1
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Ghosh B, Bera S, Ghosh P, Samanta R. Rh(III)-Catalyzed mild straightforward synthesis of quinoline-braced cyclophane macrocycles via migratory insertion. Chem Commun (Camb) 2021; 57:13134-13137. [PMID: 34807203 DOI: 10.1039/d1cc04418d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient Rh(III)-catalyzed straightforward strategy is developed for the synthesis of quinoline braced cyclophane macrocycles via methyl (sp3) C-H functionalization. The method is mild, simple and regioselective with various ring sizes and has good functional group tolerance. The method proceeds via C8-methyl metalation, metal-carbene formation and a subsequent migratory insertion. High dilution is not necessary for this macrocyclization and the only byproduct is nitrogen. A preliminary investigation shows that the C-H metalation step is the rate-determining step.
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Affiliation(s)
- Bidhan Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Satabdi Bera
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Pintu Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Rajarshi Samanta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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2
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Bouz G, Zitko J. Inhibitors of aminoacyl-tRNA synthetases as antimycobacterial compounds: An up-to-date review. Bioorg Chem 2021; 110:104806. [PMID: 33799176 DOI: 10.1016/j.bioorg.2021.104806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are crucial for the correct assembly of amino acids to cognate tRNA to maintain the fidelity of proteosynthesis. AaRSs have become a hot target in antimicrobial research. Three aaRS inhibitors are already in clinical practice; antibacterial mupirocin inhibits the synthetic site of isoleucyl-tRNA synthetase, antifungal tavaborole inhibits the editing site of leucyl-tRNA synthetase, and antiprotozoal halofuginone inhibits proline-tRNA synthetase. According to the World Health Organization, tuberculosis globally remains the leading cause of death from a single infectious agent. The rising incidence of multidrug-resistant tuberculosis is alarming and urges the search for new antimycobacterial compounds, preferably with yet unexploited mechanism of action. In this literature review, we have covered the up-to-date state in the field of inhibitors of mycobacterial aaRSs. The most studied aaRS in mycobacteria is LeuRS with at least four structural types of inhibitors, followed by TyrRS and AspRS. Inhibitors of MetRS, LysRS, and PheRS were addressed in a single significant study each. In many cases, the enzyme inhibition activity translated into micromolar or submicromolar inhibition of growth of mycobacteria. The most promising aaRS inhibitor as an antimycobacterial compound is GSK656 (compound 8), the only aaRS inhibitor in clinical trials (Phase IIa) for systemic use against tuberculosis. GSK656 is orally available and shares the oxaborole tRNA-trapping mechanism of action with antifungal tavaborole.
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Affiliation(s)
- Ghada Bouz
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University
| | - Jan Zitko
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University.
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3
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4
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Gram-scale preparation of the antibiotic lead compound salicyl-AMS, a potent inhibitor of bacterial salicylate adenylation enzymes. Methods Enzymol 2020. [PMID: 32416922 DOI: 10.1016/bs.mie.2020.04.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Salicyl-AMS (1) is a potent inhibitor of salicylate adenylation enzymes used in bacterial siderophore biosynthesis and a promising lead compound for the treatment of tuberculosis. An optimized, multigram synthesis is presented, which provides salicyl-AMS as its sodium salt (1·Na) in three synthetic steps followed by a two-step salt formation process. The synthesis proceeds in 11.6% overall yield from commercially available adenosine 2',3'-acetonide and provides highly purified material.
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5
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Vickery CR, McCulloch IP, Sonnenschein EC, Beld J, Noel JP, Burkart MD. Dissecting modular synthases through inhibition: A complementary chemical and genetic approach. Bioorg Med Chem Lett 2020; 30:126820. [PMID: 31812466 DOI: 10.1016/j.bmcl.2019.126820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/23/2023]
Abstract
Modular synthases, such as fatty acid, polyketide, and non-ribosomal peptide synthases (NRPSs), are sophisticated machineries essential in both primary and secondary metabolism. Various techniques have been developed to understand their genetic background and enzymatic abilities. However, uncovering the actual biosynthetic pathways remains challenging. Herein, we demonstrate a pipeline to study an assembly line synthase by interrogating the enzymatic function of each individual enzymatic domain of BpsA, a NRPS that produces the blue 3,3'-bipyridyl pigment indigoidine. Specific inhibitors for each biosynthetic domain of BpsA were obtained or synthesized, and the enzymatic performance of BpsA upon addition of each inhibitor was monitored by pigment development in vitro and in living bacteria. The results were verified using genetic mutants to inactivate each domain. Finally, the results complemented the currently proposed biosynthetic pathway of BpsA.
