1
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Bague D, Wang R, Hodge D, Mikati MO, Roma JS, Boshoff HI, Dailey AL, Girma M, Couch RD, Odom John AR, Dowd CS. Inhibition of DXR in the MEP pathway with lipophilic N-alkoxyaryl FR900098 analogs. RSC Med Chem 2024; 15:2422-2439. [PMID: 39026652 PMCID: PMC11253873 DOI: 10.1039/d3md00642e] [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: 11/16/2023] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
In Mycobacterium tuberculosis (Mtb) and Plasmodium falciparum (Pf), the methylerythritol phosphate (MEP) pathway is responsible for isoprene synthesis. This pathway and its products are vital to bacterial/parasitic metabolism and survival, and represent an attractive set of drug targets due to their essentiality in these pathogens but absence in humans. The second step in the MEP pathway is the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) to MEP and is catalyzed by 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR). Natural products fosmidomycin and FR900098 inhibit DXR, but are too polar to reach the desired target inside some cells, such as Mtb. Synthesized FR900098 analogs with lipophilic substitution in the position α to the phosphorous atom showed promise, resulting in increased activity against Mtb and Pf. Here, an α substitution, consisting of a 3,4-dichlorophenyl substituent, in combination with various O-linked alkylaryl substituents on the hydroxamate moiety is utilized in the synthesis of a novel series of FR900098 analogs. The purpose of the O-linked alkylaryl substituents is to further enhance DXR inhibition by extending the structure into the adjacent NADPH binding pocket, blocking the binding of both DXP and NADPH. Of the initial O-linked alkylaryl substituted analogs, compound 6e showed most potent activity against Pf parasites at 3.60 μM. Additional compounds varying the phenyl ring of 6e were synthesized. The most potent phosphonic acids, 6l and 6n, display nM activity against PfDXR and low μM activity against Pf parasites. Prodrugs of these compounds were less effective against Pf parasites but showed modest activity against Mtb cells. Data from this series of compounds suggests that this combination of substituents can be advantageous in designing a new generation of antimicrobials.
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Affiliation(s)
- Darean Bague
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Ruiqin Wang
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Dana Hodge
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
| | - Marwa O Mikati
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Jose S Roma
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Allyson L Dailey
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Misgina Girma
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
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2
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Li SR, Zeng CM, Peng XM, Chen JP, Li S, Zhou CH. Benzopyrone-mediated quinolones as potential multitargeting antibacterial agents. Eur J Med Chem 2023; 262:115878. [PMID: 37866337 DOI: 10.1016/j.ejmech.2023.115878] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
A new type of benzopyrone-mediated quinolones (BMQs) was rationally designed and efficiently synthesized as novel potential antibacterial molecules to overcome the global increasingly serious drug resistance. Some synthesized BMQs effectively suppressed the growth of the tested strains, outperforming clinical drugs. Notably, ethylidene-derived BMQ 17a exhibited superior antibacterial potential with low MICs of 0.5-2 μg/mL to clinical drugs norfloxacin, it not only displayed rapid bactericidal performance and inhibited bacterial biofilm formation, but also showed low toxicity toward human red blood cells and normal MDA-kb2 cells. Mechanistic investigation demonstrated that BMQ 17a could effectually induce bacterial metabolic disorders and promote the enhancement of reactive oxygen species to disrupt the bacterial antioxidant defense system. It was found that the active molecule BMQ 17a could not only form supramolecular complex with lactate dehydrogenase, which disturbed the biological functions, but also effectively embed into calf thymus DNA, thus affecting the normal function of DNA and achieving cell death. This work would provide an insight into developing new molecules to reduce drug resistance and expand antibacterial spectrum.
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Affiliation(s)
- Shu-Rui Li
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Chun-Mei Zeng
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Xin-Mei Peng
- School of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities, Duyun, 558000, China.
| | - Jin-Ping Chen
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Shuo Li
- School of Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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3
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Ayadi N, Descamps A, Legigan T, Dussart-Gautheret J, Monteil M, Migianu-Griffoni E, Ben Ayed T, Deschamp J, Lecouvey M. Synthesis of Aminobisphosphinates through a Cascade Reaction between Hypophosphorous Acid and Bis(trimethylsilyl)imidates Mediated by ZnI 2. Molecules 2023; 28:6226. [PMID: 37687054 PMCID: PMC10489009 DOI: 10.3390/molecules28176226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Among phosphorylated derivatives, phosphinates occupy a prominent place due to their ability to be bioisosteres of phosphates and carboxylates. These properties imply the necessity to develop efficient methodologies leading to phosphinate scaffolds. In recent years, our team has explored the nucleophilic potential of silylated phosphonite towards various electrophiles. In this paper, we propose to extend our study to other electrophiles. We describe here the implementation of a cascade reaction between (trimethylsilyl)imidates and hypophosphorous acid mediated by a Lewis acid allowing the synthesis of aminomethylenebisphosphinate derivatives. The present study focuses on methodological development including a careful NMR monitoring of the cascade reaction. The optimized conditions were successfully applied to various aliphatic and aromatic substituted (trimethylsilyl)imidates, leading to the corresponding AMBPi in moderate to good yields.
