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Sivaramalingam SS, Jothivel D, Govindarajan DK, Kadirvelu L, Sivaramakrishnan M, Chithiraiselvan DD, Kandaswamy K. Structural and functional insights of sortases and their interactions with antivirulence compounds. Curr Res Struct Biol 2024; 8:100152. [PMID: 38989133 PMCID: PMC11231552 DOI: 10.1016/j.crstbi.2024.100152] [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: 12/31/2023] [Revised: 05/18/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Sortase proteins play a crucial role as integral membrane proteins in anchoring bacterial surface proteins by recognizing them through a Cell-Wall Sorting (CWS) motif and cleaving them at specific sites before initiating pilus assembly. Both sortases and their substrate proteins are major virulence factors in numerous Gram-positive pathogens, making them attractive targets for antimicrobial intervention. Recognizing the significance of virulence proteins, a comprehensive exploration of their structural and functional characteristics is essential to enhance our understanding of pilus assembly in diverse Gram-positive bacteria. Therefore, this review article discusses the structural features of different classes of sortases and pilin proteins, primarily serving as substrates for sortase-assembled pili. Moreover, it thoroughly examines the molecular-level interactions between sortases and their inhibitors, providing insights from both structural and functional perspectives. In essence, this review article will provide a contemporary and complete understanding of both sortase pathways and various strategies to target them effectively to counteract the virulence.
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Affiliation(s)
- Sowmiya Sri Sivaramalingam
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Deepsikha Jothivel
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Deenadayalan Karaiyagowder Govindarajan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
| | - Lohita Kadirvelu
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Muthusaravanan Sivaramakrishnan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
- Department of Biotechnology, Mepco Schlenk Engineering College, Tamil Nadu, India
| | - Dhivia Dharshika Chithiraiselvan
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
| | - Kumaravel Kandaswamy
- Research Center for Excellence in Microscopy, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, 641049, Tamil Nadu, India
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2
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Kumari P, Banerjee SK, Murty US, Ravichandiran V, Mohan U. Harnessing the combined effect of antivirulence agent trans-chalcone with bactericidal curcumin against sortase A enzyme to tackle Gram-positive bacterial infections. Folia Microbiol (Praha) 2024; 69:639-652. [PMID: 37930610 DOI: 10.1007/s12223-023-01097-1] [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] [Received: 11/02/2022] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Gram-positive bacteria are responsible for a wide range of infections in humans. In most Gram-positive bacteria, sortase A plays a significant role in attaching virulence factors to the bacteria's cell wall. These cell surface proteins play a significant role in virulence and pathogenesis. Even though antibiotics are available to treat these infections, there is a continuous search for an alternative strategy due to an increase in antibiotic resistance. Thus, using anti-sortase drugs to combat these bacterial infections may be a promising approach. Here, we describe a method for targeting Gram-positive bacterial infection by combining curcumin and trans-chalcone as sortase A inhibitors. We have used curcumin and trans-chalcone alone and in combination as a sortase A inhibitor. We have seen ~78%, ~43%, and ~94% inhibition when treated with curcumin, trans-chalcone, and a combination of both compounds, respectively. The compounds have also shown a significant effect on biofilm formation, IgG binding, protein A recruitment, and IgG deposition. We discovered that combining curcumin and trans-chalcone is more effective against Gram-positive bacteria than either compound alone. The present work demonstrated that a combination of these natural compounds could be used as an antivirulence therapy against Gram-positive bacterial infection.
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Affiliation(s)
- Poonam Kumari
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, 781101, India
| | - Sanjay K Banerjee
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, 781101, India
| | | | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, 700054, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, 700054, India.
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3
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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4
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Wei X, Liu J, Xu Z, Wang D, Zhu Q, Chen Q, Xu W. Research progress on the pharmacological mechanism, in vivo metabolism and structural modification of Erianin. Biomed Pharmacother 2024; 173:116295. [PMID: 38401517 DOI: 10.1016/j.biopha.2024.116295] [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] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
Erianin is an important bibenzyl compound in dendrobium and has a wide spectrum of pharmacological properties. Since Erianin was discovered, abundant results have been achieved in the in vitro synthesis, structural modification, and pharmacological mechanism research. Researchers have developed a series of simple and efficient in vitro synthesis methods to improve the shortcomings of poor water solubility by replacing the chemical structure or coating it in nanomaterials. Erianin has a broad anti-tumor spectrum and significant anti-tumor effects. In addition, Erianin also has pharmacological actions like immune regulation, anti-inflammatory, and anti-angiogenesis. A comprehensive understanding of the synthesis, metabolism, structural modification, and pharmacological action pathways of Erianin is of great value for the utilization of Erianin. Therefore, this review conducts a relatively systematic look back at Erianin from the above four aspects, to give a reference for the evolvement and further appliance of Erianin.
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Affiliation(s)
- Xin Wei
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Jiajia Liu
- University of Science and Technology of China, Hefei 230026, PR China; Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, PR China
| | - Ziming Xu
- University of Science and Technology of China, Hefei 230026, PR China; Department of Ophthalmology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, PR China
| | - Dan Wang
- University of Science and Technology of China, Hefei 230026, PR China; Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, PR China
| | - Qizhi Zhu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Qi Chen
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Weiping Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China; Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, PR China; Anhui Provincial Key Laboratory of Tumor Immunotherapy and Nutrition Therapy, Hefei 230001, PR China.
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Wang Y, Wu Z, Wang Z, Du H, Xiao S, Lu L, Wang Z. Analyses of the Antibiofilm Activity of o-Phenanthroline Monohydrate against Enterococcus faecalis and Staphylococcus aureus and the Mechanisms Underlying These Effects. ACS Infect Dis 2024; 10:638-649. [PMID: 38258383 DOI: 10.1021/acsinfecdis.3c00516] [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: 01/24/2024]
Abstract
Enterococcus faecalis and Staphylococcus aureus exhibit robust biofilm formation capabilities, the formation of which is closely linked to pathogenicity and drug resistance, thereby resulting in host infection and treatment failure. o-Phenanthroline monohydrate (o-Phen) and its derivatives demonstrate a wide range of antibacterial and antifungal activities. In this study, we aimed to explore the antibiofilm activity of o-Phen to E. faecalis and S. aureus and provide insights into the molecular mechanisms for combating biofilm resistance. We demonstrated that o-Phen possesses significant antibacterial and antibiofilm properties against E. faecalis and S. aureus, inducing alterations in bacterial morphology, compromising cell membrane integrity, and exhibiting synergistic effects with β-lactam antibiotics at sub-MIC concentrations. The adhesion ability and automatic condensation capacity of, and synthesis of, extracellular polymers by E. faecalis cells were reduced by o-Phen, resulting in the inhibition of biofilm formation. Importantly, transcriptome analysis revealed 354 upregulated and 456 downregulated genes in o-Phen-treated E. faecalis. Differentially expressed genes were enriched in 11 metabolism-related pathways, including amino acid metabolism, pyrimidine metabolism, and glycolysis/gluconeogenesis. Moreover, the oppA, CeuA, and ZnuB genes involved in the ABC transport system, and the PBP1A penicillin-binding protein-coding genes sarA and mrcA were significantly downregulated. The multidrug efflux pump system and membrane permeability genes mdtG and hlyD, and bacterial adhesion-related genes, including adcA and fss2 were also downregulated, while mraZ and ASP23 were upregulated. Thus, o-Phen is anticipated to be an effective alternative drug for the treatment of E. faecalis and S. aureus biofilm-associated infections.
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Affiliation(s)
- Yu Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhouhui Wu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhiwen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Heng Du
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Shuang Xiao
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Lin Lu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
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Merde İB, Önel GT, Türkmenoğlu B, Gürsoy Ş, Dilek E, Özçelik AB, Uysal M. Synthesis of (
p‐
tolyl)‐3(2
H
)pyridazinone Derivatives as Novel Acetylcholinesterase Inhibitors. ChemistrySelect 2022. [DOI: 10.1002/slct.202201606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- İrem Bozbey Merde
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
| | - Gülce Taşkor Önel
- Department of Analytical Chemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
| | - Burçin Türkmenoğlu
- Department of Analytical Chemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
| | - Şule Gürsoy
- Department of Biochemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
| | - Esra Dilek
- Department of Biochemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
| | - Azime Berna Özçelik
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Gazi University 06330 Ankara Turkey
| | - Mehtap Uysal
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Erzincan Binali Yıldırım University Yalnızbağ 24002 Erzincan Turkey
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7
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Barthels F, Meyr J, Hammerschmidt SJ, Marciniak T, Räder HJ, Ziebuhr W, Engels B, Schirmeister T. 2-Sulfonylpyrimidines as Privileged Warheads for the Development of S. aureus Sortase A Inhibitors. Front Mol Biosci 2022; 8:804970. [PMID: 35047562 PMCID: PMC8763382 DOI: 10.3389/fmolb.2021.804970] [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: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with emerging multiresistant isolates causing a significant burden to public health systems. We identified 2-sulfonylpyrimidines as a new class of potent inhibitors against S. aureus sortase A acting by covalent modification of the active site cysteine 184. Series of derivatives were synthesized to derive structure-activity relationship (SAR) with the most potent compounds displaying low micromolar KI values. Studies on the inhibition selectivity of homologous cysteine proteases showed that 2-sulfonylpyrimidines reacted efficiently with protonated cysteine residues as found in sortase A, though surprisingly, no reaction occurred with the more nucleophilic cysteine residue from imidazolinium-thiolate dyads of cathepsin-like proteases. By means of enzymatic and chemical kinetics as well as quantum chemical calculations, it could be rationalized that the SNAr reaction between protonated cysteine residues and 2-sulfonylpyrimidines proceeds in a concerted fashion, and the mechanism involves a ternary transition state with a conjugated base. Molecular docking and enzyme inhibition at variable pH values allowed us to hypothesize that in sortase A this base is represented by the catalytic histidine 120, which could be substantiated by QM model calculation with 4-methylimidazole as histidine analog.