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Affiliation(s)
- Christopher R Vickery
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian P McCulloch
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Eva C Sonnenschein
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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6
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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7
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Bythrow GV, Mohandas P, Guney T, Standke LC, Germain GA, Lu X, Ji C, Levendosky K, Chavadi SS, Tan DS, Quadri LEN. Kinetic Analyses of the Siderophore Biosynthesis Inhibitor Salicyl-AMS and Analogues as MbtA Inhibitors and Antimycobacterial Agents. Biochemistry 2019; 58:833-847. [PMID: 30582694 DOI: 10.1021/acs.biochem.8b01153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a paramount need for expanding the drug armamentarium to counter the growing problem of drug-resistant tuberculosis. Salicyl-AMS, an inhibitor of salicylic acid adenylation enzymes, is a first-in-class antibacterial lead compound for the development of tuberculosis drugs targeting the biosynthesis of salicylic-acid-derived siderophores. In this study, we determined the Ki of salicyl-AMS for inhibition of the salicylic acid adenylation enzyme MbtA from Mycobacterium tuberculosis (MbtAtb), designed and synthesized two new salicyl-AMS analogues to probe structure-activity relationships (SAR), and characterized these two analogues alongside salicyl-AMS and six previously reported analogues in biochemical and cell-based studies. The biochemical studies included determination of kinetic parameters ( Kiapp, konapp, koff, and tR) and analysis of the mechanism of inhibition. For these studies, we optimized production and purification of recombinant MbtAtb, for which Km and kcat values were determined, and used the enzyme in conjunction with an MbtAtb-optimized, continuous, spectrophotometric assay for MbtA activity and inhibition. The cell-based studies provided an assessment of the antimycobacterial activity and postantibiotic effect of the nine MbtAtb inhibitors. The antimycobacterial properties were evaluated using a strain of nonpathogenic, fast-growing Mycobacterium smegmatis that was genetically engineered for MbtAtb-dependent susceptibility to MbtA inhibitors. This convenient model system greatly facilitated the cell-based studies by bypassing the methodological complexities associated with the use of pathogenic, slow-growing M. tuberculosis. Collectively, these studies provide new information on the mechanism of inhibition of MbtAtb by salicyl-AMS and eight analogues, afford new SAR insights for these inhibitors, and highlight several suitable candidates for future preclinical evaluation.
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Affiliation(s)
- Glennon V Bythrow
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Poornima Mohandas
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Tezcan Guney
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Lisa C Standke
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Gabrielle A Germain
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Xuequan Lu
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Keith Levendosky
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Sivagami Sundaram Chavadi
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Tri-Institutional Research Program , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Luis E N Quadri
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States.,Biochemistry Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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8
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Abstract
Atropisomerism is a dynamic type of axial chirality that is ubiquitous in medicinal chemistry. There are several examples of stable atropisomeric US FDA-approved drugs and experimental compounds, and in each case the atropisomers of these compounds possess drastically different biological activities. Rapidly interconverting atropisomerism is even more prevalent, and while such compounds are typically considered achiral, they bind their protein targets in an atroposelective fashion, with the nonrelevant atropisomer contributing little to the desired activities. It has been recently demonstrated that various properties of an interconverting atropisomer can be modulated through the synthesis of atropisomer stable and pure analogs. Herein we discuss examples of atropisomerism in drug discovery as well as challenges and opportunities moving forward.
