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Gong X, Brand CJ, Bertucci MA. Designing and synthesizing peptide-based quorum sensing modulators. Methods Enzymol 2024; 698:263-299. [PMID: 38886035 DOI: 10.1016/bs.mie.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Quorum sensing (QS) is a density-dependent bacterial communication system that uses small molecules as regulatory modulators. Synthetic changes to these molecules can up-or-down-regulate this system, leading to control of phenotypes, like competence and virulence factor production, that have implications in human health. In this chapter, a methodology for library design and screening of synthetic autoinducing peptides (AIPs) to uncover QS SARs is delineated. Additionally, procedures for the synthesis, purification and analysis of linear and cyclic AIPs are detailed. This includes solutions for potential synthetic challenges including diketopiperazine formation when using N-methyl amino acids and cyclization of peptides containing N-terminal cysteine residues. These procedures have and are currently being applied to develop potent QS modulators in Streptococcus pneumoniae, Bacillus cereus, Streptococcus gordonii and Lactiplantibacillus plantarum.
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Affiliation(s)
- Xiaotian Gong
- Department of Chemistry, Lafayette College, Easton, PA, United States
| | - Carter J Brand
- Department of Chemistry, Lafayette College, Easton, PA, United States
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2
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Jonkergouw C, Beyeh NK, Osmekhina E, Leskinen K, Taimoory SM, Fedorov D, Anaya-Plaza E, Kostiainen MA, Trant JF, Ras RHA, Saavalainen P, Linder MB. Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii. Nat Commun 2023; 14:2141. [PMID: 37059703 PMCID: PMC10104825 DOI: 10.1038/s41467-023-37749-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
The limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukaryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, both in vitro and in vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.
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Affiliation(s)
- Christopher Jonkergouw
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
| | - Ngong Kodiah Beyeh
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, MI, 48309-4479, USA
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Ekaterina Osmekhina
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Katarzyna Leskinen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland
| | - S Maryamdokht Taimoory
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
- University of Michigan, Department of Chemistry, Ann Arbor, MI, USA
| | - Dmitrii Fedorov
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Eduardo Anaya-Plaza
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - Mauri A Kostiainen
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
| | - John F Trant
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, ON, N9B 3P4, Canada
| | - Robin H A Ras
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland
- Aalto University, School of Science, Department of Applied Physics, Puumiehenkuja 2, Espoo, Finland
| | - Päivi Saavalainen
- University of Helsinki, Translational Immunology Research Program, Haartmaninkatu 8, 0014, Helsinki, Finland.
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
| | - Markus B Linder
- Aalto University, School of Chemical Engineering, Department of Bioproducts and Biosystems, Kemistintie 1, 02150, Espoo, Finland.
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3
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Milly TA, Tal-Gan Y. Targeting Peptide-Based Quorum Sensing Systems for the Treatment of Gram-Positive Bacterial Infections. Pept Sci (Hoboken) 2023; 115:e24298. [PMID: 37397504 PMCID: PMC10312355 DOI: 10.1002/pep2.24298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023]
Abstract
Bacteria utilize a cell density-dependent communication system called quorum sensing (QS) to coordinate group behaviors. In Gram-positive bacteria, QS involves the production of and response to auto-inducing peptide (AIP) signaling molecules to modulate group phenotypes, including pathogenicity. As such, this bacterial communication system has been identified as a potential therapeutic target against bacterial infections. More specifically, developing synthetic modulators derived from the native peptide signal paves a new way to selectively block the pathogenic behaviors associated with this signaling system. Moreover, rational design and development of potent synthetic peptide modulators allows in depth understanding of the molecular mechanisms that drive QS circuits in diverse bacterial species. Overall, studies aimed at understanding the role of QS in microbial social behavior could result in the accumulation of significant knowledge of microbial interactions, and consequently lead to the development of alternative therapeutic agents to treat bacterial infectivity. In this review, we discuss recent advances in the development of peptide-based modulators to target QS systems in Gram-positive pathogens, with a focus on evaluating the therapeutic potential associated with these bacterial signaling pathways.
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Affiliation(s)
- Tahmina A. Milly
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada, 89557, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada, 89557, United States
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Wang HM, Seo CD, Lee KJ, Park JH, Lim HS. Evaluation of the cell permeability of bicyclic peptoids and bicyclic peptide-peptoid hybrids. Bioorg Chem 2022; 127:105976. [DOI: 10.1016/j.bioorg.2022.105976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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Bajpai P, Sharma A, Chaube N. Projective assessment of Indian juveniles with conduct disorder. ASIA PACIFIC JOURNAL OF COUNSELLING AND PSYCHOTHERAPY 2022. [DOI: 10.1080/21507686.2022.2098350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Prakhar Bajpai
- Teaching and Research Assistant, School of Forensic Psychology, National Forensic Sciences University, Gandhinagar campus, Gujarat, India
| | - Abha Sharma
- Principal, Vivekanand College of Education, Aligarh, Uttar Pradesh, India
| | - Nandita Chaube
- Assistant Professor, School of Forensic Psychology, National Forensic Sciences University, Gandhinagar campus, Gujarat, India
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Bhukta S, Samal SK, Vasudevan S, Sarveswari HB, Shanmugam K, Princy SA, Dandela R. A Prospective Diversity of Antibacterial Small Peptidomimetic and Quorum Sensing Mediated Drug: A Review. ChemistrySelect 2022. [DOI: 10.1002/slct.202102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Swadhapriya Bhukta
- Institute of Chemical Technology-Indian Oil Odisha Campus Department of Industrial and Engineering Chemistry Bhubaneswar 751013 Odisha India
| | - Sangram Keshari Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies Indian Council of Medical Research-Regional Medical Research Center Bhubaneswar 751013 Odisha India
| | - Sahana Vasudevan
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Hema Bhagavathi Sarveswari
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Karthi Shanmugam
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - S. Adline Princy
- Quorum Sensing Laboratory Centre for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA University Thanjavur 613401 Tamil Nadu India
| | - Rambabu Dandela
- Institute of Chemical Technology-Indian Oil Odisha Campus Department of Industrial and Engineering Chemistry Bhubaneswar 751013 Odisha India
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7
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Lu L, Li M, Yi G, Liao L, Cheng Q, Zhu J, Zhang B, Wang Y, Chen Y, Zeng M. Screening strategies for quorum sensing inhibitors in combating bacterial infections. J Pharm Anal 2021; 12:1-14. [PMID: 35573879 PMCID: PMC9073242 DOI: 10.1016/j.jpha.2021.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/04/2021] [Accepted: 03/25/2021] [Indexed: 01/20/2023] Open
Abstract
Interference with quorum sensing (QS) represents an antivirulence strategy with a significant promise for the treatment of bacterial infections and a new approach to restoring antibiotic tolerance. Over the past two decades, a novel series of studies have reported that quorum quenching approaches and the discovery of quorum sensing inhibitors (QSIs) have a strong impact on the discovery of anti-infective drugs against various types of bacteria. The discovery of QSI was demonstrated to be an appropriate strategy to expand the anti-infective therapeutic approaches to complement classical antibiotics and antimicrobial agents. For the discovery of QSIs, diverse approaches exist and develop in-step with the scale of screening as well as specific QS systems. This review highlights the latest findings in strategies and methodologies for QSI screening, involving activity-based screening with bioassays, chemical methods to seek bacterial QS pathways for QSI discovery, virtual screening for QSI screening, and other potential tools for interpreting QS signaling, which are innovative routes for future efforts to discover additional QSIs to combat bacterial infections. Interference with QSrepresents a promising antivirulence strategy for the treatment of bacterial infections. The discovery ofQSIs was demonstrated as an appropriate strategy to expand the anti-infective therapeutic arsenal to complement classical antibiotics and antimicrobial agents. For the discovery of QSIs, diverse approaches exist and develop in-step with the scale of screening and targeted QS systems. Few previous reviews have summarized the strategies and approaches of QSI screening, whereas this review highlights the recent findings in QSI screening strategies and methodologies.
