1
|
Hintzen JCJ, Abujubara H, Tietze D, Tietze AA. The Complete Assessment of Small Molecule and Peptidomimetic Inhibitors of Sortase A Towards Antivirulence Treatment. Chemistry 2024; 30:e202401103. [PMID: 38716707 DOI: 10.1002/chem.202401103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Indexed: 06/20/2024]
Abstract
This review covers the most recent advances in the development of inhibitors for the bacterial enzyme sortase A (SrtA). Sortase A (SrtA) is a critical virulence factor, present ubiquitously in Gram-positive bacteria of which many are pathogenic. Sortases are key enzymes regulating bacterial adherence to host cells, by anchoring extracellular matrix-binding proteins to the bacterial outer cell wall. By targeting virulence factors, effective treatment can be achieved, without inducing antibiotic resistance to the treatment. This is a potentially more sustainable, long-term approach to treating bacterial infections, including ones that display multiple resistance to current therapeutics. There are many promising approaches available for SrtA inhibition, some of which have the potential to advance into further clinical development, with peptidomimetic and in vivo active small molecules being among the most promising. There are currently no approved drugs on the market targeting SrtA, despite its promise, adding to the relevance of this review article, as it extends to the pharmaceutical industry additionally to academic researchers.
Collapse
Affiliation(s)
- Jordi C J Hintzen
- University of Gothenburg, Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, Kemigården 4, 412 96, Göteborg, Sweden
| | - Helal Abujubara
- University of Gothenburg, Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, Kemigården 4, 412 96, Göteborg, Sweden
| | - Daniel Tietze
- University of Gothenburg, Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, Kemigården 4, 412 96, Göteborg, Sweden
| | - Alesia A Tietze
- University of Gothenburg, Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, Kemigården 4, 412 96, Göteborg, Sweden
| |
Collapse
|
2
|
Amacher JF, Antos JM. Sortases: structure, mechanism, and implications for protein engineering. Trends Biochem Sci 2024; 49:596-610. [PMID: 38692993 DOI: 10.1016/j.tibs.2024.04.003] [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: 11/06/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Sortase enzymes are critical cysteine transpeptidases on the surface of bacteria that attach proteins to the cell wall and are involved in the construction of bacterial pili. Due to their ability to recognize specific substrates and covalently ligate a range of reaction partners, sortases are widely used in protein engineering applications via sortase-mediated ligation (SML) strategies. In this review, we discuss recent structural studies elucidating key aspects of sortase specificity and the catalytic mechanism. We also highlight select recent applications of SML, including examples where fundamental studies of sortase structure and function have informed the continued development of these enzymes as tools for protein engineering.
Collapse
Affiliation(s)
- Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
| | - John M Antos
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, Sacchettini J, Cai JJ, Subashchandrabose S. Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli. J Bacteriol 2024:e0011224. [PMID: 38856220 DOI: 10.1128/jb.00112-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Urinary tract infections (UTIs) are a major global health problem and are caused predominantly by uropathogenic Escherichia coli (UPEC). UTIs are a leading cause of prescription antimicrobial use. Incessant increase in antimicrobial resistance in UPEC and other uropathogens poses a serious threat to the current treatment practices. Copper is an effector of nutritional immunity that impedes the growth of pathogens during infection. We hypothesized that copper would augment the toxicity of select small molecules against bacterial pathogens. We conducted a small molecule screening campaign with a library of 51,098 molecules to detect hits that inhibit a UPEC ΔtolC mutant in a copper-dependent manner. A molecule, denoted as E. coli inhibitor or ECIN, was identified as a copper-responsive inhibitor of wild-type UPEC strains. Our gene expression and metal content analysis results demonstrate that ECIN works in concert with copper to exacerbate Cu toxicity in UPEC. ECIN has a broad spectrum of activity against pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus. Subinhibitory levels of ECIN eliminate UPEC biofilm formation. Transcriptome analysis of UPEC treated with ECIN reveals induction of multiple stress response systems. Furthermore, we demonstrate that L-cysteine rescues the growth of UPEC exposed to ECIN. In summary, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC.IMPORTANCEUrinary tract infection (UTI) is a ubiquitous infectious condition affecting millions of people annually. Uropathogenic Escherichia coli (UPEC) is the predominant etiological agent of UTI. However, UTIs are becoming increasingly difficult to resolve with antimicrobials due to increased antimicrobial resistance in UPEC and other uropathogens. Here, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC. In addition to E. coli, this small molecule also inhibits pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus.
