1
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Zhang W, Liu Y, Jang H, Nussinov R. Slower CDK4 and faster CDK2 activation in the cell cycle. Structure 2024; 32:1269-1280.e2. [PMID: 38703777 PMCID: PMC11316634 DOI: 10.1016/j.str.2024.04.012] [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: 11/19/2023] [Revised: 02/08/2024] [Accepted: 04/09/2024] [Indexed: 05/06/2024]
Abstract
Dysregulation of cyclin-dependent kinases (CDKs) impacts cell proliferation, driving cancer. Here, we ask why the cyclin-D/CDK4 complex governs cell cycle progression through the longer G1 phase, whereas cyclin-E/CDK2 regulates the shorter G1/S phase transition. We consider available experimental cellular and structural data including cyclin-E's high-level burst, sustained duration of elevated cyclin-D expression, and explicit solvent molecular dynamics simulations of the inactive monomeric and complexed states, to establish the conformational tendencies along the landscape of the distinct activation scenarios of cyclin-D/CDK4 and cyclin-E/CDK2 in the G1 phase and G1/S transition of the cell cycle, respectively. These lead us to propose slower activation of cyclin-D/CDK4 and rapid activation of cyclin-E/CDK2. We provide the mechanisms through which this occurs, offering innovative CDK4 drug design considerations. Our insightful mechanistic work addresses a compelling cell cycle regulation question and illuminates the distinct activation speeds between the G1 and the G1/S phases, which are crucial for function.
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Affiliation(s)
- Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; 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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Mudaliar D, Mansky RH, White A, Baudhuin G, Hawkinson J, Wong H, Walters MA, Gomez-Pastor R. Discovery of a CK2α'-Biased ATP-Competitive Inhibitor from a High-Throughput Screen of an Allosteric-Inhibitor-Like Compound Library. ACS Chem Neurosci 2024; 15:2703-2718. [PMID: 38908003 DOI: 10.1021/acschemneuro.4c00062] [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: 06/24/2024] Open
Abstract
Protein kinase CK2 is a holoenzyme composed of two regulatory subunits (CK2β) and two catalytic subunits (CK2α and CK2α'). CK2 controls several cellular processes, including proliferation, inflammation, and cell death. However, CK2α and CK2α' possess different expression patterns and substrates and therefore impact each of these processes differently. Elevated CK2α participates in the development of cancer, while increased CK2α' has been associated with neurodegeneration, especially Huntington's disease (HD). HD is a fatal disease for which no effective therapies are available. Genetic deletion of CK2α' in HD mouse models has ameliorated neurodegeneration. Therefore, pharmacological inhibition of CK2α' presents a promising therapeutic strategy for treating HD. However, current CK2 inhibitors are unable to discriminate between CK2α and CK2α' due to their high structural homology, especially in the targeted ATP-binding site. Using computational analyses, we found a potential type IV ("D" pocket) allosteric site that contained different residues between CK2α and CK2α' and was distal from the ATP-binding pocket featured in both kinases. We decided to look for allosteric modulators that might interact in a biased fashion with the type IV pocket on both CK2α and CK2α'. We screened a commercial library containing ∼29,000 allosteric-kinase-inhibitor-like compounds using a CK2α' activity-dependent ADP-Glo Kinase assay. Obtained hits were counter-screened against CK2α using the ADP-Glo Kinase assay, revealing two CK2α'-biased compounds. These two compounds might serve as the basis for further medicinal chemistry optimization for the potential treatment of HD.