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Affiliation(s)
- Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
- Corresponding author.
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Guojuan Yi
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Li Liao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Qiang Cheng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Jie Zhu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Bin Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yingying Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yong Chen
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Ming Zeng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
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Samarasimhareddy M, Shamir M, Shalev DE, Hurevich M, Friedler A. A Rapid and Efficient Building Block Approach for Click Cyclization of Peptoids. Front Chem 2020; 8:405. [PMID: 32509731 PMCID: PMC7248394 DOI: 10.3389/fchem.2020.00405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Cyclic peptide-peptoid hybrids possess improved stability and selectivity over linear peptides and are thus better drug candidates. However, their synthesis is far from trivial and is usually difficult to automate. Here we describe a new rapid and efficient approach for the synthesis of click-based cyclic peptide-peptoid hybrids. Our methodology is based on a combination between easily synthesized building blocks, automated microwave assisted solid phase synthesis and bioorthogonal click cyclization. We proved the concept of this method using the INS peptide, which we have previously shown to activate the HIV-1 integrase enzyme. This strategy enabled the rapid synthesis and biophysical evaluation of a library of cyclic peptide-peptoid hybrids derived from HIV-1 integrase in high yield and purity. The new cyclic hybrids showed improved biological activity and were significantly more stable than the original linear INS peptide.
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Affiliation(s)
| | - Mai Shamir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, Jerusalem, Israel
| | - Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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9
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Gordon CP. Synthetic strategies to access staphylococcus auto-inducing peptides as quorum sensing modulators. Org Biomol Chem 2020; 18:379-390. [PMID: 31844862 DOI: 10.1039/c9ob02038a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The accessory gene regulator (agr) quorum-sensing system is arguably the most important regulator of staphylococcus virulence and has been the focus of tremendous interest in the development of effective therapies for pathogenic bacterial infections. With regards to chemotherapeutic based strategies, the significant proportion of currently reported agr-system modulating molecules are mimics of the native ArgC substrate, which is a thioester-based macrocyclic peptide know as the auto-inducing peptide. Over the past two decades, more than two-hundred synthetic analogues have been reported. This review traces the development of the synthetic strategies employed to synthesise these analogues with a particular focus on macrocyclisation. At present these synthetic approaches can be clustered into five broad categories (1) solution-phase cyclisation, (2) immobilised carbodiimide assisted cyclisation, (3) concomitant on-resin cleavage and macrocyclisation, (4) Boc-compatible chemoselective thioesterification, and (5) Fmoc-compatible chemoselective thioesterification. The advantages and limitation provided by each of the approaches are compared and contrasted with a view towards potential reaction scale-up.
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Affiliation(s)
- Christopher P Gordon
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith South DC, NSW 2751, Australia.
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10
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Vasquez JK, West KHJ, Yang T, Polaske TJ, Cornilescu G, Tonelli M, Blackwell HE. Conformational Switch to a β-Turn in a Staphylococcal Quorum Sensing Signal Peptide Causes a Dramatic Increase in Potency. J Am Chem Soc 2020; 142:750-761. [PMID: 31859506 DOI: 10.1021/jacs.9b05513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the solution-phase structures of native signal peptides and related analogs capable of either strongly agonizing or antagonizing the AgrC quorum sensing (QS) receptor in the emerging pathogen Staphylococcus epidermidis. Chronic S. epidermidis infections are often recalcitrant to traditional therapies due to antibiotic resistance and formation of robust biofilms. The accessory gene regulator (agr) QS system plays an important role in biofilm formation in this opportunistic pathogen, and the binding of an autoinducing peptide (AIP) signal to its cognate transmembrane receptor (AgrC) is responsible for controlling agr. Small molecules or peptides capable of modulating this binding event are of significant interest as probes to investigate both the agr system and QS as a potential antivirulence target. We used NMR spectroscopy to characterize the structures of the three native S. epidermidis AIP signals and five non-native analogs with distinct activity profiles in the AgrC-I receptor from S. epidermidis. These studies revealed a suite of structural motifs critical for ligand activity. Interestingly, a unique β-turn was present in the macrocycles of the two most potent AgrC-I modulators, in both an agonist and an antagonist, which was distinct from the macrocycle conformation in the less-potent AgrC-I modulators and in the native AIP-I itself. This previously unknown β-turn provides a structural rationale for these ligands' respective biological activity profiles. Development of analogs to reinforce the β-turn resulted in our first antagonist with subnanomolar potency in AgrC-I, while analogs designed to contain a disrupted β-turn were dramatically less potent relative to their parent compounds. Collectively, these studies provide new insights into the AIP:AgrC interactions crucial for QS activation in S. epidermidis and advance the understanding of QS at the molecular level.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Korbin H J West
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Tian Yang
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Thomas J Polaske
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Helen E Blackwell
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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11
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Horswill AR, Gordon CP. Structure-Activity Relationship Studies of Small Molecule Modulators of the Staphylococcal Accessory Gene Regulator. J Med Chem 2019; 63:2705-2730. [PMID: 31658413 DOI: 10.1021/acs.jmedchem.9b00798] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The accessory gene regulator (agr) quorum-sensing system is arguably the most important regulator of Staphylococcus virulence. The agr-system serves a crucial role in pathogenesis by triggering substantive gene expression alterations to up-regulate the production of a wide variety of virulence determinants such as exoenzymes (proteases, lipases, nucleases) and downregulate the expression of surface binding proteins. Accordingly, the agr-system represents a compelling target for the development of antivirulence therapeutics as potential adjuncts, or alternatives, to conventional bactericidal and bacteriostatic antibiotics. Despite this potential, to date, no agr-system inhibitors have progressed to the clinic; however, several promising lead compounds have been identified through screens of synthetic and natural product libraries. On the basis of the molecular components within the agr-system, the current contingent of regulating compounds can be clustered into three broad groups, AgrA-P3 activation inhibitors, AgrB-AgrD processing inhibitors, and AgrC-AIP interaction inhibitors. This review aims to provide an overview of the development, structure-activity-relationships, and limitations of compounds within each of these groups in addition to the current opportunities for developing next-generation anologs.
