51
|
Castro-Falcón G, Hahn D, Reimer D, Hughes CC. Thiol Probes To Detect Electrophilic Natural Products Based on Their Mechanism of Action. ACS Chem Biol 2016; 11:2328-36. [PMID: 27294329 DOI: 10.1021/acschembio.5b00924] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
New methods are urgently needed to find novel natural products as structural leads for the development of new drugs against emerging diseases such as cancer and multiresistant bacterial infections. Here we introduce a reactivity-guided drug discovery approach for electrophilic natural products, a therapeutically relevant class of natural products that covalently modify their cellular targets, in crude extracts. Using carefully designed halogenated aromatic reagents, the process furnishes derivatives that are UV-active and highly conspicuous via mass spectrometry by virtue of an isotopically unique bromine or chlorine tag. In addition to the identification of high-value metabolites, the process facilitates the difficult task of structure elucidation by providing derivatives that are primed for X-ray crystallographic analysis. We show that a cysteine probe efficiently and chemoselectively labels enone-, β-lactam-, and β-lactone-based electrophilic natural products (parthenolide, andrographolide, wortmannin, penicillin G, salinosporamide), while a thiophenol probe preferentially labels epoxide-based electrophilic natural products (triptolide, epoxomicin, eponemycin, cyclomarin, salinamide). Using the optimized method, we were able to detect and isolate the epoxide-bearing natural product tirandalydigin from Salinispora and thereby link an orphan gene cluster to its gene product.
Collapse
Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology
and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Dongyup Hahn
- Center for Marine Biotechnology
and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Daniela Reimer
- Center for Marine Biotechnology
and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chambers C. Hughes
- Center for Marine Biotechnology
and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
52
|
Feng Y, Zhang Y, Ebright RH. Structural basis of transcription activation. Science 2016; 352:1330-3. [PMID: 27284196 DOI: 10.1126/science.aaf4417] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/09/2016] [Indexed: 01/25/2023]
Abstract
Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σ(A) holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.
Collapse
Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
53
|
Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
Collapse
|
54
|
Ray L, Yamanaka K, Moore BS. A Peptidyl-Transesterifying Type I Thioesterase in Salinamide Biosynthesis. Angew Chem Int Ed Engl 2016; 55:364-7. [PMID: 26553755 PMCID: PMC4715598 DOI: 10.1002/anie.201508576] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Indexed: 11/10/2022]
Abstract
Salinamide A belongs to a rare class of bicyclic depsipeptide antibiotics in which the installation of a (4-methylhexa-2,4-dienoyl)glycine handle across a hexadepsipeptide core contributes to its chemical complexity and biological properties. Herein, we report the genetic and biochemical basis for salinamide construction in the marine bacterium Streptomyces sp. CNB-091, which involves a novel intermolecular transesterification reaction catalyzed by a type I thioesterase. Heterologous expression studies revealed the central role of the nonribosomal peptide synthetase Sln9 in constructing and installing the distinctive acylglycine "basket handle" of salinamide. Biochemical characterization of the Sln9 thioesterase domain established that transesterification of the serine residue of desmethylsalinamide E with acylated glycyl thioesters yields desmethylsalinamide C.
Collapse
Affiliation(s)
- Lauren Ray
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
| | - Kazuya Yamanaka
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
- Yokohama Research Center, JNC Corporation, Yokohama 236-8605 (Japan)
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92037 (USA).
| |
Collapse
|
55
|
Ray L, Yamanaka K, Moore BS. A Peptidyl-Transesterifying Type I Thioesterase in Salinamide Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
56
|
CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. Proc Natl Acad Sci U S A 2015; 112:E4178-87. [PMID: 26195788 PMCID: PMC4534225 DOI: 10.1073/pnas.1502368112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg(2+) ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. We report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.
Collapse
|
57
|
Feng Y, Degen D, Wang X, Gigliotti M, Liu S, Zhang Y, Das D, Michalchuk T, Ebright YW, Talaue M, Connell N, Ebright RH. Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles. Structure 2015; 23:1470-1481. [PMID: 26190576 DOI: 10.1016/j.str.2015.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 11/30/2022]
Abstract
CBR hydroxamidines are small-molecule inhibitors of bacterial RNA polymerase (RNAP) discovered through high-throughput screening of synthetic-compound libraries. CBR pyrazoles are structurally related RNAP inhibitors discovered through scaffold hopping from CBR hydroxamidines. CBR hydroxamidines and pyrazoles selectively inhibit Gram-negative bacterial RNAP and exhibit selective antibacterial activity against Gram-negative bacteria. Here, we report crystal structures of the prototype CBR hydroxamidine, CBR703, and a CBR pyrazole in complex with E. coli RNAP holoenzyme. In addition, we define the full resistance determinant for CBR703, show that the binding site and resistance determinant for CBR703 do not overlap the binding sites and resistance determinants of other characterized RNAP inhibitors, show that CBR703 exhibits no or minimal cross-resistance with other characterized RNAP inhibitors, and show that co-administration of CBR703 with other RNAP inhibitors results in additive antibacterial activities. The results set the stage for structure-based optimization of CBR inhibitors as antibacterial drugs.
