-binding sites than atypical complexes. Our results help explain three notable features of cyclin/CDK function in the cell cycle: (i) why CDK4 and cyclin-D have exceptionally high specificity for each other; (ii) why both cyclin-A and cyclin-B strongly activate CDK1, whereas CDK2 is only strongly activated by cyclin-A; and (iii) why cyclin-E normally activates CDK2 but not CDK1. Overall, this work reveals the binding modalities of cyclin/CDK complexes, how the modalities lead to the preference for typical complexes versus atypical complexes, and how binding modalities differ between typical complexes. Our observations suggest targeting CDK catalytic actions through destabilizing their native differential cyclin interfaces.
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Affiliation(s)
- Michael T Bergman
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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2
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Wang L, Li S, Xiang S, Liu H, Sun H. Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation. J Chem Inf Model 2024; 64:6899-6911. [PMID: 39172502 DOI: 10.1021/acs.jcim.4c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Cyclin-dependent kinases (CDKs), including CDK12 and CDK13, play crucial roles in regulating the cell cycle and RNA polymerase II activity, making them vital targets for cancer therapies. SR4835 is a selective inhibitor of CDK12/13, showing significant potential for treating triple-negative breast cancer. To elucidate the selective mechanism of SR4835 among three CDKs (CDK13/12/9), we developed an innovative enhanced sampling method, integrated well-tempered metadynamics-umbrella sampling (IMUS). IMUS synergistically combines the comprehensive pathway exploration capability of well-tempered metadynamics (WT-MetaD) with the precise free energy calculation capability of umbrella sampling, enabling the efficient and accurate characterization of drug-target interactions. The accurate calculation of binding free energy and the detailed analysis of the kinetic mechanism of the drug-target interaction using IMUS successfully elucidate the drug selectivity mechanism targeting the three CDKs, showing that the selectivity is primarily arising from differences in the stability of H-bonds within the Hinge region of the kinases and the interaction patterns during the protein-ligand recognition process. These findings also underscore the utility of IMUS in efficiently and accurately capturing drug-target interaction processes with clear mechanisms.
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Affiliation(s)
- Lingling Wang
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Shu Li
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Sutong Xiang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Huanxiang Liu
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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3
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Biswas B, Huang YH, Craik DJ, Wang CK. The prospect of substrate-based kinase inhibitors to improve target selectivity and overcome drug resistance. Chem Sci 2024; 15:13130-13147. [PMID: 39183924 PMCID: PMC11339801 DOI: 10.1039/d4sc01088d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/02/2024] [Indexed: 08/27/2024] Open
Abstract
Human kinases are recognized as one of the most important drug targets associated with cancer. There are >80 FDA-approved kinase inhibitors to date, most of which work by inhibiting ATP binding to the kinase. However, the frequent development of single-point mutations within the kinase domain has made overcoming drug resistance a major challenge in drug discovery today. Targeting the substrate site of kinases can offer a more selective and resistance-resilient solution compared to ATP inhibition but has traditionally been challenging. However, emerging technologies for the discovery of drug leads using recombinant display and stabilization of lead compounds have increased interest in targeting the substrate site of kinases. This review discusses recent advances in the substrate-based inhibition of protein kinases and the potential of such approaches for overcoming the emergence of resistance.
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Affiliation(s)
- Biswajit Biswas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia 4072
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia 4072
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia 4072
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD 4072 Australia 4072
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4
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Ikram S, Sayyah E, Durdağı S. Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interaction. Chembiochem 2024; 25:e202400008. [PMID: 38622060 DOI: 10.1002/cbic.202400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.
