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Das BC, Chokkalingam P, Shareef MA, Shukla S, Das S, Saito M, Weiss LM. Methionine aminopeptidases: Potential therapeutic target for microsporidia and other microbes. J Eukaryot Microbiol 2024:e13036. [PMID: 39036929 DOI: 10.1111/jeu.13036] [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: 04/05/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 07/23/2024]
Abstract
Methionine aminopeptidases (MetAPs) have emerged as a target for medicinal chemists in the quest for novel therapeutic agents for treating cancer, obesity, and other disorders. Methionine aminopeptidase is a metalloenzyme with two structurally distinct forms in humans, MetAP-1 and MetAP-2. The MetAP2 inhibitor fumagillin, which was used as an amebicide in the 1950s, has been used for the successful treatment of microsporidiosis in humans; however, it is no longer commercially available. Despite significant efforts and investments by many pharmaceutical companies, no new MetAP inhibitors have been approved for the clinic. Several lead compounds have been designed and synthesized by researchers as potential inhibitors of MetAP and evaluated for their potential activity in a wide range of diseases. MetAP inhibitors such as fumagillin, TNP-470, beloranib, and reversible inhibitors and their analogs guide new prospects for MetAP inhibitor development in the ongoing quest for new pharmacological indications. This perspective provides insights into recent advances related to MetAP, as a potential therapeutic target in drug discovery, bioactive small molecule MetAP2 inhibitors, and data on the role of MetAP-2 as a therapeutic target for microsporidiosis.
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Affiliation(s)
- Bhaskar C Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
- Department of Medicine and Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Parthiban Chokkalingam
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
| | - Mohammed Adil Shareef
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
| | - Srushti Shukla
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
| | - Sasmita Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York, USA
| | - Mariko Saito
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, USA
| | - Louis M Weiss
- Departments of Pathology and Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York, USA
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Tamang A, Kaur A, Thakur D, Thakur A, Thakur BK, Shivani, Swarnkar M, Pal PK, Hallan V, Pandey SS. Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production. Appl Microbiol Biotechnol 2024; 108:247. [PMID: 38427084 PMCID: PMC10907472 DOI: 10.1007/s00253-024-13076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/04/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.
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Affiliation(s)
- Anish Tamang
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amanpreet Kaur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Deepali Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Ankita Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Babit Kumar Thakur
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shivani
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohit Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
| | - Probir K Pal
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vipin Hallan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shiv Shanker Pandey
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Development and Validation of a Sensitive, Specific and Reproducible UPLC-MS/MS Method for the Quantification of OJT007, A Novel Anti-Leishmanial Agent: Application to a Pharmacokinetic Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094624. [PMID: 33925369 PMCID: PMC8123827 DOI: 10.3390/ijerph18094624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/16/2022]
Abstract
OJT007 is a methionine aminopeptidase 1 (MetAP1) inhibitor with potent anti-proliferative effects against Leishmania Major. In order to study its pharmacokinetics as a part of the drug development process, a sensitive, specific, and reproducible ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed and validated. Voriconazole was used as the internal standard to generate standard curves ranging from 5 to 1000 ng/mL. The separation was achieved using a UPLC system equipped with an Acquity UPLC BEH C18 column (2.1 × 50 mm, 1.7 μm) with 0.1% formic acid in acetonitrile and 0.1% formic acid in water as the mobile phase under gradient elution at a flow rate of 0.4 mL/min. The mass analysis was performed with a 4000 QTRAP® mass spectrometer using multiple-ion reaction monitoring (MRM) in the positive mode, with the transition of m/z 325 → m/z 205 for OJT007 and m/z 350 → m/z 101 for voriconazole. The intra- and inter-day precision and accuracy were within ±15%. The mean extraction recovery and the matrix effect were 95.1% and 7.96%, respectively, suggesting no significant matrix interfering with the quantification of the drug in rat plasma. This study was successfully used for the pharmacokinetic evaluation of OJT007 using the rat as an animal model.