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9
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Po P, Delaney E, Gamper H, Szantai-Kis DM, Speight L, Tu L, Kosolapov A, Petersson EJ, Hou YM, Deutsch C. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. J Mol Biol 2017; 429:1873-1888. [PMID: 28483649 DOI: 10.1016/j.jmb.2017.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 12/17/2022]
Abstract
All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the life-sustaining tasks of faithfully decoding mRNA and catalyzing peptide bond formation at the peptidyl transferase center (PTC). The ribosome has evolved an exit tunnel to host the elongating new peptide, protect it from proteolytic digestion, and guide its emergence. It is here that the nascent chain begins to fold. This folding process depends on the rate of translation at the PTC. We report here that besides PTC events, translation kinetics depend on steric constraints on nascent peptide side chains and that confined movements of cramped side chains within and through the tunnel fine-tune elongation rates.
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Affiliation(s)
- Pengse Po
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Delaney
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lee Speight
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - LiWei Tu
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrey Kosolapov
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Ji C, Sharma I, Pratihar D, Hudson LL, Maura D, Guney T, Rahme LG, Pesci EC, Coleman JP, Tan DS. Designed Small-Molecule Inhibitors of the Anthranilyl-CoA Synthetase PqsA Block Quinolone Biosynthesis in Pseudomonas aeruginosa. ACS Chem Biol 2016; 11:3061-3067. [PMID: 27658001 PMCID: PMC5117135 DOI: 10.1021/acschembio.6b00575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
The Gram-negative bacterial pathogen Pseudomonas aeruginosa uses three interconnected intercellular
signaling systems regulated
by the transcription factors LasR, RhlR, and MvfR (PqsR), which mediate
bacterial cell–cell communication via small-molecule natural
products and control the production of a variety of virulence factors.
The MvfR system is activated by and controls the biosynthesis of the
quinolone quorum sensing factors HHQ and PQS. A key step in the biosynthesis
of these quinolones is catalyzed by the anthranilyl-CoA synthetase
PqsA. To develop inhibitors of PqsA as novel potential antivirulence
antibiotics, we report herein the design and synthesis of sulfonyladeonsine-based
mimics of the anthranilyl-AMP reaction intermediate that is bound
tightly by PqsA. Biochemical, microbiological, and pharmacological
studies identified two potent PqsA inhibitors, anthranilyl-AMS (1) and anthranilyl-AMSN (2), that decreased HHQ
and PQS production in P. aeruginosa strain
PA14. However, these compounds did not inhibit
production of the virulence factor pyocyanin. Moreover, they exhibited
limited bacterial penetration in compound accumulation studies. This
work provides the most potent PqsA inhibitors reported to date and
sets the stage for future efforts to develop analogues with improved
cellular activity to investigate further the complex relationships
between quinolone biosynthesis and virulence factor production in P. aeruginosa and the therapeutic potential of targeting
PqsA.
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Affiliation(s)
| | | | | | - L. Lynn Hudson
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - Damien Maura
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
| | | | - Laurence G. Rahme
- Department
of Surgery, Harvard Medical School and Massachusettts General Hospital, 50
Blossom Street, Boston, Massachusetts 02114, United States
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Shriners Hospitals for
Children Boston, Boston, Massachusetts 02114, United States
| | - Everett C. Pesci
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
| | - James P. Coleman
- Department
of Microbiology and Immunology, The Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, United States
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11
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Balhara M, Chaudhary R, Ruhil S, Singh B, Dahiya N, Parmar VS, Jaiwal PK, Chhillar AK. Siderophores; iron scavengers: the novel & promising targets for pathogen specific antifungal therapy. Expert Opin Ther Targets 2016; 20:1477-1489. [PMID: 27797604 DOI: 10.1080/14728222.2016.1254196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The recent emergence of resistance, toxicity paradigm and limited efficacy of conventional antifungal drugs necessitate the identification of de novo targets in fungal metabolism. One of the most critical physiological processes during in vivo pathogenesis is maintenance of iron homeostasis. The most life threatening opportunistic human fungal pathogens like Aspergillus, Candida and Cryptococcus exploit the siderophore mediated iron uptake mechanism either for survival, virulence, propagation or resistance to oxidative stress envisaged in vivo during infection. Areas covered: In this review, we will highlight the metabolic pathways; specifically siderophore biosynthesis, uptake and utilisation, triggered in the fungal pathogens in iron starving conditions and the various putative targets viable in these pathways to be recruited as novel therapeutic antidotes either via biosynthetic enzymes catalytic site inhibitors or as drug conjugates through trojan horse approach and further role in the development of fungal specific reliable diagnostic markers. Expert opinion: Siderophores are the weapons released by a pathogen to conquer the battle for iron acquisition. Hence, the fungal siderophore biosynthetic pathways along with their uptake and utilisation mechanisms represent an ideal target for pathogen specific, host friendly therapeutic strategy which would block the proliferation of parasite without causing any harm to the mammalian host.