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Affiliation(s)
- Fabian Barthels
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Stefan J Hammerschmidt
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Tessa Marciniak
- Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | | | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Tanja Schirmeister
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
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8
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Malik A, Subramaniyam S, Kim CB, Manavalan B. SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information. Comput Struct Biotechnol J 2021; 20:165-174. [PMID: 34976319 PMCID: PMC8703055 DOI: 10.1016/j.csbj.2021.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Sortase enzymes are cysteine transpeptidases that embellish the surface of Gram-positive bacteria with various proteins thereby allowing these microorganisms to interact with their neighboring environment. It is known that several of their substrates can cause pathological implications, so researchers have focused on the development of sortase inhibitors. Currently, six different classes of sortases (A-F) are recognized. However, with the extensive application of bacterial genome sequencing projects, the number of potential sortases in the public databases has exploded, presenting considerable challenges in annotating these sequences. It is very laborious and time-consuming to characterize these sortase classes experimentally. Therefore, this study developed the first machine-learning-based two-layer predictor called SortPred, where the first layer predicts the sortase from the given sequence and the second layer predicts their class from the predicted sortase. To develop SortPred, we constructed an original benchmarking dataset and investigated 31 feature descriptors, primarily on five feature encoding algorithms. Afterward, each of these descriptors were trained using a random forest classifier and their robustness was evaluated with an independent dataset. Finally, we selected the final model independently for both layers depending on the performance consistency between cross-validation and independent evaluation. SortPred is expected to be an effective tool for identifying bacterial sortases, which in turn may aid in designing sortase inhibitors and exploring their functions. The SortPred webserver and a standalone version are freely accessible at: https://procarb.org/sortpred.
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Affiliation(s)
- Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul 03016, Republic of Korea
| | | | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea
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9
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Identification of Novel Antistaphylococcal Hit Compounds Targeting Sortase A. Molecules 2021; 26:molecules26237095. [PMID: 34885677 PMCID: PMC8658998 DOI: 10.3390/molecules26237095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/04/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a causative agent of many hospital- and community-acquired infections with the tendency to develop resistance to all known antibiotics. Therefore, the development of novel antistaphylococcal agents is of urgent need. Sortase A is considered a promising molecular target for the development of antistaphylococcal agents. The main aim of this study was to identify novel sortase A inhibitors. In order to find novel antistaphylococcal agents, we performed phenotypic screening of a library containing 15512 compounds against S. aureus ATCC43300. The molecular docking of hits was performed using the DOCK program and 10 compounds were selected for in vitro enzymatic activity inhibition assay. Two inhibitors were identified, N,N-diethyl-N′-(5-nitro-2-(quinazolin-2-yl)phenyl)propane-1,3-diamine (1) and acridin-9-yl-(1H-benzoimidazol-5-yl)-amine (2), which decrease sortase A activity with IC50 values of 160.3 µM and 207.01 µM, respectively. It was found that compounds 1 and 2 possess antibacterial activity toward 29 tested multidrug resistant S. aureus strains with MIC values ranging from 78.12 to 312.5 mg/L. These compounds can be used for further structural optimization and biological research.
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10
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Inhibitors of Sortases of Gram-Positive Bacteria and their Role in the Treatment of Infectious Diseases (Review). Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02488-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Sapra R, Rajora AK, Kumar P, Maurya GP, Pant N, Haridas V. Chemical Biology of Sortase A Inhibition: A Gateway to Anti-infective Therapeutic Agents. J Med Chem 2021; 64:13097-13130. [PMID: 34516107 DOI: 10.1021/acs.jmedchem.1c00386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus is the leading cause of hospital-acquired infections. The enzyme sortase A, present on the cell surface of S. aureus, plays a key role in bacterial virulence without affecting the bacterial viability. Inhibition of sortase A activity offers a powerful but clinically less explored therapeutic strategy, as it offers the possibility of not inducing any selective pressure on the bacteria to evolve drug-resistant strains. In this Perspective, we offer a chemical space narrative for the design of sortase A inhibitors, as delineated into three broad domains: peptidomimetics, natural products, and synthetic small molecules. This provides immense opportunities for medicinal chemists to alleviate the ever-growing crisis of antibiotic resistance.
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Affiliation(s)
- Rachit Sapra
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Amit K Rajora
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Pushpendra Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Govind P Maurya
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nalin Pant
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi-110016, India
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12
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Exploiting pilus-mediated bacteria-host interactions for health benefits. Mol Aspects Med 2021; 81:100998. [PMID: 34294411 DOI: 10.1016/j.mam.2021.100998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023]
Abstract
Surface pili (or fimbriae) are an important but conspicuous adaptation of several genera and species of Gram-negative and Gram-positive bacteria. These long and non-flagellar multi-subunit adhesins mediate the initial contact that a bacterium has with a host or environment, and thus have come to be regarded as a key colonization factor for virulence activity in pathogens or niche adaptation in commensals. Pili in pathogenic bacteria are well recognized for their roles in the adhesion to host cells, colonization of tissues, and establishment of infection. As an 'anti-adhesive' ploy, targeting pilus-mediated attachment for disruption has become a potentially effective alternative to using antibiotics. In this review, we give a description of the several structurally distinct bacterial pilus types thus far characterized, and as well offer details about the intricacy of their individual structure, assembly, and function. With a molecular understanding of pilus biogenesis and pilus-mediated host interactions also provided, we go on to describe some of the emerging new approaches and compounds that have been recently developed to prevent the adhesion, colonization, and infection of piliated bacterial pathogens.
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13
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Selvaraj C, Selvaraj G, Mohamed Ismail R, Vijayakumar R, Baazeem A, Wei DQ, Singh SK. Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors. Saudi J Biol Sci 2021; 28:3650-3659. [PMID: 34220215 PMCID: PMC8241892 DOI: 10.1016/j.sjbs.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/25/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Bacillus anthracis is a gram positive, deadly spore forming bacteria causing anthrax and these bacteria having the complex mechanism in the cell wall envelope, which can adopt the changes in environmental conditions. In this, the membrane bound cell wall proteins are said to progressive drug target for the inhibition of Bacillus anthracis. Among the cell wall proteins, the SrtA is one of the important mechanistic protein, which mediate the ligation with LPXTG motif by forming the amide bonds. The SrtA plays the vital role in cell signalling, cell wall formation, and biofilm formations. Inhibition of SrtA leads to rupture of the cell wall and biofilm formation, and that leads to inhibition of Bacillus anthracis and thus, SrtA is core important enzyme to study the inhibition mechanism. In this study, we have examined 28 compounds, which have the inhibitory activity against the Bacillus anthracis SrtA for developing the 3D-QSAR and also, compounds binding selectivity with both open and closed SrtA conformations, obtained from 100 ns of MD simulations. The binding site loop deviate in forming the open and closed gate mechanism is investigated to understand the inhibitory profile of reported compounds, and results show the closed state active site conformations are required for ligand binding specificity. Overall, the present study may offer an opportunity for better understanding of the mechanism of action and can be aided to further designing of a novel and highly potent SrtA inhibitors.