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Affiliation(s)
- Saima Ikram
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Ehsan Sayyah
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
- Molecular Therapy Lab (MTL), Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, 34353, Istanbul, Türkiye
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5
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. Int J Mol Sci 2024; 25:5368. [PMID: 38791406 PMCID: PMC11121299 DOI: 10.3390/ijms25105368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
The allosteric inhibition of insulin-like growth factor receptor 1 kinase (IGF1RK) is a potential strategy to overcome selectivity barriers for targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives that have been reported as allosteric inhibitors of IGF1RK. We further studied the dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation: forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen-bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the positioning of chemical substituents with different pharmacophore features at the R1 indole ring influences molecular interactions and binding conformations of indole-butyl-amine derivatives and, hence, dramatically affects their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA;
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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6
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Verma J, Vashisth H. Structural Models for a Series of Allosteric Inhibitors of IGF1R Kinase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588115. [PMID: 38617226 PMCID: PMC11014618 DOI: 10.1101/2024.04.04.588115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The allosteric inhibition of Insulin-like Growth Factor Receptor 1 Kinase (IGF1RK) is a potential strategy to overcome selectivity barriers in targeting receptor tyrosine kinases. We constructed structural models of a series of 12 indole-butyl-amine derivatives which have been reported as allosteric inhibitors of IGF1RK. We further studied dynamics and interactions of each inhibitor in the allosteric pocket via all-atom explicit-solvent molecular dynamics (MD) simulations. We discovered that a bulky carbonyl substitution at the R1 indole ring is structurally unfavorable for inhibitor binding in the IGF1RK allosteric pocket. Moreover, we found that the most potent derivative (termed C11) acquires a distinct conformation, forming an allosteric pocket channel with better shape complementarity and interactions with the receptor. In addition to a hydrogen bonding interaction with V1063, the cyano derivative C11 forms a stable hydrogen bond with M1156, which is responsible for its unique binding conformation in the allosteric pocket. Our findings show that the position of chemical substituents at the R1 indole ring with different pharmacophore features influences molecular interactions and binding conformations of the indole-butyl-amine derivatives, hence dramatically affecting their potencies. Our results provide a structural framework for the design of allosteric inhibitors with improved affinities and specificities against IGF1RK.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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7
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Henderson SH, Sorrell FJ, Bennett JM, Fedorov O, Hanley MT, Godoi PH, Ruela de Sousa R, Robinson S, Navratilova IH, Elkins JM, Ward SE. Imidazo[1,2-b]pyridazines as inhibitors of DYRK kinases. Eur J Med Chem 2024; 269:116292. [PMID: 38479168 DOI: 10.1016/j.ejmech.2024.116292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/07/2024]
Abstract
Selective inhibitors of DYRK1A are of interest for the treatment of cancer, Type 2 diabetes and neurological disorders. Optimization of imidazo [1,2-b]pyridazine fragment 1 through structure-activity relationship exploration and in silico drug design efforts led to the discovery of compound 17 as a potent cellular inhibitor of DYRK1A with selectivity over much of the kinome. The binding mode of compound 17 was elucidated with X-ray crystallography, facilitating the rational design of compound 29, an imidazo [1,2-b]pyridazine with improved kinase selectivity with respect to closely related CLK kinases.
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Affiliation(s)
- Scott H Henderson
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9RH, UK.
| | - Fiona J Sorrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - James M Bennett
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Marcus T Hanley
- Medicines Discovery Institute, Cardiff University, CF10 3AT, UK
| | - Paulo H Godoi
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil
| | - Roberta Ruela de Sousa
- Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil
| | - Sean Robinson
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Iva Hopkins Navratilova
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK; University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK; Structural Genomics Consortium, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, Av. Dr. André Tosello, 550, Barão Geraldo, Campinas, SP, 13083-886, Brazil.
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, CF10 3AT, UK.
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8
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Wang L, Bohmer MJ, Wang J, Nardella F, Calla J, Laureano De Souza M, Schindler KA, Montejo L, Mittal N, Rocamora F, Treat M, Charlton JT, Tumwebaze PK, Rosenthal PJ, Cooper RA, Chakrabarti R, Winzeler EA, Chakrabarti D, Gray NS. Discovery of Potent Antimalarial Type II Kinase Inhibitors with Selectivity over Human Kinases. J Med Chem 2024; 67:1460-1480. [PMID: 38214254 PMCID: PMC10950204 DOI: 10.1021/acs.jmedchem.3c02046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
While progress has been made in the effort to eradicate malaria, the disease remains a significant threat to global health. Acquired resistance to frontline treatments is emerging in Africa, urging a need for the development of novel antimalarial agents. Repurposing human kinase inhibitors provides a potential expedited route given the availability of a diverse array of kinase-targeting drugs that are approved or in clinical trials. Phenotypic screening of a library of type II human kinase inhibitors identified compound 1 as a lead antimalarial, which was initially developed to target human ephrin type A receptor 2 (EphA2). Here, we report a structure-activity relationship study and lead optimization of compound 1, which led to compound 33, with improved antimalarial activity and selectivity.
