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Uthale A, Anantram A, Sulkshane P, Degani M, Teni T. Identification of bicyclic compounds that act as dual inhibitors of Bcl-2 and Mcl-1. Mol Divers 2022:10.1007/s11030-022-10494-6. [PMID: 35909144 DOI: 10.1007/s11030-022-10494-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/02/2022] [Indexed: 10/16/2022]
Abstract
Elevated expression of anti-apoptotic proteins, such as Bcl-2 and Mcl-1 contributes to poor prognosis and resistance to current treatment modalities in multiple cancers. Here, we report the design, synthesis and characterization of benzimidazole chalcone and flavonoid scaffold-derived bicyclic compounds targeting both Bcl-2 and Mcl-1 by optimizing the structural differences in the binding sites of both these proteins. Initial docking screen of Bcl-2 and Mcl-1 with pro-apoptotic protein Bim revealed possible hits with optimal binding energies. All the optimized bicyclic compounds were screened for their in vitro cytotoxic activity against two oral cancer cell lines (AW8507 and AW13516) which express high levels of Bcl-2 and Mcl-1. Compound 4d from the benzimidazole chalcone series and compound 6d from the flavonoid series exhibited significant cytotoxic activity (IC50 7.12 μM and 17.18 μM, respectively) against AW13516 cell line. Time Resolved-Fluorescence Resonance Energy Transfer (TR-FRET) analysis further demonstrated that compound 4d and compound 6d could effectively inhibit the Bcl-2 and Mcl-1 proteins by displacing their BH3 binding partners. Both compounds exhibited potent activation of canonical pathway of apoptosis evident from appearance of cleaved Caspase-3 and PARP. Further, treatment of oral cancer cells with the inhibitors induced dissociation of the BH3 only protein Bim from Mcl-1 and Bak from Bcl-2 but failed to release Bax from Bcl-xL thereby confirming the nature of compounds as BH3-mimetics selectively targeting Bcl-2 and Mcl-1. Our study thus identifies bicyclic compounds as promising candidates for anti-apoptotic Bcl-2/Mcl-1 dual inhibitors with a potential for further development.
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Affiliation(s)
- Abhay Uthale
- Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India
| | - Aarti Anantram
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India
| | - Prasad Sulkshane
- Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India
| | - Mariam Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Tanuja Teni
- Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, India.
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2
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El‐Shahat M. Advances in the reduction of quinolines to 1,2,3,4‐tetrahydroquinolines. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mahmoud El‐Shahat
- Photochemistry Department Chemical Industries Research Institute, National Research Centre, Scopus affiliation ID 60014618 Giza Egypt
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3
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Ikeda K, Kezuka Y, Nonaka T, Yonezawa T, Osawa M, Katoh E. Comprehensive Approach of 19F Nuclear Magnetic Resonance, Enzymatic, and In Silico Methods for Site-Specific Hit Selection and Validation of Fragment Molecules that Inhibit Methionine γ-Lyase Activity. J Med Chem 2021; 64:14299-14310. [PMID: 34582207 DOI: 10.1021/acs.jmedchem.1c00766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragment-based screening using 19F NMR (19F-FS) is an efficient method for exploring seed and lead compounds for drug discovery. Here, we demonstrate the utility and merits of using 19F-FS for methionine γ-lyase-binding fragments, together with a 19F NMR-based competition and mutation assay, as well as enzymatic and in silico methods. 19F NMR-based assays provided useful information on binding between 19F-FS hit fragments and target proteins. Although the 19F-FS and enzymatic assay were weakly correlated, they show that the 19F-FS hit fragments contained compounds with inhibitory activity. Furthermore, we found that in silico calculations partially account for the differences in activity levels between the 19F-FS hits as per NMR analysis. A comprehensive approach combining the 19F-FS and other methods not only identified fragment hits but also distinguished structural differences in chemical groups with diverse activity levels.