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Affiliation(s)
- Chandrabose Selvaraj
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
| | - Gurudeeban Selvaraj
- Centre for Research in Molecular Modelling, Concordia University, 5618 Montreal, Quebec, Canada
| | - Randa Mohamed Ismail
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Department of Microbiology and Immunology, Veterinary Research Division, National Research Center (NRC), Giza, Egypt
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
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Wang L, Poque S, Laamanen K, Saarela J, Poso A, Laitinen T, Valkonen JPT. In Vitro Identification and In Vivo Confirmation of Inhibitors for Sweet Potato Chlorotic Stunt Virus RNA Silencing Suppressor, a Viral RNase III. J Virol 2021; 95:e00107-21. [PMID: 33827953 PMCID: PMC8315922 DOI: 10.1128/jvi.00107-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/28/2021] [Indexed: 11/20/2022] Open
Abstract
Sweet potato virus disease (SPVD), caused by synergistic infection of Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV), is responsible for substantial yield losses all over the world. However, there are currently no approved treatments for this severe disease. The crucial role played by RNase III of SPCSV (CSR3) as an RNA silencing suppressor during the viruses' synergistic interaction in sweetpotato makes it an ideal drug target for developing antiviral treatment. In this study, high-throughput screening (HTS) of small molecular libraries targeting CSR3 was initiated by a virtual screen using Glide docking, allowing the selection of 6,400 compounds out of 136,353. We subsequently developed and carried out kinetic-based HTS using fluorescence resonance energy transfer technology, which isolated 112 compounds. These compounds were validated with dose-response assays including kinetic-based HTS and binding affinity assays using surface plasmon resonance and microscale thermophoresis. Finally, the interference of the selected compounds with viral accumulation was verified in planta In summary, we identified five compounds belonging to two structural classes that inhibited CSR3 activity and reduced viral accumulation in plants. These results provide the foundation for developing antiviral agents targeting CSR3 to provide new strategies for controlling sweetpotato virus diseases.IMPORTANCE We report here a high-throughput inhibitor identification method that targets a severe sweetpotato virus disease caused by coinfection with two viruses (SPCSV and SPFMV). The disease is responsible for up to 90% yield losses. Specifically, we targeted the RNase III enzyme encoded by SPCSV, which plays an important role in suppressing the RNA silencing defense system of sweetpotato plants. Based on virtual screening, laboratory assays, and confirmation in planta, we identified five compounds that could be used to develop antiviral drugs to combat the most severe sweetpotato virus disease.
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Affiliation(s)
- Linping Wang
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Sylvain Poque
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Karoliina Laamanen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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15
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Nitulescu G, Margina D, Zanfirescu A, Olaru OT, Nitulescu GM. Targeting Bacterial Sortases in Search of Anti-Virulence Therapies with Low Risk of Resistance Development. Pharmaceuticals (Basel) 2021; 14:ph14050415. [PMID: 33946434 PMCID: PMC8147154 DOI: 10.3390/ph14050415] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Increasingly ineffective antibiotics and rapid spread of multi- and pan-resistant bacteria represent a global health threat; hence, the need of developing new antimicrobial medicines. A first step in this direction is identifying new molecular targets, such as virulence factors. Sortase A represents a virulence factor essential for the pathogenesis of Gram-positive pathogens, some of which have a high risk for human health. We present here an exhaustive collection of sortases inhibitors grouped by relevant chemical features: vinyl sulfones, 3-aryl acrylic acids and derivatives, flavonoids, naphtoquinones, anthraquinones, indoles, pyrrolomycins, isoquinoline derivatives, aryl β-aminoethyl ketones, pyrazolethiones, pyridazinones, benzisothiazolinones, 2-phenyl-benzoxazole and 2-phenyl-benzofuran derivatives, thiadiazoles, triazolothiadiazoles, 2-(2-phenylhydrazinylidene)alkanoic acids, and 1,2,4-thiadiazolidine-3,5-dione. This review focuses on highlighting their structure–activity relationships, using the half maximal inhibitory concentration (IC50), when available, as an indicator of each compound effect on a specific sortase. The information herein is useful for acquiring knowledge on diverse natural and synthetic sortases inhibitors scaffolds and for understanding the way their structural variations impact IC50. It will hopefully be the inspiration for designing novel effective and safe sortase inhibitors in order to create new anti-infective compounds and to help overcoming the current worldwide antibiotic shortage.
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16
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Zrelovs N, Kurbatska V, Rudevica Z, Leonchiks A, Fridmanis D. Sorting out the Superbugs: Potential of Sortase A Inhibitors among Other Antimicrobial Strategies to Tackle the Problem of Antibiotic Resistance. Antibiotics (Basel) 2021; 10:164. [PMID: 33562778 PMCID: PMC7916047 DOI: 10.3390/antibiotics10020164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/22/2022] Open
Abstract
Rapid spread of antibiotic resistance throughout the kingdom bacteria is inevitably bringing humanity towards the "post-antibiotic" era. The emergence of so-called "superbugs"-pathogen strains that develop resistance to multiple conventional antibiotics-is urging researchers around the globe to work on the development or perfecting of alternative means of tackling the pathogenic bacteria infections. Although various conceptually different approaches are being considered, each comes with its advantages and drawbacks. While drug-resistant pathogens are undoubtedly represented by both Gram(+) and Gram(-) bacteria, possible target spectrum across the proposed alternative approaches of tackling them is variable. Numerous anti-virulence strategies aimed at reducing the pathogenicity of target bacteria rather than eliminating them are being considered among such alternative approaches. Sortase A (SrtA) is a membrane-associated cysteine protease that catalyzes a cell wall sorting reaction by which surface proteins, including virulence factors, are anchored to the bacterial cell wall of Gram(+) bacteria. Although SrtA inhibition seems perspective among the Gram-positive pathogen-targeted antivirulence strategies, it still remains less popular than other alternatives. A decrease in virulence due to inactivation of SrtA activity has been extensively studied in Staphylococcus aureus, but it has also been demonstrated in other Gram(+) species. In this manuscript, results of past studies on the discovery of novel SrtA inhibitory compounds and evaluation of their potency were summarized and commented on. Here, we discussed the rationale behind the inhibition of SrtA, raised some concerns on the comparability of the results from different studies, and touched upon the possible resistance mechanisms as a response to implementation of such therapy in practice. The goal of this article is to encourage further studies of SrtA inhibitory compounds.
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Affiliation(s)
| | | | | | | | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, LV-1067 Riga, Latvia; (N.Z.); (V.K.); (Z.R.); (A.L.)
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17
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Thappeta KRV, Zhao LN, Nge CE, Crasta S, Leong CY, Ng V, Kanagasundaram Y, Fan H, Ng SB. In-Silico Identified New Natural Sortase A Inhibitors Disrupt S. aureus Biofilm Formation. Int J Mol Sci 2020; 21:ijms21228601. [PMID: 33202690 PMCID: PMC7696255 DOI: 10.3390/ijms21228601] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022] Open
Abstract
Sortase A (SrtA) is a membrane-associated enzyme that anchors surface-exposed proteins to the cell wall envelope of Gram-positive bacteria such as Staphylococcus aureus. As SrtA is essential for Gram-positive bacterial pathogenesis but dispensable for microbial growth or viability, SrtA is considered a favorable target for the enhancement of novel anti-infective drugs that aim to interfere with key bacterial virulence mechanisms, such as biofilm formation, without developing drug resistance. Here, we used virtual screening to search an in-house natural compound library and identified two natural compounds, N1287 (Skyrin) and N2576 ((4,5-dichloro-1H-pyrrol-2-yl)-[2,4-dihydroxy-3-(4-methyl-pentyl)-phenyl]-methanone) that inhibited the enzymatic activity of SrtA. These compounds also significantly reduced the growth of S. aureus but possessed moderate mammalian toxicity. Furthermore, S. aureus strains treated with these compounds exhibited reduction in adherence to host fibrinogen, as well as biofilm formation. Hence, these compounds may represent an anti-infective therapy without the side effects of antibiotics.
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Affiliation(s)
- Kishore Reddy Venkata Thappeta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
| | - Li Na Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore;
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, #3-09 Proteos, Singapore 138673, Singapore
| | - Choy Eng Nge
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
| | - Veronica Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore;
- Correspondence: (Y.K.); (H.F.); (S.B.N.); Tel.: +65-6586-9508 (Y.K.); +65-6478-8500 (H.F.); +65-6478-8513 (S.B.N.)
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore;
- Correspondence: (Y.K.); (H.F.); (S.B.N.); Tel.: +65-6586-9508 (Y.K.); +65-6478-8500 (H.F.); +65-6478-8513 (S.B.N.)
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (K.R.V.T.); (C.E.N.); (S.C.); (C.Y.L.); (V.N.)
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore;
- Correspondence: (Y.K.); (H.F.); (S.B.N.); Tel.: +65-6586-9508 (Y.K.); +65-6478-8500 (H.F.); +65-6478-8513 (S.B.N.)