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Affiliation(s)
- Lushun Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Monica J Bohmer
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Flore Nardella
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Jaeson Calla
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Lukas Montejo
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nimisha Mittal
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Mayland Treat
- School of Public Health, University of California, Berkeley California 94704, United States
| | - Jordan T Charlton
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94110, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | - Ratna Chakrabarti
- Division of Cancer Research, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University California, San Diego, La Jolla, California 92093, United States
| | - Debopam Chakrabarti
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
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9
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Kommer DC, Stamatiou K, Vagnarelli P. Cell Cycle-Specific Protein Phosphatase 1 (PP1) Substrates Identification Using Genetically Modified Cell Lines. Methods Mol Biol 2024; 2740:37-61. [PMID: 38393468 DOI: 10.1007/978-1-0716-3557-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The identification of protein phosphatase 1 (PP1) holoenzyme substrates has proven to be a challenging task. PP1 can form different holoenzyme complexes with a variety of regulatory subunits, and many of those are cell cycle regulated. Although several methods have been used to identify PP1 substrates, their cell cycle specificity is still an unmet need. Here, we present a new strategy to investigate PP1 substrates throughout the cell cycle using clustered regularly interspersed short palindromic repeats (CRISPR)-Cas9 genome editing and generate cell lines with endogenously tagged PP1 regulatory subunit (regulatory interactor of protein phosphatase one, RIPPO). RIPPOs are tagged with the auxin-inducible degron (AID) or ascorbate peroxidase 2 (APEX2) modules, and PP1 substrate identification is conducted by SILAC proteomic-based approaches. Proteins in close proximity to RIPPOs are first identified through mass spectrometry (MS) analyses using the APEX2 system; then a list of differentially phosphorylated proteins upon RIPPOs rapid degradation (achieved via the AID system) is compiled via SILAC phospho-mass spectrometry. The "in silico" overlap between the two proteomes will be enriched for PP1 putative substrates. Several methods including fluorescence resonance energy transfer (FRET), proximity ligation assays (PLA), and in vitro assays can be used as substrate validations approaches.
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Affiliation(s)
- Dorothee C Kommer
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | | | - Paola Vagnarelli
- College of Health, Medicine and Life Science, Brunel University London, London, UK.
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10
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Silnitsky S, Rubin SJS, Zerihun M, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases. Int J Mol Sci 2023; 24:17600. [PMID: 38139428 PMCID: PMC10743896 DOI: 10.3390/ijms242417600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein kinases are one of the most significant drug targets in the human proteome, historically harnessed for the treatment of cancer, cardiovascular disease, and a growing number of other conditions, including autoimmune and inflammatory processes. Since the approval of the first kinase inhibitors in the late 1990s and early 2000s, the field has grown exponentially, comprising 98 approved therapeutics to date, 37 of which were approved between 2016 and 2021. While many of these small-molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP binding pocket have been massively successful for oncological indications, their poor selectively for protein kinase isozymes have limited them due to toxicities in their application to other disease spaces. Thus, recent attention has turned to the use of alternative allosteric binding mechanisms and improved drug platforms such as modified peptides to design protein kinase modulators with enhanced selectivity and other pharmacological properties. Herein we review the role of different protein kinase C (PKC) isoforms in cancer and cardiovascular disease, with particular attention to PKC-family inhibitors. We discuss translational examples and carefully consider the advantages and limitations of each compound (Part I). We also discuss the recent advances in the field of protein kinase modulators, leverage molecular docking to model inhibitor-kinase interactions, and propose mechanisms of action that will aid in the design of next-generation protein kinase modulators (Part II).