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Affiliation(s)
- Kazuyoshi Ikeda
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Yuichiro Kezuka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Takamasa Nonaka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Etsuko Katoh
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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4
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Negi A, Murphy PV. Development of Mcl-1 inhibitors for cancer therapy. Eur J Med Chem 2020; 210:113038. [PMID: 33333396 DOI: 10.1016/j.ejmech.2020.113038] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The myeloid leukemia cell differentiation protein (Mcl-1) is an anti-apoptotic protein of the B-cell lymphoma 2 (Bcl-2) family, which regulates cellular apoptosis. Mcl-1 expression plays a key role in survival of cancer cells and therefore serves as a promising target in cancer therapy. Besides, its importance as a cancer target, various peptides and small-molecule inhibitors have been successfully designed and synthesized, yet no Mcl-1 inhibitor is approved for clinical use. However, recent development on the understanding of Mcl-1's role in key cellular processes in cancer and an upsurge of reports highlighting its association in various anticancer drug resistance supports the view that Mcl-1 is a key target in various cancers, especially hematological cancers. This review compiles structures of a variety of inhibitors of Mcl-1 reported to date. These include inhibitors based on a diverse range of heterocycles (e.g. indole, imidazole, thiophene, nicotinic acid, piperazine, triazine, thiazole, isoindoline), oligomers (terphenyl, quaterpyridine), polyphenol, phenalene, anthranilic acid, anthraquinone, macrocycles, natural products, and metal-based complexes. In addition, an effort has been made to summarize the structure activity relationships, based on a variety of assays, of some important classes of Mcl-1 inhibitors, giving affinities and selectivities for Mcl-1 compared to other Bcl-2 family members. A focus has been placed on categorizing the inhibitors based on their core frameworks (scaffolds) to appeal to the chemical biologist or medicinal chemist.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Paul V Murphy
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
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5
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Berthold D, Breit B. Asymmetric Total Syntheses of (−)-Angustureine and (−)-Cuspareine via Rhodium-Catalyzed Hydroamination. Org Lett 2019; 22:565-568. [DOI: 10.1021/acs.orglett.9b04334] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dino Berthold
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
| | - Bernhard Breit
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
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6
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Eshon J, Gerstner NC, Schomaker JM. Oxidative allene amination for the synthesis of nitrogen-containing heterocycles. ARKIVOC 2018; 2018:204-233. [PMID: 31903453 PMCID: PMC6941799 DOI: 10.24820/ark.5550190.p010.670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The prevalence of stereochemically complex amines in natural products, pharmaceuticals and other bioactive compounds, coupled with the challenges inherent in their preparation, has inspired our work to develop new and versatile methodologies for the synthesis of amine-containing stereotriads ('triads'). The key step is a highly chemo-, regio-, and stereoselective transition-metal catalyzed nitrene transfer reaction that transforms one of the cumulated double bonds of an allene precursor into a bicyclic methyleneaziridine intermediate. This account summarizes our strategies to rapidly elaborate such intermediates into stereochemically rich, densely functionalized amine triads, nitrogen heterocycles, aminated carbocycles and other useful synthetic building blocks.