Collapse
Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David Degen
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Xinyue Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gigliotti
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shuang Liu
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Deepankar Das
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Trevor Michalchuk
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yon W Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Meliza Talaue
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Nancy Connell
- Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
58
|
Structural biology of bacterial RNA polymerase. Biomolecules 2015; 5:848-64. [PMID: 25970587 PMCID: PMC4496699 DOI: 10.3390/biom5020848] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022] Open
Abstract
Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.
Collapse
|
59
|
Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS. X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein. J Med Chem 2015; 58:3156-71. [PMID: 25798859 DOI: 10.1021/acs.jmedchem.5b00050] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Squaramides constitute a novel class of RNA polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the RNA polymerase switch region. An iterative chemistry program increased the fraction unbound to human plasma protein from below minimum detection levels, i.e., <1% to 4-6%, while retaining biochemical potency. Since in vitro antimicrobial activity against an efflux-negative strain of Haemophilus influenzae was 4- to 8-fold higher, the combined improvement was at least 20- to 60-fold. Cocrystal structures of Escherichia coli RNA polymerase with two key squaramides showed displacement of the switch 2, predicted to interfere with the conformational change of the clamp domain and/or with binding of template DNA, a mechanism akin to that of natural product myxopyronin. Furthermore, the structures confirmed the chemical features required for biochemical potency. The terminal isoxazole and benzyl rings bind into distinct relatively narrow, hydrophobic pockets, and both are required for biochemical potency. In contrast, the linker composed of squarate and piperidine accesses different conformations in their respective cocrystal structures with RNA polymerase, reflecting its main role of proper orientation of the aforementioned terminal rings. These observations further explain the tolerance of hydrophilic substitutions in the linker region that was exploited to improve the fraction unbound to human plasma protein while retaining biochemical potency.
Collapse
Affiliation(s)
- Vadim Molodtsov
- †Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | | | | | | | | | | | - Craig E Masse
- ⊥Nimbus Therapeutics, Inc., Cambridge, Massachusetts 02141, United States
| | | | - Katsuhiko S Murakami
- †Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
60
|
Hassan HM, Degen D, Jang KH, Ebright RH, Fenical W. Salinamide F, new depsipeptide antibiotic and inhibitor of bacterial RNA polymerase from a marine-derived Streptomyces sp. J Antibiot (Tokyo) 2015; 68:206-9. [PMID: 25227504 PMCID: PMC4363298 DOI: 10.1038/ja.2014.122] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/10/2014] [Accepted: 08/13/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Hossam M Hassan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - David Degen
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Richard H Ebright
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
61
|
Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K. A new antibiotic kills pathogens without detectable resistance. Nature 2015; 517:455-9. [PMID: 25561178 PMCID: PMC7414797 DOI: 10.1038/nature14098] [Citation(s) in RCA: 1585] [Impact Index Per Article: 176.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/19/2014] [Indexed: 01/28/2023]
Abstract
Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.
Collapse
Affiliation(s)
- Losee L Ling
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Tanja Schneider
- 1] Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, University of Bonn, Bonn 53115, Germany [2] German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53115 Bonn, Germany
| | - Aaron J Peoples
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Amy L Spoering
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Ina Engels
- 1] Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, University of Bonn, Bonn 53115, Germany [2] German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53115 Bonn, Germany
| | - Brian P Conlon
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, Massachusetts 02115, USA
| | - Anna Mueller
- 1] Institute of Medical Microbiology, Immunology and Parasitology-Pharmaceutical Microbiology Section, University of Bonn, Bonn 53115, Germany [2] German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53115 Bonn, Germany
| | - Till F Schäberle
- 1] German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 53115 Bonn, Germany [2] Institute for Pharmaceutical Biology, University of Bonn, Bonn 53115, Germany
| | - Dallas E Hughes
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Slava Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | | | | | | | - Douglas R Cohen
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Cintia R Felix
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | | | | | - Anthony G Nitti
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Ashley M Zullo
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Chao Chen
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, Massachusetts 02115, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, Massachusetts 02115, USA
| |
Collapse
|
62
|
Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
Collapse
Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | | |
Collapse
|