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Zhao J, Zhu Y, Han J, Lin YW, Aichem M, Wang J, Chen K, Velkov T, Schreiber F, Li J. Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model. Microorganisms 2020; 8:microorganisms8111793. [PMID: 33207684 PMCID: PMC7696501 DOI: 10.3390/microorganisms8111793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/22/2023] Open
Abstract
Multidrug-resistant (MDR) Acinetobacter baumannii is a critical threat to human health globally. We constructed a genome-scale metabolic model iAB5075 for the hypervirulent, MDR A. baumannii strain AB5075. Predictions of nutrient utilization and gene essentiality were validated using Biolog assay and a transposon mutant library. In vivo transcriptomics data were integrated with iAB5075 to elucidate bacterial metabolic responses to the host environment. iAB5075 contains 1530 metabolites, 2229 reactions, and 1015 genes, and demonstrated high accuracies in predicting nutrient utilization and gene essentiality. At 4 h post-infection, a total of 146 metabolic fluxes were increased and 52 were decreased compared to 2 h post-infection; these included enhanced fluxes through peptidoglycan and lipopolysaccharide biosynthesis, tricarboxylic cycle, gluconeogenesis, nucleotide and fatty acid biosynthesis, and altered fluxes in amino acid metabolism. These flux changes indicate that the induced central metabolism, energy production, and cell membrane biogenesis played key roles in establishing and enhancing A. baumannii bloodstream infection. This study is the first to employ genome-scale metabolic modeling to investigate A. baumannii infection in vivo. Our findings provide important mechanistic insights into the adaption of A. baumannii to the host environment and thus will contribute to the development of new therapeutic agents against this problematic pathogen.
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Affiliation(s)
- Jinxin Zhao
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
- Correspondence: (Y.Z.); (J.L.); Tel.: +61-3-99029178 (Y.Z.); +61-3-99039172 (J.L.); Fax: +61-3-99056450 (J.L.)
| | - Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Yu-Wei Lin
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Michael Aichem
- Department of Computer and Information Science, University of Konstanz, 78457 Konstanz, Germany; (M.A.); (F.S.)
| | - Jiping Wang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Ke Chen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
| | - Tony Velkov
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, 78457 Konstanz, Germany; (M.A.); (F.S.)
| | - Jian Li
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (J.Z.); (Y.-W.L.); (J.W.); (K.C.)
- Correspondence: (Y.Z.); (J.L.); Tel.: +61-3-99029178 (Y.Z.); +61-3-99039172 (J.L.); Fax: +61-3-99056450 (J.L.)
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Ekpenyong O, Gao X, Ma J, Cooper C, Nguyen L, Olaleye OA, Liang D, Xie H. Pre-Clinical Pharmacokinetics, Tissue Distribution and Physicochemical Studies of CLBQ14, a Novel Methionine Aminopeptidase Inhibitor for the Treatment of Infectious Diseases. Drug Des Devel Ther 2020; 14:1263-1277. [PMID: 32280198 PMCID: PMC7127848 DOI: 10.2147/dddt.s238148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/16/2020] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION CLBQ14, a derivative of 8-hydroxyquinoline, exerts its chemotherapeutic effect by inhibiting methionine aminopeptidase (MetAP), the enzyme responsible for the post-translational modification of several proteins and polypeptides. MetAP is a novel target for infectious diseases. CLBQ14 is selective and highly potent against replicating and latent Mycobacterium tuberculosis making it an appealing lead for further development. METHODS The physicochemical properties (solubility, pH stability and lipophilicity), in vitro plasma stability and metabolism, pre-clinical pharmacokinetics, plasma protein binding and tissue distribution of CLBQ14 in adult male Sprague-Dawley rats were characterized. RESULTS At room temperature, CLBQ14 is practically insoluble in water (<0.07 mg/mL) but freely soluble in dimethyl acetamide (>80 mg/mL); it has a log P value of 3.03 ± 0.04. CLBQ14 exhibits an inverse Z-shaped pH decomposition profile; it is stable at acidic pH but is degraded at a faster rate at basic pH. It is highly bound to plasma proteins (>91%), does not partition to red blood cells (B/P ratio: 0.83 ± 0.03), and is stable in mouse, rat, monkey and human plasma. CLBQ14 exhibited a bi-exponential pharmacokinetics after intravenous administration in rats, bioavailability of 39.4 and 90.0%, respectively from oral and subcutaneous route. We observed a good correlation between predicted and observed rat clearance, 1.90 ± 0.17 L/kg/h and 1.67 ± 0.08 L/kg/h, respectively. Human hepatic clearance predicted from microsomal stability data and from the single species scaling were 0.80 L/hr/kg and 0.69 L/h/kg, respectively. CLBQ14 is extensively distributed in rats; following a 5 mg/kg intravenous administration, lowest and highest concentrations of 15.6 ± 4.20 ng/g of heart and 405.9 ± 77.11 ng/g of kidneys, respectively, were observed. In vitro CYP reaction phenotyping demonstrates that CLBQ14 is metabolized primarily by CYP 1A2. CONCLUSION CLBQ14 possess appealing qualities of a drug candidate. The studies reported herein are imperative to the development of CLBQ14 as a new chemical entity for infectious diseases.