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Affiliation(s)
- Nouha Ayadi
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
- Department of Chemistry, Université de Carthage-INSAT—Eco-Chimie Lab (LR21ES02), Centre Urbain Nord B.P.N. 676, Tunis 1080, Tunisia;
| | - Aurélie Descamps
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Thibaut Legigan
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Jade Dussart-Gautheret
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Maelle Monteil
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Evelyne Migianu-Griffoni
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Taïcir Ben Ayed
- Department of Chemistry, Université de Carthage-INSAT—Eco-Chimie Lab (LR21ES02), Centre Urbain Nord B.P.N. 676, Tunis 1080, Tunisia;
| | - Julia Deschamp
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
| | - Marc Lecouvey
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT UMR CNRS 7244, 1 Rue de Chablis, F-93000 Bobigny, France; (N.A.); (A.D.); (J.D.-G.); (M.M.); (E.M.-G.)
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4
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Liquid chromatography-mass spectrometry analyses of polyprenyl phosphates in Escherichia coli cells in which genes for isoprenoid synthesis are amplified. J Biosci Bioeng 2023; 135:382-388. [PMID: 36868984 DOI: 10.1016/j.jbiosc.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/05/2023]
Abstract
Overproduction of isopentenyl diphosphate by the amplification of the genes for the methylerythritol 4-phosphate pathway, dxs and dxr, is known to be deleterious for the growth of Escherichia coli. We hypothesized that overproduction of one of the endogenous isoprenoids, in addition to isopentenyl diphosphate itself, might be the cause of the reported reduced growth rate and attempted to identify the causative agent. In order to analyze polyprenyl phosphates, they were methylated by the reaction with diazomethane. The resulting dimethyl esters of polyprenyl phosphates with carbon numbers from 40 to 60 were quantitated by high-performance liquid chromatography-mass spectrometric analysis detecting ion peaks of the sodium ion adducts. The E. coli was transformed by a multi-copy plasmid carrying both the dxs and dxr genes. Amplification of dxs and dxr significantly increased the levels of polyprenyl phosphates and 2-octaprenylphenol. The levels of Z,E-mixed polyprenyl phosphates with carbon numbers of 50-60 in the strain in which ispB was co-amplified with dxs and dxr were lower than those in the control strain where only dxs and dxr were amplified. The levels of (all-E)-octaprenyl phosphate and 2-octaprenylphenol in the strains in which ispU/rth or crtE was co-amplified with dxs and dxr were lower than those in the control strain. Although the increase in the level of each isoprenoid intermediate was blocked, the growth rates of these strains were not restored. Neither polyprenyl phosphates nor 2-octaprenylphenol can be determined to be the cause of the growth rate reduction seen with dxs and dxr amplification.
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5
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Yuan Q, Liu HW, Cai ZJ, Ji SJ. Direct 1,1-Bisphosphonation of Isocyanides: Atom- and Step-Economical Access to Bisphosphinoylaminomethanes. ACS OMEGA 2021; 6:8495-8501. [PMID: 33817511 PMCID: PMC8015124 DOI: 10.1021/acsomega.1c00160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
An atom- and step-economical strategy for the synthesis of bisphosphinoylaminomethanes is reported. This metal-free bisphosphinylation reaction proceeded smoothly through a base-mediated direct 1,1-bisphosphonation of phosphine oxides and isocyanides under mild conditions. The present method offers a facile, efficient, and general approach to a broad range of bisphosphinoylaminomethane derivatives in moderate to good yields.
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6
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Huang H, Han YS, Chen J, Shi LY, Wei LL, Jiang TT, Yi WJ, Yu Y, Li ZB, Li JC. The novel potential biomarkers for multidrug-resistance tuberculosis using UPLC-Q-TOF-MS. Exp Biol Med (Maywood) 2020; 245:501-511. [PMID: 32046521 DOI: 10.1177/1535370220903464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The lack of rapid and efficient diagnostics impedes largely the epidemic control of multidrug-resistant tuberculosis, and might misguide the therapeutic strategies as well. This study aimed to identify novel multidrug-resistant tuberculosis biomarkers to improve the early intervention, symptomatic treatment and control of the prevalence of multidrug-resistant tuberculosis. The serum small molecule metabolites in healthy controls, patients with drug-susceptible tuberculosis, and patients with multidrug-resistant tuberculosis were screened using ultra-high-performance liquid chromatography combined with quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS). The differentially abundant metabolites were filtered out through multidimensional statistical analysis and bioinformatics analysis. Compared with drug-susceptible tuberculosis patients and healthy controls, the levels of 13 metabolites in multidrug-resistant tuberculosis patients altered. Among them, the most significant changes were found in N1-Methyl-2-pyridone-5-carboxamide (N1M2P5C), 1-Myristoyl-sn-glycerol-3-phosphocholine (MG3P), Caprylic acid (CA), and D-Xylulose (DX). And a multidrug-resistant tuberculosis/drug-susceptible tuberculosis differential diagnostic model was built based on these four metabolites, achieved the accuracy, sensitivity, and specificity of 0.928, 86.7%, and 86.7%, respectively. The enrichment analysis of metabolic pathways showed that the phospholipid remodeling of cell membranes was active in multidrug-resistant tuberculosis patients. In addition, in patients with tuberculosis, the metabolites of dipalmitoyl phosphatidylcholine (DPPC), a major component of pulmonary surfactant, were down-regulated. N1M2P5C, MG3P, CA, and DX may have the potential to serve as novel multidrug-resistant tuberculosis biomarkers. This research provides a preliminary experimental basis to further investigate potential multidrug-resistant tuberculosis biomarkers. Impact statement The MDR-TB incidence remains high, making the effective control of TB epidemic yet challenging. Rapid and accurate diagnosis is vitally important for improving the therapeutic efficacy and controlling the prevalence of drug resistance TB. Metabolomics has dramatic potential to distinguish MDR-TB and DS-TB. N1M2P5C, MG3P, CA, and DX that we identified in this study might have potential as novel MDR-TB biomarkers. The phospholipid remodeling of cell membranes was highly active in MDR-TB. The DPPC metabolites in TB were significantly down-regulated. This work aimed to investigate potential MDR-TB biomarkers to enhance the clinical diagnostic efficacy. The metabolic pathway distinctly altered in MDR-TB might provide novel targets to develop new anti-TB drugs.
