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Qandeel BM, Mowafy S, Abouzid K, Farag NA. Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations. BMC Chem 2024; 18:14. [PMID: 38245752 PMCID: PMC10800075 DOI: 10.1186/s13065-023-01110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.
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Affiliation(s)
- Basma M Qandeel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt
| | - Khaled Abouzid
- Department of Pharmaceutical Chemistry, College of Pharmacy, Ain-Shams University, Abbasia, 11566, Egypt
| | - Nahla A Farag
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
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2
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Komogortsev AN, Lichitskii BV, Melekhina VG. 1,1'-Carbonyldiimidazole-mediated transformation of allomaltol containing hydrazides into substituted 3-acetyltetronic acids. Org Biomol Chem 2023; 21:7224-7230. [PMID: 37642509 DOI: 10.1039/d3ob01136d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
For the first time, the reaction of allomaltol containing hydrazides with 1,1'-carbonyldiimidazole (CDI) was studied. It was shown that under the considered conditions, 3-hydroxy-4-pyranone derivatives were transformed into 3-acetyltetronic acids bearing a pyrrolidin-2-one moiety. We have found that the key intermediates of the investigated process are substituted 6-oxa-1-azaspiro[4.5]dec-7-ene-2,9-diones. The structures of one final product and one intermediate were confirmed by X-ray analysis. The disclosed reaction was tested using a wide range of substituted allomaltols with various carboxamide units. It was demonstrated that in the case of hetaryl containing hydrazides and hydroxamic acids, the direction of the process is completely changed and cyclization into substituted pyrano[3,2-b]pyrans occurs.
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Affiliation(s)
- Andrey N Komogortsev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
| | - Boris V Lichitskii
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
| | - Valeriya G Melekhina
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
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3
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Li M, Chen Y, Wang L, Lu C, Chen P, Jin Y, Li J, Gao F, Shang Z, Lin W. Investigations into the antibacterial effects and potential mechanism of gambogic acid and neogambogic acid. Front Microbiol 2022; 13:1045291. [PMID: 36578570 PMCID: PMC9791066 DOI: 10.3389/fmicb.2022.1045291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
The growing threat of antibiotic-resistant bacterial infections to public health necessitates the development of novel antibacterial agents. Inhibiting bacterial cell wall synthesis has remained a key focus for antibiotic development. Our search for inhibitors of undecaprenyl diphosphate synthase (UPPS), an essential enzyme required for bacterial cell wall formation, revealed that two primary components of gamboge, gambogic acid (GA) and neogambogic acid (NGA), significantly inhibited the activity of Enterococcus faecalis UPPS (EfaUPPS) with the half maximal inhibitory concentrations (IC50) of 3.08 μM and 3.07 μM, respectively. In the in vitro antibacterial assay, both GA and NGA also exhibited inhibitory activities against E. faecalis with the minimal inhibitory concentrations (MICs) of 2 μg/mL. Using microscale thermophoresis, molecular docking, and enzymatic assays, we further confirmed that GA and NGA occupy the substrate binding pocket of EfaUPPS with micro-molar binding affinity, preventing the natural substrates farnesyl diphosphate (FPP) from entering. Mutagenesis analysis revealed that L91 and L146 are two key residues in the binding between GA/NGA and UPPS. Furthermore, we also demonstrated that GA and NGA can improve E. faecalis-induced undesirable inflammation in a mouse infection model. Taken together, our findings provide a basis for structural optimization of GA/NGA to develop improved antibiotic leads and enhance treatment success rates in clinical practice.
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Affiliation(s)
- Mingzhu Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China,*Correspondence: Yuan Chen,
| | - Lijuan Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chujie Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peiying Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanling Jin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiacong Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fei Gao
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- School of Pharmaeutical Sciences, Shandong University, Jinan, China,Zhuo Shang,
| | - Wei Lin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Nanjing, China,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Nanjing, China,Wei Lin,
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4
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Discovery, total syntheses and potent anti-inflammatory activity of pyrrolinone-fused benzoazepine alkaloids Asperazepanones A and B from Aspergillus candidus. Commun Chem 2022; 5:80. [PMID: 36697682 PMCID: PMC9814288 DOI: 10.1038/s42004-022-00696-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/27/2022] [Indexed: 01/28/2023] Open
Abstract
Natural products are well established as an important resource and play an important role in drug discovery. Here, two pyrrolinone-fused benzoazepine alkaloids, (+)-asperazepanones A (1) and B (2) with a 6/7/5 ring system, together with the artifact (-)-asperazepanone A (1), were isolated from the coral-derived Aspergillus candidus fungus. Their structures including absolute configurations were elucidated by extensive spectroscopic methods, single crystal X-ray diffraction, and ECD calculations. Furthermore, total syntheses of (±)-1 and (±)-2 have been achieved starting from the commercially L-aspartic acid diethyl ester hydrochloride and monoethyl malonate in 7 and 8 steps, respectively. The key step in the syntheses was an intramolecular Friedel-Crafts reaction to build the unique tricyclic skeleton. Interestingly, (+)-2 not only showed obviously inhibitory activity against NO production, but also inhibited potent LPS-induced expression of TNF-α and IL-6 at the concentration of 0.1 μM. It thus represents a potentially promising lead for anti-inflammatory drug discovery.
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5
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Zhang R, Genov M, Pretsch A, Pretsch D, Moloney MG. Mediation of metal chelation in cysteine-derived tetramate systems. Chem Sci 2021; 12:16106-16122. [PMID: 35024133 PMCID: PMC8672780 DOI: 10.1039/d1sc05542a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
A study of bicyclic tetramates modified with a bulky ester, which leads to steric hindrance of distal chelating atoms as a route for the alteration of metal binding ability is reported. This approach required the development of a direct method for the synthesis of different esters of cysteine from cystine, which then provided access to bicyclic tetramates by Dieckmann cyclisation. Further derivation to ketones and carboxamides by Grignard addition and transamination reactions respectively provided rapid access to a chemical library of tetramates with diverse substitution. Of interest is that bicyclic tetramate ketones and carboxamides showed different tautomeric and metal binding behaviour in solution. Significantly, in both systems, the incorporation of bulky C-5 esters at the bridging position not only reduced metal binding, but also enhanced antibacterial potencies against Gram-positive MRSA bacteria. Those tetramates with antibacterial activity which was not metal dependent showed physiochemical properties of MSA of 559-737 Å2, MW of 427-577 Da, clogP of 1.8-6.1, clogD7.4 of -1.7 to 3.7, PSA of 83-109 Å2 and relative PSA of 12-15% and were generally Lipinski rule compliant. A subset of tetramates exhibited good selectivity towards prokaryotic bacterial cells. Given that the work reported herein is synthesis-led, without the underpinning detailed mechanistic understanding of biological/biochemical mechanism, that the most active compounds occupy a small region of chemical space as defined by MW, clogP, PSA and %PSA is of interest. Overall, the bicyclic tetramate template is a promising structural motif for the development of novel antibacterial drugs, with good anti-MRSA potencies and appropriate drug-like physiochemical properties, coupled with a potential for multi-targeting mechanisms and low eukaryotic cytotoxicity.