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Affiliation(s)
- Oscar Ekpenyong
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Xiuqing Gao
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Jing Ma
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Candace Cooper
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Linh Nguyen
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Omonike A Olaleye
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Dong Liang
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Huan Xie
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
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Tillery LM, Barrett KF, Dranow DM, Craig J, Shek R, Chun I, Barrett LK, Phan IQ, Subramanian S, Abendroth J, Lorimer DD, Edwards TE, Van Voorhis WC. Toward a structome of Acinetobacter baumannii drug targets. Protein Sci 2020; 29:789-802. [PMID: 31930600 DOI: 10.1002/pro.3826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.
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Affiliation(s)
- Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Justin Craig
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Roger Shek
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Ian Chun
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
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Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation. Int J Med Microbiol 2019; 309:288-298. [PMID: 31126750 DOI: 10.1016/j.ijmm.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/28/2019] [Accepted: 03/17/2019] [Indexed: 12/31/2022] Open
Abstract
N-terminal methionine excision (NME) is a proteolytic pathway that cleaves the N-termini of proteins, a process that influences where proteins localise in the cell and their turnover rates. In bacteria, protein biosynthesis is initiated by formylated methionine start tRNA (fMet-tRNAfMet). The formyl group is attached by formyltransferase (FMT) and is subsequently removed by peptide deformylase (PDF) in most but not all proteins. Methionine aminopeptidase then cleaves deformylated methionine to complete the process. Components of NME, particularly PDF, are promising therapeutic targets for bacterial pathogens. In Mycoplasma hyopneumoniae, a genome-reduced, major respiratory pathogen of swine, pdf and fmt are absent from its genome. Our bioinformatic analysis uncovered additional enzymes involved in formylated N-terminal methionine (fnMet) processing missing in fourteen mycoplasma species, including M. hyopneumoniae but not in Mycoplasma pneumoniae, a major respiratory pathogen of humans. Consistent with our bioinformatic studies, an analysis of in-house tryptic peptide libraries confirmed the absence of fnMet in M. hyopneumoniae proteins but, as expected fnMet peptides were detected in the proteome of M. pneumoniae. Additionally, computational molecular modelling of M. hyopneumoniae translation initiation factors reveal structural and sequence differences in areas known to interact with fMet-tRNAfMet. Our data suggests that some mycoplasmas have evolved a translation process that does not require fnMet.
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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A simple, sensitive and reliable LC-MS/MS method for the determination of 7-bromo-5-chloroquinolin-8-ol (CLBQ14), a potent and selective inhibitor of methionine aminopeptidases: Application to pharmacokinetic studies. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1097-1098:35-43. [PMID: 30199748 DOI: 10.1016/j.jchromb.2018.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/23/2018] [Accepted: 08/25/2018] [Indexed: 01/09/2023]
Abstract
CLBQ14 is an 8-hydroxyquinoline analogue that inhibits methionine aminopeptidase (MetAP), an enzyme responsible for the post-translational modification of several proteins and polypeptides. MetAP has been validated as druggable target for some infectious diseases, and its inhibitors have been investigated as potential therapeutic agents. In this study, we developed and validated a liquid chromatography tandem-mass spectrometry (LC-MS/MS) method for the quantification of CLBQ14 in solution, and in rat plasma and urine. This method was applied to the pharmacokinetic evaluation of CLBQ14 in adult male Sprague Dawley (SD) rats. Chromatographic separation was achieved using an ultra-high-performance liquid chromatography (UHPLC) system equipped with Waters XTerra MS C18 column (3.5 μm, 125 Å, 2.1 × 50 mm) using 0.1% formic acid in acetonitrile/water gradient system as mobile phase. Chromatographic analysis was performed with a 4000 QTRAP® mass spectrometer using MRM in positive mode for CLBQ14 transition [M + H]+m/z 257.919 → m/z 151.005, and IS (clioquinol) transition [M + H]+m/z 305.783 → m/z 178.917. CLBQ14 was extracted from plasma and urine samples by protein precipitation. The retention times for CLBQ14 and IS were 1.31 and 1.40 min respectively. The standard curves were linear for CLBQ14 concentration ranging from 1 to 1000 ng/mL. The intra-day and inter-day accuracy and precision were found to be within 15% of the nominal concentration. Extraction recoveries were >96.3% and 96.6% from rat plasma and urine respectively, and there was no significant matrix effect from the biological matrices. CLBQ14 is stable in samples subjected to expected storage, preparation, and handling conditions. Pharmacokinetic studies revealed that CLBQ14 has a bi-exponential disposition in SD rats, is extensively distributed with a long plasma half-life and is eliminated primarily by liver metabolism.