Collapse
Affiliation(s)
- Braden S Hanson
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Amanuel Hailemariam
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - Yongjian Yang
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Faras Mohamed
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Dwight Baker
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James Sacchettini
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Ramadan AMAA, Zidan SAH, Shehata RM, El-Sheikh HH, Ameen F, Stephenson SL, Al-Bedak OAHM. Antioxidant, antibacterial, and molecular docking of methyl ferulate and oleic acid produced by Aspergillus pseudodeflectus AUMC 15761 utilizing wheat bran. Sci Rep 2024; 14:3183. [PMID: 38326360 PMCID: PMC10850474 DOI: 10.1038/s41598-024-52045-z] [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: 07/31/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Secondary metabolites (SMs) are the primary source of therapeutics and lead chemicals in medicine. They have been especially important in the creation of effective cures for conditions such as cancer, malaria, bacterial and fungal infections, neurological and cardiovascular problems, and autoimmune illnesses. In the present study, Aspergillus pseudodeflectus AUMC 15761 was demonstrated to use wheat bran in solid state fermentation (SSF) at optimum conditions (pH 7.0 at 30 °C after 10 days of incubation and using sodium nitrate as a nitrogen source) to produce methyl ferulate and oleic acid with significant antioxidant and antibacterial properties. Gas chromatography-mass spectrometry (GC-MS) analysis of the crude methanol extract revealed eleven peaks that indicated the most common chemical components. Purification of methyl ferulate and oleic acid was carried out by column chromatography, and both compounds were identified by in-depth spectroscopic analysis, including 1D and 2D NMR and HR-ESI-MS. DPPH activity increased as the sample concentration increased. IC50 values of both compounds obtained were 73.213 ± 11.20 and 104.178 ± 9.53 µM, respectively. Also, the MIC value for methyl ferulate against Bacillus subtilis and Staphylococcus aureus was 0.31 mg/mL, while the corresponding MIC values for oleic acid were 1.25 mg/mL and 0.62 mg/mL for both bacterial strains, respectively. Molecular modeling calculations were carried out to reveal the binding mode of methyl ferulate and oleic acid within the binding site of the crucial proteins of Staphylococcus aureus. The docking results were found to be well correlated with the experimental data.
Collapse
Affiliation(s)
| | - Sabry Ahmed Hussein Zidan
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, 71524, Egypt
| | - Reda Mohamed Shehata
- Department of Botany & Microbiology, Faculty of Science, Al Azhar University, Cairo, Egypt
- The Regional Center for Mycology and Biotechnology (RCMB), Al Azhar University, Cairo, Egypt
| | - Hussein Hosny El-Sheikh
- Department of Botany & Microbiology, Faculty of Science, Al Azhar University, Cairo, Egypt
- The Regional Center for Mycology and Biotechnology (RCMB), Al Azhar University, Cairo, Egypt
| | - Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia.