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Affiliation(s)
- Deepti Mudaliar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rachel H Mansky
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Angel White
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Grace Baudhuin
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | | | - Henry Wong
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rocio Gomez-Pastor
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, Minnesota 55414, United States
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3
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Chakraborty S, Ahler E, Simon JJ, Fang L, Potter ZE, Sitko KA, Stephany JJ, Guttman M, Fowler DM, Maly DJ. Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics. Cell Chem Biol 2024; 31:207-220.e11. [PMID: 37683649 PMCID: PMC10902203 DOI: 10.1016/j.chembiol.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/03/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Kinase inhibitors are effective cancer therapies, but resistance often limits clinical efficacy. Despite the cataloging of numerous resistance mutations, our understanding of kinase inhibitor resistance is still incomplete. Here, we comprehensively profiled the resistance of ∼3,500 Src tyrosine kinase mutants to four different ATP-competitive inhibitors. We found that ATP-competitive inhibitor resistance mutations are distributed throughout Src's catalytic domain. In addition to inhibitor contact residues, residues that participate in regulating Src's phosphotransferase activity were prone to the development of resistance. Unexpectedly, we found that a resistance-prone cluster of residues located on the top face of the N-terminal lobe of Src's catalytic domain contributes to autoinhibition by reducing catalytic domain dynamics, and mutations in this cluster led to resistance by lowering inhibitor affinity and promoting kinase hyperactivation. Together, our studies demonstrate how drug resistance profiling can be used to define potential resistance pathways and uncover new mechanisms of kinase regulation.
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Affiliation(s)
- Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ethan Ahler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Jessica J Simon
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Katherine A Sitko
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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4
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Mudaliar D, Mansky RH, White A, Baudhuin G, Hawkinson J, Wong H, Walters MA, Gomez-Pastor R. Identification of CK2α' selective inhibitors by the screening of an allosteric-kinase-inhibitor-like compound library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576328. [PMID: 38328231 PMCID: PMC10849513 DOI: 10.1101/2024.01.18.576328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Protein Kinase CK2 is a holoenzyme composed of two regulatory subunits (CK2β) and two catalytic subunits (CK2α and CK2α'). CK2 controls several cellular processes including proliferation, inflammation, and cell death. However, CK2α and CK2α' possess different expression patterns and substrates and therefore impact each of these processes differently. Elevated CK2α participates in the development of cancer, while increased CK2α' has been associated with neurodegeneration, especially Huntington's disease (HD). HD is a fatal disease for which no effective therapies are available. Genetic deletion of CK2α' in HD mouse models has ameliorated neurodegeneration. Therefore, pharmacological inhibition of CK2α' presents a promising therapeutic strategy for treating HD. However, current CK2 inhibitors are unable to discriminate between CK2α and CK2α' due to their high structural homology, especially in the targeted ATP binding site. Using computational analyses, we found a potential Type IV ("D" pocket) allosteric site on CK2α' that contained different residues than CK2α and was distal from the ATP binding pocket featured in both kinases. With this potential allosteric site in mind, we screened a commercial library containing ~29,000 allosteric-kinase-inhibitor-like compounds using a CK2α' activity-dependent ADP-Glo™ Kinase assay. Obtained hits were counter-screened against CK2α revealing two CK2α' selective compounds. These two compounds might serve as the basis for further medicinal chemistry optimization for the potential treatment of HD.
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Affiliation(s)
- Deepti Mudaliar
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rachel H Mansky
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Angel White
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Grace Baudhuin
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
| | - Jon Hawkinson
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Henry Wong
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rocio Gomez-Pastor
- Department of Neuroscience, University of Minnesota, School of Medicine, Minneapolis, Minnesota 55414, United States
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5