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Affiliation(s)
- Ruirui Zhang
- The Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Miroslav Genov
- Oxford Antibiotic Group The Oxford Science Park, Magdalen Centre Oxford OX4 4GA UK
| | - Alexander Pretsch
- Oxford Antibiotic Group The Oxford Science Park, Magdalen Centre Oxford OX4 4GA UK
| | - Dagmar Pretsch
- Oxford Antibiotic Group The Oxford Science Park, Magdalen Centre Oxford OX4 4GA UK
| | - Mark G Moloney
- The Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK .,Oxford Suzhou Centre for Advanced Research Building A, 388 Ruo Shui Road, Suzhou Industrial Park Jiangsu 215123 P. R. China
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6
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Princiotto S, Jayasinghe L, Dallavalle S. Recent advances in the synthesis of naturally occurring tetronic acids. Bioorg Chem 2021; 119:105552. [PMID: 34929518 DOI: 10.1016/j.bioorg.2021.105552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
During the last decades the interest towards natural products containing the tetronic acid moiety augmented significantly, due to their challenging structures and to the wide range of biological activities they display. This increasing enthusiasm has led to noteworthy advances in the development of innovative methodologies for the construction of the butenolide nucleus. This review provides an overview of the progress in the synthesis of tetronic acid as a structural key motif of natural compounds, covering the last 15 years. Herein, the most representative synthetic pathways towards structurally diverse natural tetronic acids are grouped according to the strategy followed. The first part describes the functionalization of a preformed tetronic acid core by intermolecular reactions (cross-coupling reactions, nucleophilic substitution, multicomponent reactions) whereas the second part deals with intramolecular approaches (Dieckmann, cycloaddition or ring expansion reactions) to construct the heterocyclic core. This rational subcategorization allowed us to make some considerations about the best approaches for the synthesis of specific substrates, including modern intriguing methodologies such as microwave irradiation, solid phase anchoring, bio-transformations and continuous flow processes.
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Affiliation(s)
- Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
| | | | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy; National Institute of Fundamental Studies, Kandy 20000, Sri Lanka.
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7
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Poliseno V, Chaves S, Brunetti L, Loiodice F, Carrieri A, Laghezza A, Tortorella P, Magalhães JD, Cardoso SM, Santos MA, Piemontese L. Derivatives of Tenuazonic Acid as Potential New Multi-Target Anti-Alzheimer's Disease Agents. Biomolecules 2021; 11:111. [PMID: 33467709 PMCID: PMC7830597 DOI: 10.3390/biom11010111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is generally recognized as a multifactorial neurodegenerative pathology with an increasing impact on society. Tenuazonic acid (TA) is a natural compound that was recently identified as a potential multitarget ligand with anti-cholinesterase, anti-amyloidogenic and antioxidant activities. Using its structure as a chemical scaffold, we synthesized and evaluated new derivatives (1-5), including tenuazonic-donepezil (TA-DNP) hybrids (4 and 5) due to the clinical importance of the anti-AD drug donepezil. These novel compounds all achieved activity in the micromolar range towards all selected targets and demonstrated to be potentially orally absorbed. Moreover, a selected compound (1) was further investigated as a chelating agent towards copper (II), zinc (II) and iron (III) and showed good chelating ability (pFe = 16.6, pCu = 11.6, pZn = 6.0 at pH 7.4). Therefore, the TA motif can be considered an interesting building block in the search for innovative multi-functional anti-neurodegenerative drugs, as exemplified by hybrid 5, a promising non-cytotoxic lead compound adequate for the early stages of AD, and capable of ameliorating the oxidative status of SH-SY5Y human neuroblastoma cells.
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Affiliation(s)
- Viviana Poliseno
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Sílvia Chaves
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Leonardo Brunetti
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
| | - Fulvio Loiodice
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
| | - Antonio Carrieri
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
| | - Antonio Laghezza
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
| | - Paolo Tortorella
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
| | - João D. Magalhães
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.D.M.); (S.M.C.)
| | - Sandra M. Cardoso
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (J.D.M.); (S.M.C.)
- Institute of Molecular and Cell Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - M. Amélia Santos
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Luca Piemontese
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari “A. Moro”, via E. Orabona 4, 70125 Bari, Italy; (V.P.); (L.B.); (F.L.); (A.C.); (A.L.); (P.T.)
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8
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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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9
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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10
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Chen M, Lu AM, Hu Y, Yang CL. QSAR studies of phenylhydrazine-substituted tetronic acid derivatives based on the 1 H NMR and 13 C NMR chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:285-293. [PMID: 30632625 DOI: 10.1002/mrc.4830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/27/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
The quantitative structure-activity relationship models of 40 phenylhydrazine-substituted tetronic acid derivatives were established between the 1 H nuclear magnetic resonance (NMR) and 13 C NMR chemical shifts and the antifungal activity against Fusarium graminearum, Botrytis cinerea, Rhizoctonia cerealis, and Colletotrichum capsici. The models were validated by R, R2 , RA2 , variance inflation factor, F, and P values testing and residual analysis. It was concluded from the models that the 13 C NMR chemical shifts of C8, C10, C7, and the 1 H NMR chemical shifts of Ha contributed positively to the activity against Fusarium graminearum, Botrytis cinerea, Colletotrichum capsici, and Rhizoctonia cerealis, respectively. The models indicated that decreasing the election cloud density of specific nucleuses in compounds, for example, by the substituting of electron withdrawing groups, would improve the antifungal activity. These models demonstrated the practical application meaning of chemical shifts in the quantitative structure-activity relationship study. Furthermore, a practical guide was provided for further structural optimization of the antifungal phenylhydrazine-substituted tetronic acid derivatives based on the 1 H NMR and 13 C NMR chemical shifts.