| | - Steven L Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, USA
| | | |
Collapse
|
8
|
Desai N, Jadeja D, Monapara J, Panda SK, Rana MK, Dave B. Design, synthesis, antimicrobial activity, DFT, and molecular docking studies of pyridine-pyrazole-based dihydro-1,3,4-oxadiazoles against various bacterial and fungal targets. J Biochem Mol Toxicol 2023; 37:e23377. [PMID: 37098749 DOI: 10.1002/jbt.23377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Antimicrobial resistance which is increasing at an alarming rate is a severe public health issue worldwide. Hence, the development of novel antibiotics is an urgent need as microbes have developed resistance against available antibiotics. In search of novel antimicrobial agents, a convenient route for the preparation of substituted 3-(1-phenyl-3-(p-tolyl)-1H-pyrazol-4-yl)-1-(2-phenyl-5-(pyridin-3-yl)-1,3,4-oxadiazol-3(2H)-yl)prop-2-en-1-ones (6a-6o) has been adopted by using pyridine-3-carbohydrazide and various aromatic aldehydes. The newly synthesized compounds were characterized by using various spectral techniques, for example, IR, 1 H NMR, 13 C NMR, and mass spectroscopy. Synthesized hybrids were studied for in vitro antimicrobial potency against various bacterial and fungal strains. Antibacterial results revealed that compounds 6e, 6h, 6i, 6l, and 6m were found to be most active against bacterial strains as they showed minimum inhibitory concentration (MIC) value of 62.5 μg/mL while compounds 6d, 6e, and 6h showed MIC value of 200 μg/mL against Candida albicans. The quantum parameters that relate to the bioavailability of the compounds were computed, followed by docking with different bacterial and fungal targets like sortase A, dihydrofolate reductase, thymidylate kinase, gyrase B, sterol 14-alpha demethylase. The experimental and computational results are in good agreement.
Collapse
Affiliation(s)
- Nisheeth Desai
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Dharmpalsinh Jadeja
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Jahnvi Monapara
- Division of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India
| | - Bharti Dave
- School of Science, Indrashil University, Kadi, Gujarat, India
| |
Collapse
|
9
|
Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
Collapse
Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| |
Collapse
|
10
|
Ivleva EA, Zaborskaya MS, Shiryaev VA, Klimochkin YN. One pot synthesis of bridgehead amino alcohols from diamantoid hydrocarbons. SYNTHETIC COMMUN 2023. [DOI: 10.1080/00397911.2023.2177173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Elena A. Ivleva
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Maria S. Zaborskaya
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Vadim A. Shiryaev
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Yuri N. Klimochkin
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| |
Collapse
|
11
|
Shulga DA, Kudryavtsev KV. Theoretical Studies of Leu-Pro-Arg-Asp-Ala Pentapeptide (LPRDA) Binding to Sortase A of Staphylococcus aureus. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238182. [PMID: 36500275 PMCID: PMC9890316 DOI: 10.3390/molecules27238182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Sortase A (SrtA) of Staphylococcus aureus is a well-defined molecular target to combat the virulence of these clinically important bacteria. However up to now no efficient drugs or even clinical candidates are known, hence the search for such drugs is still relevant and necessary. SrtA is a complex target, so many straight-forward techniques for modeling using the structure-based drug design (SBDD) fail to produce the results they used to bring for other, simpler, targets. In this work we conduct theoretical studies of the binding/activity of Leu-Pro-Arg-Asp-Ala (LPRDA) polypeptide, which was recently shown to possess antivirulence activity against S. aureus. Our investigation was aimed at establishing a framework for the estimation of the key interactions and subsequent modification of LPRDA, targeted at non-peptide molecules, with better drug-like properties than the original polypeptide. Firstly, the available PDB structures are critically analyzed and the criteria to evaluate the quality of the ligand-SrtA complex geometry are proposed. Secondly, the docking protocol was investigated to establish its applicability to the LPRDA-SrtA complex prediction. Thirdly, the molecular dynamics studies were carried out to refine the geometries and estimate the stability of the complexes, predicted by docking. The main finding is that the previously reported partially chaotic movement of the β6/β7 and β7/β8 loops of SrtA (being the intrinsically disordered parts related to the SrtA binding site) is exaggerated when SrtA is complexed with LPRDA, which in turn reveals all the signs of the flexible and structurally disordered molecule. As a result, a wealth of plausible LPRDA-SrtA complex conformations are hard to distinguish using simple modeling means, such as docking. The use of more elaborate modeling approaches may help to model the system reliably but at the cost of computational efficiency.