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18
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Design and Synthesis of Small Molecules as Potent Staphylococcus aureus Sortase A Inhibitors. Antibiotics (Basel) 2020; 9:antibiotics9100706. [PMID: 33081148 PMCID: PMC7602840 DOI: 10.3390/antibiotics9100706] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 01/25/2023] Open
Abstract
The widespread and uncontrollable emergence of antibiotic-resistant bacteria, especially methicillin-resistant Staphylococcus aureus, has promoted a wave of efforts to discover a new generation of antibiotics that prevent or treat bacterial infections neither as bactericides nor bacteriostats. Due to its crucial role in virulence and its nonessentiality in bacterial survival, sortase A has been considered as a great target for new antibiotics. Sortase A inhibitors have emerged as promising alternative antivirulence agents against bacteria. Herein, the structural and preparative aspects of some small synthetic organic compounds that block the pathogenic action of sortase A have been described.
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19
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Possible drugs for the treatment of bacterial infections in the future: anti-virulence drugs. J Antibiot (Tokyo) 2020; 74:24-41. [PMID: 32647212 DOI: 10.1038/s41429-020-0344-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
Antibiotic resistance is a global threat that should be urgently resolved. Finding a new antibiotic is one way, whereas the repression of the dissemination of virulent pathogenic bacteria is another. From this point of view, this paper summarizes first the mechanisms of conjugation and transformation, two important processes of horizontal gene transfer, and then discusses the approaches for disarming virulent pathogenic bacteria, that is, virulence factor inhibitors. In contrast to antibiotics, anti-virulence drugs do not impose a high selective pressure on a bacterial population, and repress the dissemination of antibiotic resistance and virulence genes. Disarmed virulence factors make virulent pathogens avirulent bacteria or pathobionts, so that we human will be able to coexist with these disarmed bacteria peacefully.
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20
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Gosschalk JE, Chang C, Sue CK, Siegel SD, Wu C, Kattke MD, Yi SW, Damoiseaux R, Jung ME, Ton-That H, Clubb RT. A Cell-based Screen in Actinomyces oris to Identify Sortase Inhibitors. Sci Rep 2020; 10:8520. [PMID: 32444661 PMCID: PMC7244523 DOI: 10.1038/s41598-020-65256-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/20/2020] [Indexed: 12/12/2022] Open
Abstract
Sortase enzymes are attractive antivirulence drug targets that attach virulence factors to the surface of Staphylococcus aureus and other medically significant bacterial pathogens. Prior efforts to discover a useful sortase inhibitor have relied upon an in vitro activity assay in which the enzyme is removed from its native site on the bacterial surface and truncated to improve solubility. To discover inhibitors that are effective in inactivating sortases in vivo, we developed and implemented a novel cell-based screen using Actinomyces oris, a key colonizer in the development of oral biofilms. A. oris is unique because it exhibits sortase-dependent growth in cell culture, providing a robust phenotype for high throughput screening (HTS). Three molecules representing two unique scaffolds were discovered by HTS and disrupt surface protein display in intact cells and inhibit enzyme activity in vitro. This represents the first HTS for sortase inhibitors that relies on the simple metric of cellular growth and suggests that A. oris may be a useful platform for discovery efforts targeting sortase.
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Affiliation(s)
- Jason E Gosschalk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, USA
| | - Chungyu Chang
- Division of Oral Biology and Medicine, University of California, Los Angeles, USA
| | - Christopher K Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, USA
| | - Sara D Siegel
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Chenggang Wu
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Michele D Kattke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, USA
| | - Sung Wook Yi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Robert Damoiseaux
- Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, USA.,California NanoSystems Institute, University of California, Los Angeles, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA, 90095, USA
| | - Hung Ton-That
- Division of Oral Biology and Medicine, University of California, Los Angeles, USA. .,Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, USA.
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA. .,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, USA. .,Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA, 90095, USA.
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21
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Barthels F, Marincola G, Marciniak T, Konhäuser M, Hammerschmidt S, Bierlmeier J, Distler U, Wich PR, Tenzer S, Schwarzer D, Ziebuhr W, Schirmeister T. Asymmetric Disulfanylbenzamides as Irreversible and Selective Inhibitors of Staphylococcus aureus Sortase A. ChemMedChem 2020; 15:839-850. [PMID: 32118357 PMCID: PMC7318353 DOI: 10.1002/cmdc.201900687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/07/2020] [Indexed: 12/19/2022]
Abstract
Staphylococcus aureus is one of the most frequent causes of nosocomial and community-acquired infections, with drug-resistant strains being responsible for tens of thousands of deaths per year. S. aureus sortase A inhibitors are designed to interfere with virulence determinants. We have identified disulfanylbenzamides as a new class of potent inhibitors against sortase A that act by covalent modification of the active-site cysteine. A broad series of derivatives were synthesized to derive structure-activity relationships (SAR). In vitro and in silico methods allowed the experimentally observed binding affinities and selectivities to be rationalized. The most active compounds were found to have single-digit micromolar Ki values and caused up to a 66 % reduction of S. aureus fibrinogen attachment at an effective inhibitor concentration of 10 μM. This new molecule class exhibited minimal cytotoxicity, low bacterial growth inhibition and impaired sortase-mediated adherence of S. aureus cells.
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Affiliation(s)
- Fabian Barthels
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Gabriella Marincola
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Tessa Marciniak
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Matthias Konhäuser
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Stefan Hammerschmidt
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
| | - Jan Bierlmeier
- Interfaculty Institute of BiochemistryEberhard-Karls-University of TübingenHoppe-Seyler-Strasse 472076TübingenGermany
| | - Ute Distler
- Institute for ImmunologyUniversity Medical CenterJohannes-Gutenberg-University of MainzLangenbeckstr. 155131MainzGermany
- Focus Program Translational Neuroscience (FTN)University Medical CenterLangenbeckstr. 155131MainzGermany
| | - Peter R. Wich
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
- School of Chemical EngineeringUniversity of New South WalesScience and Engineering BuildingSydneyNSW 2052Australia
| | - Stefan Tenzer
- Institute for ImmunologyUniversity Medical CenterJohannes-Gutenberg-University of MainzLangenbeckstr. 155131MainzGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryEberhard-Karls-University of TübingenHoppe-Seyler-Strasse 472076TübingenGermany
| | - Wilma Ziebuhr
- Institute for Molecular Infection BiologyJulius-Maximilians-University of WürzburgJosef-Schneider-Strasse 297080WürzburgGermany
| | - Tanja Schirmeister
- Institute for Pharmacy and BiochemistryJohannes-Gutenberg-University of MainzStaudinger Weg 555128MainzGermany
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22
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Saini M, Mehta DK, Das R. Biological Evaluation and Molecular Docking Studies of Synthesized 5-Substituted-2-chlorophenyl-4-chloro Derivatives Bearing Pyridazinone Moiety. LETT ORG CHEM 2020. [DOI: 10.2174/1570178616666190705152605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemical modification of pyridazinone may lead to a potent therapeutic agent. In this study,
biological properties of pyridazinone derivatives were evaluated by assessing their antimicrobial and
in-vitro antioxidant activities. The reaction of a mucochloric acid and 3-chloro-phenylhydrazine hydrochloride
led to the formation of 5-aryl-4-chloro-2-(3-chloro-phenyl)-2H-pyridazin-3-one derivatives
2(a-j). The target compounds were synthesized using nucleophilic substitution reaction. In-silico molecular
docking studies of the synthesized compounds were carried out with the help of V-Life Science
MDS 4.6 software using GRIP batch docking method to find out which derivative had a better docking.
The newly synthesized compounds were characterized by FTIR, 1HNMR, 13C-NMR, MS, and elemental
analysis. Antimicrobial and in-vitro antioxidant activity study of the novel synthesized compounds
were screened. Compounds 2f and 2g showed good antimicrobial having an MIC 12.5 μg/mL
against Staphylococcus aureus and Candida albicans and in-vitro antioxidant activities having an IC50
50.84. The experimental results were further supported by molecular docking analysis with better interaction
patterns.
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Affiliation(s)
- Minaxi Saini
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana- 133207, India
| | - Dinesh Kumar Mehta
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana- 133207, India
| | - Rina Das
- M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana- 133207, India
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23
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Jaudzems K, Kurbatska V, Je̅kabsons A, Bobrovs R, Rudevica Z, Leonchiks A. Targeting Bacterial Sortase A with Covalent Inhibitors: 27 New Starting Points for Structure-Based Hit-to-Lead Optimization. ACS Infect Dis 2020; 6:186-194. [PMID: 31724850 DOI: 10.1021/acsinfecdis.9b00265] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Because of its essential role as a bacterial virulence factor, enzyme sortase A (SrtA) has become an attractive target for the development of new antivirulence drugs against Gram-positive infections. Here we describe 27 compounds identified as covalent inhibitors of Staphylococcus aureus SrtA by screening a library of approximately 50 000 compounds using a FRET assay followed by NMR-based validation and binding reversibility analysis. Nineteen of these compounds displayed only moderate to weak cytotoxicity, with CC50 against NIH 3T3 mice fibroblast cells ranging from 12 to 740 μM. Analysis using covalent docking suggests that the inhibitors initially associate via hydrophobic interactions, followed by covalent bond formation between the SrtA active site cysteine and an electrophilic center of the inhibitor. The compounds represent good starting points that have the potential to be developed into broad spectrum antivirulence agents as exemplified by hit-to-lead optimization of one of the compounds.