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Affiliation(s)
- Meenakshi Balhara
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Renu Chaudhary
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Sonam Ruhil
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Bharat Singh
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Nisha Dahiya
- b Division of Epidemiology and Communicable Diseases , Indian Council of Medical Research , Delhi , India
| | - Virinder S Parmar
- c Bioorganic Laboratory, Department of Chemistry , University of Delhi , Delhi , India
| | - Pawan K Jaiwal
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Anil K Chhillar
- a Centre for Biotechnology , Maharshi Dayanand University , Rohtak , Haryana , India
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12
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Design, synthesis, and biological evaluation of α-hydroxyacyl-AMS inhibitors of amino acid adenylation enzymes. Bioorg Med Chem Lett 2016; 26:5340-5345. [PMID: 27692545 DOI: 10.1016/j.bmcl.2016.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/09/2016] [Indexed: 11/22/2022]
Abstract
Biosynthesis of bacterial natural-product virulence factors is emerging as a promising antibiotic target. Many such natural products are produced by nonribosomal peptide synthetases (NRPS) from amino acid precursors. To develop selective inhibitors of these pathways, we have previously described aminoacyl-AMS (sulfamoyladenosine) macrocycles that inhibit NRPS amino acid adenylation domains but not mechanistically-related aminoacyl-tRNA synthetases. To improve the cell permeability of these inhibitors, we explore herein replacement of the α-amino group with an α-hydroxy group. In both macrocycles and corresponding linear congeners, this leads to decreased biochemical inhibition of the cysteine adenylation domain of the Yersina pestis siderophore synthetase HMWP2, which we attribute to loss of an electrostatic interaction with a conserved active-site aspartate. However, inhibitory activity can be regained by installing a cognate β-thiol moiety in the linear series. This provides a path forward to develop selective, cell-penetrant inhibitors of the biosynthesis of virulence factors to probe their biological functions and potential as therapeutic targets.
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13
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Krieger JP, Ricci G, Lesuisse D, Meyer C, Cossy J. Harnessing C−H Activation of Benzhydroxamates as a Macrocyclization Strategy: Synthesis of Structurally Diverse Macrocyclic Isoquinolones. Chemistry 2016; 22:13469-73. [DOI: 10.1002/chem.201602332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Jean-Philippe Krieger
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
| | - Gino Ricci
- Sanofi Process Development; 45 chemin de Mételine BP15 04210 Sisteron Cedex France
| | - Dominique Lesuisse
- R&D Sanofi; 1 avenue Pierre Brossolette 91385 Chilly-Mazarin Cedex France
| | - Christophe Meyer
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
| | - Janine Cossy
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
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14
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Matarlo JS, Evans CE, Sharma I, Lavaud LJ, Ngo SC, Shek R, Rajashankar KR, French JB, Tan DS, Tonge PJ. Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. Biochemistry 2015; 54:6514-6524. [PMID: 26394156 DOI: 10.1021/acs.biochem.5b00966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.
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Affiliation(s)
- Joe S Matarlo
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Christopher E Evans
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Indrajeet Sharma
- Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Lubens J Lavaud
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Stephen C Ngo
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Roger Shek
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Building 436E, Argonne National Laboratory, Argonne, IL 60439
| | - Jarrod B French
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400
| | - Derek S Tan
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065.,Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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15
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Efficient functionalization of 2-amino-6-chloropurine derivatives at C-8 via 8-lithiated species. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.09.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Lamb AL. Breaking a pathogen's iron will: Inhibiting siderophore production as an antimicrobial strategy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1054-70. [PMID: 25970810 DOI: 10.1016/j.bbapap.2015.05.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022]
Abstract
The rise of antibiotic resistance is a growing public health crisis. Novel antimicrobials are sought, preferably developing nontraditional chemical scaffolds that do not inhibit standard targets such as cell wall synthesis or the ribosome. Iron scavenging has been proposed as a viable target, because bacterial and fungal pathogens must overcome the nutritional immunity of the host to be virulent. This review highlights the recent work toward exploiting the biosynthetic enzymes of siderophore production for the design of next generation antimicrobials.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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17
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Davis TD, Gerry CJ, Tan DS. General platform for systematic quantitative evaluation of small-molecule permeability in bacteria. ACS Chem Biol 2014; 9:2535-44. [PMID: 25198656 PMCID: PMC4245172 DOI: 10.1021/cb5003015] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery.