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Affiliation(s)
- Huai Huang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Yu-Shuai Han
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Jing Chen
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310013, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing University Affiliated Hospital, Shaoxing 312099, China
| | - Ting-Ting Jiang
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Wen-Jing Yi
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Yi Yu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhi-Bin Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
| | - Ji-Cheng Li
- Medical Research Center, Yue Bei People's Hospital, Shaoguan 512025, China.,Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
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7
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Kaboudin B, Esfandiari H, Moradi A, Kazemi F, Aoyama H. ZnCl2-Mediated Double Addition of Dialkylphosphite to Nitriles for the Synthesis of 1-Aminobisphosphonates. J Org Chem 2019; 84:14943-14948. [DOI: 10.1021/acs.joc.9b02298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Babak Kaboudin
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-66731, Iran
| | - Hesam Esfandiari
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-66731, Iran
| | - Atieh Moradi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-66731, Iran
| | - Foad Kazemi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang, Zanjan 45137-66731, Iran
| | - Hiroshi Aoyama
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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8
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Romanenko VD. α-Heteroatom-substituted gem-Bisphosphonates: Advances in the Synthesis and Prospects for Biomedical Application. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190401141844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Functionalized gem-bisphosphonic acid derivatives being pyrophosphate isosteres are of great synthetic and biological interest since they are currently the most important class of drugs developed for the treatment of diseases associated with the disorder of calcium metabolism, including osteoporosis, Paget’s disease, and hypercalcemia. In this article, we will try to give an in-depth overview of the methods for obtaining α- heteroatom-substituted methylenebisphosphonates and acquaint the reader with the synthetic strategies that are used to develop biologically important compounds of this type.
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Affiliation(s)
- Vadim D. Romanenko
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1-Murmanska Street, Kyiv-94, 02660, Ukraine
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9
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Strobykina IY, Nemtarev AV, Garifullin BF, Voloshina AD, Sapunova AS, Kataev VE. Synthesis and Biological Activity of Alkane-1,1-diylbis(phosphonates) of Diterpenoid Isosteviol. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428019010044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E. Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis. J Med Chem 2019; 62:2564-2581. [PMID: 30730737 DOI: 10.1021/acs.jmedchem.8b01878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report that alkyl-substituted bisphosphonates have activity against Bacillus anthracis Sterne (0.40 μg/mL), Mycobacterium smegmatis (1.4 μg/mL), Bacillus subtilis (1.0 μg/mL), and Staphylococcus aureus (13 μg/mL). In many cases, there is no effect of serum binding, as well as low activity against a human embryonic kidney cell line. Targeting of isoprenoid biosynthesis is involved with 74 having IC50 values of ∼100 nM against heptaprenyl diphosphate synthase and 200 nM against farnesyl diphosphate synthase. B. subtilis growth inhibition was rescued by addition of farnesyl diphosphate, menaquinone-4 (MK-4), or undecaprenyl phosphate (UP), and the combination of MK-4 and UP resulted in a 25× increase in ED50, indicating targeting of both quinone and cell wall biosynthesis. Clostridioides difficile was inhibited by 74, and since this organism does not synthesize quinones, cell wall biosynthesis is the likely target. We also solved three X-ray structures of inhibitors bound to octaprenyl diphosphate and/or undecaprenyl diphosphate synthases.
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Affiliation(s)
| | | | | | | | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | | | | | | | | | - Xu Han
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease , West Lafayette , Indiana 47907 , United States
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11
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Bodrin GV, Pasechnik MP, Matveeva AG, Aysin RR, Matveev SV, Goryunov EI, Strelkova TV, Brel VK. The First 1-Hydroxypropylidenebisphosphonic Acid with 1,8-Naphthyridinone Substituent: Synthesis and Structure. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218090050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Sanders S, Bartee D, Harrison MJ, Phillips PD, Koppisch AT, Freel Meyers CL. Growth medium-dependent antimicrobial activity of early stage MEP pathway inhibitors. PLoS One 2018; 13:e0197638. [PMID: 29771999 PMCID: PMC5957436 DOI: 10.1371/journal.pone.0197638] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023] Open
Abstract
The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.
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Affiliation(s)
- Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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13
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Wang X, Dowd CS. The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis. ACS Infect Dis 2018; 4:278-290. [PMID: 29390176 DOI: 10.1021/acsinfecdis.7b00176] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a severe infectious disease in need of new chemotherapies especially for drug-resistant cases. To meet the urgent requirement of new TB drugs with novel modes of action, the TB research community has been validating numerous targets from several biosynthetic pathways. The methylerythritol phosphate (MEP) pathway is utilized by Mtb for the biosynthesis of isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), the universal five-carbon building blocks of isoprenoids. While being a common biosynthetic pathway in pathogens, the MEP pathway is completely absent in humans. Due to its unique presence in pathogens as well as the essentiality of the MEP pathway in Mtb, the enzymes in this pathway are promising targets for the development of new drugs against tuberculosis. In this Review, we discuss three enzymes in the MEP pathway: 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (IspC/DXR), and 2 C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF), which appear to be the most promising antitubercular drug targets. Structural and mechanistic features of these enzymes are reviewed, as well as selected inhibitors that show promise as antitubercular agents.
