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Abbas AA, Dawood KM. Anticancer therapeutic potential of benzofuran scaffolds. RSC Adv 2023; 13:11096-11120. [PMID: 37056966 PMCID: PMC10086673 DOI: 10.1039/d3ra01383a] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023] Open
Abstract
Benzofuran moiety is the main component of many biologically active natural and synthetic heterocycles. These heterocycles have unique therapeutic potentials and are involved in various clinical drugs. The reported results confirmed the extraordinary inhibitory potency of such benzofurans against a panel of human cancer cell lines compared with a wide array of reference anticancer drugs. Several publications about the anticancer potencies of benzofuran-based heterocycles were encountered. The recent developments of anticancer activities of both natural and synthetic benzofuran scaffolds during 2019-2022 are thoroughly covered. Many of the described benzofurans are promising candidates for development as anticancer agents based on their outstanding inhibitory potency against a panel of human cancer cells compared with reference anticancer drugs. These findings encourage medicinal chemists to explore new areas to improve human health and reduce suffering.
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Affiliation(s)
- Ashraf A Abbas
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt +20-2-35727556 +20-2-35676602
| | - Kamal M Dawood
- Department of Chemistry, Faculty of Science, Cairo University Giza 12613 Egypt +20-2-35727556 +20-2-35676602
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2
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Guo Y, Han Y, Li Z, Ji J, Zhu T, Du Y, Dong S. A new inhibitor of human peptide deformylase suppresses cell proliferation and induces cell apoptosis and autophagy in cancers. Anticancer Drugs 2023; 34:483-494. [PMID: 36730491 DOI: 10.1097/cad.0000000000001444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human peptide deformylase (hsPDF) has been found overexpressed in many cancer cells and its inhibitors exhibit antitumor activity. Studies were performed to validate that hsPDF is a good antitumor target. The inhibitory effect of PDF64 on hsPDF enzymatic activity was measured and confirmed by computation analysis. Antiproliferation activity was determined and in-vivo antitumor activity were analyzed in HCT116 and HL60 nude mice xenografts. Mitochondrial membrane potential (MMP), cell apoptosis, and autophagic cell death were analyzed by flow cytometry. ATP level was quantified using an ATP assay kit. Protein expression and kinase phosphorylation were determined by western blotting. A new hsPDF inhibitor PDF64 was identified. It showed evident antiproliferation activity in 10 cancer cells and significantly suppressed tumor growth in HCT116 and HL60 xenografts. It induced an obvious decrease in MMP and caused apparent cell apoptosis and autophagy in HCT116 and Jurkat cells. PDF64 treatment also led to an evident decrease in cellular ATP levels in these cells. Moreover, PDF64 downregulated c-Myc expression and had some effects on extracellular regulated protein kinases (ERK) and protein kinase B (Akt)/ mammalian target of rapamycin (mTOR) pathways. PDF64 exhibited good antitumor effects both in vivo and in vitro . It caused cell apoptosis and autophagic death in HCT116 and Jurkat cells. The effects may be mediated by inhibiting c-Myc expression and ERK or PI3K-Akt-mTOR pathway. Therefore, PDF64 may be a promising reagent for antitumor drug development, which further supports that hsPDF is a good antitumor drug target.
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Affiliation(s)
- Yanzhi Guo
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
| | - Yuqiao Han
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
| | - Ziyan Li
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
| | - Jiali Ji
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
| | - Tong Zhu
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
| | - Yijie Du
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Suzhen Dong
- Shanghai Engineering Research Centre of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University
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Design, one-pot synthesis, molecular docking study, and antibacterial evaluation of novel 2H-chromene based imidazo[1,2-a]pyridine derivatives as potent peptide deformylase inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Liu R, Zhang S, Huang M, Guo Z, Li L, Li M, Wu L, Guan Q, Zhang W. Design, synthesis and bioevaluation of 2,7-diaryl-pyrazolo[1,5-a]pyrimidines as tubulin polymerization inhibitors. Bioorg Chem 2021; 115:105220. [PMID: 34352709 DOI: 10.1016/j.bioorg.2021.105220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 11/26/2022]
Abstract
Two series of 2,7-diaryl-pyrazolo[1,5-a]pyrimidines as tubulin polymerization inhibitors were designed to restrict bioactive configuration of (E,Z)-vinylogous CA-4. All of the target compounds were synthesized and then evaluated for their in vitro antiproliferative activities against three cancer cell lines (MCF-7, SGC-7901 and A549). Among them, 6d exhibited the most potent antiproliferative activity against the MCF-7 with IC50 value of 0.047 μM. Moreover, 6d significantly inhibited tubulin polymerization, disrupted microtubule networks, arrested cell cycle at G2/M phase, induced apoptosis and hindered cancer cell migration. Colchicine competition assay and molecular docking studies suggested that 6d could interact with tubulin by binding to the colchicine site.