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Parsons M, Parsons B, Dean M, DeRocher AE, Islam Z, Maly DJ, Jensen BC. An essential Trypanosoma brucei protein kinase: a functional analysis of regulation and the identification of inhibitors. FRONTIERS IN PARASITOLOGY 2023; 2:1272378. [PMID: 38099268 PMCID: PMC10720658 DOI: 10.3389/fpara.2023.1272378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Introduction The protein serine/threonine kinase AEK1 is essential in the pathogenic stage of Trypanosoma brucei, the causative agent of African trypanosomiasis. AEK1 is a member of the AGC protein kinase family, although it is not closely related to a specific human AGC kinase. Our previous chemical genetic studies showed that targeted inhibition of AEK1 in parasites expressing analog-sensitive AEK1 blocked parasite growth and enhanced survival of infected mice. Methods To further validate AEK1 as a drug target, we used the chemical genetic system to determine the effect of a 24 hour loss of AEK1 activity on cell viability at the clonal level. A panel of 429 protein kinase inhibitors were screened against the wild-type protein for binding, using time-resolved fluorescence energy transfer (TR-FRET). The role of phosphorylation sites and motifs was probed by determining whether expression of proteins harboring mutations in these sequences could rescue AEK1 conditional knockout parasites. To determine the effect that mutations in the phosphosites have on the kinase activity of cellular AEK1 we compared the in vitro kinase activity of mutant and wild-type proteins immunoprecipitated from parasite lysates using the exogenous substrate MBP. Finally, the tagged AEK1 protein was localized by deconvolution microscopy. Results After a 24 hour exposure to an AEK1 inhibitory analog in the chemical genetic system, less than five percent of the remaining live cells can clonally expand, further validating AEK1 as a drug target. In the AEK1 inhibitor screening assay, we identified 17 hit compounds. Complementation studies showed that of the two known phosphorylation sites in the activation loop; mutation of one abolished function while mutation of the other had no discernable effect. Mutation of the other two AEK1 phosphosites gave intermediate phenotypes. Mutations in either the hydrophobic motif at the C-terminus of the protein or in the region of AEK1 predicted to bind the hydrophobic motif were also required for function. All parasites with defective AEK1 showed reduced proliferation and defects in cytokinesis, although the tested mutations differed in terms of the extent of cell death. Kinase activity of immunoprecipitated AEK1 phosphosite mutants largely paralleled the effects seen in complementation studies, although the mutation of the phosphosite adjacent to the hydrophobic motif had a greater impact on activity than predicted by the complementation studies. AEK1 was localized to cytoplasmic puncta distinct from glycosomes and acidocalcisomes. Discussion The rapid loss of viability of cells inhibited for AEK1 supports the idea that a short course of treatment that target AEK1 may be sufficient for treatment of people or animals infected with T. brucei. Key regulatory elements between AEK1 and its closest mammalian homolog appear to be largely conserved despite the vast evolutionary distance between mammals and T. brucei. The presence of AEK1 in cytoplasmic puncta raises the possibility that its localization may also play a role in functional activity.
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Affiliation(s)
- Marilyn Parsons
- Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA
| | - Ben Parsons
- Seattle Children’s Research Institute, Seattle, WA, USA
| | - Marissa Dean
- Seattle Children’s Research Institute, Seattle, WA, USA
| | | | - Zeba Islam
- Department of Chemistry, University of Washington, Seattle, WA
| | - Dustin J. Maly
- Department of Chemistry, University of Washington, Seattle, WA
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Pratap Reddy Gajulapalli V. Development of Kinase-Centric Drugs: A Computational Perspective. ChemMedChem 2023; 18:e202200693. [PMID: 37442809 DOI: 10.1002/cmdc.202200693] [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: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
Kinases are prominent drug targets in the pharmaceutical and research community due to their involvement in signal transduction, physiological responses, and upon dysregulation, in diseases such as cancer, neurological and autoimmune disorders. Several FDA-approved small-molecule drugs have been developed to combat human diseases since Gleevec was approved for the treatment of chronic myelogenous leukemia. Kinases were considered "undruggable" in the beginning. Several FDA-approved small-molecule drugs have become available in recent years. Most of these drugs target ATP-binding sites, but a few target allosteric sites. Among kinases that belong to the same family, the catalytic domain shows high structural and sequence conservation. Inhibitors of ATP-binding sites can cause off-target binding. Because members of the same family have similar sequences and structural patterns, often complex relationships between kinases and inhibitors are observed. To design and develop drugs with desired selectivity, it is essential to understand the target selectivity for kinase inhibitors. To create new inhibitors with the desired selectivity, several experimental methods have been designed to profile the kinase selectivity of small molecules. Experimental approaches are often expensive, laborious, time-consuming, and limited by the available kinases. Researchers have used computational methodologies to address these limitations in the design and development of effective therapeutics. Many computational methods have been developed over the last few decades, either to complement experimental findings or to forecast kinase inhibitor activity and selectivity. The purpose of this review is to provide insight into recent advances in theoretical/computational approaches for the design of new kinase inhibitors with the desired selectivity and optimization of existing inhibitors.
