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Maciunas LJ, Rotsides P, D'Lauro EJ, Brady S, Beld J, Loll PJ. The VanS sensor histidine kinase from type-B VRE recognizes vancomycin directly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.09.548278. [PMID: 37503228 PMCID: PMC10369886 DOI: 10.1101/2023.07.09.548278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
V ancomycin- r esistant e nterococci (VRE) are among the most common causes of nosocomial infections and have been prioritized as targets for new therapeutic development. Many genetically distinct types of VRE have been identified; however, they all share a common suite of resistance genes that function together to confer resistance to vancomycin. Expression of the resistance phenotype is controlled by the VanRS two-component system. This system senses the presence of the antibiotic, and responds by initiating transcription of resistance genes. VanS is a transmembrane sensor histidine kinase, and plays a fundamental role in antibiotic resistance by detecting vancomycin or its effects; it then transduces this signal to the VanR transcription factor, thereby alerting the organism to the presence of the antibiotic. Despite the critical role played by VanS, fundamental questions remain about its function, and in particular about how it senses vancomycin. Here, we focus on a purified VanRS system from one of the most clinically prevalent forms of VRE, type B. We show that in a native-like membrane environment, the autokinase activity of type-B VanS is strongly stimulated by vancomycin. We additionally demonstrate that this effect is mediated by a direct physical interaction between the antibiotic and the type-B VanS protein, and localize the interacting region to the protein's periplasmic domain. This represents the first time that a direct sensing mechanism has been confirmed for any VanS protein. Significance Statement When v ancomycin- r esistant e nterococci (VRE) sense the presence of vancomycin, they remodel their cell walls to block antibiotic binding. This resistance phenotype is controlled by the VanS protein, a histidine kinase that senses the antibiotic or its effects and signals for transcription of resistance genes. However, the mechanism by which VanS detects the antibiotic has remained unclear, with no consensus emerging as to whether the protein interacts directly with vancomycin, or instead detects some downstream consequence of vancomycin's action. Here, we show that for one of the most clinically relevant types of VRE, type B, VanS is activated by direct binding of the antibiotic. Such mechanistic insights will likely prove useful in circumventing vancomycin resistance.
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Alenazi NA, Aleanizy FS, Alqahtani FY, Aldossari AA, Alanazi MM, Alfaraj R. Anti-quorum sensing activity of poly-amidoamine dendrimer generation 5 dendrimer loaded kinase inhibitor peptide against methicillin-resistant Staphylococcus aureus. Saudi Pharm J 2024; 32:101932. [PMID: 38261946 PMCID: PMC10797154 DOI: 10.1016/j.jsps.2023.101932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a significant concern in both healthcare and community settings, as it causes numerous infections worldwide with high morbidity and mortality rates. One promising strategy is to target the quorum sensing (QS) system of MRSA using a dendrimer loaded with kinase inhibitor peptide. The present investigation has formulated a poly-amidoamine dendrimer (PAMAM) G5 dendrimer that is loaded with Quorum Quencher (QQ) peptide, which functions as a histidine kinase inhibitor. The particle average size of the formulated G5-QQ3 complex was determined to be 276 nm, and polydispersity index values of 0.33. The MIC50 for the formulated nanoparticles was 18 μM as demonstrated by a growth assay. Furthermore, the G5-QQ3 complex was able to inhibit the hemolysis activity of the MRSA with a concentration of 10 μM, and for Staphylococcus aureus was 3 μM. The G5-QQ3 complex possesses the ability to inhibit, penetrate, and eradicate biofilm in MRSA, Staphylococcus aureus, and different agr mutants with inhibition percentages ranging from 60 to 72%. Furthermore, live/dead viability assay confirmed the ability of the formulated nanoparticles to effectively kill all strains within the biofilm structure as evidenced by a confocal microscope, and the cytotoxicity of the G5-QQ3 complex was dose-dependent (p < 0.05). against RAW 264.7 cells. In general, the study confirmed that encapsulating QQ3 peptide within PAMAM G5 dendrimer results in a potent anti-virulence and anti-bacterial action and suggests a synergistic effect. The findings of this study have significant implications for the development of new treatments for MRSA infections, which are a major public health concern.
