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Lee LC, Peng YH, Chang HH, Hsu T, Lu CT, Huang CH, Hsueh CC, Kung FC, Kuo CC, Jiaang WT, Wu SY. Xanthine Derivatives Reveal an Allosteric Binding Site in Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2). J Med Chem 2021; 64:11288-11301. [PMID: 34337952 PMCID: PMC8389891 DOI: 10.1021/acs.jmedchem.1c00663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Methylenetetrahydrofolate
dehydrogenase 2 (MTHFD2) plays an important
role in one-carbon metabolism. The MTHFD2 gene is upregulated in various
cancers but very low or undetectable in normal proliferating cells,
and therefore a potential target for cancer treatment. In this study,
we present the structure of MTHFD2 in complex with xanthine derivative 15, which allosterically binds to MTHFD2 and coexists with
the substrate analogue. A kinetic study demonstrated the uncompetitive
inhibition of MTHFD2 by 15. Allosteric inhibitors often
provide good selectivity and, indeed, xanthine derivatives are highly
selective for MTHFD2. Moreover, several conformational changes were
observed upon the binding of 15, which impeded the binding
of the cofactor and phosphate to MTHFD2. To the best of our knowledge,
this is the first study to identify allosteric inhibitors targeting
the MTHFD family and our results would provide insights on the inhibition
mechanism of MTHFD proteins and the development of novel inhibitors.
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Affiliation(s)
- Lung-Chun Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Yi-Hui Peng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Hsin-Huei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Tsu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Cheng-Tai Lu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Chih-Hsiang Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Ching-Cheng Hsueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Fang-Chun Kung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan, ROC
| | - Weir-Torn Jiaang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County 350 Taiwan, ROC
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2
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Kirschner S, Döbber A, Krebs M, Witt C, Hartke B, Peifer C. The Impact of Electronic Effects on Photolysis: A Model Study on the 4,5‐Dimethoxy‐2‐nitrobenzyl Caged
N
‐Phenylpyrimidine‐2‐amine Scaffold. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.201900285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Stefan Kirschner
- Department of Pharmaceutical and Medicinal ChemistryChristian-Albrechts-University of Kiel Gutenbergstraße 76 24118 Kiel Germany
| | - Alexander Döbber
- Department of Pharmaceutical and Medicinal ChemistryChristian-Albrechts-University of Kiel Gutenbergstraße 76 24118 Kiel Germany
| | - Melanie Krebs
- Department of Pharmaceutical and Medicinal ChemistryChristian-Albrechts-University of Kiel Gutenbergstraße 76 24118 Kiel Germany
| | - Christopher Witt
- Institute for Physical ChemistryChristian-Albrechts-University of Kiel Max-Eyth-Str. 2 24118 Kiel Germany
| | - Bernd Hartke
- Institute for Physical ChemistryChristian-Albrechts-University of Kiel Max-Eyth-Str. 2 24118 Kiel Germany
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal ChemistryChristian-Albrechts-University of Kiel Gutenbergstraße 76 24118 Kiel Germany
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3
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Markossian S, Ang KK, Wilson CG, Arkin MR. Small-Molecule Screening for Genetic Diseases. Annu Rev Genomics Hum Genet 2018; 19:263-288. [PMID: 29799800 DOI: 10.1146/annurev-genom-083117-021452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic determinants of many diseases, including monogenic diseases and cancers, have been identified; nevertheless, targeted therapy remains elusive for most. High-throughput screening (HTS) of small molecules, including high-content analysis (HCA), has been an important technology for the discovery of molecular tools and new therapeutics. HTS can be based on modulation of a known disease target (called reverse chemical genetics) or modulation of a disease-associated mechanism or phenotype (forward chemical genetics). Prominent target-based successes include modulators of transthyretin, used to treat transthyretin amyloidoses, and the BCR-ABL kinase inhibitor Gleevec, used to treat chronic myelogenous leukemia. Phenotypic screening successes include modulators of cystic fibrosis transmembrane conductance regulator, splicing correctors for spinal muscular atrophy, and histone deacetylase inhibitors for cancer. Synthetic lethal screening, in which chemotherapeutics are screened for efficacy against specific genetic backgrounds, is a promising approach that merges phenotype and target. In this article, we introduce HTS technology and highlight its contributions to the discovery of drugs and probes for monogenic diseases and cancer.
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Affiliation(s)
- Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Kenny K Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Christopher G Wilson
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA; , , ,
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4
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Bajusz D, Ferenczy GG, Keserű GM. Property-based characterization of kinase-like ligand space for library design and virtual screening. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00253b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A property-based desirability scoring scheme has been developed for kinase-focused library design and ligand-based pre-screening of large compound sets.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- Budapest 1117
- Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- Budapest 1117
- Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- Budapest 1117
- Hungary
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5
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Colon and rectal cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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6
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Abstract
The incidence of malignant melanoma is increasing annually. Early stages can be cured with surgical intervention but metastatic disease has generally had a dismal prognosis with few effective interventions. A half of all melanomas possess a BRAF mutation, which can be targeted by specific inhibitors. Vemurafenib is an orally active, purposely designed mutant BRAF inhibitor, which has recently been shown to have a survival benefit measured in months in metastatic patients. In this article, the authors discuss the scientific rationale, drug development process and clinical trials that have led to vemurafenib becoming the first BRAF inhibitor approved for the treatment of patients with mutant BRAF metastatic melanoma.