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Affiliation(s)
- Xu Wang
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
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Ermer MA, Kottmann SC, Otten JE, Wittmer A, Poxleitner P, Pelz K. In Vitro Investigation of the Antimicrobial Effect of Three Bisphosphonates Against Different Bacterial Strains. J Oral Maxillofac Surg 2017; 76:553-560. [PMID: 28916324 DOI: 10.1016/j.joms.2017.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022]
Abstract
PURPOSE Since the first descriptions of medication-related osteonecrosis of the jaw (MRONJ) in 2003, the pathogenesis has remained unanswered. Recent histomorphometric studies have found several microorganisms, including Actinomyces, Bacillus, Fusobacterium, Staphylococcus, Streptococcus, Selenomonas, Treponema, and Candida albicans in necrotic bone. Polymerase chain reaction studies have recently confirmed the occurrence of 48 genera. Only a few studies have examined the antimicrobial effect of bisphosphonates (BPs). The influence of bacterial growth on the etiology remains unclear. The aim of the present study was the in vitro investigation of the antimicrobial effect of 3 BPs against different bacterial strains. MATERIALS AND METHODS The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 48 strains from 40 species were determined in microdilution assays against pamidronic, ibandronic, and zoledronic acid. RESULTS Growth of gram-positive oral microbiota, which account for most microorganisms in MRONJ, was present for 2 of 22 species; 6 of 26 gram-negative species and 9 of 13 anaerobes were inhibited. The MIC values were compared with the BP bone concentrations from previous reports. Of the 48 strains, 9 had an MIC or MBC less than the bone concentrations. CONCLUSIONS The results of the present study have demonstrated that BPs have an inhibitory effect on selected bacterial species and might inhibit the growth of some relevant pathogens in osteonecrosis. However, most of the species tested were unaffected at the concentration levels assumed present in the human jawbone. The clinical relevance of these in vitro data will better be clarified with reliable data on the BP concentrations in the human jawbone. The present study has provided a first approach toward the assessment of the interaction of oral bacteria and BPs.
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Affiliation(s)
- Michael A Ermer
- Consultant, Department of Oral and Maxillofacial Surgery, University Medical Center Freiburg, Freiburg, Germany.
| | - Simon C Kottmann
- Private Practitioner, Department of Oral and Maxillofacial Surgery, University Medical Center Freiburg, Freiburg, Germany
| | - Jörg-Elard Otten
- Professor, Department of Oral and Maxillofacial Surgery, University Medical Center Freiburg, Freiburg, Germany
| | - Annette Wittmer
- Medical Technical Assistant, Department of Hygiene and Microbiology, Albert-Ludwigs-Universität, Freiburg, Freiburg, Germany
| | - Philipp Poxleitner
- Resident, Department of Oral and Maxillofacial Surgery, University Medical Center Freiburg, Freiburg, Germany
| | - Klaus Pelz
- Consultant, Department of Hygiene and Microbiology, Albert-Ludwigs-Universität, Freiburg, Freiburg, Germany
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Ramakrishna K, Thomas JM, Sivasankar C. A Green Approach to the Synthesis of α-Amino Phosphonate in Water Medium: Carbene Insertion into the N–H Bond by Cu(I) Catalyst. J Org Chem 2016; 81:9826-9835. [DOI: 10.1021/acs.joc.6b01940] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kankanala Ramakrishna
- Catalysis and Energy Laboratory
(A Central University), Department of Chemistry Pondicherry University, Puducherry 605014, India
| | - Jisha Mary Thomas
- Catalysis and Energy Laboratory
(A Central University), Department of Chemistry Pondicherry University, Puducherry 605014, India
| | - Chinnappan Sivasankar
- Catalysis and Energy Laboratory
(A Central University), Department of Chemistry Pondicherry University, Puducherry 605014, India
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Desai J, Wang Y, Wang K, Malwal SR, Oldfield E. Isoprenoid Biosynthesis Inhibitors Targeting Bacterial Cell Growth. ChemMedChem 2016; 11:2205-2215. [PMID: 27571880 PMCID: PMC5160999 DOI: 10.1002/cmdc.201600343] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/05/2022]
Abstract
We synthesized potential inhibitors of farnesyl diphosphate synthase (FPPS), undecaprenyl diphosphate synthase (UPPS), or undecaprenyl diphosphate phosphatase (UPPP), and tested them in bacterial cell growth and enzyme inhibition assays. The most active compounds were found to be bisphosphonates with electron-withdrawing aryl-alkyl side chains which inhibited the growth of Gram-negative bacteria (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa) at ∼1-4 μg mL-1 levels. They were found to be potent inhibitors of FPPS; cell growth was partially "rescued" by the addition of farnesol or overexpression of FPPS, and there was synergistic activity with known isoprenoid biosynthesis pathway inhibitors. Lipophilic hydroxyalkyl phosphonic acids inhibited UPPS and UPPP at micromolar levels; they were active (∼2-6 μg mL-1 ) against Gram-positive but not Gram-negative organisms, and again exhibited synergistic activity with cell wall biosynthesis inhibitors, but only indifferent effects with other inhibitors. The results are of interest because they describe novel inhibitors of FPPS, UPPS, and UPPP with cell growth inhibitory activities as low as ∼1-2 μg mL-1 .