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Affiliation(s)
- Naifa A. Alenazi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Fadilah S. Aleanizy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Fulwah Y. Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Abdullah A. Aldossari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Mohammed M. Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Rihaf Alfaraj
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
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3
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Arya R, Kim T, Youn JW, Bae T, Kim KK. Identification of an antivirulence agent targeting the master regulator of virulence genes in Staphylococcus aureus. Front Cell Infect Microbiol 2023; 13:1268044. [PMID: 38029271 PMCID: PMC10644738 DOI: 10.3389/fcimb.2023.1268044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The emergence of bactericidal antibiotic-resistant strains has increased the demand for alternative therapeutic agents, such as antivirulence agents targeting the virulence regulators of pathogens. Staphylococcus aureus exoprotein expression (sae) locus, the master regulator of virulence gene expression in multiple drug-resistant S. aureus, is a promising therapeutic target. In this study, we screened a small-molecule library using a SaeRS green fluorescent protein (GFP)-reporter that responded to transcription controlled by the sae locus. We identified the compound, N-(2-methylcyclohexyl)-11-oxo-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide (SKKUCS), as an efficient repressor of sae-regulated GFP activity. SKKUCS inhibited hemolysin production and reduced α-hemolysin-mediated cell lysis. Moreover, SKKUCS substantially reduced the expression levels of various virulence genes controlled by the master regulators, sae, and the accessory gene regulator (agr), demonstrating its potential as an antivirulence reagent targeting the key virulence regulators. Furthermore, autokinase inhibition assay and molecular docking suggest that SKKUCS inhibits the kinase activity of SaeS and potentially targets the active site of SaeS kinase, possibly inhibiting ATP binding. Next, we evaluated the efficacy and toxicity of SKKUCS in vivo using murine models of staphylococcal intraperitoneal and skin infections. Treatment with SKKUCS markedly increased animal survival and significantly decreased the bacterial burden in organs and skin lesion sizes. These findings highlight SKKUCS as a potential antivirulence drug for drug-resistant staphylococcal infections.
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Affiliation(s)
- Rekha Arya
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Truc Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
| | - Joo Won Youn
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Institute of Antibacterial Resistance Research and Therapeutics, Suwon, Republic of Korea
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4
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Polaske TJ, West KHJ, Zhao K, Widner DL, York JT, Blackwell HE. Chemical and biomolecular insights into the Staphylococcus aureus agr quorum sensing system: Current progress and ongoing challenges. Isr J Chem 2023; 63:e202200096. [PMID: 38765792 PMCID: PMC11101167 DOI: 10.1002/ijch.202200096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 03/19/2023]
Abstract
Staphylococcus aureus is a ubiquitous bacterium that has become a major threat to human health due to its extensive toxin production and tremendous capacity for antibiotic resistance (e.g., MRSA "superbug" infections). Amid a worsening antibiotic resistance crisis, new strategies to combat this deadly microbe that remove the selective pressure of traditional approaches are in high demand. S. aureus utilizes an accessory gene regulator (agr) quorum sensing network to monitor its local cellular population and trigger a devastating communal attack, like an invading horde, once a threshold cell density has been reached. The role of the agr system in a range of disease types is still being unraveled. Herein, we discuss the present-day biochemical understanding of agr along with unresolved details, describe its connection to the progression of infection, and review how chemical strategies have been implemented to study and intercept this signaling pathway. This research is illuminating the potential of agr as an anti-virulence target in S. aureus and should inform the study of similar, yet less studied, agr systems in related bacterial pathogens.
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Affiliation(s)
- Thomas J. Polaske
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Korbin H. J. West
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Ke Zhao
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Danielle L. Widner
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Jordan T. York
- 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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5
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The role of sensory kinase proteins in two-component signal transduction. Biochem Soc Trans 2022; 50:1859-1873. [DOI: 10.1042/bst20220848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Two-component systems (TCSs) are modular signaling circuits that regulate diverse aspects of microbial physiology in response to environmental cues. These molecular circuits comprise a sensor histidine kinase (HK) protein that contains a conserved histidine residue, and an effector response regulator (RR) protein with a conserved aspartate residue. HKs play a major role in bacterial signaling, since they perceive specific stimuli, transmit the message across the cytoplasmic membrane, and catalyze their own phosphorylation, and the trans-phosphorylation and dephosphorylation of their cognate response regulator. The molecular mechanisms by which HKs co-ordinate these functions have been extensively analyzed by genetic, biochemical, and structural approaches. Here, we describe the most common modular architectures found in bacterial HKs, and address the operation mode of the individual functional domains. Finally, we discuss the use of these signaling proteins as drug targets or as sensing devices in whole-cell biosensors with medical and biotechnological applications.