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Affiliation(s)
- Alexander R Horswill
- Veterans Affairs Eastern Colorado Health Care System, Aurora, Colorado 80045, United States.,Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Christopher P Gordon
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith South DC, NSW 2751, Australia.,Molecular Medicine Research Group, School of Medicine, Westerm Sydney University, Building 30, Campbelltown, NSW 2560, Australia
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12
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Abstract
Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N-substituted glycines where side-chains are located on the nitrogen atom of the amide backbone rather than the α-carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids.
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Affiliation(s)
| | - Steven L. Cobb
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
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13
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Karathanasi G, Bojer MS, Baldry M, Johannessen BA, Wolff S, Greco I, Kilstrup M, Hansen PR, Ingmer H. Linear peptidomimetics as potent antagonists of Staphylococcus aureus agr quorum sensing. Sci Rep 2018; 8:3562. [PMID: 29476092 PMCID: PMC5824847 DOI: 10.1038/s41598-018-21951-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/14/2018] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is an important pathogen causing infections in humans and animals. Increasing problems with antimicrobial resistance has prompted the development of alternative treatment strategies, including antivirulence approaches targeting virulence regulation such as the agr quorum sensing system. agr is naturally induced by cyclic auto-inducing peptides (AIPs) binding to the AgrC receptor and cyclic peptide inhibitors have been identified competing with AIP binding to AgrC. Here, we disclose that small, linear peptidomimetics can act as specific and potent inhibitors of the S. aureus agr system via intercepting AIP-AgrC signal interaction at low micromolar concentrations. The corresponding linear peptide did not have this ability. This is the first report of a linear peptide-like molecule that interferes with agr activation by competitive binding to AgrC. Prospectively, these peptidomimetics may be valuable starting scaffolds for the development of new inhibitors of staphylococcal quorum sensing and virulence gene expression.
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Affiliation(s)
- Georgia Karathanasi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Martin Saxtorph Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Bárdur Andréson Johannessen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Sanne Wolff
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Ines Greco
- Department of Drug Design and Farmacology, Faculty of Health and Medical Sciences University of Copenhagen, Universitetsparken 2, 2100, København, Denmark
| | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Metabolic Signaling and Regulation, Technical University of Denmark, Matematiktorvet, 2800, Lyngby, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Farmacology, Faculty of Health and Medical Sciences University of Copenhagen, Universitetsparken 2, 2100, København, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark.
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14
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Vasquez JK, Tal-Gan Y, Cornilescu G, Tyler KA, Blackwell HE. Simplified AIP-II Peptidomimetics Are Potent Inhibitors of Staphylococcus aureus AgrC Quorum Sensing Receptors. Chembiochem 2017; 18:413-423. [PMID: 28006082 DOI: 10.1002/cbic.201600516] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 01/13/2023]
Abstract
The bacterial pathogen Staphylococcus aureus controls many aspects of virulence by using the accessory gene regulator (agr) quorum sensing (QS) system. The agr system is activated by a macrocyclic peptide signal known as an autoinducing peptide (AIP). We sought to develop structurally simplified mimetics of AIPs for use as chemical tools to study QS in S. aureus. Herein, we report new peptidomimetic AgrC receptor inhibitors based on a tail-truncated AIP-II peptide that have almost analogous inhibitory activities to the parent peptide. Structural comparison of one of these peptidomimetics to the parent peptide and a highly potent, all-peptide-derived, S. aureus agr inhibitor (AIP-III D4A) revealed a conserved hydrophobic motif and overall amphipathic nature. Our results suggest that the AIP scaffold is amenable to structural mimicry and minimization for the development of synthetic agr inhibitors.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.,Present address: Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kimberly A Tyler
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
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15
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Barreto ADFS, Dos Santos VA, Andrade CKZ. Synthesis of acylhydrazino-peptomers, a new class of peptidomimetics, by consecutive Ugi and hydrazino-Ugi reactions. Beilstein J Org Chem 2016; 12:2865-2872. [PMID: 28144359 PMCID: PMC5238544 DOI: 10.3762/bjoc.12.285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/21/2016] [Indexed: 12/25/2022] Open
Abstract
Herein we describe a versatile approach for the synthesis of acylhydrazino-peptomers, a new class of peptidomimetics. The key idea in this approach is based on a simple route using a one-pot hydrazino-Ugi four-component reaction followed by a hydrazinolysis or hydrolysis reaction and subsequent hydrazino-Ugi reaction or classical Ugi reaction for the construction of acyclic acylhydrazino-peptomers. The consecutive multicomponent reactions produced a variety of acylhydrazino-peptomers in moderate to excellent yields (47–90%). These compounds are multifunctional intermediates that can be further functionalized to obtain new peptidomimetics with potential biological activity.
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Affiliation(s)
- Angélica de Fátima S Barreto
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, CP 4478, 70910-970 Brasília-DF, Brazil
| | - Veronica Alves Dos Santos
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, CP 4478, 70910-970 Brasília-DF, Brazil
| | - Carlos Kleber Z Andrade
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, CP 4478, 70910-970 Brasília-DF, Brazil
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16
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Furukawa A, Townsend CE, Schwochert J, Pye CR, Bednarek MA, Lokey RS. Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem 2016; 59:9503-9512. [PMID: 27690434 DOI: 10.1021/acs.jmedchem.6b01246] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (Papp) > 1 × 10-6 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.