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Affiliation(s)
- Janish Desai
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801
| | - Yang Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Ke Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Satish R Malwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
| | - Eric Oldfield
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801
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Abstract
Background:
Bisphosphonates are drugs commonly used for the medication and prevention of diseases caused by decreased mineral density. Despite such important medicinal use, they display a variety of physiologic activities, which make them promising anti-cancer, anti-protozoal, antibacterial and antiviral agents.
Objective:
To review physiological activity of bisphosphonates with special emphasis on their ongoing and potential applications in medicine and agriculture.
Method:
Critical review of recent literature data.
Results:
Comprehensive review of activities revealed by bisphosphonates.
Conclusion:
although bisphosphonates are mostly recognized by their profound effects on bone physiology their medicinal potential has not been fully evaluated yet. Literature data considering enzyme inhibition suggest possibilities of far more wide application of these compounds. These applications are, however, limited by their low bioavailability and therefore intensive search for new chemical entities overcoming this shortage are carried out.
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18
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Siva Prasad S, Jayaprakash SH, Syamasundar C, Sreelakshmi P, Bhuvaneswar C, Vijaya Bhaskar B, Rajendra W, Nayak SK, Suresh Reddy C. Tween 20-/H 2O Promoted Green Synthesis, Computational and Antibacterial Activity of Amino Acid Substituted Methylene Bisphosphonates. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2015.1054928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- S. Siva Prasad
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - S. H. Jayaprakash
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Ch. Syamasundar
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - P. Sreelakshmi
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - C. Bhuvaneswar
- Division of Molecular Biology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - B. Vijaya Bhaskar
- Division of Molecular Biology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - W. Rajendra
- Division of Molecular Biology, Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - S. K. Nayak
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - C. Suresh Reddy
- Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
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19
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Teixeira FC, Lucas C, Curto MJM, Teixeira APS, Duarte MT, André V. Novel Bisphosphonates Derived from 1H-Indazole, 1H-Pyrazolo[3,4-b]Pyridine, and 1H-Pyrazolo[3,4-b]Quinoline. HETEROATOM CHEMISTRY 2015. [DOI: 10.1002/hc.21282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fátima C. Teixeira
- Laboratório Nacional de Energia e Geologia; I.P., Estrada do Paço do Lumiar; 22, 1649-038 Lisboa Portugal
| | - Carla Lucas
- Laboratório Nacional de Energia e Geologia; I.P., Estrada do Paço do Lumiar; 22, 1649-038 Lisboa Portugal
| | - M. João M. Curto
- Laboratório Nacional de Energia e Geologia; I.P., Estrada do Paço do Lumiar; 22, 1649-038 Lisboa Portugal
| | - António P. S. Teixeira
- Departamento de Química; Escola de Ciências e Tecnologia, Centro de Química de Évora, Instituto de Investigação e Formação Avançada, Universidade de Évora; 7000-671 Évora Portugal
- Centro de Química Estrutural; Instituto Superior Técnico, Universidade de Lisboa; 1049-001 Lisboa Portugal
| | - M. Teresa Duarte
- Centro de Química Estrutural; Instituto Superior Técnico, Universidade de Lisboa; 1049-001 Lisboa Portugal
| | - Vânia André
- Centro de Química Estrutural; Instituto Superior Técnico, Universidade de Lisboa; 1049-001 Lisboa Portugal
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20
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Goldeman W, Nasulewicz-Goldeman A. Synthesis and biological evaluation of aminomethylidenebisphosphonic derivatives of β-arylethylamines. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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21
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Kinetic release studies of nitrogen-containing bisphosphonate from gum acacia crosslinked hydrogels. Int J Biol Macromol 2015; 73:115-23. [DOI: 10.1016/j.ijbiomac.2014.10.064] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/01/2014] [Accepted: 10/25/2014] [Indexed: 11/17/2022]
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22
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Wang AE, Chang Z, Sun WT, Huang PQ. General and Chemoselective Bisphosphonylation of Secondary and Tertiary Amides. Org Lett 2015; 17:732-5. [DOI: 10.1021/acs.orglett.5b00004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ai-E Wang
- Department
of Chemistry, Fujian Provincial Key Laboratory of Chemical Biology,
College of Chemistry and Chemical Engineering, and Collaborative Innovation
Centre of Chemistry for Energy Materials, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Zong Chang
- Department
of Chemistry, Fujian Provincial Key Laboratory of Chemical Biology,
College of Chemistry and Chemical Engineering, and Collaborative Innovation
Centre of Chemistry for Energy Materials, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Wei-Ting Sun
- Department
of Chemistry, Fujian Provincial Key Laboratory of Chemical Biology,
College of Chemistry and Chemical Engineering, and Collaborative Innovation
Centre of Chemistry for Energy Materials, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Pei-Qiang Huang
- Department
of Chemistry, Fujian Provincial Key Laboratory of Chemical Biology,
College of Chemistry and Chemical Engineering, and Collaborative Innovation
Centre of Chemistry for Energy Materials, Xiamen University, Xiamen, Fujian 361005, P. R. China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
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23
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Zhu W, Wang Y, Li K, Gao J, Huang CH, Chen CC, Ko TP, Zhang Y, Guo RT, Oldfield E. Antibacterial drug leads: DNA and enzyme multitargeting. J Med Chem 2015; 58:1215-27. [PMID: 25574764 DOI: 10.1021/jm501449u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 °C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R(2) = 0.89, S. aureus; R(2) = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA ΔTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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24