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Affiliation(s)
- Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
- Department of Organic Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Viktorija Kurbatska
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, Riga LV-1067, Latvia
| | - Atis Je̅kabsons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Zhanna Rudevica
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, Riga LV-1067, Latvia
| | - Ainars Leonchiks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, Riga LV-1067, Latvia
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24
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Nitulescu G, Mihai DP, Nicorescu IM, Olaru OT, Ungurianu A, Zanfirescu A, Nitulescu GM, Margina D. Discovery of natural naphthoquinones as sortase A inhibitors and potential anti-infective solutions against Staphylococcus aureus. Drug Dev Res 2019; 80:1136-1145. [PMID: 31486108 DOI: 10.1002/ddr.21599] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/11/2022]
Abstract
Three natural naphthoquinones were screened to find new anti-virulence agents as inhibitors against sortase A from Staphylococcus aureus (SaSrtA) by quantifying the increase in fluorescence intensity upon substrate cleavage at various concentrations. The 5-hydroxy-1,4-naphthalenedione derivatives, juglone and plumbagin, demonstrated a potent inhibitory effect, with IC50 values of 1.78 μM, respectively, 16.71 μM. The related 2-hydroxy-1,4-naphthalenedione derivative, lawsone, demonstrated the selectivity of the chemical scaffold having no significant effect on SaSrtA. The experimental assay was reinforced by molecular docking experiments, antimicrobial, and toxicological studies. Molecular docking studies and the electrophilic character analysis suggest bonding to the enzyme active cysteine residue by a Michael addition reaction. None of the compounds had a significant effect on the concentration of total thiol proteins in the Daphnia magna toxicological assay after 24 hr exposure. Juglone and plumbagin moderately inhibited biofilm formation with no significant effect on bacterial growth of S. aureus, Enterococcus faecalis, and Staphylococcus epidermidis, indicating a selective anti-virulence profile.
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Affiliation(s)
| | - Dragos P Mihai
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | - Octavian T Olaru
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Anca Ungurianu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Anca Zanfirescu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | - Denisa Margina
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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25
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Wehrli PM, Uzelac I, Olsson T, Jacso T, Tietze D, Gottfries J. Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A. Bioorg Med Chem 2019; 27:115043. [PMID: 31420255 DOI: 10.1016/j.bmc.2019.115043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/27/2022]
Abstract
High-throughput screening of small-molecule libraries has led to the identification of thiadiazoles as a new class of inhibitors against Staphylococcus aureus sortase A (SrtA). N-(5-((4-nitrobenzyl)thio)-1,3,4-thiadiazol-2-yl)nicotinamide (IC50 = 3.8 µM) was identified as a potent inhibitor of SrtA after synthetic modification of hit compounds. Additional ligands developed in this study displayed affinities in the low micromolar range without affecting bacterial growth in vitro. The study also suggest a new mode of action through covalent binding to the active site cysteine.
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Affiliation(s)
- Patrick M Wehrli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Ivana Uzelac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Tomas Jacso
- Structure & Biophysics, Discovery Sciences, AstraZeneca R&D, Sweden; Early Discovery, Department of Biology, Nuevolution AB, Denmark
| | - Daniel Tietze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Gottfries
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
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26
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Structural studies of Staphylococcus aureus Sortase inhibiton via Conus venom peptides. Arch Biochem Biophys 2019; 671:87-102. [DOI: 10.1016/j.abb.2019.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022]
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27
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Craft KM, Nguyen JM, Berg LJ, Townsend SD. Methicillin-resistant Staphylococcus aureus (MRSA): antibiotic-resistance and the biofilm phenotype. MEDCHEMCOMM 2019; 10:1231-1241. [PMID: 31534648 PMCID: PMC6748282 DOI: 10.1039/c9md00044e] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022]
Abstract
Staphylococcus aureus (S. aureus) is an asymptomatic colonizer of 30% of all human beings. While generally benign, antibiotic resistance contributes to the success of S. aureus as a human pathogen. Resistance is rapidly evolved through a wide portfolio of mechanisms including horizontal gene transfer and chromosomal mutation. In addition to traditional resistance mechanisms, a special feature of S. aureus pathogenesis is its ability to survive on both biotic and abiotic surfaces in the biofilm state. Due to this characteristic, S. aureus is a leading cause of human infection. Methicillin-resistant S. aureus (MRSA) in particular has emerged as a widespread cause of both community- and hospital-acquired infections. Currently, MRSA is responsible for 10-fold more infections than all multi-drug resistant (MDR) Gram-negative pathogens combined. Recently, MRSA was classified by the World Health Organization (WHO) as one of twelve priority pathogens that threaten human health. In this targeted mini-review, we discuss MRSA biofilm production, the relationship of biofilm production to antibiotic resistance, and front-line techniques to defeat the biofilm-resistance system.
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Affiliation(s)
- Kelly M Craft
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Johny M Nguyen
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Lawrence J Berg
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
| | - Steven D Townsend
- Department of Chemistry , Vanderbilt University , 7300 Stevenson Science Center , Nashville , TN 37235 , USA .
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28
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Wójcik M, Eleftheriadis N, Zwinderman MRH, Dömling ASS, Dekker FJ, Boersma YL. Identification of potential antivirulence agents by substitution-oriented screening for inhibitors of Streptococcus pyogenes sortase A. Eur J Med Chem 2018; 161:93-100. [PMID: 30343193 DOI: 10.1016/j.ejmech.2018.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 10/28/2022]
Abstract
Antimicrobial resistance resulting in ineffective treatment of infectious diseases is an increasing global problem, particularly in infections with pathogenic bacteria. In some bacteria, such as Streptococcus pyogenes, the pathogenicity is strongly linked to the attachment of virulence factors. Their attachment to the cellular membrane is a transpeptidation reaction, catalyzed by sortase enzymes. As such, sortases pose an interesting target for the development of new antivirulence strategies that could yield novel antimicrobial drugs. Using the substitution-oriented fragment screening (SOS) approach, we discovered a potent and specific inhibitor (C10) of sortase A from S. pyogenes. The inhibitor C10 showed high specificity towards S. pyogenes sortase A, with an IC50 value of 10 μM and a Kd of 60 μM. We envision that this inhibitor could be employed as a starting point for further exploration of sortase's potential as therapeutic target for antimicrobial drug development.
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Affiliation(s)
- Magdalena Wójcik
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
| | - Nikolaos Eleftheriadis
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands; University of Groningen, Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, the Netherlands.
| | - Martijn R H Zwinderman
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
| | - Alexander S S Dömling
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Drug Design, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
| | - Frank J Dekker
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
| | - Ykelien L Boersma
- University of Groningen, Groningen Research Institute of Pharmacy, Department of Chemical and Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
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Erianin against Staphylococcus aureus Infection via Inhibiting Sortase A. Toxins (Basel) 2018; 10:toxins10100385. [PMID: 30249042 PMCID: PMC6215257 DOI: 10.3390/toxins10100385] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/08/2018] [Accepted: 09/20/2018] [Indexed: 02/04/2023] Open
Abstract
With continuous emergence and widespread of multidrug-resistant Staphylococcus aureus infections, common antibiotics have become ineffective in treating these infections in the clinical setting. Anti-virulence strategies could be novel, effective therapeutic strategies against drug-resistant bacterial infections. Sortase A (srtA), a transpeptidase in gram-positive bacteria, can anchor surface proteins that play a vital role in pathogenesis of these bacteria. SrtA is known as a potential antivirulent drug target to treat bacterial infections. In this study, we found that erianin, a natural bibenzyl compound, could inhibit the activity of srtA in vitro (half maximal inhibitory concentration-IC50 = 20.91 ± 2.31 μg/mL, 65.7 ± 7.2 μM) at subminimum inhibitory concentrations (minimum inhibitory concentrations-MIC = 512 μg/mL against S. aureus). The molecular mechanism underlying the inhibition of srtA by erianin was identified using molecular dynamics simulation: erianin binds to srtA residues Ile182, Val193, Trp194, Arg197, and Ile199, forming a stable bond via hydrophobic interactions. In addition, the activities of S. aureus binding to fibronectin and biofilm formation were inhibited by erianin, when co-culture with S. aureus. In vivo, erianin could improve the survival in mice that infected with S. aureus by tail vein injection. Experimental results showed that erianin is a potential novel therapeutic compound against S. aureus infections via affecting srtA.