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Affiliation(s)
- Josephine Eshon
- Department of Chemistry, 1101 University Avenue, Madison, WI 53706, U.S.A
| | - Nels C Gerstner
- Department of Chemistry, 1101 University Avenue, Madison, WI 53706, U.S.A
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7
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A Small-Molecule Inhibitor of Bax and Bak Oligomerization Prevents Genotoxic Cell Death and Promotes Neuroprotection. Cell Chem Biol 2017; 24:493-506.e5. [PMID: 28392146 DOI: 10.1016/j.chembiol.2017.03.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/29/2016] [Accepted: 03/13/2017] [Indexed: 11/24/2022]
Abstract
Aberrant apoptosis can lead to acute or chronic degenerative diseases. Mitochondrial outer membrane permeabilization (MOMP) triggered by the oligomerization of the Bcl-2 family proteins Bax/Bak is an irreversible step leading to execution of apoptosis. Here, we describe the discovery of small-molecule inhibitors of Bax/Bak oligomerization that prevent MOMP. We demonstrate that these molecules disrupt multiple, but not all, interactions between Bax dimer interfaces thereby interfering with the formation of higher-order oligomers in the MOM, but not recruitment of Bax to the MOM. Small-molecule inhibition of Bax/Bak oligomerization allowed cells to evade apoptotic stimuli and rescued neurons from death after excitotoxicity, demonstrating that oligomerization of Bax is essential for MOMP. Our discovery of small-molecule Bax/Bak inhibitors provides novel tools for the investigation of the mechanisms leading to MOMP and will ultimately facilitate development of compounds inhibiting Bax/Bak in acute and chronic degenerative diseases.
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8
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Gowthaman R, Miller SA, Rogers S, Khowsathit J, Lan L, Bai N, Johnson DK, Liu C, Xu L, Anbanandam A, Aubé J, Roy A, Karanicolas J. DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites. J Med Chem 2015; 59:4152-70. [PMID: 26126123 DOI: 10.1021/acs.jmedchem.5b00150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions represent an exciting and challenging target class for therapeutic intervention using small molecules. Protein interaction sites are often devoid of the deep surface pockets presented by "traditional" drug targets, and crystal structures reveal that inhibitors typically engage these sites using very shallow binding modes. As a consequence, modern virtual screening tools developed to identify inhibitors of traditional drug targets do not perform as well when they are instead deployed at protein interaction sites. To address the need for novel inhibitors of important protein interactions, here we introduce an alternate docking strategy specifically designed for this regime. Our method, termed DARC (Docking Approach using Ray-Casting), matches the topography of a surface pocket "observed" from within the protein to the topography "observed" when viewing a potential ligand from the same vantage point. We applied DARC to carry out a virtual screen against the protein interaction site of human antiapoptotic protein Mcl-1 and found that four of the top-scoring 21 compounds showed clear inhibition in a biochemical assay. The Ki values for these compounds ranged from 1.2 to 21 μM, and each had ligand efficiency comparable to promising small-molecule inhibitors of other protein-protein interactions. These hit compounds do not resemble the natural (protein) binding partner of Mcl-1, nor do they resemble any known inhibitors of Mcl-1. Our results thus demonstrate the utility of DARC for identifying novel inhibitors of protein-protein interactions.
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Affiliation(s)
- Ragul Gowthaman
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Sven A Miller
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Steven Rogers
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jittasak Khowsathit
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Lan Lan
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Nan Bai
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - David K Johnson
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Chunjing Liu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Liang Xu
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Asokan Anbanandam
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Jeffrey Aubé
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - Anuradha Roy
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
| | - John Karanicolas
- Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States
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9
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Synthesis of some new 2′-amino-2-fluoro-5′-oxo-1′-(4-phenylthiazole-2-yl)-1′,4′,5′,6′,7′,8′-hexahydro-3,4′-biquinoline-3′-carbonitrile derivatives and biological evaluation as antimicrobial agents. JOURNAL OF SAUDI CHEMICAL SOCIETY 2015. [DOI: 10.1016/j.jscs.2011.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Garg Y, Gahalawat S, Pandey SK. An enantioselective approach to 2-alkyl substituted tetrahydroquinolines: total synthesis of (+)-angustureine. RSC Adv 2015. [DOI: 10.1039/c5ra05987a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A simple and highly efficient synthetic approach to enantiopure 2-alkyl substituted tetrahydroquinoline 1 skeleton from aldehydes as starting materials and its application to the total synthesis of (+)-angustureine 2 is described.