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7
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Zhang W, Liu Y, Jang H, Nussinov R. Cell cycle progression mechanisms: slower cyclin-D/CDK4 activation and faster cyclin-E/CDK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553605. [PMID: 37790340 PMCID: PMC10542123 DOI: 10.1101/2023.08.16.553605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Dysregulation of cyclin-dependent kinases (CDKs) impacts cell proliferation, driving cancer. Here, we ask why the cyclin-D/CDK4 complex governs cell cycle progression through the longer G1 phase, whereas cyclin-E/CDK2 regulates the short G1/S phase transition. We consider the experimentally established high-level bursting of cyclin-E, and sustained duration of elevated cyclin-D expression in the cell, available experimental cellular and structural data, and comprehensive explicit solvent molecular dynamics simulations to provide the mechanistic foundation of the distinct activation scenarios of cyclin-D/CDK4 and cyclin-E/CDK2 in the G1 phase and G1/S transition of the cell cycle, respectively. These lead us to propose slower activation of cyclin-D/CDK4 and rapid activation of cyclin-E/CDK2. Importantly, we determine the mechanisms through which this occurs, offering innovative CDK4 drug design considerations. Our insightful mechanistic work addresses the compelling cell cycle regulation question and illuminates the distinct activation speeds in the G1 versus G1/S phases, which are crucial for cell function.
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Affiliation(s)
- Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, U.S.A
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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8
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Du S, Alvarado JJ, Wales TE, Moroco JA, Engen JR, Smithgall TE. ATP-site inhibitors induce unique conformations of the acute myeloid leukemia-associated Src-family kinase, Fgr. Structure 2022; 30:1508-1517.e3. [PMID: 36115344 PMCID: PMC9637690 DOI: 10.1016/j.str.2022.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
The Src-family kinase Fgr is expressed primarily in myeloid hematopoietic cells and contributes to myeloid leukemia. Here, we present X-ray crystal structures of Fgr bound to the ATP-site inhibitors A-419259 and TL02-59, which show promise as anti-leukemic agents. A-419259 induces a closed Fgr conformation, with the SH3 and SH2 domains engaging the SH2-kinase linker and C-terminal tail, respectively. In the Fgr:A-419259 complex, the activation loop of one monomer inserts into the active site of the other, providing a snapshot of trans-autophosphorylation. By contrast, TL02-59 binding induced SH2 domain displacement from the C-terminal tail and SH3 domain release from the linker. Solution studies using HDX MS were consistent with the crystal structures, with A-419259 reducing and TL02-59 enhancing solvent exposure of the SH3 domain. These structures demonstrate that allosteric connections between the kinase and regulatory domains of Src-family kinases are regulated by the ligand bound to the active site.
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Affiliation(s)
- Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jamie A Moroco
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
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9
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Marotta G, Basagni F, Rosini M, Minarini A. Role of Fyn Kinase Inhibitors in Switching Neuroinflammatory Pathways. Curr Med Chem 2021; 29:4738-4755. [PMID: 34939537 DOI: 10.2174/0929867329666211221153719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/22/2022]
Abstract
Fyn kinase is a member of the Src non-receptor tyrosine kinase family. Fyn is involved in multiple signaling pathways extending from cell proliferation and differentiation to cell adhesion and cell motility, and it has been found to be overexpressed in various types of cancers. In the central nervous system, Fyn exerts several different functions such as axon-glial signal transduction, oligodendrocyte maturation and myelination, and it is implicated in neuroinflammatory processes. Based on these premises, Fyn emerges as an attractive target in cancer and neurodegenerative disease therapy, particularly Alzheimer disease (AD), based on its activation by Aβ via cellular prion protein and its interaction with tau protein. However, Fyn is also a challenging target since the Fyn inhibitors discovered so far, due to the relevant homology of Fyn with other kinases, suffer from off-target effects. This review covers the efforts performed in the last decade to identify and optimize small molecules that effectively inhibit Fyn, both in enzymatic and in cell assays, including drug repositioning practices, as an opportunity of therapeutic intervention in neurodegeneration.