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30
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Phenotypic Variation during Biofilm Formation: Implications for Anti-Biofilm Therapeutic Design. MATERIALS 2018; 11:ma11071086. [PMID: 29949876 PMCID: PMC6073711 DOI: 10.3390/ma11071086] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 12/20/2022]
Abstract
Various bacterial species cycle between growth phases and biofilm formation, of which the latter facilitates persistence in inhospitable environments. These phases can be generally characterized by one or more cellular phenotype(s), each with distinct virulence factor functionality. In addition, a variety of phenotypes can often be observed within the phases themselves, which can be dependent on host conditions or the presence of nutrient and oxygen gradients within the biofilm itself (i.e., microenvironments). Currently, most anti-biofilm strategies have targeted a single phenotype; this approach has driven effective, yet incomplete, protection due to the lack of consideration of gene expression dynamics throughout the bacteria’s pathogenesis. As such, this article provides an overview of the distinct phenotypes found within each biofilm development phase and demonstrates the unique anti-biofilm solutions each phase offers. However, we conclude that a combinatorial approach must be taken to provide complete protection against biofilm forming bacterial and their resulting diseases.
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31
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Zhang J, Wang M, Tang R, Liu Y, Lei C, Huang Y, Nie Z, Yao S. Transpeptidation-Mediated Assembly of Tripartite Split Green Fluorescent Protein for Label-Free Assay of Sortase Activity. Anal Chem 2018; 90:3245-3252. [DOI: 10.1021/acs.analchem.7b04756] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Juan Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Menglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Rui Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yanan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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32
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Vermote A, Van Calenbergh S. Small-Molecule Potentiators for Conventional Antibiotics against Staphylococcus aureus. ACS Infect Dis 2017; 3:780-796. [PMID: 28889735 DOI: 10.1021/acsinfecdis.7b00084] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance constitutes a global health problem, while the discovery and development of novel antibiotics is stagnating. Methicillin-resistant Staphylococcus aureus, responsible for the establishment of recalcitrant, biofilm-related infections, is a well-known and notorious example of a highly resistant micro-organism. Since resistance development is unavoidable with conventional antibiotics that target bacterial viability, it is vital to develop alternative treatment options on top. Strategies aimed at more subtle manipulation of bacterial behavior have recently attracted attention. Here, we provide a literature overview of several small-molecule potentiators for antibiotics, identified for the treatment of Staphylococcus aureus infection. Typically, these potentiators are not bactericidal by themselves and function by reversing resistance mechanisms, by attenuating Staphylococcus aureus virulence, and/or by interfering with quorum sensing.
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Affiliation(s)
- Arno Vermote
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
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33
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New 2-Phenylthiazoles as Potential Sortase A Inhibitors: Synthesis, Biological Evaluation and Molecular Docking. Molecules 2017; 22:molecules22111827. [PMID: 29077016 PMCID: PMC6150342 DOI: 10.3390/molecules22111827] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 10/22/2017] [Indexed: 01/21/2023] Open
Abstract
Sortase A inhibition is a well establish strategy for decreasing bacterial virulence by affecting numerous key processes that control biofilm formation, host cell entry, evasion and suppression of the immune response and acquisition of essential nutrients. A meta-analysis of structures known to act as Sortase A inhibitors provided the starting point for identifying a new potential scaffold. Based on this template a series of new potential Sortase A inhibitors, that contain the 2-phenylthiazole moiety, were synthesized. The physicochemical characterisation confirmed the identity of the proposed structures. Antibacterial activity evaluation showed that the new compounds have a reduced activity against bacterial cell viability. However, the compounds prevent biofilm formation at very low concentrations, especially in the case of E. faecalis. Molecular docking studies performed estimate that this is most likely due to the inhibition of Sortase A. The new compounds could be used as add-on therapies together with known antibacterial agents in order to combat multidrug-resistance enterococcal infections.
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34
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Nitulescu G, Nicorescu IM, Olaru OT, Ungurianu A, Mihai DP, Zanfirescu A, Nitulescu GM, Margina D. Molecular Docking and Screening Studies of New Natural Sortase A Inhibitors. Int J Mol Sci 2017; 18:E2217. [PMID: 29065551 PMCID: PMC5666896 DOI: 10.3390/ijms18102217] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 10/13/2017] [Accepted: 10/20/2017] [Indexed: 11/16/2022] Open
Abstract
To date, multi-drug resistant bacteria represent an increasing health threat, with a high impact on mortality, morbidity, and health costs on a global scale. The ability of bacteria to rapidly and permanently acquire new virulence factors and drug-resistance elements requires the development of new antimicrobial agents and selection of new proper targets, such as sortase A. This specific bacterial target plays an important role in the virulence of many Gram-positive pathogens, and its inhibition should produce a mild evolutionary pressure which will not favor the development of resistance. A primary screening using a fluorescence resonance energy transfer assay was used to experimentally evaluate the inhibitory activity of several compounds on sortase A. Using molecular docking and structure-activity relationship analyses, several lead inhibitors were identified, which were further tested for antimicrobial activity using the well diffusion test and minimum inhibitory concentration. The toxicity was assessed using the Daphnia magna test and used as a future screening filter. Three natural compounds were identified in this study as promising candidates for further development into therapeutically useful anti-infective agents that could be used to treat infections caused by multi-drug resistant bacterial pathogens which include sortase A in their enzymatic set.
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Affiliation(s)
- Georgiana Nitulescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Isabela Madalina Nicorescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Octavian Tudorel Olaru
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Anca Ungurianu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Dragos Paul Mihai
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Anca Zanfirescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - George Mihai Nitulescu
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
| | - Denisa Margina
- Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania.
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35
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Kaminskyy D, Kryshchyshyn A, Lesyk R. Recent developments with rhodanine as a scaffold for drug discovery. Expert Opin Drug Discov 2017; 12:1233-1252. [PMID: 29019278 DOI: 10.1080/17460441.2017.1388370] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Rhodanines, as one of the 4-thiazolidinones subtypes, are recognized as privileged heterocycles in medicinal chemistry. The main achievements include the development of drug-like molecules with numerous biological activities as well as approved drugs. Among rhodanines, 5-ene-rhodanines are of special interest, and are often claimed as pan assay interference compounds due to Michael acceptor functionality. Areas covered: Herein, the synthetic protocols for rhodanines and their transformation are reviewed. Biological activity is briefly discussed as well as biotargets, mode of actions and optimization directions. Furthermore, the utilization of 5-ene-rhodanines in Michael additions are discussed while both pro and contra arguments have been outlined within medicinal chemistry application. Expert opinion: Rhodanines remain privileged heterocycles in drug discovery. They are accessible building blocks for optimization and transformation into related heterocycles, simplified analogues and fused heterocycles with a thiazolidine framework. Michael acceptor functionality, as well as the thesis about low selectivity towards biotargets of rhodanines, must be confirmed experimentally and it cannot be based on just the presence of conjugated α,β-unsaturated carbonyl. Moreover, the positive aspects of Michael acceptors must be considered as well as their multitarget properties. New criteria for target affinity must be found. In conclusion, rhodanines are generally not problematic per se.
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Affiliation(s)
- Danylo Kaminskyy
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Anna Kryshchyshyn
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Roman Lesyk
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
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36
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Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors. Chem Biol Drug Des 2017; 90:327-344. [PMID: 28160417 DOI: 10.1111/cbdd.12962] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/25/2017] [Accepted: 01/28/2017] [Indexed: 12/24/2022]
Abstract
Staphylococcus aureus is a leading cause of hospital-acquired infections in the USA and is a major health concern as methicillin-resistant S. aureus and other antibiotic-resistant strains are common. Compounds that inhibit the S. aureus sortase (SrtA) cysteine transpeptidase may function as potent anti-infective agents as this enzyme attaches virulence factors to the bacterial cell wall. While a variety of SrtA inhibitors have been discovered, the vast majority of these small molecules have not been optimized using structure-based approaches. Here we have used NMR spectroscopy to determine the molecular basis through which pyridazinone-based small molecules inhibit SrtA. These inhibitors covalently modify the active cysteine thiol and partially mimic the natural substrate of SrtA by inducing the closure of an active site loop. Computational and synthetic chemistry methods led to second-generation analogues that are ~70-fold more potent than the lead molecule. These optimized molecules exhibit broad-spectrum activity against other types of class A sortases, have reduced cytotoxicity, and impair SrtA-mediated protein display on S. aureus cell surface. Our work shows that pyridazinone analogues are attractive candidates for further development into anti-infective agents, and highlights the utility of employing NMR spectroscopy and solubility-optimized small molecules in structure-based drug discovery.