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Affiliation(s)
- Yuvraj Garg
- School of Chemistry and Biochemistry
- Thapar University
- Patiala 147001
- India
| | - Suraksha Gahalawat
- School of Chemistry and Biochemistry
- Thapar University
- Patiala 147001
- India
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11
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Collins I, Jones AM. Diversity-oriented synthetic strategies applied to cancer chemical biology and drug discovery. Molecules 2014; 19:17221-55. [PMID: 25350364 PMCID: PMC6270883 DOI: 10.3390/molecules191117221] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 12/22/2022] Open
Abstract
How can diversity-oriented strategies for chemical synthesis provide chemical tools to help shape our understanding of complex cancer pathways and progress anti-cancer drug discovery efforts? This review (surveying the literature from 2003 to the present) considers the applications of diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS) and associated strategies to cancer biology and drug discovery, summarising the syntheses of novel and often highly complex scaffolds from pluripotent or synthetically versatile building blocks. We highlight the role of diversity-oriented synthetic strategies in producing new chemical tools to interrogate cancer biology pathways through the assembly of relevant libraries and their application to phenotypic and biochemical screens. The use of diversity-oriented strategies to explore structure-activity relationships in more advanced drug discovery projects is discussed. We show how considering appropriate and variable focus in library design has provided a spectrum of DOS approaches relevant at all stages in anti-cancer drug discovery.
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Affiliation(s)
- Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
| | - Alan M Jones
- Division of Chemistry and Environmental Science, School of Science and the Environment, Faculty of Science and Engineering, Manchester Metropolitan University, John Dalton Building, Chester Street, Manchester M1 5GD, UK.
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12
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Prediction of anti-tumor chemical probes of a traditional Chinese medicine formula by HPLC fingerprinting combined with molecular docking. Eur J Med Chem 2014; 83:294-306. [DOI: 10.1016/j.ejmech.2014.06.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 05/29/2014] [Accepted: 06/17/2014] [Indexed: 11/24/2022]
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13
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Weatherly CD, Guzei IA, Schomaker JM. Stereocontrolled Synthesis of 1,3-Diamino-2-ols by Aminohydroxylation of Bicyclic Methylene-Aziridines. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Satyanarayana G, Pflästerer D, Helmchen G. Enantioselective Syntheses of Tetrahydroquinolines Based on Iridium-Catalyzed Allylic Substitutions: Total Syntheses of (+)-Angustureine and (-)-Cuspareine. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100981] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Sridharan V, Suryavanshi PA, Menéndez JC. Advances in the chemistry of tetrahydroquinolines. Chem Rev 2011; 111:7157-259. [PMID: 21830756 DOI: 10.1021/cr100307m] [Citation(s) in RCA: 771] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Vellaisamy Sridharan
- Departamento de Química Orgánica y Farmacéutica, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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16
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Synthesis and molecular modeling study of new trimeric quinoline derivatives. Bioorg Chem 2011; 39:143-50. [DOI: 10.1016/j.bioorg.2011.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 07/01/2011] [Accepted: 07/03/2011] [Indexed: 11/21/2022]
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17
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Schulz MN, Landström J, Bright K, Hubbard RE. Design of a Fragment Library that maximally represents available chemical space. J Comput Aided Mol Des 2011; 25:611-20. [DOI: 10.1007/s10822-011-9461-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 07/13/2011] [Indexed: 12/01/2022]
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18
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Synthesis and biological activities of new di- and trimeric quinoline derivatives. Bioorg Med Chem 2010; 18:7132-43. [DOI: 10.1016/j.bmc.2010.07.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/12/2010] [Accepted: 07/13/2010] [Indexed: 11/17/2022]
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19
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Dalafave D. Design of Druglike Small Molecules for Possible Inhibition of Antiapoptotic BCL-2, BCL-W, and BFL-1 Proteins. Biomed Eng Comput Biol 2010. [DOI: 10.4137/becb.s5575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
New druglike small molecules with possible anticancer applications were computationally designed. The molecules formed stable complexes with antiapoptotic BCL-2, BCL-W, and BFL-1 proteins. These findings are novel because, to the best of the author's knowledge, molecules that bind all three of these proteins are not known. A drug based on them should be more economical and better tolerated by patients than a combination of drugs, each targeting a single protein. The calculated drug-related properties of the molecules were similar to those found in most commercial drugs. The molecules were designed and evaluated following a simple, yet effective procedure. The need for substantial computational resources often precludes researchers in many countries and small institutions from participating in the field. The procedure presented here offsets the problem by reducing the cost of involvement. The procedure can be used efficiently in the early phases of drug discovery to evaluate promising lead compounds in time- and cost-effective ways.