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Affiliation(s)
- Giambattista Marotta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126-Bologna. Italy
| | - Filippo Basagni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126-Bologna. Italy
| | - Michela Rosini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126-Bologna. Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126-Bologna. Italy
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10
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Abdelhameed RFA, Ibrahim AK, Elfaky MA, Habib ES, Mahamed MI, Mehanna ET, Darwish KM, Khodeer DM, Ahmed SA, Elhady SS. Antioxidant and Anti-Inflammatory Activity of Cynanchum acutum L. Isolated Flavonoids Using Experimentally Induced Type 2 Diabetes Mellitus: Biological and In Silico Investigation for NF-κB Pathway/miR-146a Expression Modulation. Antioxidants (Basel) 2021; 10:antiox10111713. [PMID: 34829584 PMCID: PMC8615122 DOI: 10.3390/antiox10111713] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Cynanchum acutum L. is a climbing vine that belongs to the family Apocynaceae. Using different chromatographic techniques, seven compounds were isolated from the methanolic extract of the plant. The isolated compounds include six flavonoid compounds identified as rutin (1), quercetin-3-O-neohesperidoside (2), quercetin-3-O-β-galactoside (3), isoquercitrin (4), quercetin (5), and kaempferol 3-O-β-glucoside (6), in addition to a coumarin, scopoletin (7). The structures of the compounds were elucidated based on 1D NMR spectroscopy and high-resolution mass spectrometry (HR-MS), and by comparison with data reported in the literature. The first five compounds were selected for in vivo investigation of their anti-inflammatory and antioxidant properties in a rat model of type 2 diabetes. All tested compounds significantly reduced oxidative stress and increased erythrocyte lysate levels of antioxidant enzymes, along with the amelioration of the serum levels of inflammatory markers. Upregulation of miR-146a expression and downregulation of nuclear factor kappa B (NF-κB) expression were detected in the liver and adipose tissue of rats treated with the isolated flavonoids. Results from the biological investigation and those from the validated molecular modeling approach on two biological targets of the NF-κB pathway managed to highlight the superior anti-inflammatory activity of quercetin-3-O-galactoside (3) and quercetin (5), as compared to other bioactive metabolites.
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Affiliation(s)
- Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (E.S.H.); (M.I.M.); (S.A.A.)
- Department of Pharmacognosy, Faculty of Pharmacy, Galala University, New Galala 43713, Egypt
| | - Amany K. Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (E.S.H.); (M.I.M.); (S.A.A.)
- Correspondence: (A.K.I.); (E.T.M.)
| | - Mahmoud A. Elfaky
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.E.); (S.S.E.)
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Eman S. Habib
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (E.S.H.); (M.I.M.); (S.A.A.)
| | - Mayada I. Mahamed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (E.S.H.); (M.I.M.); (S.A.A.)
| | - Eman T. Mehanna
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (A.K.I.); (E.T.M.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Dina M. Khodeer
- Department of Pharmacology, and Toxicology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Safwat A. Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (E.S.H.); (M.I.M.); (S.A.A.)
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.E.); (S.S.E.)
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11
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Garlick JM, Sturlis SM, Bruno PA, Yates JA, Peiffer AL, Liu Y, Goo L, Bao L, De Salle SN, Tamayo-Castillo G, Brooks CL, Merajver SD, Mapp AK. Norstictic Acid Is a Selective Allosteric Transcriptional Regulator. J Am Chem Soc 2021; 143:9297-9302. [PMID: 34137598 PMCID: PMC8717358 DOI: 10.1021/jacs.1c03258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inhibitors of transcriptional protein-protein interactions (PPIs) have high value both as tools and for therapeutic applications. The PPI network mediated by the transcriptional coactivator Med25, for example, regulates stress-response and motility pathways, and dysregulation of the PPI networks contributes to oncogenesis and metastasis. The canonical transcription factor binding sites within Med25 are large (∼900 Å2) and have little topology, and thus, they do not present an array of attractive small-molecule binding sites for inhibitor discovery. Here we demonstrate that the depsidone natural product norstictic acid functions through an alternative binding site to block Med25-transcriptional activator PPIs in vitro and in cell culture. Norstictic acid targets a binding site comprising a highly dynamic loop flanking one canonical binding surface, and in doing so, it both orthosterically and allosterically alters Med25-driven transcription in a patient-derived model of triple-negative breast cancer. These results highlight the potential of Med25 as a therapeutic target as well as the inhibitor discovery opportunities presented by structurally dynamic loops within otherwise challenging proteins.