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Affiliation(s)
- Akihiro Furukawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.,Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd. , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
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17
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Yang T, Tal-Gan Y, Paharik AE, Horswill AR, Blackwell HE. Structure-Function Analyses of a Staphylococcus epidermidis Autoinducing Peptide Reveals Motifs Critical for AgrC-type Receptor Modulation. ACS Chem Biol 2016; 11:1982-91. [PMID: 27159024 DOI: 10.1021/acschembio.6b00120] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Staphylococcus epidermidis is frequently implicated in human infections associated with indwelling medical devices due to its ubiquity in the skin flora and formation of robust biofilms. The accessory gene regulator (agr) quorum sensing (QS) system plays a prominent role in the establishment of biofilms and infection by this bacterium. Agr activation is mediated by the binding of a peptide signal (or autoinducing peptide, AIP) to its cognate AgrC receptor. Many questions remain about the role of QS in S. epidermidis infections, as well as in mixed-microbial populations on a host, and chemical modulators of its agr system could provide novel insights into this signaling network. The AIP ligand provides an initial scaffold for the development of such probes; however, the structure-activity relationships (SARs) for activation of S. epidermidis AgrC receptors by AIPs are largely unknown. Herein, we report the first SAR analyses of an S. epidermidis AIP by performing systematic alanine and d-amino acid scans of the S. epidermidis AIP-I. On the basis of these results, we designed and identified potent, pan-group inhibitors of the AgrC receptors in the three S. epidermidis agr groups, as well as a set of AIP-I analogs capable of selective AgrC inhibition in either specific S. epidermidis agr groups or in another common staphylococcal species, S. aureus. In addition, we uncovered a non-native peptide agonist of AgrC-I that can strongly inhibit S. epidermidis biofilm growth. Together, these synthetic analogs represent new and readily accessible probes for investigating the roles of QS in S. epidermidis colonization and infections.
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Affiliation(s)
- Tian Yang
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Yftah Tal-Gan
- Department
of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, Nevada 89557, United States
| | - Alexandra E. Paharik
- Department
of Microbiology, University of Iowa Carver College of Medicine, 431 Newton Rd., Iowa City, Iowa 52242, United States
| | - Alexander R. Horswill
- Department
of Microbiology, University of Iowa Carver College of Medicine, 431 Newton Rd., Iowa City, Iowa 52242, United States
| | - Helen E. Blackwell
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
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18
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Tal-Gan Y, Ivancic M, Cornilescu G, Yang T, Blackwell HE. Highly Stable, Amide-Bridged Autoinducing Peptide Analogues that Strongly Inhibit the AgrC Quorum Sensing Receptor in Staphylococcus aureus. Angew Chem Int Ed Engl 2016; 55:8913-7. [PMID: 27276693 DOI: 10.1002/anie.201602974] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/19/2016] [Indexed: 12/20/2022]
Abstract
Blocking quorum sensing (QS) pathways has attracted considerable interest as an approach to suppress virulence in bacterial pathogens. Toward this goal, we recently developed analogues of a native autoinducing peptide (AIP-III) signal that can inhibit AgrC-type QS receptors and attenuate virulence phenotypes in Staphylococcus aureus. Application of these compounds is limited, however, as they contain hydrolytically unstable thioester linkages and have only low aqueous solubilities. Herein, we report amide-linked AIP analogues with greatly enhanced hydrolytic stabilities and solubilities relative to our prior analogues, whilst maintaining strong potencies as AgrC receptor inhibitors in S. aureus. These compounds represent powerful tools for the study of QS.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
- Current address: Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Monika Ivancic
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
- Current address: Department of Chemistry, University of Vermont, 82 University Pl., Burlington, VT, 05405, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Tian Yang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
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19
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Tal-Gan Y, Ivancic M, Cornilescu G, Yang T, Blackwell HE. Highly Stable, Amide-Bridged Autoinducing Peptide Analogues that Strongly Inhibit the AgrC Quorum Sensing Receptor inStaphylococcus aureus. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
- Current address: Department of Chemistry; University of Nevada, Reno; 1664 N. Virginia St. Reno NV 89557 USA
| | - Monika Ivancic
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
- Current address: Department of Chemistry; University of Vermont; 82 University Pl. Burlington VT 05405 USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility; University of Wisconsin-Madison; 433 Babcock Dr. Madison WI 53706 USA
| | - Tian Yang
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
| | - Helen E. Blackwell
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
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20
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Butterfoss GL, Drew K, Renfrew PD, Kirshenbaum K, Bonneau R. Conformational preferences of peptide-peptoid hybrid oligomers. Biopolymers 2016; 102:369-78. [PMID: 24919990 DOI: 10.1002/bip.22516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/04/2014] [Accepted: 06/08/2014] [Indexed: 11/07/2022]
Abstract
Peptomers are oligomeric molecules composed of both α-amino acids and N-substituted glycine monomers, thus creating a hybrid of peptide and peptoid units. Peptomers have been used in several applications such as antimicrobials, protease inhibitors, and antibody mimics. Despite the considerable promise of peptomers as chemically diverse molecular scaffolds, we know little about their conformational tendencies. This lack of knowledge limits the ability to implement computational approaches for peptomer design. Here we computationally evaluate the local structural propensities of the peptide-peptoid linkage. We find some general similarities between the peptide residue conformational preferences and the Ramachandran distribution of residues that precede proline in folded protein structures. However, there are notable differences. For example, several β-turn motifs are disallowed when the i+2 residue is also a peptoid monomer. Significantly, the lowest energy geometry, when dispersion forces are accounted for, corresponds to a "cis-Pro touch-turn" conformation, an unusual turn motif that has been observed at protein catalytic centers and binding sites. The peptomer touch-turn thus represents a useful design element for the construction of folded oligomers capable of molecular recognition and as modules in the assembly of structurally complex peptoid-protein hybrid macromolecules.