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Affiliation(s)
- Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
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11
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Wang Z, Tan J, Li M, Gao C, Li W, Xu J, Guo C, Chen Z, Cai R. Clickable Photoreactive ATP-Affinity Probe for Global Profiling of ATP-Binding Proteins. Anal Chem 2023; 95:17533-17540. [PMID: 37993803 DOI: 10.1021/acs.analchem.3c02694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Adenosine triphosphate (ATP) is the major energy carrier in organisms, and there are many cellular proteins that can bind to ATP. Among these proteins, kinases are key regulators in several cell signaling processes, and aberrant kinase signaling contributes to the development of many human diseases, including cancer. Hence, small-molecule kinase inhibitors have been successfully used for the treatment of various diseases. Since the ATP-binding pockets are similar for many kinases, it is very important to evaluate the selectivity of different kinase inhibitors. We report here a clickable ATP photoaffinity probe for the global profiling of ATP-binding proteins. After incubating the protein lysate with the ATP probe followed by ultraviolet (UV) irradiation, ATP-binding proteins were labeled with an alkyne handle for subsequent biotin conjugation through click chemistry. Labeled proteins were enriched with streptavidin beads, digested with trypsin, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). More than 400 ATP-binding proteins, including approximately 200 kinases, could be identified in a single LC-MS/MS run in the data-dependent acquisition mode. We then applied this method to the analysis of targets of three selected ATP-competitive kinase inhibitors. We were able to successfully identify some of their reported target proteins from label-free quantification results and validated the results using Western blot analyses. Together, we developed a clickable ATP photoaffinity probe for proteome-wide profiling of ATP-binding proteins and demonstrated that this chemoproteomic method is amenable to high-throughput target identification of kinase inhibitors.
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Affiliation(s)
- Zhiming Wang
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Jing Tan
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
| | - Mengxuan Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Can Gao
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Wenwen Li
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Jing Xu
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
| | - Changchuan Guo
- Shandong Institute for Food and Drug Control, Jinan 250101, Shandong, China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, Shandong, China
| | - Rong Cai
- Institute of Pharmaceutical Analysis, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen 518057, Guangdong, China
- Suzhou Research Institute, Shandong University, Suzhou 215123, Jiangsu, China
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12
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Tanabe M, Sakate R, Nakabayashi J, Tsumura K, Ohira S, Iwato K, Kimura T. A novel in silico scaffold-hopping method for drug repositioning in rare and intractable diseases. Sci Rep 2023; 13:19358. [PMID: 37938624 PMCID: PMC10632405 DOI: 10.1038/s41598-023-46648-1] [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: 06/16/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
In the field of rare and intractable diseases, new drug development is difficult and drug repositioning (DR) is a key method to improve this situation. In this study, we present a new method for finding DR candidates utilizing virtual screening, which integrates amino acid interaction mapping into scaffold-hopping (AI-AAM). At first, we used a spleen associated tyrosine kinase inhibitor as a reference to evaluate the technique, and succeeded in scaffold-hopping maintaining the pharmacological activity. Then we applied this method to five drugs and obtained 144 compounds with diverse structures. Among these, 31 compounds were known to target the same proteins as their reference compounds and 113 compounds were known to target different proteins. We found that AI-AAM dominantly selected functionally similar compounds; thus, these selected compounds may represent improved alternatives to their reference compounds. Moreover, the latter compounds were presumed to bind to the targets of their references as well. This new "compound-target" information provided DR candidates that could be utilized for future drug development.
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Affiliation(s)
- Mao Tanabe
- Laboratory of Rare Disease Information and Resource Library, Center for Intractable Diseases and ImmunoGenomics Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Ryuichi Sakate
- Laboratory of Rare Disease Information and Resource Library, Center for Intractable Diseases and ImmunoGenomics Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Jun Nakabayashi
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Kyosuke Tsumura
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Shino Ohira
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Kaoru Iwato
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Tomonori Kimura
- Reverse Translational Research Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-City, Osaka, Japan.
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan.
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
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13
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Qiao K, Liang Z, Wang A, Wu Q, Yang S, Ma Y, Li S, Schiwy S, Jiang J, Zhou S, Ye Q, Hollert H, Gui W. Waterborne Tebuconazole Exposure Induces Male-Biased Sex Differentiation in Zebrafish ( Danio rerio) Larvae via Aromatase Inhibition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16764-16778. [PMID: 37890152 DOI: 10.1021/acs.est.3c03181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Tebuconazole is a widely used fungicide for various crops that targets sterol 14-α-demethylase (CYP51) in fungi. However, attention has shifted to aromatase (CYP19) due to limited research indicating its reproductive impact on aquatic organisms. Herein, zebrafish were exposed to 0.5 mg/L tebuconazole at different developmental stages. The proportion of males increased significantly after long-term exposure during the sex differentiation phase (0-60, 5-60, and 19-60 days postfertilization (dpf)). Testosterone levels increased and 17β-estradiol and cyp19a1a expression levels decreased during the 5-60 dpf exposure, while the sex ratio was equally distributed on coexposure with 50 ng/L 17β-estradiol. Chemically activated luciferase gene expression bioassays determined that the male-biased sex differentiation was not caused by tebuconazole directly binding to sex hormone receptors. Protein expression and phosphorylation levels were specifically altered in the vascular endothelial growth factor signaling pathway despite excluding the possibility of tebuconazole directly interacting with kinases. Aromatase was selected for potential target analysis. Molecular docking and aromatase activity assays demonstrated the interactions between tebuconazole and aromatase, highlighting that tebuconazole poses a threat to fish populations by inducing a gender imbalance.
