1
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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2
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Treisman M, Coe L, Zhao Y, Sasi VM, Gullick J, Hansen MH, Ly A, Leichthammer V, Hess C, Machell DL, Schittenhelm RB, Hooper J, Jackson CJ, Tailhades J, De Voss JJ, Cryle MJ. An Engineered Biarylitide Cross-Linking P450 from RiPP Biosynthesis Generates Alternative Cyclic Peptides. Org Lett 2024; 26:1828-1833. [PMID: 38417822 DOI: 10.1021/acs.orglett.3c04366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Cytochrome-P450-mediated cross-linking of ribosomally encoded peptides (RiPPs) is rapidly expanding and displays great potential for biocatalysis. Here, we demonstrate that active site engineering of the biarylitide cross-linking enzyme P450Blt enables the formation of His-X-Tyr and Tyr-X-Tyr cross-linked peptides, thus showing how such P450s can be further exploited to produce alternate cyclic tripeptides with controlled cross-linking states.
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Affiliation(s)
- Maxine Treisman
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Laura Coe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Vishnu Mini Sasi
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Jemma Gullick
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Mathias H Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Aviva Ly
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Victor Leichthammer
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Caroline Hess
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Daniel L Machell
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Joel Hooper
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Colin J Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Acton, ACT 2601, Australia
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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3
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Liu CL, Wang ZJ, Shi J, Yan ZY, Zhang GD, Jiao RH, Tan RX, Ge HM. P450-Modified Multicyclic Cyclophane-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides. Angew Chem Int Ed Engl 2024; 63:e202314046. [PMID: 38072825 DOI: 10.1002/anie.202314046] [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: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Cyclic peptides with cyclophane linkers are an attractive compound type owing to the fine-tuned rigid three-dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C-C and C-O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450-modified multicyclic RiPPs, we set out to find cryptic and unknown P450-modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450-modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450-modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450-modified multicyclic RiPPs with different cyclophane linkers through heterologous expression. Further mutation of the key ring-forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane-containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.
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Affiliation(s)
- Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zi Jie Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Guo Dong Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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4
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Koehler MFT, Chen YC, Chen Y, Chen Y, Crawford JJ, Durk MR, Garland K, Hanan EJ, Higuchi RI, Hu H, Ly CQ, Paraselli PG, Roberts TC, Schwarz JB, Smith PA, Yu Z, Heise CE. Lipid Tales: Optimizing Arylomycin Membrane Anchors. ACS Med Chem Lett 2023; 14:1524-1530. [PMID: 37974942 PMCID: PMC10641904 DOI: 10.1021/acsmedchemlett.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023] Open
Abstract
Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts, no new antibiotic class with activity against Gram-negative bacteria has been approved in over 50 years. LepB inhibitors (LepBi) based on the arylomycin class of natural products are a novel class of antibiotics and function by inhibiting the bacterial type I signal peptidase (SPase) in Gram-negative bacteria. One critical aspect of LepBi development involves optimization of the membrane-anchored lipophilic portion of the molecule. We therefore developed an approach that assesses the effect of this portion on the complicated equilibria of plasma protein binding, crossing the outer membrane of Gram-negative bacteria and anchoring in the bacterial inner membrane to facilitate SPase binding. Our findings provide important insights into the development of antibacterial agents where the target is associated with the inner membrane of Gram-negative bacteria.
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Affiliation(s)
- Michael F. T. Koehler
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yi-Chen Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yongsheng Chen
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Yuan Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - James J. Crawford
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Matthew R. Durk
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Keira Garland
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Emily J. Hanan
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | - Huiyong Hu
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Cuong Q. Ly
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | | | - Jacob B. Schwarz
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Peter A. Smith
- Department
of Infectious Disease, Genentech, Inc., South San Francisco, California 94080, United States
| | - Zhiyong Yu
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Christopher E. Heise
- Department
of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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5
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Armstrong DW, Berthod A. Occurrence of D-amino acids in natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:47. [PMID: 37932633 PMCID: PMC10628113 DOI: 10.1007/s13659-023-00412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023]
Abstract
Since the identified standard genetic code contains 61 triplet codons of three bases for the 20 L-proteinogenic amino acids (AAs), no D-AA should be found in natural products. This is not what is observed in the living world. D-AAs are found in numerous natural compounds produced by bacteria, algae, fungi, or marine animals, and even vertebrates. A review of the literature indicated the existence of at least 132 peptide natural compounds in which D-AAs are an essential part of their structure. All compounds are listed, numbered and described herein. The two biosynthetic routes leading to the presence of D-AA in natural products are: non-ribosomal peptide synthesis (NRPS), and ribosomally synthesized and post-translationally modified peptide (RiPP) synthesis which are described. The methods used to identify the AA chirality within naturally occurring peptides are briefly discussed. The biological activity of an all-L synthetic peptide is most often completely different from that of the D-containing natural compounds. Analyzing the selected natural compounds showed that D-Ala, D-Val, D-Leu and D-Ser are the most commonly encountered D-AAs closely followed by the non-proteinogenic D-allo-Thr. D-Lys and D-Met were the least prevalent D-AAs in naturally occurring compounds.
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Affiliation(s)
- Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019, USA.
| | - Alain Berthod
- Institut des Sciences Analytiques, CNRS, University of Lyon 1, 69100, Villeurbanne, France
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6
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Wang L, Li K, Ye T, Huang L, Wu H, Zhang J, Xie H, Liu Y, Zeng J, Cheng P. Visible-Light-Promoted α-Benzylation of N-Phenyl α-Amino Acids to α-Amino Phenylpropanoids. J Org Chem 2023; 88:11924-11934. [PMID: 37560787 DOI: 10.1021/acs.joc.3c01196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
A new method for the synthesis of α-amino phenylpropanoids under blue light-emitting diode irradiation has been developed through α-C-H benzylation of readily available N-phenyl glycine ester with benzyl oxalates as a coupling partner under mild conditions. A range of N-phenyl glycine esters were successfully converted to α-amino phenylpropanoid products in moderate to good yields. The utility of this methodology is underlined by its application to the late-state modification of natural products.