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Affiliation(s)
- Min Chen
- Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory of Pesticide Science, Nanjing Agricultural University, Nanjing, China
| | - Ai-Min Lu
- Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory of Pesticide Science, Nanjing Agricultural University, Nanjing, China
| | - Ying Hu
- Project Department, Changzhou Yuangu Intellectual Property Agency Ltd, Changzhou, China
| | - Chun-Long Yang
- Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Key Laboratory of Pesticide Science, Nanjing Agricultural University, Nanjing, China
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11
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Jukič M, Rožman K, Sova M, Barreteau H, Gobec S. Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis. Front Microbiol 2019; 9:3322. [PMID: 30692977 PMCID: PMC6339874 DOI: 10.3389/fmicb.2018.03322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report the successful implementation of virtual screening in the discovery of new inhibitors of undecaprenyl pyrophosphate synthase (UppS) from Escherichia coli. UppS is an essential enzyme in the biosynthesis of bacterial cell wall. It catalyzes the condensation of farnesyl pyrophosphate (FPP) with eight consecutive isopentenyl pyrophosphate units (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate. The latter serves as a lipid carrier for peptidoglycan synthesis, thus representing an important target in the antibacterial drug design. A pharmacophore model was designed on a known bisphosphonate BPH-629 and used to prepare an enriched compound library that was further docked into UppS conformational ensemble generated by molecular dynamics experiment. The docking resulted in three anthranilic acid derivatives with promising inhibitory activity against UppS. Compound 2 displayed high inhibitory potency (IC50 = 25 μM) and good antibacterial activity against E. coli BW25113 ΔtolC strain (MIC = 0.5 μg/mL).
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Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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12
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New β-lactam - Tetramic acid hybrids show promising antibacterial activities. Bioorg Med Chem Lett 2018; 28:3105-3112. [PMID: 30097368 DOI: 10.1016/j.bmcl.2018.07.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 11/21/2022]
Abstract
β-Lactams are the most important class of antibiotics, for which the emergence of resistance threatens their utility. As such, we explored the extent to which the tetramic acid motif, frequently found in naturally occurring antibiotics, can be used to generate novel β-lactam antibiotics with improved antibacterial activity. We synthesized new ampicillin - tetramic acid, cephalosporin - tetramic acid, and cephamycin - tetramic acid analogs and evaluated their activities against problematic Gram-positive and Gram-negative pathogens. Amongst the analogs, a 7-aminocephalosporanic acid analog, 3397, and a 7-amino-3-vinyl cephalosporanic acid, 3436, showed potent activities against S. aureus NRS 70 (MRSA) with MICs of 6.25 μg/mL and 3.13 μg/mL respectively. These new analogs were ≥16-fold more potent than cefaclor and cephalexin. Additionally, a Δ2 cephamycin - tetramic acid analog 3474 which contained a basic guanidinium substituent at the 5-position of the tetramic acid core displayed potent activity against several clinical strains of K. pneumoniae and E. coli.
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13
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Dai W, Chen W, Debnath B, Wu Y, Neamati N. Synthesis, Structure–Activity Relationship Studies, and ADMET Properties of 3‐Aminocyclohex‐2‐en‐1‐ones as Chemokine Receptor 2 (CXCR2) Antagonists. ChemMedChem 2018; 13:916-930. [PMID: 29493096 DOI: 10.1002/cmdc.201800027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/23/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Weiyang Dai
- Department of Medicinal Chemistry, College of Pharmacy University of Michigan 1600 Huron Parkway Ann Arbor MI USA
- Key Laboratory of Drug Targeting and Drug Delivery, System of Ministry of Education, West China School of Pharmacy Sichuan University No. 17 People's South Road Chengdu 610041 P.R. China
| | - Wenmin Chen
- Department of Medicinal Chemistry, College of Pharmacy University of Michigan 1600 Huron Parkway Ann Arbor MI USA
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy University of Michigan 1600 Huron Parkway Ann Arbor MI USA
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery, System of Ministry of Education, West China School of Pharmacy Sichuan University No. 17 People's South Road Chengdu 610041 P.R. China
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy University of Michigan 1600 Huron Parkway Ann Arbor MI USA
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14
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Sadamitsu Y, Komatsuki K, Saito K, Yamada T. Access to Tetronic Acids via Silver-Catalyzed CO2 Incorporation into Conjugated Ynones. Org Lett 2017; 19:3191-3194. [DOI: 10.1021/acs.orglett.7b01309] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuta Sadamitsu
- Department of Chemistry, Keio University, 3-14-1
Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Keiichi Komatsuki
- Department of Chemistry, Keio University, 3-14-1
Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kodai Saito
- Department of Chemistry, Keio University, 3-14-1
Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Tohru Yamada
- Department of Chemistry, Keio University, 3-14-1
Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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15
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Wang Y, Desai J, Zhang Y, Malwal SR, Shin CJ, Feng X, Sun H, Liu G, Guo RT, Oldfield E. Bacterial Cell Growth Inhibitors Targeting Undecaprenyl Diphosphate Synthase and Undecaprenyl Diphosphate Phosphatase. ChemMedChem 2016; 11:2311-2319. [PMID: 27578312 PMCID: PMC5155509 DOI: 10.1002/cmdc.201600342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Indexed: 11/09/2022]
Abstract
We synthesized a series of benzoic acids and phenylphosphonic acids and investigated their effects on the growth of Staphylococcus aureus and Bacillus subtilis. One of the most active compounds, 5-fluoro-2-(3-(octyloxy)benzamido)benzoic acid (7, ED50 ∼0.15 μg mL-1 ) acted synergistically with seven antibiotics known to target bacterial cell-wall biosynthesis (a fractional inhibitory concentration index (FICI) of ∼0.35, on average) but had indifferent effects in combinations with six non-cell-wall biosynthesis inhibitors (average FICI∼1.45). The most active compounds were found to inhibit two enzymes involved in isoprenoid/bacterial cell-wall biosynthesis: undecaprenyl diphosphate synthase (UPPS) and undecaprenyl diphosphate phosphatase (UPPP), but not farnesyl diphosphate synthase, and there were good correlations between bacterial cell growth inhibition, UPPS inhibition, and UPPP inhibition.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Janish Desai
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Yonghui Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Satish R Malwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Christopher J Shin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Xinxin Feng
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Hong Sun
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Guizhi Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA.