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Wang J, Xiong Z, Li S, Wang Y. Exploiting exogenous MEP pathway genes to improve the downstream isoprenoid pathway effects and enhance isoprenoid production in Escherichia coli. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
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26
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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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27
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Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A 2014; 111:E2530-9. [PMID: 24927548 DOI: 10.1073/pnas.1409061111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We used in silico methods to screen a library of 1,013 compounds for possible binding to the allosteric site in farnesyl diphosphate synthase (FPPS). Two of the 50 predicted hits had activity against either human FPPS (HsFPPS) or Trypanosoma brucei FPPS (TbFPPS), the most active being the quinone methide celastrol (IC50 versus TbFPPS ∼ 20 µM). Two rounds of similarity searching and activity testing then resulted in three leads that were active against HsFPPS with IC50 values in the range of ∼ 1-3 µM (as compared with ∼ 0.5 µM for the bisphosphonate inhibitor, zoledronate). The three leads were the quinone methides taxodone and taxodione and the quinone arenarone, compounds with known antibacterial and/or antitumor activity. We then obtained X-ray crystal structures of HsFPPS with taxodione+zoledronate, arenarone+zoledronate, and taxodione alone. In the zoledronate-containing structures, taxodione and arenarone bound solely to the homoallylic (isopentenyl diphosphate, IPP) site, not to the allosteric site, whereas zoledronate bound via Mg(2+) to the same site as seen in other bisphosphonate-containing structures. In the taxodione-alone structure, one taxodione bound to the same site as seen in the taxodione+zoledronate structure, but the second located to a more surface-exposed site. In differential scanning calorimetry experiments, taxodione and arenarone broadened the native-to-unfolded thermal transition (Tm), quite different to the large increases in ΔTm seen with biphosphonate inhibitors. The results identify new classes of FPPS inhibitors, diterpenoids and sesquiterpenoids, that bind to the IPP site and may be of interest as anticancer and antiinfective drug leads.
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Sub-inhibitory fosmidomycin exposures elicits oxidative stress in Salmonella enterica serovar Typhimurium LT2. PLoS One 2014; 9:e95271. [PMID: 24751777 PMCID: PMC3994034 DOI: 10.1371/journal.pone.0095271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 03/26/2014] [Indexed: 01/16/2023] Open
Abstract
Fosmidomycin is a time-dependent nanomolar inhibitor of methylerythritol phosphate (MEP) synthase, which is the enzyme that catalyzes the first committed step in the MEP pathway to isoprenoids. Importantly, fosmidomycin is one of only a few MEP pathway-specific inhibitors that exhibits antimicrobial activity. Most inhibitors identified to date only exhibit activity against isolated pathway enzymes. The MEP pathway is the sole route to isoprenoids in many bacteria, yet has no human homologs. The development of inhibitors of this pathway holds promise as novel antimicrobial agents. Similarly, analyses of the bacterial response toward MEP pathway inhibitors provides valuable information toward the understanding of how emergent resistance may ultimately develop to this class of antibiotics. We have examined the transcriptional response of Salmonella enterica serovar typhimurium LT2 to sub-inhibitory concentrations of fosmidomycin via cDNA microarray and RT-PCR. Within the regulated genes identified by microarray were a number of genes encoding enzymes associated with the mediation of reactive oxygen species (ROS). Regulation of a panel of genes implicated in the response of cells to oxidative stress (including genes for catalases, superoxide dismutases, and alkylhydrogen peroxide reductases) was investigated and mild upregulation in some members was observed as a function of fosmidomycin exposure over time. The extent of regulation of these genes was similar to that observed for comparable exposures to kanamycin, but differed significantly from tetracycline. Furthermore, S. typhimurium exposed to sub-inhibitory concentrations of fosmidomycin displayed an increased sensitivity to exogenous H2O2 relative to either untreated controls or kanamycin-treated cells. Our results suggest that endogenous oxidative stress is one consequence of exposures to fosmidomycin, likely through the temporal depletion of intracellular isoprenoids themselves, rather than other mechanisms that have been proposed to facilitate ROS accumulation in bacteria (e.g. cell death processes or the ability of the antibiotic to redox cycle).
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29
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30
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Smith JM, Warrington NV, Vierling RJ, Kuhn ML, Anderson WF, Koppisch AT, Freel Meyers CL. Targeting DXP synthase in human pathogens: enzyme inhibition and antimicrobial activity of butylacetylphosphonate. J Antibiot (Tokyo) 2014; 67:77-83. [PMID: 24169798 PMCID: PMC3946878 DOI: 10.1038/ja.2013.105] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 09/20/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
The unique methylerythritol phosphate pathway for isoprenoid biosynthesis is essential in most bacterial pathogens. The first enzyme in this pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes a distinct thiamin diphosphate (ThDP)-dependent reaction to form DXP from D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate and represents a potential anti-infective drug target. We have previously demonstrated that the unnatural bisubstrate analog, butylacetylphosphonate (BAP), exhibits selective inhibition of Escherichia coli DXP synthase over mammalian ThDP-dependent enzymes. Here, we report the selective inhibition by BAP against recombinant DXP synthase homologs from Mycobacterium tuberculosis, Yersinia pestis and Salmonella enterica. We also demonstrate antimicrobial activity of BAP against both Gram-negative and Gram-positive strains (including E. coli, S. enterica and Bacillus anthracis), and several clinically isolated pathogens. Our results suggest a mechanism of action involving inhibition of DXP synthase and show that BAP acts synergistically with established antimicrobial agents, highlighting a potential strategy to combat emerging resistance in bacterial pathogens.