Collapse
Affiliation(s)
- Dmitry A. Shulga
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
- Correspondence: (D.A.S.); (K.V.K.)
| | - Konstantin V. Kudryavtsev
- Laboratory of Molecular Pharmacology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997 Moscow, Russia
- Correspondence: (D.A.S.); (K.V.K.)
| |
Collapse
|
12
|
Kumar V, Murmu S, Krishnan V. Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis. Biochimie 2022; 200:140-152. [PMID: 35654243 DOI: 10.1016/j.biochi.2022.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
Several strains and species of lactic acid bacteria (LAB) are widely used in fermented foods, including dairy products and also as probiotics, because of their contribution to various health benefits in humans. Sortase enzymes decorate the bacterial cell wall with different surface proteins and pili for facilitating the interactions with host and environment for the colonization and beneficial effects. While the sortases and sortase anchored proteins from pathogens have been the prime focus of the research in the past, sortases from many non-pathogenic bacteria, including LAB strains, have attracted attention for their potential applications in vaccine delivery and other clinical interventions. Here, we report the purification and functional characterization of two sortases (housekeeping SrtA and pilus-specific SrtC) from a probiotic Lactococcus lactis. The purified sortases were found to be active against the putative LPXTG motif-based peptide substrates, albeit with differences. The in-silico analysis provides insights into the residues involved in substrate binding and specificity. Overall, this study sheds new light on the aspects of structure, substrate specificity, and function of sortases from non-pathogenic bacteria, which may have physiological ramifications as well as their applications in sortase-mediated protein bioconjugation.
Collapse
Affiliation(s)
- Vijay Kumar
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Sumit Murmu
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India.
| |
Collapse
|
13
|
Volynets GP, Barthels F, Hammerschmidt SJ, Moshynets OV, Lukashov SS, Starosyla SA, Vyshniakova HV, Iungin OS, Bdzhola VG, Prykhod'ko AO, Syniugin AR, Sapelkin VM, Yarmoluk SM, Schirmeister T. Identification of novel small-molecular inhibitors of Staphylococcus aureus sortase A using hybrid virtual screening. J Antibiot (Tokyo) 2022; 75:321-332. [PMID: 35440771 PMCID: PMC9016125 DOI: 10.1038/s41429-022-00524-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 01/18/2023]
Abstract
Staphylococcus aureus is one of the most dangerous pathogens commonly associated with high levels of morbidity and mortality. Sortase A is considered as a promising molecular target for the development of antistaphylococcal agents. Using hybrid virtual screening approach and FRET analysis, we have identified five compounds able to decrease the activity of sortase A by more than 50% at the concentration of 200 µM. The most promising compound was 2-(2-amino-3-chloro-benzoylamino)-benzoic acid which was able to inhibit S. aureus sortase A at the IC50 value of 59.7 µM. This compound was selective toward sortase A compared to other four cysteine proteases - cathepsin L, cathepsin B, rhodesain, and the SARS-CoV2 main protease. Microscale thermophoresis experiments confirmed that this compound bound sortase A with KD value of 189 µM. Antibacterial and antibiofilm assays also confirmed high specificity of the hit compound against two standard and three wild-type, S. aureus hospital infection isolates. The effect of the compound on biofilms produced by two S. aureus ATCC strains was also observed suggesting that the compound reduced biofilm formation by changing the biofilm structure and thickness.