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Affiliation(s)
- Kun Qiao
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zhuoying Liang
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Aoxue Wang
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qiong Wu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
- Patent Examination Cooperation (Henan) Center of the Patent Office, CNIPA, Zhengzhou 450046, P. R. China
| | - Siyu Yang
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yongfang Ma
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Shuying Li
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, P. R. China
| | - Sabrina Schiwy
- Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jinhua Jiang
- Institute of Agro-Products Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P. R. China
| | - Shengli Zhou
- Zhejiang Province Environmental Monitoring Center, Hangzhou 310012, P. R. China
| | - Qingfu Ye
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Henner Hollert
- Department Evolutionary Ecology and Environmental Toxicology, Faculty Biological Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department Environmental Media Related Ecotoxicology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 57392 Schmallenberg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325 Frankfurt am Main, Germany
| | - Wenjun Gui
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, P. R. China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, P. R. China
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14
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Moradi M, Mousavi A, Emamgholipour Z, Giovannini J, Moghimi S, Peytam F, Honarmand A, Bach S, Foroumadi A. Quinazoline-based VEGFR-2 inhibitors as potential anti-angiogenic agents: A contemporary perspective of SAR and molecular docking studies. Eur J Med Chem 2023; 259:115626. [PMID: 37453330 DOI: 10.1016/j.ejmech.2023.115626] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/14/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Angiogenesis, the formation of new blood vessels from the existing vasculature, is pivotal in the migration, growth, and differentiation of endothelial cells in normal physiological conditions. In various types of tumour microenvironments, dysregulated angiogenesis plays a crucial role in supplying oxygen and nutrients to cancerous cells, leading to tumour size growth. VEGFR-2 tyrosine kinase has been extensively studied as a critical regulator of angiogenesis; thus, inhibition of VEGFR-2 has been widely used for cancer treatments in recent years. Quinazoline nucleus is a privileged and versatile scaffold with a broad range of pharmacological activity, especially in the field of tyrosine kinase inhibitors with more than twenty small molecule inhibitors approved by the US Food and Drug Administration in the last two decades. As of now, the U.S. FDA has approved eleven small chemical inhibitors of VEGFR-2 for various types of malignancies, with a prime example being vandetanib, a quinazoline derivative, which is a multi targeted kinase inhibitor used for the treatment of late-stage medullary thyroid cancer. Despite of prosperous discovery and development of VEGFR-2 down regulator drugs, there still exists limitations in clinical efficacy, adverse effects, a high rate of clinical discontinuation and drug resistance. Therefore, there is an urgent need for the design and synthesis of more selective and effective inhibitors to tackle these challenges. Through the gathering of this review, we have strived to broaden the extent of our view over the entire scope of quinazoline-based VEGFR-2 inhibitors. Herein, we give an overview of the importance and advancement status of reported structures, highlighting the SAR, biological evaluations and their binding modes.
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Affiliation(s)
- Mahfam Moradi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mousavi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Emamgholipour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Johanna Giovannini
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680, Roscoff, France
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Peytam
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Honarmand
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Stéphane Bach
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680, Roscoff, France; Sorbonne Université, CNRS, FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680, Roscoff, France; Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa.
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.
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15
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Gu S, Liu H, Liu L, Hou T, Kang Y. Artificial intelligence methods in kinase target profiling: Advances and challenges. Drug Discov Today 2023; 28:103796. [PMID: 37805065 DOI: 10.1016/j.drudis.2023.103796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Kinases have a crucial role in regulating almost the full range of cellular processes, making them essential targets for therapeutic interventions against various diseases. Accurate kinase-profiling prediction is vital for addressing the selectivity/specificity challenges in kinase drug discovery, which is closely related to lead optimization, drug repurposing, and the understanding of potential drug side effects. In this review, we provide an overview of the latest advancements in machine learning (ML)-based and deep learning (DL)-based quantitative structure-activity relationship (QSAR) models for kinase profiling. We highlight current trends in this rapidly evolving field and discuss the existing challenges and future directions regarding experimental data set construction and model architecture design. Our aim is to offer practical insights and guidance for the development and utilization of these approaches.