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Affiliation(s)
- Jessica M Smith
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicole V Warrington
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Ryan J Vierling
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Andrew T Koppisch
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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31
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Zhang Y, Lin FY, Li K, Zhu W, Liu YL, Cao R, Pang R, Lee E, Axelson J, Hensler M, Wang K, Molohon KJ, Wang Y, Mitchell DA, Nizet V, Oldfield E. HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis. ACS Med Chem Lett 2012; 3:402-406. [PMID: 22662288 DOI: 10.1021/ml300038t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We report the discovery of antibacterial leads, keto- and diketo-acids, targeting two prenyl transferases: undecaprenyl diphosphate synthase (UPPS) and dehydrosqualene synthase (CrtM). The leads were suggested by the observation that keto- and diketo-acids bind to the active site Mg(2+)/Asp domain in HIV-1 integrase, and similar domains are present in prenyl transferases. We report the x-ray crystallographic structures of one diketo-acid and one keto-acid bound to CrtM, which supports the Mg(2+) binding hypothesis, together with the x-ray structure of one diketo-acid bound to UPPS. In all cases, the inhibitors bind to a farnesyl diphosphate substrate-binding site. Compound 45 had cell growth inhibition MIC(90) values of ~250-500 ng/mL against S. aureus, 500 ng/mL against Bacillus anthracis, 4 μg/mL against Listeria monocytogenes and Enterococcus faecium, and 1 μg/mL against Streptococcus pyogenes M1, but very little activity against E. coli (DH5α, K12) or human cell lines.
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Affiliation(s)
- Yonghui Zhang
- PrenylX Research Institute, Zhangjiagang, 215600, People's Republic of
China
| | | | | | | | | | | | | | | | | | - Mary Hensler
- Department of Pediatrics and
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
92093, United States
| | | | | | | | | | - Victor Nizet
- Department of Pediatrics and
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
92093, United States
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NMR, potentiometric and ESI-MS combined studies on the zinc(II) magnesium(II) and calcium(II) complexation by (morpholin-1-yl)methane-1,1-diphosphonic acid and its thio-analog. Polyhedron 2012. [DOI: 10.1016/j.poly.2011.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Dozier JK, Distefano MD. An enzyme-coupled continuous fluorescence assay for farnesyl diphosphate synthases. Anal Biochem 2011; 421:158-63. [PMID: 22085443 DOI: 10.1016/j.ab.2011.10.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/03/2011] [Accepted: 10/21/2011] [Indexed: 01/01/2023]
Abstract
Farnesyl diphosphate synthase (FDPS) catalyzes the conversion of isopentenyl diphosphate and dimethylallyl diphosphate to farnesyl diphosphate, a crucial metabolic intermediate in the synthesis of cholesterol, ubiquinone, and prenylated proteins; consequently, much effort has gone into developing inhibitors that target FDPS. Currently most FDPS assays either use radiolabeled substrates and are discontinuous or monitor pyrophosphate release and not farnesyl diphosphate (FPP) creation. Here we report the development of a continuous coupled enzyme assay for FDPS activity that involves the subsequent incorporation of the FPP product of that reaction into a peptide via the action of protein farnesyltransferase (PFTase). By using a dansylated peptide whose fluorescence quantum yield increases upon farnesylation, the rate of FDPS-catalyzed FPP production can be measured. We show that this assay is more sensitive than existing coupled assays, that it can be used to conveniently monitor FDPS activity in a 96-well plate format, and that it can reproduce IC(50) values for several previously reported FDPS inhibitors. This new method offers a simple, safe, and continuous method to assay FDPS activity that should greatly facilitate the screening of inhibitors of this important target.
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Affiliation(s)
- Jonathan K Dozier
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des 2011; 78:323-32. [PMID: 21696546 PMCID: PMC3155669 DOI: 10.1111/j.1747-0285.2011.01164.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relaxed complex scheme, a virtual-screening methodology that accounts for protein receptor flexibility, was used to identify a low-micromolar, non-bisphosphonate inhibitor of farnesyl diphosphate synthase. Serendipitously, we also found that several predicted farnesyl diphosphate synthase inhibitors were low-micromolar inhibitors of undecaprenyl diphosphate synthase. These results are of interest because farnesyl diphosphate synthase inhibitors are being pursued as both anti-infective and anticancer agents, and undecaprenyl diphosphate synthase inhibitors are antibacterial drug leads.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, CA 92093, USA.
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Maahs MP, Azambuja AA, Campos MM, Salum FG, Cherubini K. Association between bisphosphonates and jaw osteonecrosis: A study in Wistar rats. Head Neck 2011; 33:199-207. [DOI: 10.1002/hed.21422] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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36
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Minaeva LI, Patrikeeva LS, Kabachnik MM, Beletskaya IP, Orlinson BS, Novakov IA. Synthesis of novel aminomethylenebisphosphonates and bisphosphonic acids, containing adamantyl fragment. HETEROATOM CHEMISTRY 2010. [DOI: 10.1002/hc.20656] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Nuclear magnetic resonance-based quantification of organic diphosphates. Anal Biochem 2010; 408:316-20. [PMID: 20833124 DOI: 10.1016/j.ab.2010.08.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 08/25/2010] [Indexed: 11/21/2022]
Abstract
Phosphorylated compounds are ubiquitous in life. Given their central role, many such substrates and analogs have been prepared for subsequent evaluation. Prior to biological experiments, it is typically necessary to determine the concentration of the target molecule in solution. Here we describe a method where concentrations of stock solutions of organic diphosphates and bisphosphonates are quantified using (31)P nuclear magnetic resonance (NMR) spectroscopy with standard instrumentation using a capillary tube with a secondary standard. The method is specific and is applicable down to a concentration of 200 μM. The capillary tube provides the reference peak for quantification and deuterated solvent for locking.