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10
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Helgren TR, Seven ES, Chen C, Edwards TE, Staker BL, Abendroth J, Myler PJ, Horn JR, Hagen TJ. The identification of inhibitory compounds of Rickettsia prowazekii methionine aminopeptidase for antibacterial applications. Bioorg Med Chem Lett 2018; 28:1376-1380. [PMID: 29551481 PMCID: PMC5908248 DOI: 10.1016/j.bmcl.2018.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 11/25/2022]
Abstract
Methionine aminopeptidase (MetAP) is a dinuclear metalloprotease responsible for the cleavage of methionine initiator residues from nascent proteins. MetAP activity is necessary for bacterial proliferation and is therefore a projected novel antibacterial target. A compound library consisting of 294 members containing metal-binding functional groups was screened against Rickettsia prowazekii MetAP to determine potential inhibitory motifs. The compounds were first screened against the target at a concentration of 10 µM and potential hits were determined to be those exhibiting greater than 50% inhibition of enzymatic activity. These hit compounds were then rescreened against the target in 8-point dose-response curves and 11 compounds were found to inhibit enzymatic activity with IC50 values of less than 10 µM. Finally, compounds (1-5) were docked against RpMetAP with AutoDock to determine potential binding mechanisms and the results were compared with crystal structures deposited within the PDB.
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Affiliation(s)
- Travis R Helgren
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Elif S Seven
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Congling Chen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA
| | - Jan Abendroth
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.
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11
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Žalubovskis R, Winum JY. Inhibitors of Selected Bacterial Metalloenzymes. Curr Med Chem 2018; 26:2690-2714. [PMID: 29611472 DOI: 10.2174/0929867325666180403154018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022]
Abstract
The utilization of bacterial metalloenzymes, especially ones not having mammalian (human) counterparts, has drawn attention to develop novel antibacterial agents to overcome drug resistance and especially multidrug resistance. In this review, we focus on the recent achievements on the development of inhibitors of bacterial enzymes peptide deformylase (PDF), metallo-β-lactamase (MBL), methionine aminopeptidase (MetAP) and UDP-3-O-acyl- N-acetylglucosamine deacetylase (LpxC). The state of the art of the design and investigation of inhibitors of bacterial metalloenzymes is presented, and challenges are outlined and discussed.
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Affiliation(s)
- Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Latvia
| | - Jean-Yves Winum
- Institut des Biomolecules Max Mousseron, Universite de Montpellier, France
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12
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Helgren TR, Chen C, Wangtrakuldee P, Edwards TE, Staker BL, Abendroth J, Sankaran B, Housley NA, Myler PJ, Audia JP, Horn JR, Hagen TJ. Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents. Bioorg Med Chem 2017; 25:813-824. [PMID: 28089350 PMCID: PMC5319851 DOI: 10.1016/j.bmc.2016.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023]
Abstract
Methionine aminopeptidase (MetAP) is a class of ubiquitous enzymes essential for the survival of numerous bacterial species. These enzymes are responsible for the cleavage of N-terminal formyl-methionine initiators from nascent proteins to initiate post-translational modifications that are often essential to proper protein function. Thus, inhibition of MetAP activity has been implicated as a novel antibacterial target. We tested this idea in the present study by targeting the MetAP enzyme in the obligate intracellular pathogen Rickettsia prowazekii. We first identified potent RpMetAP inhibitory species by employing an in vitro enzymatic activity assay. The molecular docking program AutoDock was then utilized to compare published crystal structures of inhibited MetAP species to docked poses of RpMetAP. Based on these in silico and in vitro screens, a subset of 17 compounds was tested for inhibition of R. prowazekii growth in a pulmonary vascular endothelial cell (EC) culture infection model system. All compounds were tested over concentration ranges that were determined to be non-toxic to the ECs and 8 of the 17 compounds displayed substantial inhibition of R. prowazekii growth. These data highlight the therapeutic potential for inhibiting RpMetAP as a novel antimicrobial strategy and set the stage for future studies in pre-clinical animal models of infection.