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Affiliation(s)
- Tony D. Davis
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Christopher J. Gerry
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Derek S. Tan
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
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18
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Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL. Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism. Bioorg Med Chem 2014; 22:5961-9. [PMID: 25282647 DOI: 10.1016/j.bmc.2014.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/31/2023]
Abstract
Antibiotic resistance is a growing health concern, and new avenues of antimicrobial drug design are being actively sought. One suggested pathway to be targeted for inhibitor design is that of iron scavenging through siderophores. Here we present a high throughput screen to the isochorismate-pyruvate lyase of Pseudomonas aeruginosa, an enzyme required for the production of the siderophore pyochelin. Compounds identified in the screen are high nanomolar to low micromolar inhibitors of the enzyme and produce growth inhibition in PAO1 P. aeruginosa in the millimolar range under iron-limiting conditions. The identified compounds were also tested for enzymatic inhibition of Escherichia coli chorismate mutase, a protein of similar fold and similar chemistry, and of Yersinia enterocolitica salicylate synthase, a protein of differing fold but catalyzing the same lyase reaction. In both cases, subsets of the inhibitors from the screen were found to be inhibitory to enzymatic activity (mutase or synthase) in the micromolar range and capable of growth inhibition in their respective organisms (E. coli or Y. enterocolitica).
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Qianyi Luo
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Andrew P Riley
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Byron Taylor
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Anuradha Roy
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Ross L Stein
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Thomas E Prisinzano
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States.
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19
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Specific enrichment of nonribosomal peptide synthetase module by an affinity probe for adenylation domains. Bioorg Med Chem Lett 2013; 24:865-9. [PMID: 24398296 DOI: 10.1016/j.bmcl.2013.12.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/15/2013] [Accepted: 12/19/2013] [Indexed: 01/22/2023]
Abstract
We targeted the development of an affinity probe for adenylation (A) domains that can facilitate enrichment, identification, and quantification of A domain-containing modules in nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrids and NRPSs. A 5'-O-sulfamoyladenosine (AMS) non-hydrolyzable analogue of adenosine monophosphate (AMP) has been reported as a scaffold for the design of inhibitors exhibiting tight binding of adenylation enzymes. Here we describe the application of an affinity probe for A domains. Our synthetic probe, a biotinylated L-Phe-AMS (L-Phe-AMS-biotin) specifically targets the A domains in NRPS modules that activates L-Phe to an aminoacyladenylate intermediate in both recombinant NRPS enzyme systems and whole proteomes.
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20
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Spillane W, Malaubier JB. Sulfamic Acid and Its N- and O-Substituted Derivatives. Chem Rev 2013; 114:2507-86. [DOI: 10.1021/cr400230c] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- William Spillane
- School
of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Jean-Baptiste Malaubier
- Manufacturing Science
and
Technology, Roche Ireland Limited, Clarecastle, Co. Clare, Ireland
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21
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Vondenhoff GHM, Van Aerschot A. Aminoacyl-tRNA synthetase inhibitors as potential antibiotics. Eur J Med Chem 2011; 46:5227-36. [PMID: 21968372 DOI: 10.1016/j.ejmech.2011.08.049] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 11/29/2022]
Abstract
Increasing resistance to antibiotics is a major problem worldwide and provides the stimulus for development of new bacterial inhibitors with preferably different modes of action. In search for new leads, several new bacterial targets are being exploited beside the use of traditional screening methods. Hereto, inhibition of bacterial protein synthesis is a long-standing validated target. Aminoacyl-tRNA synthetases (aaRSs) play an indispensable role in protein synthesis and their structures proved quite conserved in prokaryotes and eukaryotes. However, some divergence has occurred allowing the development of selective aaRS inhibitors. Following an outline on the action mechanism of aaRSs, an overview will be given of already existing aaRS inhibitors, which are largely based on mimics of the aminoacyl-adenylates, the natural reaction intermediates. This is followed by a discussion on more recent developments in the field and the bioavailability problem.