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16
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Concha N, Huang J, Bai X, Benowitz A, Brady P, Grady LC, Kryn LH, Holmes D, Ingraham K, Jin Q, Pothier Kaushansky L, McCloskey L, Messer JA, O’Keefe H, Patel A, Satz AL, Sinnamon RH, Schneck J, Skinner SR, Summerfield J, Taylor A, Taylor JD, Evindar G, Stavenger RA. Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase. J Med Chem 2016; 59:7299-304. [DOI: 10.1021/acs.jmedchem.6b00746] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nestor Concha
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jianzhong Huang
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Xiaopeng Bai
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Andrew Benowitz
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Pat Brady
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - LaShadric C. Grady
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Luz Helena Kryn
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, North Carolina 27009, United States
| | - David Holmes
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Karen Ingraham
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Qi Jin
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | - Lynn McCloskey
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jeffrey A. Messer
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Heather O’Keefe
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Amish Patel
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Alexander L. Satz
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Robert H. Sinnamon
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jessica Schneck
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Steve R. Skinner
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | - Amy Taylor
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - J. David Taylor
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Ghotas Evindar
- GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Robert A. Stavenger
- GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
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17
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Han SJ, Stoltz BM. A mild and efficient approach to enantioenriched α-hydroxyethyl α,β-unsaturated δ-lactams. Tetrahedron Lett 2016; 57:2233-2235. [PMID: 27182092 DOI: 10.1016/j.tetlet.2016.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A straightforward approach toward enantioenriched α-substituted α,β-unsaturated δ-lactams is described. Although a considerable number of approches toward α,β-unsaturated δ-lactams have been reported, there are relatively few examples of enantioenriched α,δ-disubstituted α,β-unsaturated δ-lactams formation. The δ-stereocenter was formed by addition of allylmagnesium bromide to an N-tert-butylsulfinyl imine. The α,β-unsaturated δ-lactam was furnished by ring-closing metathesis. Although Baylis-Hillman chemistry failed on this cyclic compound, introduction of the hydroxyethyl group prior to ring-closing metathesis was successful. A Baylis-Hillman reaction was used to introduce the substituent at the α-position of the α,β-unsaturated lactam.
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Affiliation(s)
- Seo-Jung Han
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engi neering, California Institute of Technology, 1200 E California Boulevard, MC 101-20, Pasadena, CA 91125, USA
| | - Brian M Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engi neering, California Institute of Technology, 1200 E California Boulevard, MC 101-20, Pasadena, CA 91125, USA
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18
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Cherian PT, Deshpande A, Cheramie MN, Bruhn DF, Hurdle JG, Lee RE. Design, synthesis and microbiological evaluation of ampicillin-tetramic acid hybrid antibiotics. J Antibiot (Tokyo) 2016; 70:65-72. [PMID: 27189120 PMCID: PMC5116011 DOI: 10.1038/ja.2016.52] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/18/2016] [Indexed: 12/11/2022]
Abstract
Exploiting iron-uptake pathways by conjugating β-lactam antibiotics with iron-chelators such as catechol and hydroxamic acid is a proven strategy to overcome permeability-related resistance in Gram-negative bacteria. Since naturally occurring iron chelating tetramic acids have not been previously examined for this purpose, an exploratory series of novel ampicillin-tetramic acid hybrids that structurally resemble ureidopenicillins was designed and synthesized. The new analogs were evaluated for the ability to chelate iron and their MIC activities determined against a representative panel of clinically significant bacterial pathogens. The tetramic acid β-lactam hybrids demonstrated a high affinity to iron in the order of 10−30 M3. The hybrids were less active against Gram-positive bacteria. However, against Gram-negative bacteria, their activity was species dependent with several hybrids displaying improved activity over ampicillin against wild-type Pseudomonas aeruginosa. The anti-Gram-negative activities of the hybrids improved in the presence of clavulanic acid revealing that the tetramic acid moiety did not provide added protection against β-lactamases. Additionally, the hybrids were found to be efflux pump substrates as their activities markedly improved against pump-inactivated strains. Unlike the catechol and hydroxamic acid siderophore β-lactam conjugates, the activities of the hybrids did not improve under iron-deficient conditions. These results suggest that the tetramic acid hybrids gain permeability via different membrane receptors, or they are out competed by native bacterial siderophores with stronger affinities for iron. This study provides a foundation for the further exploitation of the tetramic acid moiety to achieve novel β-lactam anti-Gram-negative agents, providing that efflux and β-lactamase mediated resistance is addressed.
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Affiliation(s)
- Philip T Cherian
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Aditi Deshpande
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Martin N Cheramie
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David F Bruhn
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Julian G Hurdle
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.,Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College of Medicine, Bryan, TX, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA
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19
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Inokoshi J, Nakamura Y, Komada S, Komatsu K, Umeyama H, Tomoda H. Inhibition of bacterial undecaprenyl pyrophosphate synthase by small fungal molecules. J Antibiot (Tokyo) 2016; 69:798-805. [PMID: 27049441 DOI: 10.1038/ja.2016.35] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 02/09/2016] [Accepted: 02/17/2016] [Indexed: 11/09/2022]
Abstract
Viridicatumtoxin and spirohexaline, small fungal molecules with a tetracyclic scaffold and an additional spirobicyclic ring in common, were found to inhibit bacterial undecaprenyl pyrophosphate (UPP) synthase with IC50 values of 4 and 9 μm, respectively. These molecules showed weak inhibitory activity against catalytically related enzymes such as bacterial octaprenyl pyrophosphate synthase and yeast dehydrodolichyl pyrophosphate synthase, indicating that the compounds preferentially inhibit UPP synthase. They showed antimicrobial activity, particularly against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Furthermore, molecular modeling strongly suggested that the hydrophobic spirobicyclic ring of viridicatumtoxin interacts with three hydrophobic clefts of the active site in MRSA UPP synthase.