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Majumdar A, Sun Y, Shah M, Freel Meyers CL. Versatile (1)H-(31)P-(31)P COSY 2D NMR techniques for the characterization of polyphosphorylated small molecules. J Org Chem 2010; 75:3214-23. [PMID: 20408590 DOI: 10.1021/jo100042m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Di- and triphosphorylated small molecules represent key intermediates in a wide range of biological and chemical processes. The importance of polyphosphorylated species in biology and medicine underscores the need to develop methods for the detection and characterization of this compound class. We have reported two-dimensional HPP-COSY spectroscopy techniques to identify diphosphate-containing metabolic intermediates at submillimolar concentrations in the methylerythritol phosphate (MEP) isoprenoid biosynthetic pathway. (1) In this work, we explore the scope of HPP-COSY-based techniques to characterize a diverse group of small organic molecules bearing di- and triphosphorylated moieties. These include molecules containing P-O-P and P-C-P connectivities, multivalent P(III)-O-P(V) phosphorus nuclei with widely separated chemical shifts, as well as virtually overlapping (31)P resonances exhibiting strong coupling effects. We also demonstrate the utility of these experiments to rapidly distinguish between mono- and diphosphates. A detailed protocol for optimizing these experiments to achieve best performance is presented.
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Affiliation(s)
- Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, JohnsHopkins School of Medicine, Baltimore, Maryland 21205, USA
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Matczak-Jon E, Kowalik-Jankowska T, Ślepokura K, Kafarski P, Rajewska A. Specificity of the zinc(ii), magnesium(ii) and calcium(ii) complexation by (pyridin-2-yl)aminomethane-1,1-diphosphonic acids and related 1,3-(thiazol-2-yl) and 1,3-(benzothiazol-2-yl) derivatives. Dalton Trans 2010; 39:1207-21. [DOI: 10.1039/b914647d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Dąbrowska E, Burzyńska A, Mucha A, Matczak-Jon E, Sawka-Dobrowolska W, Berlicki Ł, Kafarski P. Insight into the mechanism of three component condensation leading to aminomethylenebisphosphonates. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2009.07.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Cao R, Chen CKM, Guo RT, Wang AHJ, Oldfield E. Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases. Proteins 2009; 73:431-9. [PMID: 18442135 DOI: 10.1002/prot.22066] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report the X-ray crystallographic structures of the bisphosphonate N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate (BPH-210), a potent analog of pamidronate (Aredia), bound to farnesyl diphosphate synthase (FPPS) from Trypanosoma brucei as well as to geranylgeranyl diphosphate synthase from Saccharomyces cerevisiae. BPH-210 binds to FPPS, together with 3 Mg(2+), with its long, hydrophobic phenylbutyl side-chain being located in the same binding pocket that is occupied by allylic diphosphates and other bisphosphonates. Binding is overwhelmingly entropy driven, as determined by isothermal titration calorimetry. The structure is of interest since it explains the lack of potency of longer chain analogs against FPPS, since these would be expected to have a steric clash with an aromatic ring at the distal end of the binding site. Unlike shorter chain FPPS inhibitors, such as pamidronate, BPH-210 is also found to be a potent inhibitor of human geranylgeranyl diphosphate synthase. In this case, the bisphosphonate binds only to the GGPP product inhibitory site, with only 1 (chain A) or 0 (chain B) Mg(2+), and DeltaS is much smaller and DeltaH is approximately 6 k cal more negative than in the case of FPPS binding. Overall, these results are of general interest since they show that some bisphosphonates can bind to more than one trans-prenyl synthase enzyme which, in some cases, can be expected to enhance their overall activity in vitro and in vivo.
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Affiliation(s)
- Rong Cao
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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42
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Biological Activity of Aminophosphonic Acids and Their Short Peptides. TOPICS IN HETEROCYCLIC CHEMISTRY 2009. [DOI: 10.1007/7081_2008_14] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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43
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Zhang Y, Hudock MP, Krysiak K, Cao R, Bergan K, Yin F, Leon A, Oldfield E. Activity of sulfonium bisphosphonates on tumor cell lines. J Med Chem 2007; 50:6067-79. [PMID: 17963374 DOI: 10.1021/jm700991k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We investigated three series of sulfonium bisphosphonates for their activity in inhibiting the growth of three human tumor cell lines. The first series consisted of 6 cyclic sulfonium bisphosphonates, the most active species having an (average) IC50 of 89 microM. The second consisted of 10 phenylalkyl and phenylalkoxy bisphosphonates, the most active species having an IC50 of 18 microM. The third series consisted of 17 n-alkyl sulfonium bisphosphonates, the most active species having an IC50 of approximately 240 nM. Three QSAR models showed that the experimental cell growth inhibition results could be well predicted. We also determined the structures of one sulfonium bisphosphonate bound to farnesyl diphosphate synthase, finding that it binds exclusively to the dimethylallyl diphosphate binding site. These results are of interest since they show that sulfonium bisphosphonates can have potent activity against a variety of tumor cell lines, the most active species having IC50 values much lower than conventional nitrogen-containing bisphosphonates.
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Affiliation(s)
- Yonghui Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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