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Affiliation(s)
- Heather M Shaw
- Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, Middlesex, HA6 2RN, UK
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7
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Jin F, Gao D, Zhang C, Liu F, Chu B, Chen Y, Chen YZ, Tan C, Jiang Y. Exploration of 1-(3-chloro-4-(4-oxo-4H-chromen-2-yl)phenyl)-3-phenylurea derivatives as selective dual inhibitors of Raf1 and JNK1 kinases for anti-tumor treatment. Bioorg Med Chem 2013; 21:824-31. [DOI: 10.1016/j.bmc.2012.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/31/2012] [Accepted: 04/04/2012] [Indexed: 12/19/2022]
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8
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Bollag G, Tsai J, Zhang J, Zhang C, Ibrahim P, Nolop K, Hirth P. Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discov 2012; 11:873-86. [PMID: 23060265 DOI: 10.1038/nrd3847] [Citation(s) in RCA: 543] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The identification of driver oncogenes has provided important targets for drugs that can change the landscape of cancer therapies. One such example is the BRAF oncogene, which is found in about half of all melanomas as well as several other cancers. As a druggable kinase, oncogenic BRAF has become a crucial target of small-molecule drug discovery efforts. Following a rapid clinical development path, vemurafenib (Zelboraf; Plexxikon/Roche) was approved for the treatment of BRAF-mutated metastatic melanoma in the United States in August 2011 and the European Union in February 2012. This Review describes the underlying biology of BRAF, the technology used to identify vemurafenib and its clinical development milestones, along with future prospects based on lessons learned during its development.
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Affiliation(s)
- Gideon Bollag
- Plexxikon, 91 Bolivar Drive, Berkeley, California 94710, USA.
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9
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Targeted inhibition of BRAF kinase: opportunities and challenges for therapeutics in melanoma. Biosci Rep 2012; 32:25-33. [PMID: 21981139 DOI: 10.1042/bsr20110068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malignant melanoma is the most aggressive form of skin cancer and its incidence has increased dramatically in the last two decades. Even with a high rate of success in the treatment of early stages of this malignancy, currently there are no effective strategies for the treatment of advanced metastatic melanoma. Much effort has been put into the use of different target-specific drugs, among which BRAF kinase-specific small-molecule inhibitors have rendered promising results as therapeutic agents in metastatic melanoma. Nonetheless, some side effects, such as development of SCC (squamous cell carcinoma), as well as tumour resistance and recurrence, are common limitations of this therapeutic strategy. The use of combination treatments in which different regulatory pathways or the immunological response are targeted seems to be a promising tool for the future success of melanoma therapeutics.
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10
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Singh N, Sun H, Chaudhury S, Abdulhameed MDM, Wallqvist A, Tawa G. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. J Cheminform 2012; 4:4. [PMID: 22316383 PMCID: PMC3299594 DOI: 10.1186/1758-2946-4-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/08/2012] [Indexed: 01/26/2023] Open
Abstract
Background The current chemical space of known small molecules is estimated to exceed 1060 structures. Though the largest physical compound repositories contain only a few tens of millions of unique compounds, virtual screening of databases of this size is still difficult. In recent years, the application of physicochemical descriptor-based profiling, such as Lipinski's rule-of-five for drug-likeness and Oprea's criteria of lead-likeness, as early stage filters in drug discovery has gained widespread acceptance. In the current study, we outline a kinase-likeness scoring function based on known kinase inhibitors. Results The method employs a collection of 22,615 known kinase inhibitors from the ChEMBL database. A kinase-likeness score is computed using statistical analysis of nine key physicochemical descriptors for these inhibitors. Based on this score, the kinase-likeness of four publicly and commercially available databases, i.e., National Cancer Institute database (NCI), the Natural Products database (NPD), the National Institute of Health's Molecular Libraries Small Molecule Repository (MLSMR), and the World Drug Index (WDI) database, is analyzed. Three of these databases, i.e., NCI, NPD, and MLSMR are frequently used in the virtual screening of kinase inhibitors, while the fourth WDI database is for comparison since it covers a wide range of known chemical space. Based on the kinase-likeness score, a kinase-focused library is also developed and tested against three different kinase targets selected from three different branches of the human kinome tree. Conclusions Our proposed methodology is one of the first that explores how the narrow chemical space of kinase inhibitors and its relevant physicochemical information can be utilized to build kinase-focused libraries and prioritize pre-existing compound databases for screening. We have shown that focused libraries generated by filtering compounds using the kinase-likeness score have, on average, better docking scores than an equivalent number of randomly selected compounds. Beyond library design, our findings also impact the broader efforts to identify kinase inhibitors by screening pre-existing compound libraries. Currently, the NCI library is the most commonly used database for screening kinase inhibitors. Our research suggests that other libraries, such as MLSMR, are more kinase-like and should be given priority in kinase screenings.
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Affiliation(s)
- Narender Singh
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U,S, Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
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11
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Ahn YM, Clare M, Ensinger CL, Hood MM, Lord JW, Lu WP, Miller DF, Patt WC, Smith BD, Vogeti L, Kaufman MD, Petillo PA, Wise SC, Abendroth J, Chun L, Clark R, Feese M, Kim H, Stewart L, Flynn DL. Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region. Bioorg Med Chem Lett 2010; 20:5793-8. [PMID: 20800479 DOI: 10.1016/j.bmcl.2010.07.134] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/28/2010] [Accepted: 07/30/2010] [Indexed: 11/19/2022]
Abstract
Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.
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Affiliation(s)
- Yu Mi Ahn
- Deciphera Pharmaceuticals LLC, 643 Massachusetts St, Lawrence, KS 66044, USA
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