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Affiliation(s)
- Lin Wang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Kang Li
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Tian Ye
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Lei Huang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Huilan Wu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jingxuan Zhang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Hongqi Xie
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yisong Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Pi Cheng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
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7
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Stone MC, Mychack A, Coe KA, Walker S. Combining Signal Peptidase and Lipoprotein Processing Inhibitors Overcomes Ayr Resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0011523. [PMID: 37097175 PMCID: PMC10190671 DOI: 10.1128/aac.00115-23] [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: 02/02/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Antibiotic resistance in bacterial pathogens is an ongoing public health concern. The arylomycins are a class of natural product antibiotics that target the type I signal peptidase, which carries out the terminal step in protein secretion. Here, we used transposon sequencing (Tn-Seq) to profile the effects of the optimized arylomycin derivative G0775 in Staphylococcus aureus. Our transposon libraries include both upregulation and inactivation mutants, allowing us to identify resistance mechanisms and targets for synergism. We identified several cell envelope pathways that, when inactivated, sensitize S. aureus to the arylomycin G0775. These pathways include the lipoprotein processing pathway, and we have shown that inhibitors of this pathway synergize with G0775 even though lipoprotein processing is nonessential in S. aureus. Moreover, we found that blocking this pathway completely reverses Ayr resistance, which is a major resistance mechanism to arylomycins, including G0775. Our Tn-Seq data also showed that upregulation of mprF and several other genes is protective against G0775. Because a subset of these genes was previously found in a Tn-Seq profile of the clinically important antibiotic daptomycin, we tested a set of daptomycin-nonsusceptible clinical isolates with gain-of-function mutations in mprF for susceptibility to arylomycin G0775. Despite structural and mechanistic differences between these antibiotics, we observed similar decreases in susceptibility. Taken together, our results highlight how Tn-Seq profiles that include both gene inactivation and upregulation can identify targets, antibiotic resistance mechanisms, and strategies to overcome resistance.
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Affiliation(s)
- Madeleine C. Stone
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Aaron Mychack
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn A. Coe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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8
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Keyes ED, Mifflin MC, Austin MJ, Alvey BJ, Lovely LH, Smith A, Rose TE, Buck-Koehntop BA, Motwani J, Roberts AG. Chemoselective, Oxidation-Induced Macrocyclization of Tyrosine-Containing Peptides. J Am Chem Soc 2023; 145:10071-10081. [PMID: 37119237 DOI: 10.1021/jacs.3c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Inspired by nature's wide range of oxidation-induced modifications to install cross-links and cycles at tyrosine (Tyr) and other phenol-containing residue side chains, we report a Tyr-selective strategy for the preparation of Tyr-linked cyclic peptides. This approach leverages N4-substituted 1,2,4-triazoline-3,5-diones (TADs) as azo electrophiles that react chemoselectively with the phenolic side chain of Tyr residues to form stable C-N1-linked cyclic peptides. In the developed method, a precursor 1,2,4-triazolidine-3,5-dione moiety, also known as urazole, is readily constructed at any free amine revealed on a solid-supported peptide. Once prepared, the N4-substituted urazole peptide is selectively oxidized using mild, peptide-compatible conditions to generate an electrophilic N4-substituted TAD peptide intermediate that reacts selectively under aqueous conditions with internal and terminal Tyr residues to furnish Tyr-linked cyclic peptides. The approach demonstrates good tolerance of native residue side chains and enables access to cyclic peptides ranging from 3- to 11-residues in size (16- to 38-atom-containing cycles). The identity of the installed Tyr-linkage, a stable covalent C-N1 bond, was characterized using NMR spectroscopy. Finally, we applied the developed method to prepare biologically active Tyr-linked cyclic peptides bearing the integrin-binding RGDf epitope.
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Affiliation(s)
- E Dalles Keyes
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Maxwell J Austin
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Brighton J Alvey
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Lotfa H Lovely
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andriea Smith
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Tristin E Rose
- 1200 Pharma LLC, 6100 Bristol Parkway, Culver City, California 90230, United States
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jyoti Motwani
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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9
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Adams Z, Silvestri AP, Chiorean S, Flood DT, Balo BP, Shi Y, Holcomb M, Walsh SI, Maillie CA, Pierens GK, Forli S, Rosengren KJ, Dawson PE. Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS CENTRAL SCIENCE 2023; 9:648-656. [PMID: 37122474 PMCID: PMC10141592 DOI: 10.1021/acscentsci.2c01462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Advances in the modulation of protein-protein interactions (PPIs) enable both characterization of PPI networks that govern diseases and design of therapeutics and probes. The shallow protein surfaces that dominate PPIs are challenging to target using standard methods, and approaches for accessing extended backbone structures are limited. Here, we incorporate a rigid, linear, diyne brace between side chains at the i to i+2 positions to generate a family of low-molecular-weight, extended-backbone peptide macrocycles. NMR and density functional theory studies show that these stretched peptides adopt stable, rigid conformations in solution and can be tuned to explore extended peptide conformational space. The diyne brace is formed in excellent conversions (>95%) and amenable to high-throughput synthesis. The minimalist structure-inducing tripeptide core (<300 Da) is amenable to further synthetic elaboration. Diyne-braced inhibitors of bacterial type 1 signal peptidase demonstrate the utility of the technique.
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Affiliation(s)
- Zoë
C. Adams
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anthony P. Silvestri
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Unnatural
Products, Inc., 2161
Delaware Ave, Suite A., Santa Cruz, California 95060, United States
| | - Sorina Chiorean
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brian P. Balo
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yifan Shi
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shawn I. Walsh
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Colleen A. Maillie
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gregory K. Pierens
- Centre
for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefano Forli
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - K. Johan Rosengren
- Institute
for Molecular Bioscience and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Philip E. Dawson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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10
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800 Australia
- EMBL Australia, Monash University, Clayton, Victoria, 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, 3800 Australia
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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Molinaro C, Kawasaki Y, Wanyoike G, Nishioka T, Yamamoto T, Snedecor B, Robinson SJ, Gosselin F. Engineered Cytochrome P450-Catalyzed Oxidative Biaryl Coupling Reaction Provides a Scalable Entry into Arylomycin Antibiotics. J Am Chem Soc 2022; 144:14838-14845. [PMID: 35905381 DOI: 10.1021/jacs.2c06019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the first example of a cytochrome P450-catalyzed oxidative carbon-carbon coupling process for a scalable entry into arylomycin antibiotic cores. Starting from wild-type hydroxylating cytochrome P450 enzymes and engineered Escherichia coli, a combination of enzyme engineering, random mutagenesis, and optimization of reaction conditions generated a P450 variant that affords the desired arylomycin core 2d in 84% assay yield. Furthermore, this process was demonstrated as a viable route for the production of the arylomycin antibiotic core on the gram scale. Finally, this new entry affords a viable, scalable, and practical route for the synthesis of novel Gram-negative antibiotics.