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Affiliation(s)
- Albert H Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sung Wook Yi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ethan M Weiner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brendan R Amer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher K Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | - Carly A Dillen
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Silvia Senese
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.,Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Lloyd S Miller
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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37
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Jackson PA, Widen JC, Harki DA, Brummond KM. Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions. J Med Chem 2017; 60:839-885. [PMID: 27996267 PMCID: PMC5308545 DOI: 10.1021/acs.jmedchem.6b00788] [Citation(s) in RCA: 332] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.
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Affiliation(s)
- Paul A. Jackson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - John C. Widen
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kay M. Brummond
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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38
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He W, Zhang Y, Bao J, Deng X, Batara J, Casey S, Guo Q, Jiang F, Fu L. Synthesis, biological evaluation and molecular docking analysis of 2-phenyl-benzofuran-3-carboxamide derivatives as potential inhibitors of Staphylococcus aureus Sortase A. Bioorg Med Chem 2016; 25:1341-1351. [PMID: 28094221 DOI: 10.1016/j.bmc.2016.12.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 11/26/2022]
Abstract
In Gram-positive bacteria, Sortase A (Srt A) is a critical cysteine transpeptidase that is responsible for recognizing and assembling surface virulence proteins through the recognition of a LPXTG (leucine, proline, X, threonine, and glycine, where X is any amino acid) signal. Mutants lacking genes for Srt A attenuate infections without affecting microbial viability. Here a series of 2-phenyl-benzofuran-3-carboxamide derivatives were synthesized and identified as potent Srt A inhibitors. Activity assays revealed that multiple compounds exhibited excellent inhibitory activity against Srt A compared with known Sortase A inhibitor pHMB (IC50=130μM). Structural activity relationships (SARs) demonstrated that the amide group at 3-position was essential for inhibitory activity. Replacement of the hydroxyl group at the 2-phenyl position of benzofuran with other substitutions such as a methoxyl, halogen or nitro group reduced the enzyme inhibitory activity in most cases. The compound Ia-22 was found to be the most potent inhibitor against the enzyme with an IC50 value of 30.8μM. Molecular docking studies showed Ia-22 shared similar binding pattern with substrate LPXTG in the binding pocket of Srt A (PDB: 2KID) including i-butyl stretching, L-shape pattern kinking, and H-bond interaction with Srt A functional site residues Cys184, Trp194 and Arg197.
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Affiliation(s)
- Wan He
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Yong Zhang
- School of Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jian Bao
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Xinxian Deng
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Jennifer Batara
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Shawn Casey
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Qiuyuan Guo
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China
| | - Faqin Jiang
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China.
| | - Lei Fu
- School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, PR China.
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39
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Structural Analysis of Sortase A Inhibitors. Molecules 2016; 21:molecules21111591. [PMID: 27879666 PMCID: PMC6272945 DOI: 10.3390/molecules21111591] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/12/2016] [Accepted: 11/19/2016] [Indexed: 01/18/2023] Open
Abstract
Bacterial sortases are cysteine transpeptidases that regulate the covalent linkage of several surface protein virulence factors in Gram-positive bacteria. Virulence factors play significant roles in adhesion, invasion of host tissues, biofilm formation and immune evasion, mediating the bacterial pathogenesis and infectivity. Therefore, sortases are emerging as important targets for the design of new anti-infective agents. We employed a computational study, based on structure derived descriptors and molecular fingerprints, in order to develop simple classification methods which could allow predicting low active or high active SrtA inhibitors. Our results indicate that a highly active SrtA inhibitor has a molecular weight ranging between 180 and 600, contains one up to four nitrogen atoms, up to three oxygen atoms and under 18 hydrogen atoms. Also the hydrogen acceptor number and the molecular flexibility, as assessed by the number of rotatable bounds, have emerged as the most relevant descriptors for SrtA affinity. The Bemis-Murcko scaffolding revealed favoured scaffolds as containing at least two ring structures bonded directly or merged in a condensed cycle. This data represent a valuable tool for identifying new potent SrtA inhibitors, potential anti-virulence agents targeted against Gram-positive bacteria, including multiresistant strains.
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40
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Rentero Rebollo I, McCallin S, Bertoldo D, Entenza JM, Moreillon P, Heinis C. Development of Potent and Selective S. aureus Sortase A Inhibitors Based on Peptide Macrocycles. ACS Med Chem Lett 2016; 7:606-11. [PMID: 27326335 DOI: 10.1021/acsmedchemlett.6b00045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/14/2016] [Indexed: 11/30/2022] Open
Abstract
Sortases are transpeptidase enzymes that anchor surface proteins, including virulence factors, to the cell wall of Gram-positive bacteria, and they are potential targets for the development of anti-infective agents. While several large compound libraries were searched by high-throughput screening, no high-affinity inhibitors of sortases could be developed to date. Here, we applied phage display to screen billions of peptide macrocycles against sortase A (SrtA) of Staphylococcus aureus (S. aureus). We were able to identify potent and selective inhibitors of SrtA that blocked SrtA-mediated anchoring of synthetic substrates to the surface of live S. aureus cells. A region present in all inhibitory peptides (Leu-Pro-Pro) resembled the natural substrates of SrtA (Leu-Pro-Xaa-Thr-Gly), suggesting that the macrocycles bind to the enzyme's active site and that they form similar molecular contacts as natural substrates. The evolved peptide macrocycles may be used as lead structures for the development of potent peptidomimetic SrtA inhibitors.
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Affiliation(s)
- Inmaculada Rentero Rebollo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Shawna McCallin
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Davide Bertoldo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - José Manuel Entenza
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Moreillon
- Department
of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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41
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Schatte M, Bocola M, Roth T, Martinez R, Kopetzki E, Schwaneberg U, Bönitz-Dulat M. Reporter Immobilization Assay (REIA) for Bioconjugating Reactions. Bioconjug Chem 2016; 27:1484-92. [DOI: 10.1021/acs.bioconjchem.6b00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Schatte
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | - Marco Bocola
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Ronny Martinez
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Ulrich Schwaneberg
- Lehrstuhl
für Biotechnologie, RWTH Aachen University, 52074 Aachen, Germany
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42
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Si L, Li P, Liu X, Luo L. Chinese herb medicine against Sortase A catalyzed transformations, a key role in gram-positive bacterial infection progress. J Enzyme Inhib Med Chem 2016; 31:184-196. [PMID: 27162091 DOI: 10.1080/14756366.2016.1178639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many Gram-positive bacteria can anchor their surface proteins to the cell wall peptidoglycan covalently by a common mechanism with Sortase A (SrtA), thus escaping from the host's identification of immune cells. SrtA can complete this anchoring process by cleaving LPXTG motif conserved among these surface proteins and thus these proteins anchor on the cell wall. Moreover, those SrtA mutants lose this capability to anchor these relative proteins, with these bacteria no longer infectious. Therefore, SrtA inhibitors can be promising anti-infective agents to cure bacterial infections. Chinese herb medicines (CHMs) (chosen from Science Citation Index) have exhibited inhibition on SrtA of Gram-positive pathogens irreversibly or reversibly. In general, CHMs are likely to have important long-term impact as new antibacterial compounds and sought after by academia and the pharmaceutical industry. This review mainly focuses on SrtA inhibitors from CHMs and the potential inhibiting mechanism related to chemical structures of compounds in CHMs.
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Affiliation(s)
- Lifang Si
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Pan Li
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Xiong Liu
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
| | - Lixin Luo
- a School of Bioscience & Bioengineering, South China University of Technology, Guangzhou University Town , Panyu , Guangzhou , China
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43
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Maggio B, Raffa D, Raimondi MV, Cascioferro S, Plescia F, Schillaci D, Cusimano MG, Leonchiks A, Zhulenkovs D, Basile L, Daidone G. Discovery of a New Class of Sortase A Transpeptidase Inhibitors to Tackle Gram-Positive Pathogens: 2-(2-Phenylhydrazinylidene)alkanoic Acids and Related Derivatives. Molecules 2016; 21:241. [PMID: 26907235 PMCID: PMC6273394 DOI: 10.3390/molecules21020241] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/05/2016] [Accepted: 02/12/2016] [Indexed: 12/23/2022] Open
Abstract
A FRET-based random screening assay was used to generate hit compounds as sortase A inhibitors that allowed us to identify ethyl 3-oxo-2-(2-phenylhydrazinylidene)butanoate as an example of a new class of sortase A inhibitors. Other analogues were generated by changing the ethoxycarbonyl function for a carboxy, cyano or amide group, or introducing substituents in the phenyl ring of the ester and acid derivatives. The most active derivative found was 3-oxo-2-(2-(3,4dichlorophenyl)hydrazinylidene)butanoic acid (2b), showing an IC50 value of 50 µM. For a preliminary assessment of their antivirulence properties the new derivatives were tested for their antibiofilm activity. The most active compound resulted 2a, which showed inhibition of about 60% against S. aureus ATCC 29213, S. aureus ATCC 25923, S. aureus ATCC 6538 and S. epidermidis RP62A at a screening concentration of 100 µM.