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Affiliation(s)
- Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box, 129188, Abu Dhabi, United Arab Emirates
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21
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Qvit N, Kornfeld OS. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation. J Vis Exp 2016:e53589. [PMID: 26863382 DOI: 10.3791/53589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University School of Medicine;
| | - Opher S Kornfeld
- Department of Chemical and Systems Biology, Stanford University School of Medicine
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22
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Quorum Quenching Strategy Targeting Gram-Positive Pathogenic Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 901:109-30. [PMID: 27167409 DOI: 10.1007/5584_2016_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Quorum sensing (QS) is a cell density-dependent regulatory system that orchestrates the group behavior of unicellular organisms by synchronizing the expression of certain gene(s) within the clonal community of same species. Bacterial pathogens often employ QS system to establish efficiently an infection. A large part of low GC Gram-positive bacteria belonging to phylum Firmicutes use thiolactone/lactone peptides as communication signals so-called autoinducing peptides (AIPs) to coordinate QS circuit. In particular, QS of staphylococci, enterococci, and clostridia have been intensively studied in terms of alternative target of anti-pathogenic chemotherapy independent of bactericidal antibiotics. Thus far, a number of quorum quenching (QQ) agents that targeting the QS circuit of these Gram-positive pathogens have been developed by random screening of natural compounds or rationale design of AIP antagonists. This review summarizes those QQ agents and previews their potential as post-antibiotic drugs.
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23
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Tal-Gan Y, Ivancic M, Cornilescu G, Blackwell HE. Characterization of structural elements in native autoinducing peptides and non-native analogues that permit the differential modulation of AgrC-type quorum sensing receptors in Staphylococcus aureus. Org Biomol Chem 2015; 14:113-21. [PMID: 26416476 DOI: 10.1039/c5ob01735a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus uses short macrocyclic peptides (i.e., autoinducing peptides, or AIPs) to assess its local population density in a cell-cell signaling mechanism called quorum sensing (QS). At high cell numbers, this pathogen can initiate many virulent behaviors that allow for the establishment of infection. Binding of the AIP signal to its cognate transmembrane AgrC-type receptor is a critical event in the QS signaling cascade; consequently, interference of AIP:receptor interactions may have the potential to prevent and eradicate certain S. aureus infections. To date, four pairs of AIP:AgrC receptors have been identified in S. aureus, each pair being utilized by a specific S. aureus group (I-IV). Other staphylococcal species also use closely related, but distinct, AIP:AgrC pairs to control QS. We seek to develop non-native ligands capable of intercepting AIP:AgrC binding in each S. aureus group and in related species. As these bacteria may use their respective AIP signal to attenuate the QS systems of other groups/species, such ligands would provide valuable chemical tools to probe possible interference mechanisms in a range of contexts. In the current study, we used solution-phase NMR techniques to characterize the 3-D structures of a set of known native and non-native peptides that have differential modulatory activity in certain AgrC receptors. Analysis of these structures revealed several distinct structural motifs that belay differential activity in selected S. aureus AgrC receptors (i.e., AgrC-I, AgrC-II, and AgrC-III). The results of this study can be leveraged for the design of new synthetic ligands with enhanced selectivities and potencies for these AgrC receptors.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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24
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Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SSF, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett 2015; 17:2928-31. [PMID: 26046483 DOI: 10.1021/acs.orglett.5b01162] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of peptide-to-peptoid substitutions on the passive membrane permeability of an N-methylated cyclic hexapeptide is examined. In general, substitutions maintained permeability but increased conformational heterogeneity. Diversification with nonproteinogenic side chains increased permeability up to 3-fold. Additionally, the conformational impact of peptoid substitutions within a β-turn are explored. Based on these results, the strategic incorporation of peptoid residues into cyclic peptides can maintain or improve cell permeability, while increasing access to diverse side-chain functionality.
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Affiliation(s)
- Joshua Schwochert
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Rushia Turner
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Melissa Thang
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Ray F Berkeley
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Alexandra R Ponkey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Kelsie M Rodriguez
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Bhagyashree Khunte
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Gilles Goetz
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Chris Limberakis
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- §Pharmacokinetics and Drug Metabolism, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- ⊥Pharmacokinetics and Drug Metabolism, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Alan M Mathiowetz
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - David A Price
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - R Scott Lokey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
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25
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Khan BA, Yeh AJ, Cheung GYC, Otto M. Investigational therapies targeting quorum-sensing for the treatment of Staphylococcus aureus infections. Expert Opin Investig Drugs 2015; 24:689-704. [PMID: 25704585 DOI: 10.1517/13543784.2015.1019062] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Antibiotic resistance is a serious global health concern for developed and developing nations. MRSA represents a particularly severe public health threat that is associated with high morbidity and mortality. The lack of novel antibiotics has led scientists to explore therapies targeting bacterial virulence mechanisms and virulence regulators, including those controlling cell-cell communication. AREAS COVERED The authors discuss the role of quorum-sensing in Staphylococcus aureus infections and components of the system that are being targeted using novel investigational drugs. In particular, the authors examine the role of the accessory gene regulator (Agr) system in virulence regulation of S. aureus pathogenesis. Finally, the authors present and compare natural and synthetic compounds that have been found to interfere with Agr functionality. EXPERT OPINION There is a great need to develop new therapeutic methods to combat S. aureus infections. These include anti-virulence therapies that target key global regulators involved with the establishment and propagation of infection. Several molecules have been found to interfere with S. aureus virulence regulation, especially those targeting the Agr quorum-sensing signaling molecule. These preliminary findings warrant further investigation and validation, with the goal of refining a compound that has broad-spectrum inhibitory effects on most S. aureus strains and Agr subtypes.
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Affiliation(s)
- Burhan A Khan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories , 903 S. 4th St, 1/1110, Hamilton, MT 59840 , USA
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26
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Melander RJ, Melander C. Innovative strategies for combating biofilm-based infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 831:69-91. [PMID: 25384664 DOI: 10.1007/978-3-319-09782-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Roberta J Melander
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
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27
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Tal-Gan Y, Stacy DM, Blackwell HE. N-Methyl and peptoid scans of an autoinducing peptide reveal new structural features required for inhibition and activation of AgrC quorum sensing receptors in Staphylococcus aureus. Chem Commun (Camb) 2014; 50:3000-3. [PMID: 24509706 DOI: 10.1039/c4cc00117f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the first N-methyl and peptoid residue scans of a full-length autoinducing peptide (AIP), AIP-III, used by Staphylococcus aureus for quorum sensing (QS). Biological evaluation of these AIP-III analogues uncovered new features of the AIP-III scaffold that can be tuned to develop chemical probes of QS in all four groups of S. aureus (I-IV).
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, USA.