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Affiliation(s)
- Carmela Molinaro
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yukie Kawasaki
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - George Wanyoike
- Production Technology Department, MicroBiopharm Japan Co. Ltd., 1808 Nakaizumi, Iwata, Shizuoka 438-0078, Japan
| | - Taiki Nishioka
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Tsuyoshi Yamamoto
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Brad Snedecor
- Department of Cell Culture and Bioprocess Operations, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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Szałaj N, Benediktsdottir A, Rusin D, Karlén A, Mowbray SL, Więckowska A. Bacterial type I signal peptidase inhibitors - Optimized hits from nature. Eur J Med Chem 2022; 238:114490. [DOI: 10.1016/j.ejmech.2022.114490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 11/04/2022]
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Benediktsdottir A, Lu L, Cao S, Zamaratski E, Karlén A, Mowbray SL, Hughes D, Sandström A. Antibacterial sulfonimidamide-based oligopeptides as type I signal peptidase inhibitors: Synthesis and biological evaluation. Eur J Med Chem 2021; 224:113699. [PMID: 34352713 DOI: 10.1016/j.ejmech.2021.113699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Abstract
Oligopeptide boronates with a lipophilic tail are known to inhibit the type I signal peptidase in E. coli, which is a promising drug target for developing novel antibiotics. Antibacterial activity depends on these oligopeptides having a cationic modification to increase their permeation. Unfortunately, this modification is associated with cytotoxicity, motivating the need for novel approaches. The sulfonimidamide functionality has recently gained much interest in drug design and discovery, as a means of introducing chirality and an imine-handle, thus allowing for the incorporation of additional substituents. This in turn can tune the chemical and biological properties, which are here explored. We show that introducing the sulfonimidamide between the lipophilic tail and the peptide in a series of signal peptidase inhibitors resulted in antibacterial activity, while the sulfonamide isostere and previously known non-cationic analogs were inactive. Additionally, we show that replacing the sulfonamide with a sulfonimidamide resulted in decreased cytotoxicity, and similar results were seen by adding a cationic sidechain to the sulfonimidamide motif. This is the first report of incorporation of the sulfonimidamide functional group into bioactive peptides, more specifically into antibacterial oligopeptides, and evaluation of its biological effects.
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Affiliation(s)
- Andrea Benediktsdottir
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Lu Lu
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden
| | - Sherry L Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-75123, Uppsala, Sweden; Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, Box 596, SE-751 24, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-75123, Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, BMC, Uppsala University, Box 574, SE-75123, Uppsala, Sweden.
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Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
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Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
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Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
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16
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Tan YX, Peters DS, Walsh SI, Holcomb M, Santos-Martins D, Forli S, Romesberg FE. Initial Analysis of the Arylomycin D Antibiotics. JOURNAL OF NATURAL PRODUCTS 2020; 83:2112-2121. [PMID: 32614583 DOI: 10.1021/acs.jnatprod.9b01174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The arylomycins are a class of natural product antibiotics that inhibit bacterial type I signal peptidase and are under development as therapeutics. Four classes of arylomycins are known, arylomycins A-D. Previously, we reported the synthesis and analysis of representatives of the A, B, and C classes and showed that their spectrum of activity has the potential to be much broader than originally assumed. Along with a comparison of the mechanism of acquired and innate resistance, this led us to suggest that the arylomycins are latent antibiotics, antibiotics that once possessed broad-spectrum activity, but which upon examination today, have only narrow spectrum activity due to prior selection for resistance in the course of the competition with other microorganisms that drove their evolution in the first place. Interestingly, actinocarbasin, the only identified member of the arylomycin D class, has been reported to have activity against MRSA. To confirm and understand this activity, several actinocarbasin derivatives were synthesized. We demonstrate that the previously reported structure of actinocarbasin is incorrect, identify what is likely the correct scaffold, confirm that scaffold has activity against MRSA, and determine the origin of this activity.
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Affiliation(s)
- Yun Xuan Tan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - David S Peters
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shawn I Walsh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Diogo Santos-Martins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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17
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Newman DJ, Cragg GM. Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019. JOURNAL OF NATURAL PRODUCTS 2020; 83:770-803. [PMID: 32162523 DOI: 10.1021/acs.jnatprod.9b01285] [Citation(s) in RCA: 2648] [Impact Index Per Article: 662.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This review is an updated and expanded version of the five prior reviews that were published in this journal in 1997, 2003, 2007, 2012, and 2016. For all approved therapeutic agents, the time frame has been extended to cover the almost 39 years from the first of January 1981 to the 30th of September 2019 for all diseases worldwide and from ∼1946 (earliest so far identified) to the 30th of September 2019 for all approved antitumor drugs worldwide. As in earlier reviews, only the first approval of any drug is counted, irrespective of how many "biosimilars" or added approvals were subsequently identified. As in the 2012 and 2016 reviews, we have continued to utilize our secondary subdivision of a "natural product mimic", or "NM", to join the original primary divisions, and the designation "natural product botanical", or "NB", to cover those botanical "defined mixtures" now recognized as drug entities by the FDA (and similar organizations). From the data presented in this review, the utilization of natural products and/or synthetic variations using their novel structures, in order to discover and develop the final drug entity, is still alive and well. For example, in the area of cancer, over the time frame from 1946 to 1980, of the 75 small molecules, 40, or 53.3%, are N or ND. In the 1981 to date time frame the equivalent figures for the N* compounds of the 185 small molecules are 62, or 33.5%, though to these can be added the 58 S* and S*/NMs, bringing the figure to 64.9%. In other areas, the influence of natural product structures is quite marked with, as expected from prior information, the anti-infective area being dependent on natural products and their structures, though as can be seen in the review there are still disease areas (shown in Table 2) for which there are no drugs derived from natural products. Although combinatorial chemistry techniques have succeeded as methods of optimizing structures and have been used very successfully in the optimization of many recently approved agents, we are still able to identify only two de novo combinatorial compounds (one of which is a little speculative) approved as drugs in this 39-year time frame, though there is also one drug that was developed using the "fragment-binding methodology" and approved in 2012. We have also added a discussion of candidate drug entities currently in clinical trials as "warheads" and some very interesting preliminary reports on sources of novel antibiotics from Nature due to the absolute requirement for new agents to combat plasmid-borne resistance genes now in the general populace. We continue to draw the attention of readers to the recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated"; thus we consider that this area of natural product research should be expanded significantly.