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Affiliation(s)
- Junji Inokoshi
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yuichiro Nakamura
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Saori Komada
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Katsuichiro Komatsu
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hideaki Umeyama
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Tomoda
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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20
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Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A 2015; 112:E7073-82. [PMID: 26644565 PMCID: PMC4697371 DOI: 10.1073/pnas.1521988112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is a growing need for new antibiotics. Compounds that target the proton motive force (PMF), uncouplers, represent one possible class of compounds that might be developed because they are already used to treat parasitic infections, and there is interest in their use for the treatment of other diseases, such as diabetes. Here, we tested a series of compounds, most with known antiinfective activity, for uncoupler activity. Many cationic amphiphiles tested positive, and some targeted isoprenoid biosynthesis or affected lipid bilayer structure. As an example, we found that clomiphene, a recently discovered undecaprenyl diphosphate synthase inhibitor active against Staphylococcus aureus, is an uncoupler. Using in silico screening, we then found that the anti-glioblastoma multiforme drug lead vacquinol is an inhibitor of Mycobacterium tuberculosis tuberculosinyl adenosine synthase, as well as being an uncoupler. Because vacquinol is also an inhibitor of M. tuberculosis cell growth, we used similarity searches based on the vacquinol structure, finding analogs with potent (∼0.5-2 μg/mL) activity against M. tuberculosis and S. aureus. Our results give a logical explanation of the observation that most new tuberculosis drug leads discovered by phenotypic screens and genome sequencing are highly lipophilic (logP ∼5.7) bases with membrane targets because such species are expected to partition into hydrophobic membranes, inhibiting membrane proteins, in addition to collapsing the PMF. This multiple targeting is expected to be of importance in overcoming the development of drug resistance because targeting membrane physical properties is expected to be less susceptible to the development of resistance.
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Affiliation(s)
- Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Wei Zhu
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | | | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Carolyn Shoen
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - Reese Hitchings
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Jikun Li
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Yang Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Noman Baig
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Tianhui Zhou
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Boo Kyung Kim
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Dean C Crick
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Michael Cynamon
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093;
| | - Robert B Gennis
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Department of Biochemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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21
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Meng T, Liu L, Jia H, Ren L, Feng C, Wang X, Zhao W. One-pot synthesis of 3,4-dihydropyridin-2-ones via tandem reaction of Blaise reactionintermediate and acrylic ester. Appl Organomet Chem 2015. [DOI: 10.1002/aoc.3399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tuanjie Meng
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Lantao Liu
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Huiyi Jia
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Lifeng Ren
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Cuilan Feng
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Xiaojuan Wang
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
| | - Wenxian Zhao
- Key Laboratory of New Organic Materials Synthesis; College of Chemistry and Chemical Engineering, Shangqiu Normal University; Shangqiu 476000 PR China
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22
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An efficient synthetic approach towards fully functionalized tetronic acids: the use of 1,3-dioxolane-2,4-diones as novel protected-activated synthons of α-hydroxy acids. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Cherian PT, Wu X, Yang L, Scarborough JS, Singh AP, Alam ZA, Lee RE, Hurdle JG. Gastrointestinal localization of metronidazole by a lactobacilli-inspired tetramic acid motif improves treatment outcomes in the hamster model of Clostridium difficile infection. J Antimicrob Chemother 2015; 70:3061-9. [PMID: 26286574 DOI: 10.1093/jac/dkv231] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/07/2015] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES Metronidazole, a mainstay treatment for Clostridium difficile infection (CDI), is often ineffective for severe CDI. Whilst this is thought to arise from suboptimal levels of metronidazole in the colon due to rapid absorption, empirical validation is lacking. In contrast, reutericyclin, an antibacterial tetramic acid from Lactobacillus reuteri, concentrates in the gastrointestinal tract. In this study, we modified metronidazole with reutericyclin's tetramic acid motif to obtain non-absorbed compounds, enabling assessment of the impact of pharmacokinetics on treatment outcomes. METHODS A series of metronidazole-bearing tetramic acid substituents were synthesized and evaluated in terms of anti-C. difficile activities, gastric permeability, in vivo pharmacokinetics, efficacy in the hamster model of CDI and mode of action. RESULTS Most compounds were absorbed less than metronidazole in cell-based Caco-2 permeability assays. In hamsters, lead compounds compartmentalized in the colon rather than the bloodstream with negligible levels detected in the blood, in direct contrast with metronidazole, which was rapidly absorbed into the blood and was undetectable in caecum. Accordingly, four leads were more efficacious (P < 0.05) than metronidazole in C. difficile-infected animals. Improved efficacy was not due to an alternative mode of action, as the leads retained the mode of action of metronidazole. CONCLUSIONS This study provides the clearest empirical evidence that the high absorption of metronidazole lowers treatment outcomes for CDI and suggests a role for the tetramic acid motif for colon-specific drug delivery. This approach also has the potential to lower systemic toxicity and drug interactions of nitroheterocyclic drugs for treating gastrointestine-specific diseases.
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Affiliation(s)
- Philip T Cherian
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoqian Wu
- Department of Biology, University of Texas, Arlington, TX 76019, USA Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jerrod S Scarborough
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Aman P Singh
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA Biomedical Sciences Program, Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zahidul A Alam
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Julian G Hurdle
- Department of Biology, University of Texas, Arlington, TX 76019, USA Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
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24
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Hu Y, Zhang LZ, Ren ZJ, Zhao Z, Xu WQ, Yang CL. Synthesis and Antifungal Activity of Novel Furan-2,4-dione Derivatives Containing Substituted Phenylhydrazine Moiety. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201400463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Jeong YC, Moloney MG. Antibacterial barbituric acid analogues inspired from natural 3-acyltetramic acids; synthesis, tautomerism and structure and physicochemical property-antibacterial activity relationships. Molecules 2015; 20:3582-627. [PMID: 25710842 PMCID: PMC6272196 DOI: 10.3390/molecules20033582] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/05/2015] [Accepted: 02/12/2015] [Indexed: 12/13/2022] Open
Abstract
The synthesis, tautomerism and antibacterial activity of novel barbiturates is reported. In particular, 3-acyl and 3-carboxamidobarbiturates exhibited antibacterial activity, against susceptible and some resistant Gram-positive strains of particular interest is that these systems possess amenable molecular weight, rotatable bonds and number of proton-donors/acceptors for drug design as well as less lipophilic character, with physicochemical properties and ionic states that are similar to current antibiotic agents for oral and injectable use. Unfortunately, the reduction of plasma protein affinity by the barbituric core is not sufficient to achieve activity in vivo. Further optimization to reduce plasma protein affinity and/or elevate antibiotic potency is therefore required, but we believe that these systems offer unusual opportunities for antibiotic drug discovery.