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6
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Reconstitution of the S. aureus agr quorum sensing pathway reveals a direct role for the integral membrane protease MroQ in pheromone biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2202661119. [PMID: 35939668 PMCID: PMC9388083 DOI: 10.1073/pnas.2202661119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Staphylococcus aureus, virulence is under the control of a quorum sensing (QS) circuit encoded in the accessory gene regulator (agr) genomic locus. Key to this pathogenic behavior is the production and signaling activity of a secreted pheromone, the autoinducing peptide (AIP), generated following the ribosomal synthesis and posttranslational modification of a precursor polypeptide, AgrD, through two discrete cleavage steps. The integral membrane protease AgrB is known to catalyze the first processing event, generating the AIP biosynthetic intermediate, AgrD (1-32) thiolactone. However, the identity of the second protease in this biosynthetic pathway, which removes an N-terminal leader sequence, has remained ambiguous. Here, we show that membrane protease regulator of agr QS (MroQ), an integral membrane protease recently implicated in the agr response, is directly involved in AIP production. Genetic complementation and biochemical experiments reveal that MroQ proteolytic activity is required for AIP biosynthesis in agr specificity group I and group II, but not group III. Notably, as part of this effort, the biosynthesis and AIP-sensing arms of the QS circuit were reconstituted together in vitro. Our experiments also reveal the molecular features guiding MroQ cleavage activity, a critical factor in defining agr specificity group identity. Collectively, our study adds to the molecular understanding of the agr response and Staphylococcus aureus virulence.
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7
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West KHJ, Gahan CG, Kierski PR, Calderon DF, Zhao K, Czuprynski CJ, McAnulty JF, Lynn DM, Blackwell HE. Sustained Release of a Synthetic Autoinducing Peptide Mimetic Blocks Bacterial Communication and Virulence In Vivo. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Curran G. Gahan
- University of Wisconsin-Madison Chemical and Biological Engineering UNITED STATES
| | | | - Diego F. Calderon
- University of Wisconsin-Madison Pathobiological Sciences UNITED STATES
| | - Ke Zhao
- University of Wisconsin-Madison Chemistry 1101 University Ave. 53706 Madison UNITED STATES
| | | | | | - David M. Lynn
- University of Wisconsin-Madison Chemical and Biological Engineering UNITED STATES
| | - Helen E. Blackwell
- University of Wisconsin Department of Chemistry 1101 University Ave.Room 5211a Chemistry 53706-1322 Madison UNITED STATES
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8
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West KHJ, Gahan CG, Kierski PR, Calderon DF, Zhao K, Czuprynski CJ, McAnulty JF, Lynn DM, Blackwell HE. Sustained Release of a Synthetic Autoinducing Peptide Mimetic Blocks Bacterial Communication and Virulence In Vivo. Angew Chem Int Ed Engl 2022; 61:e202201798. [PMID: 35334139 PMCID: PMC9322450 DOI: 10.1002/anie.202201798] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 11/07/2022]
Abstract
A synthetic peptide was found to block cell-to-cell signalling, or quorum sensing, in bacteria and be highly bioavailable in mouse tissue. The controlled release of this agent from degradable polymeric microparticles strongly inhibited skin infection in a wound model at levels that far surpassed the potency of the peptide when delivered conventionally.
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Affiliation(s)
- Korbin H. J. West
- Department of ChemistryUniversity of Wisconsin-Madison1101 University Ave.MadisonWI 53706USA
| | - Curran G. Gahan
- Department of Chemical and Biological EngineeringUniversity of Wisconsin-Madison1415 Engineering Dr.MadisonWI 53706USA
| | - Patricia R. Kierski
- Department of Surgical SciencesSchool of Veterinary MedicineUniversity of Wisconsin-Madison2015 Linden Dr.MadisonWI 53706USA
| | - Diego F. Calderon
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin-Madison2015 Linden Dr.MadisonWI 53706USA
| | - Ke Zhao
- Department of ChemistryUniversity of Wisconsin-Madison1101 University Ave.MadisonWI 53706USA
| | - Charles J. Czuprynski
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin-Madison2015 Linden Dr.MadisonWI 53706USA
| | - Jonathan F. McAnulty
- Department of Surgical SciencesSchool of Veterinary MedicineUniversity of Wisconsin-Madison2015 Linden Dr.MadisonWI 53706USA
| | - David M. Lynn
- Department of ChemistryUniversity of Wisconsin-Madison1101 University Ave.MadisonWI 53706USA
- Department of Chemical and Biological EngineeringUniversity of Wisconsin-Madison1415 Engineering Dr.MadisonWI 53706USA
| | - Helen E. Blackwell
- Department of ChemistryUniversity of Wisconsin-Madison1101 University Ave.MadisonWI 53706USA
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9