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Affiliation(s)
- David J Newman
- NIH Special Volunteer, Wayne, Pennsylvania 19087, United States
| | - Gordon M Cragg
- NIH Special Volunteer, Gaithersburg, Maryland 20877, United States
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19
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Inhibition of Protein Secretion in Escherichia coli and Sub-MIC Effects of Arylomycin Antibiotics. Antimicrob Agents Chemother 2019; 63:AAC.01253-18. [PMID: 30420476 DOI: 10.1128/aac.01253-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
At sufficient concentrations, antibiotics effectively eradicate many bacterial infections. However, during therapy, bacteria are unavoidably exposed to lower antibiotic concentrations, and sub-MIC exposure can result in a wide variety of other effects, including the induction of virulence, which can complicate therapy, or horizontal gene transfer (HGT), which can accelerate the spread of resistance genes. Bacterial type I signal peptidase (SPase) is an essential protein that acts at the final step of the general secretory pathway. This pathway is required for the secretion of many proteins, including many required for virulence, and the arylomycins are a class of natural product antibiotics that target SPase. Here, we investigated the consequences of exposing Escherichia coli cultures to sub-MIC levels of an arylomycin. Using multidimensional protein identification technology mass spectrometry, we found that arylomycin treatment inhibits the proper extracytoplasmic localization of many proteins, both those that appear to be SPase substrates and several that do not. The identified proteins are involved in a broad range of extracytoplasmic processes and include a number of virulence factors. The effects of arylomycin on several processes required for virulence were then individually examined, and we found that, at even sub-MIC levels, the arylomycins potently inhibit flagellation, motility, biofilm formation, and the dissemination of antibiotic resistance via HGT. Thus, we conclude that the arylomycins represent promising novel therapeutics with the potential to eradicate infections while simultaneously reducing virulence and the dissemination of resistance.
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Abstract
Signal peptidases are the membrane bound enzymes that cleave off the amino-terminal signal peptide from secretory preproteins . There are two types of bacterial signal peptidases . Type I signal peptidase utilizes a serine/lysine catalytic dyad mechanism and is the major signal peptidase in most bacteria. Type II signal peptidase is an aspartic protease specific for prolipoproteins. This chapter will review what is known about the structure, function and mechanism of these unique enzymes.
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Affiliation(s)
- Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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21
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Szałaj N, Lu L, Benediktsdottir A, Zamaratski E, Cao S, Olanders G, Hedgecock C, Karlén A, Erdélyi M, Hughes D, Mowbray SL, Brandt P. Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase. Eur J Med Chem 2018; 157:1346-1360. [DOI: 10.1016/j.ejmech.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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Zhao P, Xue Y, Gao W, Li J, Zu X, Fu D, Feng S, Bai X, Zuo Y, Li P. Actinobacteria-Derived peptide antibiotics since 2000. Peptides 2018; 103:48-59. [PMID: 29567053 DOI: 10.1016/j.peptides.2018.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 11/23/2022]
Abstract
Members of the Actinobacteria, including Streptomyces spp., Kutzneria sp. Actinoplanes spp., Actinomycete sp., Nocardia sp., Brevibacteriumsp.,Actinomadura spp., Micromonospora sp., Amycolatopsis spp., Nonomuraea spp., Nocardiopsis spp., Marinactinospora sp., Rhodococcus sp., Lentzea sp., Actinokineospora sp., Planomonospora sp., Streptomonospora sp., and Microbacterium sp., are an important source of structurally diverse classes of short peptides of ∼30 residues or fewer that will likely play an important role in new antibiotic development and discovery. Additionally, many have unique structures that make them recalcitrant to traditional modes of drug resistance via novel mechanisms, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic is urgent, and this review summarizes 199 Actinobacteria compounds published since 2000, including 35 cyclic lipopeptides containing piperazic or pipecolic acids, eight aromatic peptides, five glycopeptides, 21 bicyclic peptides, 44 other cyclic lipopeptides, five linear lipopeptides, six 2,5-diketopiperazines, one dimeric peptide, four nucleosidyl peptides, two thioamide-containing peptides, 25 thiopeptides, nine lasso peptides, and 34 typical cyclic peptides. The current and potential therapeutic applications of these peptides, including their structure, antituberculotic, antibacterial, antifungal, antiviral, anti-brugia, anti-plasmodial, and anti-trypanosomal activities, are discussed.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yanjun Zuo
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ping Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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Blaskovich MAT, Butler MS, Cooper MA. Polishing the tarnished silver bullet: the quest for new antibiotics. Essays Biochem 2017; 61:103-114. [PMID: 28258234 PMCID: PMC5869247 DOI: 10.1042/ebc20160077] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
Abstract
We are facing a potential catastrophe of untreatable bacterial infections, driven by the inexorable rise of extensively drug-resistant bacteria, coupled with a market failure of pharmaceutical and biotech companies to deliver new therapeutic options. While global recognition of the problem is finally apparent, solutions are still a long way from being implemented. In addition to drug stewardship programmes and better diagnostics, new antibiotics are desperately needed. The question remains as to how to achieve this goal. This review will examine the different strategies being applied to discover new antibiotics.
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Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
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25
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Pérez-Labrada K, Cruz-Mendoza MA, Chávez-Riveros A, Hernández-Vázquez E, Torroba T, Miranda LD. Diversity-oriented synthesis and cytotoxic activity evaluation of biaryl-containing macrocycles. Org Biomol Chem 2017; 15:2450-2458. [DOI: 10.1039/c6ob02726a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Synthesis of biaryl-containing macrocycles has been carried out through a four-step approach comprising two Ugi four component reactions and a Suzuki–Miyaura macrocyclization.
