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Prakash M, Itoh Y, Fujiwara Y, Takahashi Y, Takada Y, Mellini P, Elboray EE, Terao M, Yamashita Y, Yamamoto C, Yamaguchi T, Kotoku M, Kitao Y, Singh R, Roy R, Obika S, Oba M, Wang DO, Suzuki T. Identification of Potent and Selective Inhibitors of Fat Mass Obesity-Associated Protein Using a Fragment-Merging Approach. J Med Chem 2021; 64:15810-15824. [PMID: 34727689 DOI: 10.1021/acs.jmedchem.1c01107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fat mass obesity-associated protein (FTO) is a DNA/RNA demethylase involved in the epigenetic regulation of various genes and is considered a therapeutic target for obesity, cancer, and neurological disorders. Here, we aimed to design novel FTO-selective inhibitors by merging fragments of previously reported FTO inhibitors. Among the synthesized analogues, compound 11b, which merges key fragments of Hz (3) and MA (4), inhibited FTO selectively over alkylation repair homologue 5 (ALKBH5), another DNA/RNA demethylase. Treatment of acute monocytic leukemia NOMO-1 cells with a prodrug of 11b decreased the viability of acute monocytic leukemia cells, increased the level of the FTO substrate N6-methyladenosine in mRNA, and induced upregulation of MYC and downregulation of RARA, which are FTO target genes. Thus, Hz (3)/MA (4) hybrid analogues represent an entry into a new class of FTO-selective inhibitors.
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Affiliation(s)
- Muthuraj Prakash
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukari Takahashi
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yuri Takada
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | - Paolo Mellini
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Elghareeb E Elboray
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Mitsuhiro Terao
- SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan
| | | | - Chika Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayuki Kotoku
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yuki Kitao
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Ritesh Singh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,Department of Chemistry, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer 305817, Rajasthan, India
| | - Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.,Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Makoto Oba
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.,Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.,SANKEN, Osaka University, Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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Waltemate J, Ivanov I, Ghasemi JB, Aghaee E, Daniliuc CG, Müller K, Prinz H. 10-(4-Phenylpiperazine-1-carbonyl)acridin-9(10H)-ones and related compounds: Synthesis, antiproliferative activity and inhibition of tubulin polymerization. Bioorg Med Chem Lett 2021; 32:127687. [PMID: 33212157 DOI: 10.1016/j.bmcl.2020.127687] [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: 10/13/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 10/23/2022]
Abstract
As part of our continuing search for potent inhibitors of tubulin polymerization, two novel series of 42 10-(4-phenylpiperazine-1-carbonyl)acridin-9(10H)-ones and N-benzoylated acridones were synthesized on the basis of a retrosynthetic approach. All newly synthesized compounds were tested for antiproliferative activity and interaction with tubulin. Several analogs potently inhibited tumor cell growth. Among the compounds tested, 10-(4-(3-methoxyphenyl)piperazine-1-carbonyl)acridin-9(10H)-one (17c) exhibited excellent growth inhibitory effects on 93 tumor cell lines, with an average GI50 value of 5.4 nM. We were able to show that the strong cytotoxic effects are caused by disruption of tubulin polymerization, as supported by the EBI (N,N'-Ethylenebis(iodoacetamide)) assay and the fact that the most potent inhibitors of cancer cell growth turned out to be the most efficacious tubulin polymerization inhibitors. Potencies were nearly comparable or superior to those of the antimitotic reference compounds. Closely related to this, the most active analogs inhibited cell cycling at the G2/M phase at concentrations down to 30 nM and induced apoptosis in K562 leukemia cells. We believe that our work not only proves the excellent suitability of the acridone scaffold for the design of potent tubulin polymerization inhibitors but also enables synthetic access to further potentially interesting N-acylated acridones.
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Affiliation(s)
- Jana Waltemate
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Corrensstraße 48, D-48149 Münster, Germany
| | - Igor Ivanov
- Oncolead GmbH & Co. KG, Zugspitzstraße 5, D-85757 Karlsfeld, Germany
| | - Jahan B Ghasemi
- Drug Design in Silico Lab, Chemistry Faculty, School of Sciences, University of Tehran, Teheran, Iran
| | - Elham Aghaee
- Drug Design in Silico Lab, Chemistry Faculty, School of Sciences, University of Tehran, Teheran, Iran
| | | | - Klaus Müller
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Corrensstraße 48, D-48149 Münster, Germany
| | - Helge Prinz
- Institute of Pharmaceutical and Medicinal Chemistry, Westphalian Wilhelms-University, Corrensstraße 48, D-48149 Münster, Germany.
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Wang Z, Song T, Feng Y, Guo Z, Fan Y, Xu W, Liu L, Wang A, Zhang Z. Bcl-2/MDM2 Dual Inhibitors Based on Universal Pyramid-Like α-Helical Mimetics. J Med Chem 2016; 59:3152-62. [PMID: 26982372 DOI: 10.1021/acs.jmedchem.5b01913] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
No α-helical mimetic that exhibits Bcl-2/MDM2 dual inhibition has been rationally designed due to the different helicities of the α-helixes at their binding interfaces. Herein, we extracted a one-turn α-helix-mimicking ortho-triarene unit from o-phenylene foldamers. Linking benzamide substrates with a rotatable C-N bond, we constructed a novel semirigid pyramid-like scaffold that could support its two-turn α-helix mimicry without aromatic stacking interactions and could adopt the different dihedral angles of the key residues of p53 and BH3-only peptides. On the basis of this universal scaffold, a series of substituent groups were installed to capture the key residues of both p53TAD and BimBH3 and balance the differences of the bulks between them. Identified by FP, ITC, and NMR spectroscopy, a compound 6e (zq-1) that directly binds to Mcl-1, Bcl-2, and MDM2 with balanced submicromolar affinities was obtained. Cell-based experiments demonstrated its antitumor ability through Bcl-2/MDM2 dual inhibition simultaneously.
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Affiliation(s)
- Ziqian Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Ting Song
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yingang Feng
- Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao 266101, People's Republic of China
| | - Zongwei Guo
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Yudan Fan
- School of Life Science and Technology, Dalian University of Technology , Dalian 116024, People's Republic of China
| | - Wenjie Xu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Lu Liu
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Anhui Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
| | - Zhichao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology , No. 158-89, Zhongshan Road, Dalian 116012, People's Republic of China
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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