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Affiliation(s)
- Travis R Helgren
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Congling Chen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Phumvadee Wangtrakuldee
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Bart L Staker
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Jan Abendroth
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicole A Housley
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - Peter J Myler
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Department of Global Health and Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Jonathon P Audia
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.
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13
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Biochemical characterization of recombinant methionine aminopeptidases (MAPs) from Mycobacterium tuberculosis H37Rv. Mol Cell Biochem 2012; 365:191-202. [PMID: 22466806 DOI: 10.1007/s11010-012-1260-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/08/2012] [Indexed: 01/06/2023]
Abstract
Methionine aminopeptidase (MAP) performs the essential post-translational N-terminal methionine excision (NME) of nascent polypeptides during protein synthesis. To characterize MAP from Mycobacterium tuberculosis, two homolgues, mapA (Rv0734) and mapB (Rv2861c), were over expressed and purified as recombinant proteins in E. coli. In vitro activity assay of apo-MtbMAPs using L-Met-p-nitro anilide as substrate revealed MtbMAP A to be catalytically more efficient compared to MtbMAP B. Ni(2+) was the best activator of apo-MtbMAP A, whereas Ni(2+) and Co(2+) activated apo-MtbMAP B equally. MtbMAP B showed higher thermo-stability, but was feedback inhibited by higher concentrations of L-methionine. Aminopeptidase inhibitors like actinonin and bestatin inhibited both MtbMAPs, more prominently MtbMAP B. Among the site-directed mutants of MtbMAP B, substitution of metal-binding residue D142 completely abolished enzyme activity, whereas substitution of residues forming S1' pocket, C105S and T94C, had only moderate effects on substrate hydrolysis. Present study identified a specific insertion region in MtbMAP A sequence which differentiates it from other bacterial and eukaryotic MAPs. A deletion mutant lacking amino acids from this insertion region (MtbMAP A-∆164-176) was constructed to probe into their structural and functional role in activity and stability of MtbMAP A. The limited success in soluble expression of this deletion mutant suggests further optimizations of expression conditions or alternative bioinformatics approaches for further characterization of this deletion mutant of MtbMAP A.
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A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. J Bacteriol 2012; 194:2594-605. [PMID: 22389480 DOI: 10.1128/jb.05990-11] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ferric uptake regulator (Fur) protein is the major sensor of cellular iron status. When iron is limiting for growth, derepression of the Fur regulon increases the cellular capacity for iron uptake and mobilizes an iron-sparing response mediated in large part by a small noncoding RNA named FsrA. FsrA functions, in collaboration with three small basic proteins (FbpABC), to repress many "low-priority" iron-containing enzymes. We have used transcriptome analyses to gain insights into the scope of the iron-sparing response and to define subsets of genes dependent for their repression on FsrA, FbpAB, and/or FbpC. Enzymes of the tricarboxylic acid (TCA) cycle, including aconitase and succinate dehydrogenase (SDH), are major targets of FsrA-mediated repression, and as a consequence, flux through this pathway is significantly decreased in a fur mutant. FsrA also represses the DctP dicarboxylate permease and the iron-sulfur-containing enzyme glutamate synthase (GltAB), which serves as a central link between carbon and nitrogen metabolism. Allele-specific suppression analysis was used to document a direct RNA-RNA interaction between the FsrA small RNA (sRNA) and the gltAB leader region. We further demonstrated that distinct regions of FsrA are required for the translational repression of the GltAB and SDH enzyme complexes.
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