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Affiliation(s)
- Gaston H M Vondenhoff
- Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Minderbroedersstraat 10, BE-3000 Leuven, Belgium
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22
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Characterization of peptide chain length and constituency requirements for YejABEF-mediated uptake of microcin C analogues. J Bacteriol 2011; 193:3618-23. [PMID: 21602342 DOI: 10.1128/jb.00172-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin C (McC), a natural antibacterial compound consisting of a heptapeptide attached to a modified adenosine, is actively taken up by the YejABEF transporter, after which it is processed by cellular aminopeptidases, releasing the nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC analogues with variable length of the peptide moiety were synthesized and evaluated in order to characterize the substrate preferences of the YejABEF transporter. It was shown that a minimal peptide chain length of 6 amino acids and the presence of an N-terminal formyl-methionyl-arginyl sequence are required for transport.
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23
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24
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Drake EJ, Duckworth BP, Neres J, Aldrich CC, Gulick AM. Biochemical and structural characterization of bisubstrate inhibitors of BasE, the self-standing nonribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis. Biochemistry 2010; 49:9292-305. [PMID: 20853905 DOI: 10.1021/bi101226n] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The human pathogen Acinetobacter baumannii produces a siderophore called acinetobactin that is derived from one molecule each of threonine, histidine, and 2,3-dihydroxybenzoic acid (DHB). The activity of several nonribosomal peptide synthetase (NRPS) enzymes is used to combine the building blocks into the final molecule. The acinetobactin synthesis pathway initiates with a self-standing adenylation enzyme, BasE, that activates the DHB molecule and covalently transfers it to the pantetheine cofactor of an aryl-carrier protein of BasF, a strategy that is shared with many siderophore-producing NRPS clusters. In this reaction, DHB reacts with ATP to form the aryl adenylate and pyrophosphate. In a second partial reaction, the DHB is transferred to the carrier protein. Inhibitors of BasE and related enzymes have been identified that prevent growth of bacteria on iron-limiting media. Recently, a new inhibitor of BasE has been identified via high-throughput screening using a fluorescence polarization displacement assay. We present here biochemical and structural studies to examine the binding mode of this inhibitor. The kinetics of the wild-type BasE enzyme is shown, and inhibition studies demonstrate that the new compound exhibits competitive inhibition against both ATP and 2,3-dihydroxybenzoate. Structural examination of BasE bound to this inhibitor illustrates a novel binding mode in which the phenyl moiety partially fills the enzyme pantetheine binding tunnel. Structures of rationally designed bisubstrate inhibitors are also presented.
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Affiliation(s)
- Eric J Drake
- Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203-1102, USA
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25
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Tellam JP, Carbery DR. Development of the Ireland−Claisen Rearrangement of Alkoxy- and Aryloxy-Substituted Allyl Glycinates. J Org Chem 2010; 75:7809-21. [PMID: 20958078 DOI: 10.1021/jo1017124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James P. Tellam
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - David R. Carbery
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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26
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Zettler J, Mootz HD. Biochemical evidence for conformational changes in the cross-talk between adenylation and peptidyl-carrier protein domains of nonribosomal peptide synthetases. FEBS J 2010; 277:1159-71. [PMID: 20121951 DOI: 10.1111/j.1742-4658.2009.07551.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nonribosomal peptide synthetases serve as multidomain protein templates for producing a wealth of pharmaceutically important natural products. For the correct assembly of the desired natural product the interactions between the different catalytic centres and the reaction intermediates bound to the peptidyl carrier protein must be precisely controlled at spatial and temporal levels. We have investigated the interplay between the adenylation (A) domain and the peptidyl carrier protein in the gramicidin S synthetase I (EC 5.1.1.11) via partial tryptic digests, native PAGE and gel-filtration analysis, as well as by chemical labeling experiments. Our data imply that the 4'-phosphopantetheine moiety of the peptidyl carrier protein changes its position as a result of a conformational change in the A domain, which is induced by the binding of an amino acyl adenylate mimic. The productive interaction between the two domains at the stage of the amino acyl transfer onto the 4'-phosphopantetheine moiety is accompanied by a highly compact protein conformation of the holo-protein. These results provide the first biochemical evidence for the occurrence of conformational changes in the cross-talk between A and peptidyl carrier protein domains of a multidomain nonribosomal peptide synthetase.