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28
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Structural features of peptoid-peptide hybrids in lipid-water interfaces. FEBS Lett 2014; 588:3291-7. [DOI: 10.1016/j.febslet.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/24/2014] [Accepted: 07/14/2014] [Indexed: 12/15/2022]
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29
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Small head-to-tail macrocyclic α-peptoids. Org Lett 2014; 16:2780-3. [PMID: 24797336 DOI: 10.1021/ol501102b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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30
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Rajasekhar K, Narayanaswamy N, Mishra P, Suresh SN, Manjithaya R, Govindaraju T. Synthesis of Hybrid Cyclic Peptoids and Identification of Autophagy Enhancer. Chempluschem 2013; 79:25-30. [DOI: 10.1002/cplu.201300343] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 01/02/2023]
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31
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Tal-Gan Y, Ivancic M, Cornilescu G, Cornilescu CC, Blackwell HE. Structural characterization of native autoinducing peptides and abiotic analogues reveals key features essential for activation and inhibition of an AgrC quorum sensing receptor in Staphylococcus aureus. J Am Chem Soc 2013; 135:18436-44. [PMID: 24219181 DOI: 10.1021/ja407533e] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a major human pathogen that uses quorum sensing (QS) to control virulence. Its QS system is regulated by macrocyclic peptide signals (or autoinducing peptides (AIPs)) and their cognate transmembrane receptors (AgrCs). Four different specificity groups of S. aureus have been identified to date (groups I-IV), each of which uses a different AIP:AgrC pair. Non-native ligands capable of intercepting AIP:AgrC binding, and thereby QS, in S. aureus have attracted considerable interest as chemical tools to study QS pathways and as possible antivirulence strategies for the treatment of infection. We recently reported a set of analogues of the group-III AIP that are capable of strongly modulating the activity of all four AgrC receptors. Critical to the further development of such ligands is a detailed understanding of the structural features of both native AIPs and non-native analogues that are essential for activity. Herein, we report the first three-dimensional structural analysis of the known native AIP signals (AIPs-I-IV) and several AIP-III analogues with varied biological activities using NMR spectroscopy. Integration of these NMR studies with the known agonism and antagonism profiles of these peptides in AgrC-III revealed two key structural elements that control AIP-III (and non-native peptide) activity: (1) a tri-residue hydrophobic "knob" essential for both activation and inhibition and (2) a fourth anchor point on the exocyclic tail needed for receptor activation. These results provide strong structural support for a mechanism of AIP-mediated AgrC activation and inhibition in S. aureus , and should facilitate the design of new AgrC ligands with enhanced activities (as agonists or antagonists) and simplified chemical structures.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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32
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Abstract
Cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. Its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. With the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. An antivirulence approach by which quorum sensing is impeded has caught on as a viable means to manipulate bacterial processes, especially pathogenic traits that are harmful to human and animal health and agricultural productivity. The identification and development of chemical compounds and enzymes that facilitate quorum-sensing inhibition (QSI) by targeting signaling molecules, signal biogenesis, or signal detection are reviewed here. Overall, the evidence suggests that QSI therapy may be efficacious against some, but not necessarily all, bacterial pathogens, and several failures and ongoing concerns that may steer future studies in productive directions are discussed. Nevertheless, various QSI successes have rightfully perpetuated excitement surrounding new potential therapies, and this review highlights promising QSI leads in disrupting pathogenesis in both plants and animals.
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33
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Arya R, Princy SA. An insight into pleiotropic regulators Agr and Sar: molecular probes paving the new way for antivirulent therapy. Future Microbiol 2013; 8:1339-53. [DOI: 10.2217/fmb.13.92] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Staphylococcus aureus pathogenesis is an intricate process involving a diverse array of extracellular proteins, biofilm and cell wall components that are coordinately expressed in different stages of infection. The expression of two divergent loci, agr and sar, is increasingly recognized as a key regulator of virulence in S. aureus, and there is mounting evidence for the role of these loci in staphylococcal infections. The functional agr regulon is critical for the production of virulence factors, including α, β and δ hemolysins. The sar locus encodes SarA protein, which regulates the expression of cell wall-associated and certain extracellular proteins in agr-dependent and agr-independent pathways. Multidrug-resistant S. aureus is a leading cause of morbidity and mortality in the world and its management, especially in community-acquired methicillin-resistant S. aureus infections, has evolved comparatively little. In particular, no novel targets have been incorporated into its treatment to date. Hence, these loci appear to be the most significant and are currently at the attention of intense investigation regarding their therapeutic prospects.
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Affiliation(s)
- Rekha Arya
- Quorum Sensing Laboratory, SASTRA‘s Hub for Research & Innovation (SHRI), School of Chemical & Biotechnology, SASTRA University, Tirumalaisamudrum 613401, Thanjavur, Tamil Nadu, India
| | - S Adline Princy
- Quorum Sensing Laboratory, SASTRA‘s Hub for Research & Innovation (SHRI), School of Chemical & Biotechnology, SASTRA University, Tirumalaisamudrum 613401, Thanjavur, Tamil Nadu, India
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34
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Blackledge MS, Worthington RJ, Melander C. Biologically inspired strategies for combating bacterial biofilms. Curr Opin Pharmacol 2013; 13:699-706. [PMID: 23871261 PMCID: PMC3795836 DOI: 10.1016/j.coph.2013.07.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/11/2013] [Accepted: 07/01/2013] [Indexed: 01/07/2023]
Abstract
Infections caused by bacterial biofilms are a significant global health problem, causing considerable patient morbidity and mortality and contributing to the economic burden of infectious disease. This review describes diverse strategies to combat bacterial biofilms, focusing firstly on small molecule interference with bacterial communication and signaling pathways, including quorum sensing and two-component signal transduction systems. Secondly we discuss enzymatic approaches to the degradation of extracellular matrix components to effect biofilm dispersal. Both of these approaches are based upon non-microbicidal mechanisms of action, and thereby do not place a direct evolutionary pressure on the bacteria to develop resistance. Such approaches have the potential to, in combination with conventional antibiotics, play an important role in the eradication of biofilm based bacterial infections.