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Affiliation(s)
- Julie M Garlick
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven M Sturlis
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul A Bruno
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joel A Yates
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Amanda L Peiffer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yejun Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Laura Goo
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - LiWei Bao
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Samantha N De Salle
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Kueffer LE, Joseph RE, Andreotti AH. Reining in BTK: Interdomain Interactions and Their Importance in the Regulatory Control of BTK. Front Cell Dev Biol 2021; 9:655489. [PMID: 34249912 PMCID: PMC8260988 DOI: 10.3389/fcell.2021.655489] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
Since Dr. Ogden Bruton's 1952 paper describing the first human primary immunodeficiency disease, the peripheral membrane binding signaling protein, aptly named Bruton's tyrosine kinase (BTK), has been the target of intense study. Dr. Bruton's description of agammaglobulinemia set the stage for ultimately understanding key signaling steps emanating from the B cell receptor. BTK is a multidomain tyrosine kinase and in the decades since Dr. Bruton's discovery it has become clear that genetic defects in the regulatory domains or the catalytic domain can lead to immunodeficiency. This finding underscores the intricate regulatory mechanisms within the BTK protein that maintain appropriate levels of signaling both in the resting B cell and during an immune challenge. In recent decades, BTK has become a target for clinical intervention in treating B cell malignancies. The survival reliance of B cell malignancies on B cell receptor signaling has allowed small molecules that target BTK to become essential tools in treating patients with hematological malignancies. The first-in-class Ibrutinib and more selective second-generation inhibitors all target the active site of the multidomain BTK protein. Therapeutic interventions targeting BTK have been successful but are plagued by resistance mutations that render drug treatment ineffective for some patients. This review will examine the molecular mechanisms that drive drug resistance, the long-range conformational effects of active site inhibitors on the BTK regulatory apparatus, and emerging opportunities to allosterically target the BTK kinase to improve therapeutic interventions using combination therapies.
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Affiliation(s)
| | | | - Amy H. Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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13
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Umezawa K, Kii I. Druggable Transient Pockets in Protein Kinases. Molecules 2021; 26:molecules26030651. [PMID: 33513739 PMCID: PMC7865889 DOI: 10.3390/molecules26030651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 12/29/2022] Open
Abstract
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of recombinant enzyme proteins. Non-canonical inhibitors targeting a hidden pocket in a protein have received considerable research attention. Kii and colleagues identified an inhibitor targeting a transient pocket in the kinase DYRK1A during its folding process and termed it FINDY. FINDY exhibits a unique inhibitory profile; that is, FINDY does not inhibit the fully folded form of DYRK1A, indicating that the FINDY-binding pocket is hidden in the folded form. This intriguing pocket opens during the folding process and then closes upon completion of folding. In this review, we discuss previously established kinase inhibitors and their inhibitory mechanisms in comparison with FINDY. We also compare the inhibitory mechanisms with the growing concept of “cryptic inhibitor-binding sites.” These sites are buried on the inhibitor-unbound surface but become apparent when the inhibitor is bound. In addition, an alternative method based on cell-free protein synthesis of protein kinases may allow the discovery of small molecules that occupy these mysterious binding sites. Transitional folding intermediates would become alternative targets in drug discovery, enabling the efficient development of potent kinase inhibitors.