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Affiliation(s)
- D.S. Dalafave
- Physics Department, The College of New Jersey, Ewing, New Jersey, 08628 USA
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20
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Barelier S, Pons J, Gehring K, Lancelin JM, Krimm I. Ligand specificity in fragment-based drug design. J Med Chem 2010; 53:5256-66. [PMID: 20575554 DOI: 10.1021/jm100496j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fragment-based drug design consists of identifying low-molecular weight compounds that weakly bind to a target macromolecule and will then be modified or linked to yield potent inhibitors. The specificity of these low-complexity and low-affinity molecules has rarely been discussed in the literature. To address this question, NMR spectroscopy was used to investigate the interactions of 150 fragments with five proteins: three proteins from the Bcl-2 family (Bcl-x(L), Bcl-w, and Mcl-1), human peroxiredoxin 5, for which very few ligands have been reported, and human serum albumin, which is known to bind a large number of ligands. Our results show that the fragments are rather versatile binders and able to identify binding hot spots in very different targets. Despite the different hit rates observed related to the druggability of the proteins, two scaffolds appear as preferred binders for all proteins. Low specificity was observed between homologous proteins or unrelated poorly druggable proteins, while higher specificity could be achieved with highly druggable targets.
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Affiliation(s)
- Sarah Barelier
- Laboratoire des Sciences Analytiques, UMR CNRS 5180, Universite de Lyon, Universite Claude Bernard, Lyon 1, Bat. ESCPE Lyon, Domaine Scientifique de la Doua, 69100 Villeurbanne, France
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21
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Dalafave DS, Prisco G. Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics. Cancer Inform 2010; 9:169-77. [PMID: 20838611 PMCID: PMC2935820 DOI: 10.4137/cin.s5065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Informatics and computational design methods were used to create new molecules that could potentially bind antiapoptotic proteins, thus promoting death of cancer cells. Apoptosis is a cellular process that leads to the death of damaged cells. Its malfunction can cause cancer and poor response to conventional chemotherapy. After being activated by cellular stress signals, proapoptotic proteins bind antiapoptotic proteins, thus allowing apoptosis to go forward. An excess of antiapoptotic proteins can prevent apoptosis. Designed molecules that mimic the roles of proapoptotic proteins can promote the death of cancer cells. The goal of our study was to create new putative mimetics that could simultaneously bind several antiapoptotic proteins. Five new small molecules were designed that formed stable complexes with BCL-2, BCL-XL, and MCL-1 antiapoptotic proteins. These results are novel because, to our knowledge, there are not many, if any, small molecules known to bind all three proteins. Drug-likeness studies performed on the designed molecules, as well as previous experimental and preclinical studies on similar agents, strongly suggest that the designed molecules may indeed be promising drug candidates. All five molecules showed “drug-like” properties and had overall drug-likeness scores between 81% and 96%. A single drug based on these mimetics should cost less and cause fewer side effects than a combination of drugs each aimed at a single protein. Computer-based molecular design promises to accelerate drug research by predicting potential effectiveness of designed molecules prior to laborious experiments and costly preclinical trials.