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Affiliation(s)
- Meghan S. Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Christian Melander
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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O'Connell KMG, Hodgkinson JT, Sore HF, Welch M, Salmond GPC, Spring DR. Die Bekämpfung multiresistenter Bakterien: aktuelle Strategien zur Entdeckung neuer Antibiotika. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209979] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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O'Connell KMG, Hodgkinson JT, Sore HF, Welch M, Salmond GPC, Spring DR. Combating Multidrug-Resistant Bacteria: Current Strategies for the Discovery of Novel Antibacterials. Angew Chem Int Ed Engl 2013; 52:10706-33. [DOI: 10.1002/anie.201209979] [Citation(s) in RCA: 310] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/25/2013] [Indexed: 11/07/2022]
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37
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Sun J, Zuckermann RN. Peptoid polymers: a highly designable bioinspired material. ACS NANO 2013; 7:4715-32. [PMID: 23721608 DOI: 10.1021/nn4015714] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Affiliation(s)
- Jing Sun
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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38
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Tal-Gan Y, Stacy DM, Foegen MK, Koenig DW, Blackwell HE. Highly potent inhibitors of quorum sensing in Staphylococcus aureus revealed through a systematic synthetic study of the group-III autoinducing peptide. J Am Chem Soc 2013; 135:7869-82. [PMID: 23647400 DOI: 10.1021/ja3112115] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methods to intercept bacterial quorum sensing (QS) have attracted significant attention as potential anti-infective therapies. Staphylococcus aureus is a major human pathogen that utilizes autoinducing peptide (AIP) signals to mediate QS and thereby regulate virulence. S. aureus strains are categorized into four groups (I-IV) according to their AIP signal and cognate extracellular receptor, AgrC. Each group is associated with a certain disease profile, and S. aureus group-III strains are responsible for toxic shock syndrome and have been underestimated in other infections to date. A limited set of non-native AIP analogs have been shown to inhibit AgrC receptors; such compounds represent promising tools to study QS pathways in S. aureus . We seek to expand this set of chemical probes and report herein the first design, synthesis, and biological testing of AIP-III mimetics. A set of non-native peptides was identified that can inhibit all four of the AgrC receptors (I-IV) with picomolar IC50 values in reporter strains. These analogs also blocked hemolysis by wild-type S. aureus group I-IV strains-a virulence trait under the control of QS-at picomolar concentrations. Moreover, four of the lead AgrC inhibitors were capable of attenuating the production of toxic shock syndrome toxin-1 (also under the control of QS) by over 80% at nanomolar concentrations in a wild-type S. aureus group-III strain. These peptides represent, to our knowledge, the most potent synthetic inhibitors of QS in S. aureus known, and constitute new and readily accessible chemical tools for the study of the AgrC system and virulence in this deadly pathogen.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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39
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Gordon CP, Williams P, Chan WC. Attenuating Staphylococcus aureus virulence gene regulation: a medicinal chemistry perspective. J Med Chem 2013; 56:1389-404. [PMID: 23294220 PMCID: PMC3585718 DOI: 10.1021/jm3014635] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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Virulence gene expression in Staphylococcus aureus is tightly regulated by intricate networks of transcriptional regulators
and two-component signal transduction systems. There is now an emerging
body of evidence to suggest that the blockade of S. aureus virulence gene expression significantly attenuates infection in
experimental models. In this Perspective, we will provide insights
into medicinal chemistry strategies for the development of chemical
reagents that have the capacity to inhibit staphylococcal virulence
expression. These reagents can be broadly grouped into four categories:
(1) competitive inhibitors of the accessory gene regulator (agr) quorum sensing system, (2) inhibitors of AgrA–DNA
interactions, (3) RNAIII transcription inhibitors, and (4) inhibitors
of the SarA family of transcriptional regulators. We discuss the potential
of specific examples of antivirulence agents for the management and
treatment of staphylococcal infections.
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Affiliation(s)
- Christopher P Gordon
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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40
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Abstract
Peptoids (oligomers of N-substituted glycine residues) and peptide-peptoid hybrid polymers (peptomers) are interesting classes of compounds mimicking structure and function of biologically active peptides. The oligomeric peptidomimetics such as peptoids are particularly important compounds since they provide access to an enormous molecular diversity, by variation of the building blocks. The modular structure of peptoids, ease of synthesis, and high compatibility with existing peptide chemistry synthetic protocols, make peptoids and peptoid-containing peptidomimetics ideal tools for structure-activity and drug discovery related studies.
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41
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Leonard PG, Bezar IF, Sidote DJ, Stock AM. Identification of a hydrophobic cleft in the LytTR domain of AgrA as a locus for small molecule interactions that inhibit DNA binding. Biochemistry 2012. [PMID: 23181972 DOI: 10.1021/bi3011785] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The AgrA transcription factor regulates the quorum-sensing response in Staphylococcus aureus, controlling the production of hemolysins and other virulence factors. AgrA binds to DNA via its C-terminal LytTR domain, a domain not found in humans but common in many pathogenic bacteria, making it a potential target for antimicrobial development. We have determined the crystal structure of the apo AgrA LytTR domain and screened a library of 500 fragment compounds to find inhibitors of AgrA DNA binding activity. Using nuclear magnetic resonance, the binding site for five compounds has been mapped to a common locus at the C-terminal end of the LytTR domain, a site known to be important for DNA binding activity. Three of these compounds inhibit AgrA DNA binding. These results provide the first evidence that LytTR domains can be targeted by small organic compounds.
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Affiliation(s)
- Paul G Leonard
- Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, USA
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42
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Frost JR, Vitali F, Jacob NT, Brown MD, Fasan R. Macrocyclization of Organo-Peptide Hybrids through a Dual Bio-orthogonal Ligation: Insights from Structure-Reactivity Studies. Chembiochem 2012. [DOI: 10.1002/cbic.201200579] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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43
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Abstract
Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis patients, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: (1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, (2) chemical library screening for compounds with anti-biofilm activity, and (3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity.
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44
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Praneenararat T, Palmer AG, Blackwell HE. Chemical methods to interrogate bacterial quorum sensing pathways. Org Biomol Chem 2012; 10:8189-99. [PMID: 22948815 PMCID: PMC3480174 DOI: 10.1039/c2ob26353j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria frequently manifest distinct phenotypes as a function of cell density in a phenomenon known as quorum sensing (QS). This intercellular signalling process is mediated by "chemical languages" comprised of low-molecular weight signals, known as autoinducers, and their cognate receptor proteins. As many of the phenotypes regulated by QS can have a significant impact on the success of pathogenic or mutualistic prokaryotic-eukaryotic interactions, there is considerable interest in methods to probe and modulate QS pathways with temporal and spatial control. Such methods would be valuable for both basic research in bacterial ecology and in practical medicinal, agricultural, and industrial applications. Toward this goal, considerable recent research has been focused on the development of chemical approaches to study bacterial QS pathways. In this Perspective, we provide an overview of the use of chemical probes and techniques in QS research. Specifically, we focus on: (1) combinatorial approaches for the discovery of small molecule QS modulators, (2) affinity chromatography for the isolation of QS receptors, (3) reactive and fluorescent probes for QS receptors, (4) antibodies as quorum "quenchers," (5) abiotic polymeric "sinks" and "pools" for QS signals, and (6) the electrochemical sensing of QS signals. The application of such chemical methods can offer unique advantages for both elucidating and manipulating QS pathways in culture and under native conditions.