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Affiliation(s)
- Karell Pérez-Labrada
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
| | - Marco A. Cruz-Mendoza
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
| | - Alejandra Chávez-Riveros
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
| | - Eduardo Hernández-Vázquez
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
| | - Tomás Torroba
- Department of Chemistry
- Faculty of Science
- University of Burgos
- 09001 Burgos
- Spain
| | - Luis D. Miranda
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito Exterior S.N
- Ciudad Universitaria
- Coyoacán
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26
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De Rosa M, Lu L, Zamaratski E, Szałaj N, Cao S, Wadensten H, Lenhammar L, Gising J, Roos AK, Huseby DL, Larsson R, Andrén PE, Hughes D, Brandt P, Mowbray SL, Karlén A. Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB). Bioorg Med Chem 2016; 25:897-911. [PMID: 28038943 DOI: 10.1016/j.bmc.2016.12.003] [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: 06/10/2016] [Revised: 10/14/2016] [Accepted: 12/03/2016] [Indexed: 01/25/2023]
Abstract
Type I signal peptidases are potential targets for the development of new antibacterial agents. Here we report finding potent inhibitors of E. coli type I signal peptidase (LepB), by optimizing a previously reported hit compound, decanoyl-PTANA-CHO, through modifications at the N- and C-termini. Good improvements of inhibitory potency were obtained, with IC50s in the low nanomolar range. The best inhibitors also showed good antimicrobial activity, with MICs in the low μg/mL range for several bacterial species. The selection of resistant mutants provided strong support for LepB as the target of these compounds. The cytotoxicity and hemolytic profiles of these compounds are not optimal but the finding that minor structural changes cause the large effects on these properties suggests that there is potential for optimization in future studies.
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Affiliation(s)
- Maria De Rosa
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Lu Lu
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box 596, SE-751 24 Uppsala, Sweden
| | - Edouard Zamaratski
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Natalia Szałaj
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sha Cao
- Uppsala University, Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-751 23 Uppsala, Sweden
| | - Henrik Wadensten
- Uppsala University, Department of Pharmaceutical Biosciences, BMC, Box 591, SE-751 24 Uppsala, Sweden
| | - Lena Lenhammar
- Uppsala University Hospital, Department of Medical Sciences, Uppsala, Sweden
| | - Johan Gising
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Annette K Roos
- Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, BMC, Box 596, SE-751 24 Uppsala, Sweden
| | - Douglas L Huseby
- Uppsala University, Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-751 23 Uppsala, Sweden
| | - Rolf Larsson
- Uppsala University Hospital, Department of Medical Sciences, Uppsala, Sweden
| | - Per E Andrén
- Uppsala University, Department of Pharmaceutical Biosciences, BMC, Box 591, SE-751 24 Uppsala, Sweden
| | - Diarmaid Hughes
- Uppsala University, Department of Medical Biochemistry and Microbiology, BMC, Box 582, SE-751 23 Uppsala, Sweden
| | - Peter Brandt
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sherry L Mowbray
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box 596, SE-751 24 Uppsala, Sweden; Uppsala University, Science for Life Laboratory, Department of Cell and Molecular Biology, BMC, Box 596, SE-751 24 Uppsala, Sweden.
| | - Anders Karlén
- Uppsala University, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Box 574, SE-751 23 Uppsala, Sweden.
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27
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Zer Aviv P, Shubely M, Moskovits Y, Viskind O, Albeck A, Vertommen D, Ruthstein S, Shokhen M, Gruzman A. A New Oxopiperazin-Based Peptidomimetic Molecule Inhibits Prostatic Acid Phosphatase Secretion and Induces Prostate Cancer Cell Apoptosis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pinchas Zer Aviv
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Moran Shubely
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Yoni Moskovits
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Olga Viskind
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Amnon Albeck
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Didier Vertommen
- de Duve Institute; Université catholique de Louvain; Brussels 1200 Belgium
| | - Sharon Ruthstein
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Michael Shokhen
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Arie Gruzman
- Department of Chemistry; Bar-Ilan University; Ramat-Gan 5290002 Israel
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28
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Abstract
The type I signal peptidase of Staphylococcus aureus, SpsB, is an attractive antibacterial target because it is essential for viability and extracellularly accessible. We synthesized compound 103, a novel arylomycin-derived inhibitor of SpsB with significant potency against various clinical S. aureus strains (MIC of ~1 µg/ml). The predominant clinical strain USA300 developed spontaneous resistance to compound 103 with high frequency, resulting from single point mutations inside or immediately upstream of cro/cI, a homolog of the lambda phage transcriptional repressor cro. These cro/cI mutations led to marked (>50-fold) overexpression of three genes encoding a putative ABC transporter. Overexpression of this ABC transporter was both necessary and sufficient for resistance and, notably, circumvented the essentiality of SpsB during in vitro culture. Mutation of its predicted ATPase gene abolished resistance, suggesting a possible role for active transport; in these bacteria, resistance to compound 103 occurred with low frequency and through mutations in spsB. Bacteria overexpressing the ABC transporter and lacking SpsB were capable of secreting a subset of proteins that are normally cleaved by SpsB and instead were cleaved at a site distinct from the canonical signal peptide. These bacteria secreted reduced levels of virulence-associated proteins and were unable to establish infection in mice. This study reveals the mechanism of resistance to a novel arylomycin derivative and demonstrates that the nominal essentiality of the S. aureus signal peptidase can be circumvented by the upregulation of a putative ABC transporter in vitro but not in vivo. The type I signal peptidase of Staphylococcus aureus (SpsB) enables the secretion of numerous proteins by cleavage of the signal peptide. We synthesized an SpsB inhibitor with potent activity against various clinical S. aureus strains. The predominant S. aureus strain USA300 develops resistance to this inhibitor by mutations in a novel transcriptional repressor (cro/cI), causing overexpression of a putative ABC transporter. This mechanism promotes the cleavage and secretion of various proteins independently of SpsB and compensates for the requirement of SpsB for viability in vitro. However, bacteria overexpressing the ABC transporter and lacking SpsB secrete reduced levels of virulence-associated proteins and are unable to infect mice. This study describes a bacterial resistance mechanism that provides novel insights into the biology of bacterial secretion.