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Affiliation(s)
- Benedetta Maggio
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Demetrio Raffa
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Maria Valeria Raimondi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
- IEMEST, Istituto Euromediterraneo di Scienza e Tecnologia, Via Emerico Amari 123, I-90139 Palermo, Italy.
| | - Fabiana Plescia
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Maria Grazia Cusimano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
| | - Ainars Leonchiks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, 1067 Riga, Latvia.
| | - Dmitrijs Zhulenkovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, 1067 Riga, Latvia.
| | - Livia Basile
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale A. Doria 6 Ed. 2, Città Universitaria, I-95125 Catania, Italy.
| | - Giuseppe Daidone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy.
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44
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Exploration of multiple Sortase A protein conformations in virtual screening. Sci Rep 2016; 6:20413. [PMID: 26846342 PMCID: PMC4742773 DOI: 10.1038/srep20413] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/04/2016] [Indexed: 02/08/2023] Open
Abstract
Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.
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45
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Heras B, Scanlon MJ, Martin JL. Targeting virulence not viability in the search for future antibacterials. Br J Clin Pharmacol 2015; 79:208-15. [PMID: 24552512 DOI: 10.1111/bcp.12356] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/09/2013] [Indexed: 01/01/2023] Open
Abstract
New antibacterials need new approaches to overcome the problem of rapid antibiotic resistance. Here we review the development of potential new antibacterial drugs that do not kill bacteria or inhibit their growth, but combat disease instead by targeting bacterial virulence.
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Affiliation(s)
- Begoña Heras
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic
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46
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Chan AH, Yi SW, Terwilliger AL, Maresso AW, Jung ME, Clubb RT. Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal: A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS. J Biol Chem 2015; 290:25461-74. [PMID: 26324714 DOI: 10.1074/jbc.m115.670984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/31/2022] Open
Abstract
The endospore forming bacterium Bacillus anthracis causes lethal anthrax disease in humans and animals. The ability of this pathogen to replicate within macrophages is dependent upon the display of bacterial surface proteins attached to the cell wall by the B. anthracis Sortase A ((Ba)SrtA) enzyme. Previously, we discovered that the class A (Ba)SrtA sortase contains a unique N-terminal appendage that wraps around the body of the protein to contact the active site of the enzyme. To gain insight into its function, we determined the NMR structure of (Ba)SrtA bound to a LPXTG sorting signal analog. The structure, combined with dynamics, kinetics, and whole cell protein display data suggest that the N terminus modulates substrate access to the enzyme. We propose that it may increase the efficiency of protein display by reducing the unproductive hydrolytic cleavage of enzyme-protein covalent intermediates that form during the cell wall anchoring reaction. Notably, a key active site loop (β7/β8 loop) undergoes a disordered to ordered transition upon binding the sorting signal, potentially facilitating recognition of lipid II.
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Affiliation(s)
- Albert H Chan
- From the Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, California 90095 and
| | - Sung Wook Yi
- From the Department of Chemistry and Biochemistry
| | - Austen L Terwilliger
- the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Anthony W Maresso
- the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Robert T Clubb
- From the Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, and the Molecular Biology Institute, University of California, Los Angeles, California 90095 and
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47
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Cascioferro S, Raffa D, Maggio B, Raimondi MV, Schillaci D, Daidone G. Sortase A Inhibitors: Recent Advances and Future Perspectives. J Med Chem 2015; 58:9108-23. [DOI: 10.1021/acs.jmedchem.5b00779] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Stella Cascioferro
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
- IEMEST, Istituto Euromediterraneo di Scienza e Tecnologia, Via Emerico Amari, 123, 90139 Palermo, Italy
| | - Demetrio Raffa
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Benedetta Maggio
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Maria Valeria Raimondi
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Domenico Schillaci
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Giuseppe Daidone
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione
di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
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48
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49
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Zhu J, Xiang L, Jiang F, Zhang ZJ. Equilibrium of sortase A dimerization on Staphylococcus aureus cell surface mediates its cell wall sorting activity. Exp Biol Med (Maywood) 2015; 241:90-100. [PMID: 26129884 DOI: 10.1177/1535370215592122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/20/2015] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus sortase A (SrtA) transpeptidase is a therapeutically important membrane-bound enzyme in Gram-positive bacteria, which organizes the covalently attached cell surface proteins on the peptidoglycan cell wall of the organism. Here, we report the direct observation of the highly selective homo-dimerization of SrtA on the cell membrane. To address the biological significance of the dimerization towards enzyme function, site-directed mutagenesis was performed to generate a SrtA mutant, which exists as monomer on the cell membrane. We observed that the cell surface display of adhesive proteins in S. aureus cells expressing monomeric SrtA mutant is more prominent than the cells expressing the wild-type enzyme. A cell-based invasion assay was also performed to evaluate the activities of wild-type SrtA and its monomeric mutant as well. Our data demonstrated that S. aureus cells expressing SrtA in monomeric form invade host mammalian cells more efficiently than those expressing wild-type SrtA in dimer-monomer equilibrium. The results suggested that the monomeric form of SrtA is more active than the dimeric form of the enzyme in terms of cell surface display of virulence factors for infection. This is the first study to present the oligomerization of SrtA and its related biological function on the cell membrane. Study of SrtA dimerization has implications for understanding its catalytic mechanism at the cellular level as well as the development of novel anti-infective agents.
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Affiliation(s)
- Jie Zhu
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - Liang Xiang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA Bioengineering Department, School of Engineering, Santa Clara University, Santa Clara, CA 95053, USA
| | - Faqin Jiang
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA Department of Medicinal Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiwen J Zhang
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA Bioengineering Department, School of Engineering, Santa Clara University, Santa Clara, CA 95053, USA
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50
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Raj KK, Ganesh Kumar V, Leela Madhuri C, Mathi P, Durga Lakshmi R, Ravi M, Sri Ramudu B, Venkata Rao SV, Ramachandran D. Designing of potential inhibitors against Staphylococcus aureus sortase A: Combined analogue and structure based approach with in vitro validation. J Mol Graph Model 2015; 60:89-97. [PMID: 26119984 DOI: 10.1016/j.jmgm.2015.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus sortase A is an attractive target of Gram-positive bacteria that plays a crucial role in anchoring of surface proteins to peptidoglycan present in bacterial cell wall. Inhibiting sortase A is an elementary and essential effort in preventing the pathogenesis. In this context, in silico virtual screening of in-house database was performed using ligand based pharmacophore model as a filter. The developed pharmacophore model AAHR 11 consists of two acceptors, one hydrophobic and one ring aromatic feature. Top ranked molecule KKR1 was docked into the active site of the target. After profound analysis, it was analyzed and optimized based on the observations from its binding pose orientation. Upgraded version of KKR1 was KKR2 and has improved docking score, binding interactions and best fit in the binding pocket. KKR1 along with KKR2 were further validated using 100 ns molecular dynamic studies. Both KKR1 and KKR2 contain Indole-thiazolidine moiety and were synthesized. The disk diffusion assay has good initial results (ZI of KKR1, KKR2 were 24, 38 mm at 10 μg/mL and ZI of Ampicillin was 22 at 10 μg/mL) and calculated MICs of the molecules (KKR1 5.56±0.28 μg/mL, KKR2 1.32±0.12 μg/mL, Ampicillin 8±1.1 μg/mL) were in good agreement with standard drug Ampicillin. KKR1 has shown IC50 of 1.23±0.14 μM whereas the optimized lead molecule KKR2 show IC50 of 0.008±0.07 μM. Results from in silico were validated by in vitro studies and proved that indole-thiazolidine molecules would be useful for future development as lead molecules against S. aureus sortase A.
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Affiliation(s)
- K Kranthi Raj
- Department of Chemistry, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 510, India
| | - Veeramachaneni Ganesh Kumar
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, Guntur (Dt.), 522 502 Guntur, AP, India
| | - Chalasani Leela Madhuri
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, Guntur (Dt.), 522 502 Guntur, AP, India
| | - Pardhasaradhi Mathi
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, Guntur (Dt.), 522 502 Guntur, AP, India
| | - Ravulapati Durga Lakshmi
- Department of Electronics and Computer Engineering, K L E F University, Green Fields, Vaddeswaram, Guntur (Dt.), 522 502 Guntur, AP, India
| | - M Ravi
- Bioinformatics Division, Environmental Microbiology Lab, Department of Botany, Osmania University, Hyderabad 500 007, India
| | - B Sri Ramudu
- Department of Chemistry, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 510, India
| | - S V Venkata Rao
- Department of Chemistry, Rajiv Gandhi University of Knowledge Technologies, Nuzvid 521 201 AP, India
| | - D Ramachandran
- Department of Chemistry, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522 510, India.
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