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Affiliation(s)
| | | | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA. Fax: +1 (608) 265-4534; Tel: +1 (608) 262-1503
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45
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Olsen CA, Montero A, Leman LJ, Ghadiri MR. Macrocyclic peptoid-Peptide hybrids as inhibitors of class I histone deacetylases. ACS Med Chem Lett 2012; 3:749-53. [PMID: 24900543 DOI: 10.1021/ml300162r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/07/2012] [Indexed: 01/04/2023] Open
Abstract
We report the design, synthesis, and biological evaluation of the first macrocyclic peptoid-containing histone deacetylase (HDAC) inhibitors. The compounds selectively inhibit human class I HDAC isoforms in vitro, with no inhibition of the tubulin deacetylase activity associated with class IIb HDAC6 in cultured Jurkat cells. Compared to the natural product apicidin (1), one inhibitor (compound 10) showed equivalent potency against K-562 cells, but was more cytoselective across a panel of cancer cell lines.
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Affiliation(s)
- Christian A. Olsen
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Ana Montero
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Luke J. Leman
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
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46
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Zezzi do Valle Gomes M, Nitschke M. Evaluation of rhamnolipid and surfactin to reduce the adhesion and remove biofilms of individual and mixed cultures of food pathogenic bacteria. Food Control 2012. [DOI: 10.1016/j.foodcont.2011.11.025] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Simpson LS, Kodadek T. A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron Lett 2012; 53:2341-2344. [PMID: 22736872 DOI: 10.1016/j.tetlet.2012.02.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many macrocyclic depsipeptides or related compounds have interesting medicinal properties and often display more favorable pharmacokinetic properties than linear analogues. Therefore, there is considerable interest in the development of large combinatorial libraries of macrocyclic peptidomimetic compounds. However, such molecules cannot be easily sequenced by tandem mass spectrometry, making it difficult to identify hits isolated from library screens using one bead one compound libraries. Here we report a strategy to solve this problem by placing a methionine in both the linker connecting the cyclic molecule to the bead as well as within the cycle itself. Treatment with CNBr both linearizes the molecule at a specific position and releases the molecule from the bead, making its characterization by tandem MALDI mass spectrometry straightforward.
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Affiliation(s)
- Levi S Simpson
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185
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48
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Tsipis AC, Stalikas AV. Molecular and electronic structure, magnetotropicity and absorption spectra of benzene-trinuclear copper(I) and silver(I) trihalide columnar binary stacks. Inorg Chem 2012; 51:2541-59. [PMID: 22229767 DOI: 10.1021/ic202497j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The molecular and electronic structures, stabilities, bonding features, magnetotropicity and absorption spectra of benzene-trinuclear Cu(I) and Ag(I) trihalide columnar binary stacks with the general formula [c-M(3)(μ(2)-X)(3)](n)(C(6)H(6))(m) (M = Cu, Ag; X = halide; n, m ≤ 2) have been investigated by means of electronic structure calculation methods. The interaction of c-M(3)(μ(2)-X)(3) clusters with one and two benzene molecules yields 1:1 and 1:2 binary stacks, while benzene sandwiched 2:1 stacks are formed upon interaction of two c-M(3)(μ(2)-X)(3) clusters with one benzene molecule. In all binary stacks the plane of the alternating c-M(3)(μ(2)-X)(3) and benzene components adopts an almost parallel orientation. The separation distance between the centroids of the benzene and the proximal c-M(3)(μ(2)-X)(3) metallic cluster found in the range 2.97-3.33 Å at the B97D/Def2-TZVP level is indicative of a π···π stacking interaction mode, for the centroid separation distance is very close to the sum of the van der Waals radii of Cu···C (3.10 Å) and Ag···C (3.44 Å). Energy decomposition analysis (EDA) at the SSB-D/TZP level revealed that the dominant term in the c-M(3)(μ(2)-X)(3)···C(6)H(6) interaction arises from dispersion and electrostatic forces while the covalent interactions are predicted to be negligible. On the other hand, charge decomposition analysis (CDA) illustrated very small charge transfer from C(6)H(6) toward the c-M(3)(μ(2)-X)(3) clusters, thus reflecting weak π-base/π-acid interactions which are further corroborated by the respective electrostatic potentials and the fact that the total dipole moment vector points to the center of the metallic ring of the c-M(3)(μ(2)-X)(3) cluster. The absorption spectra of all aromatic columnar binary stacks simulated by means of TD-DFT calculations showed strong absorptions in the UV region. The main features of the simulated absorption spectra are thoroughly analyzed, and assignments of the contributing electronic transitions are given. The magnetotropicity of the binary stacks evaluated by the NICS(zz)-scan curves indicated an enhancement of the diatropicity of the inorganic ring upon interaction with the aromatic benzene molecule. Noteworthy is the slight enhancement of the diatropicity of the benzene ring, particularly in the region between the interacting rings, probably due to the superposition (coupling) of the diamagnetic ring currents of the interacting aromatic ring systems.
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Affiliation(s)
- A C Tsipis
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, 451 10 Ioannina, Greece.
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49
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Caumes C, Hjelmgaard T, Roy O, Reynaud M, Servent D, Taillefumier C, Faure S. Synthesis and binding affinities for sst receptors of cyclic peptoid SRIF-mimetics. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20265d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthesis of the first all-peptoid SRIF (Somatotropin Release-Inhibiting Factor) analogues and evaluation of their binding affinities for the five human somatostatin receptors (hsst1–5).
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Affiliation(s)
- Cécile Caumes
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Thomas Hjelmgaard
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Olivier Roy
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Morgane Reynaud
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Denis Servent
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Claude Taillefumier
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Sophie Faure
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
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50
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Lee JH, Kim HS, Lim HS. Design and Facile Solid-Phase Synthesis of Conformationally Constrained Bicyclic Peptoids. Org Lett 2011; 13:5012-5. [DOI: 10.1021/ol201773f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ji Hoon Lee
- Department of Biochemistry and Molecular Biology, and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Han-Sung Kim
- Department of Biochemistry and Molecular Biology, and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Hyun-Suk Lim
- Department of Biochemistry and Molecular Biology, and Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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