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Affiliation(s)
- D S Dalafave
- Physics Department, The College of New Jersey, Ewing, NJ, USA
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Jiang YL, Patel P, Klein SM. A fluorescein-containing, small-molecule, water-soluble receptor for cytosine free bases. Bioorg Med Chem 2010; 18:7034-42. [PMID: 20801661 DOI: 10.1016/j.bmc.2010.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/02/2010] [Accepted: 08/04/2010] [Indexed: 11/15/2022]
Abstract
In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using (15)N NMR spectroscopy and partially labeled cytosine-2,4-(13)C-1,3,4-(15)N-cytosine. Binding with the receptor 6a (the disodium form of 6) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.
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Affiliation(s)
- Yu Lin Jiang
- Department of Chemistry, College of Arts and Sciences, East Tennessee State University, Johnson City, TN 37614, United States.
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23
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Barelier S, Pons J, Marcillat O, Lancelin JM, Krimm I. Fragment-based deconstruction of Bcl-xL inhibitors. J Med Chem 2010; 53:2577-88. [PMID: 20192224 DOI: 10.1021/jm100009z] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based drug design consists of screening low-molecular-weight compounds in order to identify low-affinity ligands that are then modified or linked to yield potent inhibitors. The method thus attempts to build bioactive molecules in a modular way and relies on the hypothesis that the fragment binding mode will be conserved upon elaboration of the active molecule. If the inverse process is considered, do the fragments resulting from the deconstruction of high-affinity inhibitors recapitulate their binding mode in the large molecule? Few studies deal with this issue. Here, we report the analysis of 22 fragments resulting from the dissection of 9 inhibitors of the antiapoptotic protein Bcl-x(L). To determine if the fragments retained affinity toward the protein and identify their binding site, ligand-observed and protein-observed NMR experiments were used. The analysis of the fragments behavior illustrates the complexity of low-affinity protein-ligand interactions involved in the fragment-based construction of bioactive molecules.
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Affiliation(s)
- Sarah Barelier
- Laboratoire des Sciences Analytiques, UMR CNRS 5180, Universite de Lyon, Universite Claude Bernard, Lyon 1, Bat ESCPE Lyon, Domaine Scientifique de la Doua, 69100 Villeurbanne, France
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24
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Multicomponent synthesis of dihydrobenzoxazepinones, bearing four diversity points, as potential α-helix mimics. Mol Divers 2009; 14:425-42. [DOI: 10.1007/s11030-009-9210-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 10/24/2009] [Indexed: 10/20/2022]
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Lee EF, Czabotar PE, Yang H, Sleebs BE, Lessene G, Colman PM, Smith BJ, Fairlie WD. Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind ligands. J Biol Chem 2009; 284:30508-17. [PMID: 19726685 DOI: 10.1074/jbc.m109.040725] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antagonists of anti-apoptotic Bcl-2 family members hold promise as cancer therapeutics. Apoptosis is triggered when a peptide containing a BH3 motif or a small molecule BH3 peptidomimetic, such as ABT 737, binds to the relevant Bcl-2 family members. ABT-737 is an antagonist of Bcl-2, Bcl-x(L), and Bcl-w but not of Mcl-1. Here we describe new structures of mutant BH3 peptides bound to Bcl-x(L) and Mcl-1. These structures suggested a rationale for the failure of ABT-737 to bind Mcl-1, but a designed variant of ABT-737 failed to acquire binding affinity for Mcl-1. Rather, it was selective for Bcl-x(L), a result attributable in part to significant backbone refolding and movements of helical segments in its ligand binding site. To date there are few reported crystal structures of organic ligands in complex with their pro-survival protein targets. Our structure of this new organic ligand provided insights into the structural transitions that occur within the BH3 binding groove, highlighting significant differences in the structural properties of members of the Bcl-2 pro-survival protein family. Such differences are likely to influence and be important in the quest for compounds capable of selectively antagonizing the different family members.
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Affiliation(s)
- Erinna F Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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