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Affiliation(s)
- Shukai Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao 999078
| | - Liwei Liu
- Advanced Computing and Storage Laboratory, Central Research Institute, 2012 Laboratories, Huawei Technologies Co. Ltd, Nanjing 210000, Jiangsu, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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16
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Liang Q, Wang B, Zou F, Guo G, Wang W, Wang W, Liu Q, Shen L, Hu C, Wang W, Wang A, Huang T, He Y, Xia R, Ge J, Liu J, Liu Q. Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor. Eur J Med Chem 2023; 256:115411. [PMID: 37209613 DOI: 10.1016/j.ejmech.2023.115411] [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: 01/20/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/22/2023]
Abstract
Through a structure-based irreversible drug design approach, we have discovered a highly potent IDH1-mutant inhibitor compound 16 (IHMT-IDH1-053) (IC50 = 4.7 nM), which displays high selectivity against IDH1 mutants over IDH1 wt and IDH2 wt/mutants. The crystal structure demonstrates that 16 binds to the IDH1 R132H protein in the allosteric pocket adjacent to the NAPDH binding pocket through a covalent bond with residue Cys269. 16 inhibits 2-hydroxyglutarate (2-HG) production in IDH1 R132H mutant transfected 293T cells (IC50 = 28 nM). In addition, it inhibits the proliferation of HT1080 cell line and primary AML cells which both bear IDH1 R132 mutants. In vivo, 16 inhibits 2-HG level in a HT1080 xenograft mouse model. Our study suggested that 16 would be a new pharmacological tool to study IDH1 mutant-related pathology and the covalent binding mode provided a novel approach for designing irreversible IDH1 inhibitors.
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Affiliation(s)
- Qianmao Liang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Fengming Zou
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Gongrui Guo
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, PR China
| | - Wenliang Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Wei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, PR China
| | - Qingwang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Lijuan Shen
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Aoli Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China
| | - Tao Huang
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, PR China
| | - Yuying He
- Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, PR China
| | - Ruixiang Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, PR China
| | - Jian Ge
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, PR China.
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; University of Science and Technology of China, Hefei, Anhui, 230026, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China.
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; University of Science and Technology of China, Hefei, Anhui, 230026, PR China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, 230031, PR China; Precision Medicine Research Laboratory of Anhui Province, Hefei, Anhui, 230088, PR China.
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17
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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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18
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Xin X, Wang Y, Zhang L, Zhang D, Sha L, Zhu Z, Huang X, Mao W, Zhang J. Development and therapeutic potential of adaptor-associated kinase 1 inhibitors in human multifaceted diseases. Eur J Med Chem 2023; 248:115102. [PMID: 36640459 DOI: 10.1016/j.ejmech.2023.115102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Adaptor-Associated Kinase 1 (AAK1), a Ser/Thr protein kinase, responsible for regulating clathrin-mediated endocytosis, is ubiquitous in the central nervous system (CNS). AAK1 plays an important role in neuropathic pain and a variety of other human diseases, including viral invasion, Alzheimer's disease, Parkinson's syndrome, etc. Therefore, targeting AAK1 is a promising therapeutic strategy. However, although small molecule AAK1 inhibitors have been vigorously developed, only BMS-986176/LX-9211 has entered clinical trials. Simultaneously, new small molecule inhibitors, including BMS-911172 and LP-935509, exhibited excellent druggability. This review elaborates on the structure, biological function, and disease relevance of AAK1. We emphatically analyze the structure-activity relationships (SARs) of small molecule AAK1 inhibitors based on different binding modalities and discuss prospective strategies to provide insights into novel AAK1 therapeutic agents for clinical practice.