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Affiliation(s)
- Yong-Chul Jeong
- Chemistry Research Laboratory, Mansfield Rd, University of Oxford, OX1 3TA, UK.
| | - Mark G Moloney
- Chemistry Research Laboratory, Mansfield Rd, University of Oxford, OX1 3TA, UK.
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26
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Pelkey ET, Pelkey SJ, Greger JG. De Novo Synthesis of 3-Pyrrolin-2-Ones. ADVANCES IN HETEROCYCLIC CHEMISTRY 2015. [DOI: 10.1016/bs.aihch.2015.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Liu ZQ, Hu YJ, Chen XY, Wu Q, Lin XF. Enzymatic multicomponent reaction for simultaneous synthesis of two important scaffolds, pyridin-2-ones and α-alkylated nitriles. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des 2014; 85:756-69. [PMID: 25352216 DOI: 10.1111/cbdd.12463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/26/2014] [Accepted: 10/17/2014] [Indexed: 01/09/2023]
Abstract
With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS), are involved in bacterial cell wall biosynthesis, while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 μm inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC(50) ~0.5- to 20-μm inhibitor (depending on substrate) of cis-DPPS, a ~660-nm inhibitor of Rv3378c as well as a 4.8-μm inhibitor of cis-FPPS, opening up the possibility of multitarget inhibition involving both cell wall biosynthesis and virulence factor formation.
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Affiliation(s)
- Meekyum Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xinxin Feng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ferran Feixas
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wei Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Steffen Lindert
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shannon Bogue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - William Sinko
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - César de Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA, 92093, USA
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29
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Nielsen DU, Korsager S, Lindhardt AT, Skrydstrup T. A Palladium-Catalyzed Carbonylative-Deacetylative Sequence to 1,3-Keto Amides. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400545] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Liu YX, Cui ZP, Zhao HP, Li YH, Gu YC, Wang QM. Synthesis and Biological Activities of 3-Substituted Analogues of Tenuazonic Acid. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu-Xiu Liu
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Zhi-Peng Cui
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Hua-Ping Zhao
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Yong-Hong Li
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Yu-Cheng Gu
- Syngenta, Jealott's Hill International Research Centre; Bracknell Berks RG42 6EY United Kingdom
| | - Qing-Min Wang
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
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31
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Hu Y, Wang J, Lu A, Yang C. Synthesis, characterization, antifungal evaluation and 3D-QSAR study of phenylhydrazine substituted tetronic acid derivatives. Bioorg Med Chem Lett 2014; 24:3772-6. [DOI: 10.1016/j.bmcl.2014.06.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 11/25/2022]
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32
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Park J, Matralis AN, Berghuis AM, Tsantrizos YS. Human isoprenoid synthase enzymes as therapeutic targets. Front Chem 2014; 2:50. [PMID: 25101260 PMCID: PMC4106277 DOI: 10.3389/fchem.2014.00050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 06/25/2014] [Indexed: 12/14/2022] Open
Abstract
In the human body, the complex biochemical network known as the mevalonate pathway is responsible for the biosynthesis of all isoprenoids, which consists of a vast array of metabolites that are vital for proper cellular functions. Two key isoprenoids, farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) are responsible for the post-translational prenylation of small GTP-binding proteins, and serve as the biosynthetic precursors to numerous other biomolecules. The down-stream metabolite of FPP and GGPP is squalene, the precursor to steroids, bile acids, lipoproteins, and vitamin D. In the past, interest in prenyl synthase inhibitors focused mainly on the role of the FPP in lytic bone diseases. More recently pre-clinical and clinical studies have strongly implicated high levels of protein prenylation in a plethora of human diseases, including non-skeletal cancers, the progression of neurodegenerative diseases and cardiovascular diseases. In this review, we focus mainly on the potential therapeutic value of down-regulating the biosynthesis of FPP, GGPP, and squalene. We summarize the most recent drug discovery efforts and the structural data available that support the current on-going studies.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University Montreal, QC, Canada
| | | | - Albert M Berghuis
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology, McGill University Montreal, QC, Canada
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Chemistry, McGill University Montreal, QC, Canada
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33
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Dodbele S, Martinez CD, Troutman JM. Species differences in alternative substrate utilization by the antibacterial target undecaprenyl pyrophosphate synthase. Biochemistry 2014; 53:5042-50. [PMID: 25020247 PMCID: PMC4341984 DOI: 10.1021/bi500545g] [Citation(s) in RCA: 13] [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
![]()
Undecaprenyl pyrophosphate synthase
(UPPS) is a critical enzyme
required for the biosynthesis of polysaccharides essential for bacterial
survival. In this report, we have tested the substrate selectivity
of UPPS derived from the mammalian symbiont Bacteroides fragilis, the human pathogen Vibrio vulnificus, and the
typically benign but opportunistic pathogen Escherichia coli. An anthranilamide-containing substrate, 2-amideanilinogeranyl diphosphate
(2AA-GPP), was an effective substrate for only the B. fragilis UPPS protein, yet replacing the amide with a nitrile [2-nitrileanilinogeranyl
diphosphate (2CNA-GPP)] led to a compound that was fully functional
for UPPS from all three target organisms. These fluorescent substrate
analogues were also found to undergo increases in fluorescence upon
isoprenoid chain elongation, and this increase in fluorescence can
be utilized to monitor the activity and inhibition of UPPS in 96-well
plate assays. The fluorescence of 2CNA-GPP increased by a factor of
2.5-fold upon chain elongation, while that of 2AA-GPP increased only
1.2-fold. The 2CNA-GPP compound was therefore more versatile for screening
the activity of UPPS from multiple species of bacteria and underwent
a larger increase in fluorescence that improved its ability to detect
increases in chain length. Overall, this work describes the development
of new assay methods for UPPS and demonstrates the difference in substrate
utilization between forms of UPPS from different species, which has
major implications for UPPS inhibitor development, assay construction,
and the development of polysaccharide biosynthesis probes.