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29
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Craney A, Romesberg FE. A putative cro-like repressor contributes to arylomycin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2015; 59:3066-74. [PMID: 25753642 PMCID: PMC4432125 DOI: 10.1128/aac.04597-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/05/2015] [Indexed: 01/26/2023] Open
Abstract
Antibiotic-resistant bacteria are a significant public health concern and motivate efforts to develop new classes of antibiotics. One such class of antibiotics is the arylomycins, which target type I signal peptidase (SPase), the enzyme responsible for the release of secreted proteins from their N-terminal leader sequences. Despite the essentiality, conservation, and relative accessibility of SPase, the activity of the arylomycins is limited against some bacteria, including the important human pathogen Staphylococcus aureus. To understand the origins of the limited activity against S. aureus, we characterized the susceptibility of a panel of strains to two arylomycin derivatives, arylomycin A-C16 and its more potent analog arylomycin M131. We observed a wide range of susceptibilities to the two arylomycins and found that resistant strains were sensitized by cotreatment with tunicamycin, which inhibits the first step of wall teichoic acid synthesis. To further understand how S. aureus responds to the arylomycins, we profiled the transcriptional response of S. aureus NCTC 8325 to growth-inhibitory concentrations of arylomycin M131 and found that it upregulates the cell wall stress stimulon (CWSS) and an operon consisting of a putative transcriptional regulator and three hypothetical proteins. Interestingly, we found that mutations in the putative transcriptional regulator are correlated with resistance, and selection for resistance ex vivo demonstrated that mutations in this gene are sufficient for resistance. The results begin to elucidate how S. aureus copes with secretion stress and how it evolves resistance to the inhibition of SPase.
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Affiliation(s)
- Arryn Craney
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
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30
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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.
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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
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31
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Mohimani H, Liu WT, Kersten R, Moore BS, Dorrestein PC, Pevzner PA. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. JOURNAL OF NATURAL PRODUCTS 2014; 77:1902-9. [PMID: 25116163 PMCID: PMC4143176 DOI: 10.1021/np500370c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 05/31/2023]
Abstract
Nonribosomal peptides (NRPs) such as vancomycin and daptomycin are among the most effective antibiotics. While NRPs are biomedically important, the computational techniques for sequencing these peptides are still in their infancy. The recent emergence of mass spectrometry techniques for NRP analysis (capable of sequencing an NRP from small amounts of nonpurified material) revealed an enormous diversity of NRPs. However, as many NRPs have nonlinear structure (e.g., cyclic or branched-cyclic peptides), the standard de novo sequencing tools (developed for linear peptides) are not applicable to NRP analysis. Here, we introduce the first NRP identification algorithm, NRPquest, that performs mutation-tolerant and modification-tolerant searches of spectral data sets against a database of putative NRPs. In contrast to previous studies aimed at NRP discovery (that usually report very few NRPs), NRPquest revealed nearly a hundred NRPs (including unknown variants of previously known peptides) in a single study. This result indicates that NRPquest can potentially make MS-based NRP identification as robust as the identification of linear peptides in traditional proteomics.
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Affiliation(s)
- Hosein Mohimani
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Wei-Ting Liu
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Roland
D. Kersten
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
| | - Pavel A. Pevzner
- Department of Electrical and Computer
Engineering, Department of Chemistry and Biochemistry, Center for Marine
Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of
Pharmacy and Pharmaceutical Sciences, and Department of Computer Science
and Engineering, University of California
San Diego, La Jolla, California 92093, United States
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32
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Aldemir H, Richarz R, Gulder TAM. Das biokatalytische Repertoire natürlicher Biarylbildung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Aldemir H, Richarz R, Gulder TAM. The Biocatalytic Repertoire of Natural Biaryl Formation. Angew Chem Int Ed Engl 2014; 53:8286-93. [DOI: 10.1002/anie.201401075] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 02/04/2023]
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34
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Rao C V S, De Waelheyns E, Economou A, Anné J. Antibiotic targeting of the bacterial secretory pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1762-83. [PMID: 24534745 DOI: 10.1016/j.bbamcr.2014.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 02/06/2023]
Abstract
Finding new, effective antibiotics is a challenging research area driven by novel approaches required to tackle unconventional targets. In this review we focus on the bacterial protein secretion pathway as a target for eliminating or disarming pathogens. We discuss the latest developments in targeting the Sec-pathway for novel antibiotics focusing on two key components: SecA, the ATP-driven motor protein responsible for driving preproteins across the cytoplasmic membrane and the Type I signal peptidase that is responsible for the removal of the signal peptide allowing the release of the mature protein from the membrane. We take a bird's-eye view of other potential targets in the Sec-pathway as well as other Sec-dependent or Sec-independent protein secretion pathways as targets for the development of novel antibiotics. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Smitha Rao C V
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Evelien De Waelheyns
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium; Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, P.O. Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, P.O. Box 1385, GR-71110 Iraklio, Crete, Greece.
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
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35
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Paetzel M. Structure and mechanism of Escherichia coli type I signal peptidase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1497-508. [PMID: 24333859 DOI: 10.1016/j.bbamcr.2013.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/26/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Type I signal peptidase is the enzyme responsible for cleaving off the amino-terminal signal peptide from proteins that are secreted across the bacterial cytoplasmic membrane. It is an essential membrane bound enzyme whose serine/lysine catalytic dyad resides on the exo-cytoplasmic surface of the bacterial membrane. This review discusses the progress that has been made in the structural and mechanistic characterization of Escherichia coli type I signal peptidase (SPase I) as well as efforts to develop a novel class of antibiotics based on SPase I inhibition. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
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36
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Liu WT, Lamsa A, Wong WR, Boudreau PD, Kersten R, Peng Y, Moree WJ, Duggan BM, Moore BS, Gerwick WH, Linington RG, Pogliano K, Dorrestein PC. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. J Antibiot (Tokyo) 2013; 67:99-104. [PMID: 24149839 DOI: 10.1038/ja.2013.99] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/24/2013] [Accepted: 07/27/2013] [Indexed: 02/06/2023]
Abstract
Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh's amazing career.
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Affiliation(s)
- Wei-Ting Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Anne Lamsa
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weng Ruh Wong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Roland Kersten
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wilna J Moree
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Brendan M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- 1] Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA [2] Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA [3] Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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37
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Rao M, Feng L, Ruan L, Ge M, Sheng X. UPLC-MS-Based Metabolomic Study ofStreptomycesStrain HCCB10043 Under Different pH Conditions Reveals Important Pathways Affecting the Biosynthesis of A21978C Compounds. ANAL LETT 2013. [DOI: 10.1080/00032719.2013.800538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Liu J, Smith PA, Steed DB, Romesberg F. Efforts toward broadening the spectrum of arylomycin antibiotic activity. Bioorg Med Chem Lett 2013; 23:5654-9. [PMID: 24012184 DOI: 10.1016/j.bmcl.2013.08.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/24/2013] [Accepted: 08/05/2013] [Indexed: 11/26/2022]
Abstract
New antibiotics are needed, and one source may be 'latent' antibiotics, natural products whose once broad-spectrum activity is currently limited by the evolution of resistance in nature. We have identified a potential class of latent antibiotics, the arylomycins, which are lipopeptides with a C-terminal macrocycle that target signal peptidase and whose spectrum is limited by a resistance-conferring mutation in many bacteria. Herein, we report the synthesis and evaluation of several arylomycin derivatives, and demonstrate that both C-terminal homologation with a glycyl aldehyde and addition of a positive charge to the macrocycle increase the activity and spectrum of the arylomycin scaffold.