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Affiliation(s)
- Runlai Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Shuai Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Mingxin Huang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Zhenpeng Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Long Li
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Mi Li
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Lan Wu
- Department of Geratology, The First Affiliated Hospital, Chinese Medical University, Shenyang 110001, China.
| | - Qi Guan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
| | - Weige Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
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5
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Identification of ortho-naphthoquinones as anti-AML agents by highly efficient oxidation of phenols. Bioorg Chem 2019; 86:97-102. [DOI: 10.1016/j.bioorg.2019.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/12/2019] [Accepted: 01/12/2019] [Indexed: 01/07/2023]
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6
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Watanabe K, Mino T, Masuda C, Yoshida Y, Sakamoto M. Synthesis of 7-Allylated Benzofuran Derivatives from o-
Allyloxyethynylbenzene via Claisen Rearrangement and TBAF-Catalyzed Annulation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Kohei Watanabe
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Takashi Mino
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Chihiro Masuda
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Yasushi Yoshida
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Masami Sakamoto
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33, Yayoi-cho, Inage-ku Chiba 263-8522 Japan
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7
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Watanabe K, Mino T, Ishikawa E, Masuda C, Yoshida Y, Sakamoto M. Hydrazone–Pd-catalyzed direct intermolecular reaction of o-alkynylphenols with allylic acetates. Org Biomol Chem 2018; 16:575-584. [DOI: 10.1039/c7ob02873c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The hydrazone–palladium catalyzed direct intermolecular reaction of o-alkynylphenols with allylic acetates gave the corresponding 2-substituted-3-allylbenzofuran derivatives at room temperature.
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Affiliation(s)
- Kohei Watanabe
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Takashi Mino
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
- Molecular Chirality Research Center
| | - Eri Ishikawa
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Chihiro Masuda
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Yasushi Yoshida
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
- Molecular Chirality Research Center
| | - Masami Sakamoto
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
- Molecular Chirality Research Center
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8
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Affiliation(s)
- Kolluru Srinivas
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Chepuri V. Ramana
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Srinivas K, Sharma R, Ramana CV. Interrupting Base-Mediated Benzofuran Ring Transformation with Michael Acceptors. J Org Chem 2017; 82:9816-9823. [PMID: 28819976 DOI: 10.1021/acs.joc.7b01267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple two-stage approach for the synthesis of 3-(2-arylbenzofuran-3-yl)propanoates and propanamides has been developed employing simple acrylates and acrylamides and readily available 3-aroylbenzofurans. The key step of this process involves a base-mediated ring opening of the 3-aroylbenzofurans and subsequent Michael addition of the resulting 1,3-dicarbonyl intermediate with acrylate/acrylamide, followed by the deformylation in one-pot. The resulting products undergo an acid-mediated dehydrative cyclization to arrive at these targets.
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Affiliation(s)
- Kolluru Srinivas
- Division of Organic Chemistry, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Rashmi Sharma
- Division of Organic Chemistry, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Chepuri V Ramana
- Division of Organic Chemistry, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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Srinivas K, Dangat Y, Kommagalla Y, Vanka K, Ramana CV. Electronic Control on Linear versus Branched Alkylation of 2-/3-Aroylbenzofurans with Acrylates: Combined DFT and Synthetic Studies. Chemistry 2017; 23:7570-7581. [PMID: 28370600 DOI: 10.1002/chem.201700643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/14/2023]
Abstract
Investigations on the factors that govern unusual branched alkylation of 2-aroylbenzofurans with acrylates by Ru-catalyzed carbonyl-directed C-H activation has been carried out by calculating the kinetics associated with the two key steps-the coordination of the acrylate with the intermediate ruthenacycle and the subsequent migratory insertion reaction-studied with the help of DFT calculations. Eight possible orientations for each mode of alkylation have been considered for the calculations. From these calculations, it has been understood that there is a synergistic operation of the steric and electronic effects favoring the branched alkylation. Further DFT investigations on the alkylation of the isomeric 3-aroylbenzofurans indicated a preference for the linear alkylation and this has been verified experimentally. Overall, the observed/calculated complementary selectivity in the alkylation of 2-/3-aroylbenzofurans with acrylates reveals that the substrate-dependent charge distribution of the Ru-C bond in the intermediate ruthenacycle is an important determining factor and thus the current work opens up a new domain of substrate design for controlling regioselectivity.