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Affiliation(s)
- Koji Umezawa
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan;
| | - Isao Kii
- Laboratory for Drug Target Research, Faculty & Graduate School of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan
- Correspondence: ; Tel.: +81-265-77-1521
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14
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Shetve VV, Bhowmick S, Alissa SA, Alothman ZA, Wabaidu SM, Asmary FA, Alhajri HM, Islam MA. Identification of selective Lyn inhibitors from the chemical databases through integrated molecular modelling approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:1-27. [PMID: 33161767 DOI: 10.1080/1062936x.2020.1799433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
In the current study, the Asinex and ChEBI databases were virtually screened for the identification of potential Lyn protein inhibitors. Therefore, a multi-steps molecular docking study was carried out using the VSW utility tool embedded in Maestro user interface of the Schrödinger suite. On initial screening, molecules having a higher XP-docking score and binding free energy compared to Staurosporin were considered for further assessment. Based on in silico pharmacokinetic analysis and a common-feature pharmacophore mapping model developed from the Staurosporin, four molecules were proposed as promising Lyn inhibitors. The binding interactions of all proposed Lyn inhibitors revealed strong ligand efficiency in terms of energy score obtained in molecular modelling analyses. Furthermore, the dynamic behaviour of each molecule in association with the Lyn protein-bound state was assessed through an all-atoms molecular dynamics (MD) simulation study. MD simulation analyses were confirmed with notable intermolecular interactions and consistent stability for the Lyn protein-ligand complexes throughout the simulation. High negative binding free energy of identified four compounds calculated through MM-PBSA approach demonstrated a strong binding affinity towards the Lyn protein. Hence, the proposed compounds might be taken forward as potential next-generation Lyn kinase inhibitors for managing numerous Lyn associated diseases or health complications after experimental validation.
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Affiliation(s)
- V V Shetve
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University , Pune, India
| | - S Bhowmick
- Department of Chemical Technology, University of Calcutta , Kolkata, India
| | - S A Alissa
- Chemistry Department, College of Science, Princess Nourah Bint Abdulrahman University , Riyadh, Saudi Arabia
| | - Z A Alothman
- Department of Chemistry, College of Science, King Saud University , Riyadh, Saudi Arabia
| | - S M Wabaidu
- Department of Chemistry, College of Science, King Saud University , Riyadh, Saudi Arabia
| | - F A Asmary
- Department of Chemistry, College of Science, King Saud University , Riyadh, Saudi Arabia
| | - H M Alhajri
- Department of Chemistry, College of Science, King Saud University , Riyadh, Saudi Arabia
| | - M A Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester , Manchester, UK
- School of Health Sciences, University of Kwazulu-Natal , Durban, South Africa
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division , Pretoria, South Africa
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15
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Patel RK, Patel YK, Smithgall TE. In Vitro Evolution Reveals a Single Mutation as Sole Source of Src-Family Kinase C-Helix-out Inhibitor Resistance. ACS Chem Biol 2020; 15:2175-2184. [PMID: 32602694 PMCID: PMC8136437 DOI: 10.1021/acschembio.0c00373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding cancer cell drug resistance to protein-tyrosine kinase inhibitors, which often arises from acquired mutations in the target kinase, is central to the development of more durable therapies. Experimental systems that reveal potential paths to resistance for a given inhibitor and kinase target have an important role in preclinical development of kinase inhibitor drugs. Here, we employed a codon mutagenesis strategy to define the mutational landscape of acquired resistance in HCK, a member of the SRC tyrosine kinase family and therapeutic target in acute myeloid leukemia (AML). Using PCR-based saturation mutagenesis, we created a cDNA library designed to replace each codon in the HCK open reading frame with all possible codons. This HCK mutant library was used to transform Rat-2 fibroblasts, followed by selection for resistant colonies with A-419259, a pyrrolopyrimidine HCK inhibitor and drug lead for AML. X-ray crystallography has shown that A-419259 binding induces outward rotation of the kinase domain αC-helix, a conformation incompatible with phosphotransfer. Remarkably, only a single resistance mutation evolved during A-419259 selection: histidine substitution for threonine at the gatekeeper position in the kinase domain. Deep sequencing confirmed representation of nearly all other missense mutations across the entire HCK open reading frame. This observation suggests that A-419259 and other C-helix-out Src-family kinase inhibitors may have a narrow path to acquired resistance in the context of AML cases where Hck is an oncogenic driver.