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Khan K, Jalal K, Khan A, Al-Harrasi A, Uddin R. Comparative Metabolic Pathways Analysis and Subtractive Genomics Profiling to Prioritize Potential Drug Targets Against Streptococcus pneumoniae. Front Microbiol 2022; 12:796363. [PMID: 35222301 PMCID: PMC8866961 DOI: 10.3389/fmicb.2021.796363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/28/2021] [Indexed: 02/01/2023] Open
Abstract
Streptococcus pneumoniae is a notorious pathogen that affects ∼450 million people worldwide and causes up to four million deaths per annum. Despite availability of antibiotics (i.e., penicillin, doxycycline, or clarithromycin) and conjugate vaccines (e.g., PCVs), it is still challenging to treat because of its drug resistance ability. The rise of antibiotic resistance in S. pneumoniae is a major source of concern across the world. Computational subtractive genomics is one of the most applied techniques in which the whole proteome of the bacterial pathogen is gradually reduced to a limited number of potential therapeutic targets. Whole-genome sequencing has greatly reduced the time required and provides more opportunities for drug target identification. The goal of this work is to evaluate and analyze metabolic pathways in serotype 14 of S. pneumonia to identify potential drug targets. In the present study, 47 potent drug targets were identified against S. pneumonia by employing the computational subtractive genomics approach. Among these, two proteins are prioritized (i.e., 4-oxalocrotonate tautomerase and Sensor histidine kinase uniquely present in S. pneumonia) as novel drug targets and selected for further structure-based studies. The identified proteins may provide a platform for the discovery of a lead drug candidate that may be capable of inhibiting these proteins and, therefore, could be helpful in minimizing the associated risk related to the drug-resistant S. pneumoniae. Finally, these enzymatic proteins could be of prime interest against S. pneumoniae to design rational targeted therapy.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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10
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Bleul L, Francois P, Wolz C. Two-Component Systems of S. aureus: Signaling and Sensing Mechanisms. Genes (Basel) 2021; 13:34. [PMID: 35052374 PMCID: PMC8774646 DOI: 10.3390/genes13010034] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus encodes 16 two-component systems (TCSs) that enable the bacteria to sense and respond to changing environmental conditions. Considering the function of these TCSs in bacterial survival and their potential role as drug targets, it is important to understand the exact mechanisms underlying signal perception. The differences between the sensing of appropriate signals and the transcriptional activation of the TCS system are often not well described, and the signaling mechanisms are only partially understood. Here, we review present insights into which signals are sensed by histidine kinases in S. aureus to promote appropriate gene expression in response to diverse environmental challenges.
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Affiliation(s)
- Lisa Bleul
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tubingen, Germany;
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tubingen, Germany
| | - Patrice Francois
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals of Geneva University Medical Center, Michel Servet 1, CH-1211 Geneva, Switzerland;
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076 Tubingen, Germany;
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tubingen, Germany
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11
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Polaske TJ, Gahan CG, Nyffeler KE, Lynn DM, Blackwell HE. Identification of small molecules that strongly inhibit bacterial quorum sensing using a high-throughput lipid vesicle lysis assay. Cell Chem Biol 2021; 29:605-614.e4. [PMID: 34932995 PMCID: PMC9035047 DOI: 10.1016/j.chembiol.2021.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 01/15/2023]
Abstract
Strategies to both monitor and block bacterial quorum sensing (QS), and thus associated infections, are of significant interest. We developed a straightforward assay to monitor biosurfactants and lytic agents produced by bacteria under the control of QS. The method is based on the lysis of synthetic lipid vesicles containing the environmentally sensitive fluorescent dye calcein. This assay allows for the in situ screening of compounds capable of altering biosurfactant production by bacteria, and thereby the identification of molecules that could potentially modulate QS pathways, and avoids the constraints of many of the cell-based assays in use today. Application of this assay in a high-throughput format revealed five molecules capable of blocking vesicle lysis by S. aureus. Two of these compounds were found to almost completely inhibit agr-based QS in S. aureus and represent the most potent small-molecule-derived QS inhibitors reported in this formidable pathogen.