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Affiliation(s)
- Jian Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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39
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Schmidt B, Riemer M, Karras M. 2,2′-Biphenols via Protecting Group-Free Thermal or Microwave-Accelerated Suzuki–Miyaura Coupling in Water. J Org Chem 2013; 78:8680-8. [DOI: 10.1021/jo401398n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernd Schmidt
- Institut fuer Chemie (Organische Synthesechemie), Universitaet Potsdam, Karl-Liebknecht-Strasse 24-25,
D-14476 Potsdam-Golm, Germany
| | - Martin Riemer
- Institut fuer Chemie (Organische Synthesechemie), Universitaet Potsdam, Karl-Liebknecht-Strasse 24-25,
D-14476 Potsdam-Golm, Germany
| | - Manfred Karras
- Institut fuer Chemie (Organische Synthesechemie), Universitaet Potsdam, Karl-Liebknecht-Strasse 24-25,
D-14476 Potsdam-Golm, Germany
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Rao M, Wei W, Ge M, Chen D, Sheng X. A new antibacterial lipopeptide found by UPLC-MS from an actinomycete Streptomyces sp. HCCB10043. Nat Prod Res 2013; 27:2190-5. [PMID: 23815473 DOI: 10.1080/14786419.2013.811661] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
It is an attractive and interesting thing for us to mine the diversity of microbial metabolites by means of ultra performance liquid chromatography tandem quadrupole and time of flight high-resolution mass spectrometry. Through this method, two trace compounds, a new lipopeptide, named arylomycin A6 (1), and a known lipopeptide (arylomycin A5, 2) were found and isolated from an actinomycete Streptomyces parvus HCCB10043. The structure of the new lipopeptide was elucidated by a combination of 1D, 2D NMR (correlation spectroscopy, heteronuclear multiple quantum correlation and heteronuclear multiple bond coherence) techniques, high-resolution electrospray ionization mass spectrometry and MS/MS spectrometry and fatty acid analyses. Arylomycin A6 exhibited antibacterial activity against Staphylococcus epidermidis HCCB20256 with the minimum inhibitory concentration of 1 μg/mL. Till now, arylomycins are the third series of active secondary metabolites we found in S. parvus HCCB10043. The results strongly support and encourage the studies for mining trace natural active products from microorganisms like Streptomyces.
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Affiliation(s)
- Min Rao
- a College of Life Sciences, Nanjing Agricultural University , Nanjing , 210095 , Jiangsu Province People's Republic of China
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Hänchen A, Rausch S, Landmann B, Toti L, Nusser A, Süssmuth RD. Alanine scan of the peptide antibiotic feglymycin: assessment of amino acid side chains contributing to antimicrobial activity. Chembiochem 2013; 14:625-32. [PMID: 23447362 DOI: 10.1002/cbic.201300032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Indexed: 01/08/2023]
Abstract
The antibiotic feglymycin is a linear 13-mer peptide synthesized by the bacterium Streptomyces sp. DSM 11171. It mainly consists of the nonproteinogenic amino acids 4-hydroxyphenylglycine and 3,5-dihydroxyphenylglycine. An alanine scan of feglymycin was performed by solution-phase peptide synthesis in order to assess the significance of individual amino acid side chains for biological activity. Hence, 13 peptides were synthesized from di- and tripeptide building blocks, and subsequently tested for antibacterial activity against Staphylococcus aureus strains. Furthermore we tested the inhibition of peptidoglycan biosynthesis enzymes MurA and MurC, which are inhibited by feglymycin. Whereas the antibacterial activity is significantly based on the three amino acids D-Hpg1, L-Hpg5, and L-Phe12, the inhibitory activity against MurA and MurC depends mainly on L-Asp13. The difference in the position dependence for antibacterial activity and enzyme inhibition suggests multiple molecular targets in the modes of action of feglymycin.
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Affiliation(s)
- Anne Hänchen
- Technische Universität Berlin, Fakultät II, Institut für Chemie, Strasse des 17. Juni 124, 10623 Berlin, Germany
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Jin X, Rao M, Wei W, Ge M, Liu J, Chen D, Liang Y. Biosynthesis of new lipopentapeptides by an engineered strain of Streptomyces sp. Biotechnol Lett 2012; 34:2283-9. [DOI: 10.1007/s10529-012-1032-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/15/2012] [Indexed: 11/29/2022]
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Abstract
Staphylococcus aureus is an important human pathogen whose virulence relies on the secretion of many different proteins. In general, the secretion of most proteins in S. aureus, as well as other bacteria, is dependent on the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein to the general secretory pathway. The arylomycins are a class of natural product antibiotics that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. While wild-type S. aureus (NCTC 8325) is naturally resistant to the arylomycins, sensitivity is conferred via a point mutation in its SPase. Here, we use a synthetic arylomycin along with a sensitized strain of S. aureus and multidimensional protein identification technology (MudPIT) mass spectrometry to identify 46 proteins whose extracellular accumulation requires SPase activity. Forty-four possess identifiable Sec-type signal peptides and thus are likely canonically secreted proteins, while four also appear to possess cell wall retention signals. We also identified the soluble C-terminal domains of two transmembrane proteins, lipoteichoic acid synthase, LtaS, and O-acyteltransferase, OatA, both of which appear to have noncanonical, internal SPase cleavage sites. Lastly, we identified three proteins, HtrA, PrsA, and SAOUHSC_01761, whose secretion is induced by arylomycin treatment. In addition to elucidating fundamental aspects of the physiology and pathology of S. aureus, the data suggest that an arylomycin-based therapeutic would reduce virulence while simultaneously eradicating an infection.