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Affiliation(s)
- Samantha Dodbele
- Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
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34
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Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem 2014; 57:5693-701. [PMID: 24827744 PMCID: PMC4096218 DOI: 10.1021/jm5004649] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is a significant need for new antibiotics due to the rise in drug resistance. Drugs such as methicillin and vancomycin target bacterial cell wall biosynthesis, but methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) have now arisen and are of major concern. Inhibitors acting on new targets in cell wall biosynthesis are thus of particular interest since they might also restore sensitivity to existing drugs, and the cis-prenyl transferase undecaprenyl diphosphate synthase (UPPS), essential for lipid I, lipid II, and thus, peptidoglycan biosynthesis, is one such target. We used 12 UPPS crystal structures to validate virtual screening models and then assayed 100 virtual hits (from 450,000 compounds) against UPPS from S. aureus and Escherichia coli. The most promising inhibitors (IC50 ∼2 μM, Ki ∼300 nM) had activity against MRSA, Listeria monocytogenes, Bacillus anthracis, and a vancomycin-resistant Enterococcus sp. with MIC or IC50 values in the 0.25-4 μg/mL range. Moreover, one compound (1), a rhodanine with close structural similarity to the commercial diabetes drug epalrestat, exhibited good activity as well as a fractional inhibitory concentration index (FICI) of 0.1 with methicillin against the community-acquired MRSA USA300 strain, indicating strong synergism.
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Affiliation(s)
- William Sinko
- Pharmacology Department, University of California San Diego , La Jolla, California 92093-0365, United States
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35
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Jeong YC, Bikadi Z, Hazai E, Moloney MG. A Detailed Study of Antibacterial 3-Acyltetramic Acids and 3-Acylpiperidine-2,4-diones. ChemMedChem 2014; 9:1826-37. [DOI: 10.1002/cmdc.201402093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 12/12/2022]
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36
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Manat G, Roure S, Auger R, Bouhss A, Barreteau H, Mengin-Lecreulx D, Touzé T. Deciphering the metabolism of undecaprenyl-phosphate: the bacterial cell-wall unit carrier at the membrane frontier. Microb Drug Resist 2014; 20:199-214. [PMID: 24799078 DOI: 10.1089/mdr.2014.0035] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
During the biogenesis of bacterial cell-wall polysaccharides, such as peptidoglycan, cytoplasmic synthesized precursors should be trafficked across the plasma membrane. This essential process requires a dedicated lipid, undecaprenyl-phosphate that is used as a glycan lipid carrier. The sugar is linked to the lipid carrier at the inner face of the membrane and is translocated toward the periplasm, where the glycan moiety is transferred to the growing polymer. Undecaprenyl-phosphate originates from the dephosphorylation of its precursor undecaprenyl-diphosphate, with itself generated by de novo synthesis or by recycling after the final glycan transfer. Undecaprenyl-diphosphate is de novo synthesized by the cytosolic cis-prenyltransferase undecaprenyl-diphosphate synthase, which has been structurally and mechanistically characterized in great detail highlighting the condensation process. In contrast, the next step toward the formation of the lipid carrier, the dephosphorylation step, which has been overlooked for many years, has only started revealing surprising features. In contrast to the previous step, two unrelated families of integral membrane proteins exhibit undecaprenyl-diphosphate phosphatase activity: BacA and members of the phosphatidic acid phosphatase type 2 super-family, raising the question of the significance of this multiplicity. Moreover, these enzymes establish an unexpected link between the synthesis of bacterial cell-wall polymers and other biological processes. In the present review, the current knowledge in the field of the bacterial lipid carrier, its mechanism of action, biogenesis, recycling, regulation, and future perspective works are presented.
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Affiliation(s)
- Guillaume Manat
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Université Paris Sud , Orsay Cedex, France
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37
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Liu YX, Cui ZP, Li YH, Gu YC, Wang QM. 3-Hydrazido and 3-Hydrazono Derivatives of Tenuazonic Acid and their Herbicide Evaluation. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.1939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yu-Xiu Liu
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 People's Republic of China
| | - Zhi-Peng Cui
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 People's Republic of China
| | - Yong-Hong Li
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 People's Republic of China
| | - Yu-Cheng Gu
- Syngenta, Jealott's Hill International Research Centre; Bracknell Berks RG42 6EY UK
| | - Qing-Min Wang
- State Key Laboratory of Elemento-Organic Chemistry, Research Institute of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 People's Republic of China
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38
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Kuznetsov NY, Khrustalev VN, Strelkova TV, Bubnov YN. Diastereoselective In and Zn-mediated allylation of pyrazol-4-yl derived (R)-tert-butanesulfinyl imines: synthesis of enantiomerically pure 6-(pyrazol-4-yl)-piperidin-2,4-diones. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.tetasy.2014.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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39
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Synthesis, antibiotic activity and structure–activity relationship study of some 3-enaminetetramic acids. Bioorg Med Chem Lett 2014; 24:1901-6. [DOI: 10.1016/j.bmcl.2014.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 01/31/2023]
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40
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Liu YX, Zhao HP, Song HB, Gu YC, Wang QM. Studies on the Synthesis and Bioactivities of 4-Amino Derivatives of Tetramic Acid. J Heterocycl Chem 2014. [DOI: 10.1002/jhet.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yu-Xiu Liu
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Hua-Ping Zhao
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Hai-Bin Song
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre; Bracknell Berkshire RG42 6EY UK
| | - Qing-Min Wang
- State Key Laboratory of Elemento-Organic Chemistry; Research Institute of Elemento-Organic Chemistry, Nankai University; Tianjin 300071 People's Republic of China
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41
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Leung CY, Park J, De Schutter JW, Sebag M, Berghuis AM, Tsantrizos YS. Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. J Med Chem 2013; 56:7939-50. [PMID: 23998921 DOI: 10.1021/jm400946f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Chun Yuen Leung
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Jaeok Park
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Joris W. De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Michael Sebag
- Division
of Haematology, McGill University Health Center, Royal Victoria Hospital, C6.80,
687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1
| | - Albert M. Berghuis
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Department of Microbiology and Immunology, McGill University, 801 Sherbrooke Street
West, Montreal, Quebec, Canada H3A 0B8
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Groupe de Recherche
Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir
William Osler, Montreal, Quebec, Canada H3G 0B1
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42
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Jeong YC, Moloney MG. Synthesis and antibacterial activity of monocyclic 3-carboxamide tetramic acids. Beilstein J Org Chem 2013; 9:1899-906. [PMID: 24204399 PMCID: PMC3817595 DOI: 10.3762/bjoc.9.224] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/23/2013] [Indexed: 11/23/2022] Open
Abstract
A chemical library of carboxamide-substituted tetramates designed by analogy with antibacterial natural products, a method for their rapid construction, and the evaluation of their antibacterial activity is reported.