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Affiliation(s)
- Xin Xin
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yue Wang
- Leling Traditional Chinese Medicine Hospital, Leling, 253600, Shandong, China
| | - Lele Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Dan Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Leihao Sha
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ziyu Zhu
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaoyi Huang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wuyu Mao
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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19
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Lu H, Cheng Z, Hu Y, Tang LV. What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders? BIOLOGY 2023; 12:166. [PMID: 36829445 PMCID: PMC9952452 DOI: 10.3390/biology12020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Protein therapeutics have been widely used to treat hematological disorders. With the advent of de novo protein design, protein therapeutics are not limited to ameliorating natural proteins but also produce novel protein sequences, folds, and functions with shapes and functions customized to bind to the therapeutic targets. De novo protein techniques have been widely used biomedically to design novel diagnostic and therapeutic drugs, novel vaccines, and novel biological materials. In addition, de novo protein design has provided new options for treating hematological disorders. Scientists have designed protein switches called Colocalization-dependent Latching Orthogonal Cage-Key pRoteins (Co-LOCKR) that perform computations on the surface of cells. De novo designed molecules exhibit a better capacity than the currently available tyrosine kinase inhibitors in chronic myeloid leukemia therapy. De novo designed protein neoleukin-2/15 enhances chimeric antigen receptor T-cell activity. This new technique has great biomedical potential, especially in exploring new treatment methods for hematological disorders. This review discusses the development of de novo protein design and its biological applications, with emphasis on the treatment of hematological disorders.
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Affiliation(s)
| | | | | | - Liang V. Tang
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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20
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Generation of innervated cochlear organoid recapitulates early development of auditory unit. Stem Cell Reports 2022; 18:319-336. [PMID: 36584686 PMCID: PMC9860115 DOI: 10.1016/j.stemcr.2022.11.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022] Open
Abstract
Functional cochlear hair cells (HCs) innervated by spiral ganglion neurons (SGNs) are essential for hearing, whereas robust models that recapitulate the peripheral auditory circuity are still lacking. Here, we developed cochlear organoids with functional peripheral auditory circuity in a staging three-dimensional (3D) co-culture system by initially reprogramming cochlear progenitor cells (CPCs) with increased proliferative potency that could be long-term expanded, then stepwise inducing the differentiation of cochlear HCs, as well as the outgrowth of neurites from SGNs. The function of HCs and synapses within organoids was confirmed by a series of morphological and electrophysiological evaluations. Single-cell mRNA sequencing revealed the differentiation trajectories of CPCs toward the major cochlear cell types and the dynamic gene expression during organoid HC development, which resembled the pattern of native HCs. We established the cochlear organoids with functional synapses for the first time, which provides a platform for deciphering the mechanisms of sensorineural hearing loss.
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21
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Tang S, Xue Y, Dengqi X, Shao L. Design, development and evaluation of a prodrug-type TrkA-selective inhibitor with antinociceptive effects in vivo. Eur J Med Chem 2022; 245:114901. [DOI: 10.1016/j.ejmech.2022.114901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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22
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St. Denis JD, Chessari G, Cleasby A, Cons BD, Cowan S, Dalton SE, East C, Murray CW, O’Reilly M, Peakman T, Rapti M, Stow JL. X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor. J Med Chem 2022; 65:12319-12333. [DOI: 10.1021/acs.jmedchem.2c01044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jeffrey D. St. Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Benjamin D. Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Suzanna Cowan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Samuel E. Dalton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Marc O’Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Magdalini Rapti
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Jessie L. Stow
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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23
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Goebel GL, Qiu X, Wu P. Kinase-targeting small-molecule inhibitors and emerging bifunctional molecules. Trends Pharmacol Sci 2022; 43:866-881. [PMID: 35589447 DOI: 10.1016/j.tips.2022.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 02/07/2023]
Abstract
Kinases are among the most successful drug targets. To date, 72 small-molecule kinase inhibitors (SMKIs) have been approved by the US FDA, together with ~500 SMKIs in clinical trials. Although the topic has been heavily reviewed in recent years, an overview that focused on the currently approved SMKIs in combination with the emerging kinase-targeting bifunctional molecules is absent. Herein, we first provide an updated overview of the approved SMKIs, with an emphasis on their binding modes, classified in groups of type I and II ATP-competitive inhibitors, type III and IV allosteric inhibitors, and covalent inhibitors. We then highlight the novel chemical modalities in kinase targeting by using different types of proximity-inducing bifunctional molecules for kinase degradation and modifications.
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Affiliation(s)
- Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen DK-2100, Denmark.
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