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Affiliation(s)
- Thomas J Polaske
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA
| | - Curran G Gahan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI 53706, USA
| | - Kayleigh E Nyffeler
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, USA
| | - David M Lynn
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., 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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12
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Fihn CA, Carlson EE. Targeting a highly conserved domain in bacterial histidine kinases to generate inhibitors with broad spectrum activity. Curr Opin Microbiol 2021; 61:107-114. [PMID: 33932730 PMCID: PMC8189720 DOI: 10.1016/j.mib.2021.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/30/2022]
Abstract
With the rise in antimicrobial resistance and the dearth of effective strategies to combat this threat, the development of novel therapies is of utmost importance. Targeting of bacterial signaling through their the two-component systems (TCSs) may be a viable strategy. TCSs are comprised of a sensory histidine kinase (HK), of which a bacterium can have up to 160 distinct proteins, and a cognate response regulator (RR). The TCSs are generally non-essential for life, but control many virulence and antibiotic-resistance mechanisms. This, along with their absence in animals makes the TCSs an attractive target for antimicrobial therapy, whether as a stand-alone treatments or adjuvants for existing therapies. This review focuses on progress in the development of inhibitors that target the HK ATP-binding domain. Because this domain is highly conserved, it may be feasible to disrupt multiple TCSs within a single organism to increase effectiveness and reduce pressure for the evolution of resistance.
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Affiliation(s)
- Conrad A Fihn
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN 55454, United States; Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States; Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, United States.
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13
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Nagano M, Huang Y, Obexer R, Suga H. One-Pot In Vitro Ribosomal Synthesis of Macrocyclic Depsipeptides. J Am Chem Soc 2021; 143:4741-4750. [PMID: 33733757 DOI: 10.1021/jacs.1c00466] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report a method for the one-pot ribosomal synthesis of macrocyclic depsipeptides. This method is based on a Ser-Pro-Cys-Gly (SPCG) motif discovered by in vitro selection of peptides for the function of self-acylation in the presence of a thioester acyl donor, which forms an O-acyl isopeptide bond via intramolecular S-to-O acyl transfer. Ribosomal synthesis of linear peptides containing the SPCG motif and a backbone "acyl donor" thioester at a downstream position results in spontaneous conversion to the corresponding cyclic depsipeptides (CDPs) in a nearly independent manner of ring size and sequence context. Mutational analysis of the SPCG motif revealed that the P and G residues are dispensable to some extent, but the arrangement of residues in SXCX is crucial for efficient acyl transfer, e.g., CPSG is much less efficient. Finally, one-pot ribosomal synthesis of macrocyclic depsipeptides with various ring sizes and sequences has been demonstrated. This synthetic method can facilitate the ribosomal construction of highly diverse CDP libraries for the discovery of de novo bioactive CDPs.
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Affiliation(s)
- Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Richard Obexer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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14
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Taguchi S, Suga H. Targeting of extracellular protein-protein interactions with macrocyclic peptides. Curr Opin Chem Biol 2021; 62:82-89. [PMID: 33774472 DOI: 10.1016/j.cbpa.2021.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
Targeting of extracellular protein-protein interactions (PPI) is emerging as a major application for de novo discovered macrocyclic peptides. Modern discovery platforms can routinely identify macrocyclic peptide ligands capable of highly selective modulation of extracellular signaling pathways; amenability to chemical synthesis and natural modularity of peptides additionally provides an avenue for their further structural elaboration, while the challenge of cell internalization can be minimized. Here, we discuss the recent progress in targeting extracellular PPIs with macrocyclic peptides by focusing on a number of recent case studies. We analyze the scope and potential limitations of the discovery systems in identifying functional macrocyclic ligands. We also highlight the recent technical advancements allowing for a more streamlined discovery pipeline and our brief perspective in this field.
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Affiliation(s)
- Shota Taguchi
- Department of Advanced Interdisciplinary, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Liu Y, Davis RG, Thomas PM, Kelleher NL, Jewett MC. In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins. Biochemistry 2021; 60:161-169. [PMID: 33426883 DOI: 10.1021/acs.biochem.0c00829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, assembly, and translation (iSAT) system was established to construct functional ribosomes in cell-free systems. However, the iSAT system has not been shown to be compatible with genetic code expansion. Here, to address this gap, we develop an iSAT platform capable of manufacturing pure proteins with site-specifically incorporated ncAAs. We first establish an iSAT platform based on extracts from genomically recoded Escherichia coli lacking release factor 1 (RF-1). This permits complete reassignment of the amber codon translation function. Next, we optimize orthogonal translation system components to demonstrate the benefits of genomic RF-1 deletion on incorporation of ncAAs into proteins. Using our optimized platform, we demonstrate high-level, multi-site incorporation of p-acetyl-phenylalanine (pAcF) and p-azido-phenylalanine into superfolder green fluorescent protein (sfGFP). Mass spectrometry analysis confirms the high accuracy of incorporation for pAcF at one, two, and five amber sites in sfGFP. The iSAT system updated for ncAA incorporation sets the stage for investigating ribosomal mutations to better understand the fundamental basis of protein synthesis, manufacturing proteins with new properties, and engineering ribosomes for novel polymerization chemistries.
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