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Affiliation(s)
- Yong-Chul Jeong
- Chemistry Research Laboratory, University of Oxford, Mansfield Rd, University of Oxford, OX1 3TA, UK
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43
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Reducing the Level of Undecaprenyl Pyrophosphate Synthase Has Complex Effects on Susceptibility to Cell Wall Antibiotics. Antimicrob Agents Chemother 2013; 57:4267-4275. [PMID: 23796923 DOI: 10.1128/aac.00794-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/14/2013] [Indexed: 01/09/2023] Open
Abstract
Undecaprenyl pyrophosphate synthase (UppS) catalyzes the formation of the C55 lipid carrier (UPP) that is essential for bacterial peptidoglycan biosynthesis. We selected here a vancomycin (VAN)-resistant derivative of Bacillus subtilis W168 that contains a single-point mutation in the ribosome-binding site of the uppS gene designated uppS1 Genetic reconstruction experiments demonstrate that the uppS1 allele is sufficient to confer low-level VAN resistance and causes reduced UppS translation. The decreased level of UppS renders B. subtilis slightly more susceptible to many late-acting cell wall antibiotics, including β-lactams, but significantly more resistant to fosfomycin and d-cycloserine, antibiotics that interfere with the very early steps of cell wall synthesis. We further show that the uppS1 allele leads to slightly elevated expression of the σM regulon, possibly helping to compensate for the stress caused by a decrease in UPP levels. Notably, the uppS1 mutation increases resistance to VAN, fosfomycin, and d-cycloserine in wild-type cells, but this effect is greatly reduced or eliminated in a sigM mutant background. Our findings suggest that, although UppS is an attractive antibacterial target, incomplete inhibition of UppS function may lead to increased resistance to some cell wall-active antibiotics.
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44
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Jeong YC, Anwar M, Bikadi Z, Hazai E, Moloney MG. Natural product inspired antibacterial tetramic acid libraries with dual enzyme inhibition. Chem Sci 2013. [DOI: 10.1039/c2sc21713a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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45
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He M, Pan Z, Bai S, Li P, Zhang Y, Jin L, Hu D, Yang S, Song B. Enantioselective synthesis of β-amino esters bearing a quinazoline moiety via a Mannich-type reaction catalyzed by a cinchona alkaloid derivative. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4822-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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46
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Anti-infectious agents against MRSA. Molecules 2012; 18:204-24. [PMID: 23262449 PMCID: PMC6269750 DOI: 10.3390/molecules18010204] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/03/2012] [Accepted: 12/14/2012] [Indexed: 11/17/2022] Open
Abstract
Clinically useful antibiotics, β-lactams and vancomycin, are known to inhibit bacterial cell wall peptidoglycan synthesis. Methicillin-resistant Staphylococcus aureus (MRSA) has a unique cell wall structure consisting of peptidoglycan and wall teichoic acid. In recent years, new anti-infectious agents (spirohexaline, tripropeptin C, DMPI, CDFI, cyslabdan, 1835F03, and BPH-652) targeting MRSA cell wall biosynthesis have been discovered using unique screening methods. These agents were found to inhibit important enzymes involved in cell wall biosynthesis such as undecaprenyl pyrophosphate (UPP) synthase, FemA, flippase, or UPP phosphatase. In this review, the discovery, the mechanism of action, and the future of these anti-infectious agents are described.
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47
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Abstract
With the rise in resistance to antibiotics such as methicillin, there is a need for new drugs. We report here the discovery and X-ray crystallographic structures of 10 chemically diverse compounds (benzoic, diketo, and phosphonic acids, as well as a bisamidine and a bisamine) that inhibit bacterial undecaprenyl diphosphate synthase, an essential enzyme involved in cell wall biosynthesis. The inhibitors bind to one or more of the four undecaprenyl diphosphate synthase inhibitor binding sites identified previously, with the most active leads binding to site 4, outside the catalytic center. The most potent leads are active against Staphylococcus aureus [minimal inhibitory concentration (MIC)(90) ∼0.25 µg/mL], and one potently synergizes with methicillin (fractional inhibitory concentration index = 0.25) and is protective in a mouse infection model. These results provide numerous leads for antibacterial development and open up the possibility of restoring sensitivity to drugs such as methicillin, using combination therapies.
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48
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Inokoshi J, Nakamura Y, Hongbin Z, Uchida R, Nonaka KI, Masuma R, Tomoda H. Spirohexalines, new inhibitors of bacterial undecaprenyl pyrophosphate synthase, produced by Penicillium brasilianum FKI-3368. J Antibiot (Tokyo) 2012; 66:37-41. [DOI: 10.1038/ja.2012.83] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Structures, mechanisms and inhibitors of undecaprenyl diphosphate synthase: A cis-prenyltransferase for bacterial peptidoglycan biosynthesis. Bioorg Chem 2012; 43:51-7. [DOI: 10.1016/j.bioorg.2011.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/13/2011] [Accepted: 09/15/2011] [Indexed: 12/20/2022]
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50
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Teng KH, Liang PH. Undecaprenyl diphosphate synthase, a cis-prenyltransferase synthesizing lipid carrier for bacterial cell wall biosynthesis. Mol Membr Biol 2012; 29:267-73. [PMID: 22471620 DOI: 10.3109/09687688.2012.674162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A group of prenyltransferases produce linear lipids by catalyzing consecutive condensation reactions of farnesyl diphosphate (FPP) with specific numbers of isopentenyl diphosphate (IPP), a common building block of isoprenoid compounds. Depending on the stereochemistry of the double bonds formed during IPP condensation, these prenyltransferases are categorized as cis- and trans-types. Undecaprenyl diphosphate synthase (UPPS) that catalyzes chain elongation of FPP by consecutive condensation reactions with eight IPP, to form C₅₅ lipid carrier for bacterial cell wall biosynthesis, serves as a model for understanding cis-prenyltransferases. In this review, the current knowledge in UPPS kinetics, mechanisms, structures, and inhibitors is summarized.
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Affiliation(s)
- Kuo-Hsun Teng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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