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Affiliation(s)
- Kolluru Srinivas
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Yuvraj Dangat
- Division of Physical and Materials Chemistry, CSIR-National Chemical Laboratory, Pune-, 411008, India
| | - Yadagiri Kommagalla
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Kumar Vanka
- Division of Physical and Materials Chemistry, CSIR-National Chemical Laboratory, Pune-, 411008, India
| | - Chepuri V Ramana
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411008, India
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Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer. Molecules 2016; 21:396. [PMID: 27023495 PMCID: PMC6273975 DOI: 10.3390/molecules21040396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
Abstract
Human peptide deformylase (HsPDF) is an important target for anticancer drug discovery. In view of the limited HsPDF, inhibitors were reported, and high-throughput virtual screening (HTVS) studies based on HsPDF for developing new PDF inhibitors remain to be reported. We reported here on diverse small molecule inhibitors with excellent anticancer activities designed based on HTVS and molecular docking studies using the crystal structure of HsPDF. The compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC50s of 35.26, 29.63 and 24.63 μM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with HsPDF by several conserved hydrogen bonds. Moreover, the pharmacokinetic and toxicity properties of M7594_0037 and its derivatives were predicted using the OSIRIS property explorer. Thus, M7594_0037 and its derivatives might represent a promising scaffold for the further development of novel anticancer drugs.
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Watanabe K, Mino T, Ikematsu T, Hatta C, Yoshida Y, Sakamoto M. Hydrazone–palladium catalyzed annulation of 1-cinnamyloxy-2-ethynylbenzene derivatives. Org Chem Front 2016. [DOI: 10.1039/c6qo00112b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The annulation of 1-cinnamyloxy-2-ethynylbenzene derivatives using a hydrazone–palladium catalyst system proceeded smoothly and gave the corresponding 2-substituted-3-cinnamylbenzofurans in good-to-excellent yields.
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Affiliation(s)
- Kohei Watanabe
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Takashi Mino
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Tatsuya Ikematsu
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Chikako Hatta
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Yasushi Yoshida
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Masami Sakamoto
- Department of Applied Chemistry and Biotechnology
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
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Khanam H, Shamsuzzaman. Bioactive Benzofuran derivatives: A review. Eur J Med Chem 2015; 97:483-504. [DOI: 10.1016/j.ejmech.2014.11.039] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 12/13/2022]
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Lee SJ, Jung OS, Lee BJ, Cho KH, Lee BI. Identification of Potent Inhibitors against Human Peptide Deformylase as Anticancer Agents. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.12.3885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Randhawa H, Chikara S, Gehring D, Yildirim T, Menon J, Reindl KM. Overexpression of peptide deformylase in breast, colon, and lung cancers. BMC Cancer 2013; 13:321. [PMID: 23815882 PMCID: PMC3722014 DOI: 10.1186/1471-2407-13-321] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 06/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. Methods The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. Results PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. Conclusions This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation.
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Affiliation(s)
- Harsharan Randhawa
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
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Abdel-Aziz HA, Ahmad P, Kadi A, Al-Rashood KA, Ghabbour HA, Fun HK. Unexpected ring-opening of 3-aroylbenzo[b]furans at room temperature: a new route for the construction of phenol-substituted pyrazoles. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.04.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lee SJ, Lee SJ, Lee SK, Yoon HJ, Lee HH, Kim KK, Lee BJ, Lee BI, Suh SW. Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:784-93. [PMID: 22751663 DOI: 10.1107/s0907444912011912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 03/19/2012] [Indexed: 01/02/2023]
Abstract
Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse-hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory-tract infections, such as Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae, and leading nosocomial pathogens such as Staphylococcus aureus and Klebsiella pneumoniae with a minimum inhibitory concentration (MIC) in the range 0.1-0.8 mg ml(-1). Interestingly, the reverse-hydroxamate/nonpeptide compounds showed a 250-fold higher antimicrobial activity towards S. aureus, although the four compounds showed similar K(i) values against S. aureus PDF enzymes, with K(i) values in the 11-85 nM range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of S. aureus PDF in complex with the four inhibitors were determined at resolutions of 1.90-2.30 Å. The inhibitor-bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn(2+) ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse-hydroxamate inhibitors) appears to be correlated to S. aureus inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.
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Affiliation(s)
- Sang Jae Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-749, Republic of Korea
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