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27
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Laroche C, Kerwin SM. Lithiation and functionalization of 1-alkynylimidazoles at the 2-position. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.06.133] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Synthetic microcin C analogs targeting different aminoacyl-tRNA synthetases. J Bacteriol 2009; 191:6273-80. [PMID: 19684138 DOI: 10.1128/jb.00829-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin C (McC) is a potent antibacterial agent produced by some strains of Escherichia coli. McC consists of a ribosomally synthesized heptapeptide with a modified AMP attached through a phosphoramidate linkage to the alpha-carboxyl group of the terminal aspartate. McC is a Trojan horse inhibitor: it is actively taken inside sensitive cells and processed there, and the product of processing, a nonhydrolyzable aspartyl-adenylate, inhibits translation by preventing aminoacylation of tRNA(Asp) by aspartyl-tRNA synthetase (AspRS). Changing the last residue of the McC peptide should result in antibacterial compounds with targets other than AspRS. However, mutations that introduce amino acid substitutions in the last position of the McC peptide abolish McC production. Here, we report total chemical synthesis of three McC-like compounds containing a terminal aspartate, glutamate, or leucine attached to adenosine through a nonhydrolyzable sulfamoyl bond. We show that all three compounds function in a manner similar to that of McC, but the first compound inhibits bacterial growth by targeting AspRS while the latter two inhibit, respectively, GluRS and LeuRS. Our approach opens a way for creation of new antibacterial Trojan horse agents that target any 1 of the 20 tRNA synthetases in the cell.
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29
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Foley TL, Burkart MD. A homogeneous resonance energy transfer assay for phosphopantetheinyl transferase. Anal Biochem 2009; 394:39-47. [PMID: 19573516 DOI: 10.1016/j.ab.2009.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/24/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022]
Abstract
Phosphopantetheinyl transferase plays an essential role in activating fatty acid, polyketide, and nonribosomal peptide biosynthetic pathways, catalyzing covalent attachment of a 4'-phosphopantetheinyl group to a conserved residue within carrier protein domains. This enzyme has been validated as an essential gene to primary metabolism and presents a target for the identification of antibiotics with a new mode of action. Here we report the development of a homogeneous resonance energy transfer assay using fluorescent coenzyme A derivatives and a surrogate peptide substrate that can serve to identify inhibitors of this enzyme class. This assay lays a blueprint for translation of these techniques to other transferase enzymes that accept fluorescent substrate analogues.
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Affiliation(s)
- Timothy L Foley
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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30
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Lu X, Zhang H, Tonge PJ, Tan DS. Mechanism-based inhibitors of MenE, an acyl-CoA synthetase involved in bacterial menaquinone biosynthesis. Bioorg Med Chem Lett 2008; 18:5963-6. [PMID: 18762421 PMCID: PMC2628629 DOI: 10.1016/j.bmcl.2008.07.130] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/22/2022]
Abstract
Menaquinone (vitamin K(2)) is an essential component of the electron transfer chain in many pathogens, including Mycobacterium tuberculosis and Staphylococcus aureus, and menaquinone biosynthesis is a potential target for antibiotic drug discovery. We report herein a series of mechanism-based inhibitors of MenE, an acyl-CoA synthetase that catalyzes adenylation and thioesterification of o-succinylbenzoic acid (OSB) during menaquinone biosynthesis. The most potent compound inhibits MenE with an IC(50) value of 5.7microM.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
| | - Huaning Zhang
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Peter J. Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Derek S. Tan
- Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan–Kettering Cancer Center, New York, NY 10065, USA
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31
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Neres J, Labello NP, Somu RV, Boshoff HI, Wilson DJ, Vannada J, Chen L, Barry CE, Bennett EM, Aldrich CC. Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structure-activity relationships of the nucleobase domain of 5'-O-[N-(salicyl)sulfamoyl]adenosine. J Med Chem 2008; 51:5349-70. [PMID: 18690677 DOI: 10.1021/jm800567v] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
5'-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) is a prototype for a new class of antitubercular agents that inhibit the aryl acid adenylating enzyme (AAAE) known as MbtA involved in biosynthesis of the mycobactins. Herein, we report the structure-based design, synthesis, biochemical, and biological evaluation of a comprehensive and systematic series of analogues, exploring the structure-activity relationship of the purine nucleobase domain of Sal-AMS. Significantly, 2-phenyl-Sal-AMS derivative 26 exhibited exceptionally potent antitubercular activity with an MIC99 under iron-deficient conditions of 0.049 microM while the N-6-cyclopropyl-Sal-AMS 16 led to improved potency and to a 64-enhancement in activity under iron-deficient conditions relative to iron-replete conditions, a phenotype concordant with the designed mechanism of action. The most potent MbtA inhibitors disclosed here display in vitro antitubercular activity superior to most current first line TB drugs, and these compounds are also expected to be useful against a wide range of pathogens that require aryl-capped siderphores for virulence.