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Affiliation(s)
- Ravi K. Patel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine 450 Technology Drive, Pittsburgh, PA 15219, USA
| | | | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine 450 Technology Drive, Pittsburgh, PA 15219, USA
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16
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Potter ZE, Lau HT, Chakraborty S, Fang L, Guttman M, Ong SE, Fowler DM, Maly DJ. Parallel Chemoselective Profiling for Mapping Protein Structure. Cell Chem Biol 2020; 27:1084-1096.e4. [PMID: 32649906 PMCID: PMC7484201 DOI: 10.1016/j.chembiol.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/27/2020] [Accepted: 06/19/2020] [Indexed: 01/01/2023]
Abstract
Solution-based structural techniques complement high-resolution structural data by providing insight into the oft-missed links between protein structure and dynamics. Here, we present Parallel Chemoselective Profiling, a solution-based structural method for characterizing protein structure and dynamics. Our method utilizes deep mutational scanning saturation mutagenesis data to install amino acid residues with specific chemistries at defined positions on the solvent-exposed surface of a protein. Differences in the extent of labeling of installed mutant residues are quantified using targeted mass spectrometry, reporting on each residue's local environment and structural dynamics. Using our method, we studied how conformation-selective, ATP-competitive inhibitors affect the local and global structure and dynamics of full-length Src kinase. Our results highlight how parallel chemoselective profiling can be used to study a dynamic multi-domain protein, and suggest that our method will be a useful addition to the relatively small toolkit of existing protein footprinting techniques.
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Affiliation(s)
- Zachary E Potter
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Ho-Tak Lau
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sujata Chakraborty
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Linglan Fang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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17
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Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. ACS Chem Biol 2020; 15:2005-2016. [PMID: 32479050 DOI: 10.1021/acschembio.0c00429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule kinase inhibitors that stabilize distinct ATP binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP binding site contacts are responsible for modulating the global conformation of SFKs and whether these inhibitor-mediated allosteric effects generalize to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix αC. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix αC in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Our study highlights that an ATP-competitive inhibitor's interactions with helix αC can have a major influence on the global conformation of some tyrosine kinases.
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Affiliation(s)
| | - Jessica Vilas-Boas
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | | | | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
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18
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Asquith CRM, Laitinen T, Bennett JM, Wells CI, Elkins JM, Zuercher WJ, Tizzard GJ, Poso A. Design and Analysis of the 4-Anilinoquin(az)oline Kinase Inhibition Profiles of GAK/SLK/STK10 Using Quantitative Structure-Activity Relationships. ChemMedChem 2019; 15:26-49. [PMID: 31675459 DOI: 10.1002/cmdc.201900521] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Indexed: 01/01/2023]
Abstract
The 4-anilinoquinoline and 4-anilinoquinazoline ring systems have been the focus of significant efforts in prior kinase drug discovery programs, which have led to approved medicines. Broad kinome profiles of these compounds have now been assessed with the advent of advanced screening technologies. These ring systems, while originally designed for specific targets including epidermal growth factor receptor (EGFR), but actually display a number of potent collateral kinase targets, some of which have been associated with negative clinical outcomes. We have designed and synthesized a series of 4-anilinoquin(az)olines in order to better understand the structure-activity relationships of three main collateral kinase targets of quin(az)oline-based kinase inhibitors: cyclin G associated kinase (GAK), STE20-like serine/threonine-protein kinase (SLK) and serine/threonine-protein kinase 10 (STK10). This was achieved through a series of quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites and extensive small-molecule X-ray structural analysis.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - James M Bennett
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M Elkins
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.,Structural Genomics Consortium, Universidade Estadual de Campinas-UNICAMP, Campinas, São Paulo, 13083-886 (Brazil)
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland.,University Hospital Tübingen, Deparment of Internal Medicine VIII, University of Tübingen, 72076, Tübingen, Germany
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