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Smitha Rao CV, Anné J. Bacterial type I signal peptidases as antibiotic targets. Future Microbiol 2012; 6:1279-96. [PMID: 22082289 DOI: 10.2217/fmb.11.109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite an alarming increase in morbidity and mortality caused by multidrug-resistant bacteria, the number of antibiotics available to efficiently combat them is dwindling. Consequently, there is a pressing need for new drugs, preferably with novel modes of action to avert the problem of cross-resistance. Several new targets have been proposed, including proteins essential in the protein secretion pathway such as the type I signal peptidase (SPase), indispensable for the release of the signal peptide during secretion of Sec- and Tat-dependent proteins. The type I SPase is considered to be an attractive target because it is essential, substantially different from the eukaryotic counterpart, and its active site is located at the outer leaflet of the cytoplasmic membrane, permitting relatively easy access to potential inhibitors. A few SPase inhibitors have already been identified, but their suitability as drugs is yet to be confirmed. An overview is given on the currently known SPase inhibitors, how they can give valuable information on the structural, biochemical and target validation aspects of the SPases, the approaches to identify them, and their future potential as drugs.
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Affiliation(s)
- C V Smitha Rao
- Laboratory of Bacteriology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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Gulder T, Baran PS. Strained cyclophane natural products: Macrocyclization at its limits. Nat Prod Rep 2012; 29:899-934. [DOI: 10.1039/c2np20034a] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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Tan YX, Romesberg FE. Latent antibiotics and the potential of the arylomycins for broad-spectrum antibacterial activity. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20043k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Liu WT, Kersten RD, Yang YL, Moore BS, Dorrestein PC. Imaging mass spectrometry and genome mining via short sequence tagging identified the anti-infective agent arylomycin in Streptomyces roseosporus. J Am Chem Soc 2011; 133:18010-3. [PMID: 21999343 DOI: 10.1021/ja2040877] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, we described the discovery of anti-infective agent arylomycin and its biosynthetic gene cluster in an industrial daptomycin producing strain Streptomyces roseosporus. This was accomplished via the use of MALDI imaging mass spectrometry (IMS) along with peptidogenomic approach in which we have expanded to short sequence tagging (SST) described herein. Using IMS, we observed that prior to the production of daptomycin, a cluster of ions (1-3) was produced by S. roseosporus and correlated well with the decreased staphylococcal cell growth. With a further adopted SST peptidogenomics approach, which relies on the generation of sequence tags from tandem mass spectrometric data and query against genomes to identify the biosynthetic genes, we were able to identify these three molecules (1-3) to arylomycins, a class of broad-spectrum antibiotics that target type I signal peptidase. The gene cluster was then identified. This highlights the strength of IMS and MS guided genome mining approaches in effectively bridging the gap between phenotypes, chemotypes, and genotypes.
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Affiliation(s)
- Wei-Ting Liu
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, Unites States
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Liu J, Luo C, Smith PA, Chin JK, Page MGP, Paetzel M, Romesberg FE. Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase. J Am Chem Soc 2011; 133:17869-77. [PMID: 21999324 DOI: 10.1021/ja207318n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosylation of natural products, including antibiotics, often plays an important role in determining their physical properties and their biological activity, and thus their potential as drug candidates. The arylomycin class of antibiotics inhibits bacterial type I signal peptidase and is comprised of three related series of natural products with a lipopeptide tail attached to a core macrocycle. Previously, we reported the total synthesis of several A series derivatives, which have unmodified core macrocycles, as well as B series derivatives, which have a nitrated macrocycle. We now report the synthesis and biological evaluation of lipoglycopeptide arylomycin variants whose macrocycles are glycosylated with a deoxy-α-mannose substituent, and also in some cases hydroxylated. The synthesis of the derivatives bearing each possible deoxy-α-mannose enantiomer allowed us to assign the absolute stereochemistry of the sugar in the natural product and also to show that while glycosylation does not alter antibacterial activity, it does appear to improve solubility. Crystallographic structural studies of a lipoglycopeptide arylomycin bound to its signal peptidase target reveal the molecular interactions that underlie inhibition and also that the mannose is directed away from the binding site into solvent which suggests that other modifications may be made at the same position to further increase solubility and thus reduce protein binding and possibly optimize the pharmacokinetics of the scaffold.
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Affiliation(s)
- Jian Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Roberts TC, Schallenberger MA, Liu J, Smith PA, Romesberg FE. Initial efforts toward the optimization of arylomycins for antibiotic activity. J Med Chem 2011; 54:4954-63. [PMID: 21630667 DOI: 10.1021/jm1016126] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While most clinically used antibiotics were derived from natural products, the isolation of new broad-spectrum natural products has become increasingly rare and narrow-spectrum agents are typically deemed unsuitable for development because of intrinsic limitations of their scaffold or target. However, it is possible that the spectrum of a natural product antibiotic might be limited by specific resistance mechanisms in some bacteria, such as target mutations, and the spectra of such "latent" antibiotics might be reoptimized by derivatization, just as has been done with clinically deployed antibiotics. We recently showed that the spectrum of the arylomycin natural product antibiotics, which act via the novel mechanism of inhibiting type I signal peptidase, is broader than previously believed and that resistance in several key human pathogens is due to the presence of a specific Pro residue in the target peptidase that disrupts interactions with the lipopeptide tail of the antibiotic. To begin to test whether this natural resistance might be overcome by derivatization, we synthesized analogues with altered lipopeptide tails and identified several with an increased spectrum of activity against S. aureus. The data support the hypothesis that the arylomycins are latent antibiotics, suggest that their spectrum may be optimized by derivatization, and identify a promising scaffold upon which future optimization efforts might focus.
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Affiliation(s)
- Tucker C Roberts
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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Roberts TC, Smith PA, Romesberg FE. Synthesis and biological characterization of arylomycin B antibiotics. JOURNAL OF NATURAL PRODUCTS 2011; 74:956-961. [PMID: 21545107 PMCID: PMC3150569 DOI: 10.1021/np200163g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Antibiotics are virtually always isolated as families of related compounds, but the evolutionary forces underlying the observed diversity are generally poorly understood, and it is not even clear whether they are all expected to be biologically active. The arylomycin class of antibiotics is comprised of three related families that are differentiated by nitration, glycosylation, and hydroxylation of a conserved core scaffold. Previously, we reported the total synthesis of an A series member, arylomycin A2, as well as the A series derivative arylomycin C16 and showed that both are active against a broader spectrum of bacteria than previously appreciated. We now report the total synthesis of a B series analogue, arylomycin B-C16, and its aromatic amine derivative. While the aromatic amine loses activity against all bacteria tested, the B series compound shows activities that are similar to the A series compounds, except that it also gains activity against the important pathogen Streptococcus agalactiae.
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