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Affiliation(s)
- João Neres
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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32
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Stirrett KL, Ferreras JA, Rossi SM, Moy RL, Fonseca FV, Quadri LE. A multicopy suppressor screening approach as a means to identify antibiotic resistance determinant candidates in Yersinia pestis. BMC Microbiol 2008; 8:122. [PMID: 18644132 PMCID: PMC2500020 DOI: 10.1186/1471-2180-8-122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/21/2008] [Indexed: 11/29/2022] Open
Abstract
Background Yersinia pestis is the causative agent of plague and a potential agent of bioterrorism and biowarfare. The plague biothreat and the emergence of multidrug-resistant plague underscore the need to increase our understanding of the intrinsic potential of Y. pestis for developing antimicrobial resistance and to anticipate the mechanisms of resistance that may emerge in Y. pestis. Identification of Y. pestis genes that, when overexpressed, are capable of reducing antibiotic susceptibility is a useful strategy to expose genes that this pathogen may rely upon to evolve antibiotic resistance via a vertical modality. In this study, we explored the use of a multicopy suppressor, Escherichia coli host-based screening approach as a means to expose antibiotic resistance determinant candidates in Y. pestis. Results We constructed a multicopy plasmid-based, Y. pestis genome-wide expression library of nearly 16,000 clones in E. coli and screened the library for suppressors of the antimicrobial activity of ofloxacin, a fluoroquinolone antibiotic. The screen permitted the identification of a transcriptional regulator-encoding gene (robAYp) that increased the MIC99 of ofloxacin by 23-fold when overexpressed from a multicopy plasmid in Y. pestis. Additionally, we found that robAYp overexpression in Y. pestis conferred low-level resistance to many other antibiotics and increased organic solvent tolerance. Overexpression of robAYp also upregulated the expression of several efflux pumps in Y. pestis. Conclusion Our study provides proof of principle for the use of multicopy suppressor screening based on the tractable and easy-to-manipulate E. coli host as a means to identify antibiotic resistance determinant candidates of Y. pestis.
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Affiliation(s)
- Karen L Stirrett
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA.
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33
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Driggers EM, Hale SP, Lee J, Terrett NK. The exploration of macrocycles for drug discovery — an underexploited structural class. Nat Rev Drug Discov 2008; 7:608-24. [DOI: 10.1038/nrd2590] [Citation(s) in RCA: 984] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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34
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Cisar JS, Tan DS. Small molecule inhibition of microbial natural product biosynthesis-an emerging antibiotic strategy. Chem Soc Rev 2008; 37:1320-9. [PMID: 18568158 DOI: 10.1039/b702780j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A variety of natural products modulate critical biological processes in the microorganisms that produce them. Thus, inhibition of the corresponding natural product biosynthesis pathways represents a promising avenue to develop novel antibiotics. In this tutorial review, we describe several recent examples of designed small molecule inhibitors of microbial natural product biosynthesis and their use in evaluating this emerging antibiotic strategy.
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Affiliation(s)
- Justin S Cisar
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, NY 10065, USA
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