Collapse
Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Olena V Moshynets
- Biofilm study group, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy S Lukashov
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.,RECEPTOR.AI, Boston, MA, USA
| | - Hanna V Vyshniakova
- L.V. Gromashevsky Institute of Epidemiology and Infectious Diseases NAMS of Ukraine, 5 Amosova St, 03038, Kyiv, Ukraine
| | - Olga S Iungin
- Department of Functional Genomics, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Andrii O Prykhod'ko
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine.,Research and Development Department, Scientific Services Company Otava Ltd, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Anatolii R Syniugin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Vladislav M Sapelkin
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, 150 Zabolotnogo St, 03143, Kyiv, Ukraine
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Wang L, Wang G, Qu H, Wang K, Jing S, Guan S, Su L, Li Q, Wang D. Taxifolin, an Inhibitor of Sortase A, Interferes With the Adhesion of Methicillin-Resistant Staphylococcal aureus. Front Microbiol 2021; 12:686864. [PMID: 34295320 PMCID: PMC8290497 DOI: 10.3389/fmicb.2021.686864] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022] Open
Abstract
The evolution and spread of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant hidden risk to human public health. The majority of antibiotics used clinically have become mostly ineffective, and so the development of novel anti-infection strategies is urgently required. Since Staphylococcus aureus (S. aureus) cysteine transpeptidase sortase A (SrtA) mediates the surface-anchoring of proteins to its surface, compounds that inhibit SrtA are considered potential antivirulence treatments. Herein, we report on the efficacy of the potent SrtA inhibitor taxifolin (Tax), a flavonoid compound isolated from Chinese herbs. It was able to reversibly block the activity of SrtA with an IC50 of 24.53 ± 0.42 μM. Tax did not display toxicity toward mammalian cells or S. aureus at a concentration of 200 μM. In addition, Tax attenuated the virulence-related phenotype of SrtA in vitro by decreasing the adherence of S. aureus, reducing the formation of a biofilm, and anchoring of S. aureus protein A on its cell wall. The mechanism of the SrtA-Tax interaction was determined using a localized surface plasmon resonance assay. Subsequent mechanistic studies confirmed that Asp-170 and Gln-172 were the principal sites on SrtA with which it binds to Tax. Importantly, in vivo experiments demonstrated that Tax protects mice against pneumonia induced by lethal doses of MRSA, significantly improving their survival rate and reducing the number of viable S. aureus in the lung tissue. The present study indicates that Tax is a useful pioneer compound for the development of novel agents against S. aureus infections.
Collapse
Affiliation(s)
- Li Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Guangming Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Han Qu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Kai Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shisong Jing
- College of Animal Science, Jilin University, Changchun, China
| | - Shuhan Guan
- College of Animal Science, Jilin University, Changchun, China
| | - Liyan Su
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Qianxue Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Dacheng Wang
- College of Animal Science, Jilin University, Changchun, China
| |
Collapse
|
18
|
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.
Collapse
|
19
|
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.
Collapse
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.)
| |
Collapse
|
20
|
Klimochkin YN, Leonova MV, Ivleva EA, Kazakova AI, Zaborskaya MS. Synthesis of Cage Acylamino Derivatives in Nitric Acid Medium. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021010012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
21
|
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.
Collapse
|
22
|
Wu Z, Wu J, Lang F, Cai Z, Zeng X, Guo Y, Liu X, Pan D. Characterization of the sortase A from Lactobacillus acidophilus ATCC 4356 involved in adherence to intestinal cells. Future Microbiol 2020; 15:485-496. [PMID: 32476478 DOI: 10.2217/fmb-2019-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Aim: Confirmation of the enzymatic activity of Class A sortase (SrtA) in probiotic strain Lactobacillus acidophilus associated with the adhesion properties. Materials & methods: SrtA from L. acidophilus ATCC 4356 was purified and its enzymatic properties was investigated by site-directed mutagenesis approach and the sensitivity to metal ions was also detected. Results: SrtA of L. acidophilus ATCC4356 can recognize LPxTG and LPxTD sorting motifs. The active sites of SrtA include His137, Cys198 and Arg205. Furthermore, acacetin can increase the activity of SrtA, while phenyl vinyl sulfone could effectively inhibit the activity of SrtA with an IC50 of 143.32 μg/ml. The adhesion ability of L. acidophilus was also decreased resulting from the inhibition of SrtA activity. Conclusion: The unique properties of SrtA of L. acidophilus can provide some insights into the development of high-adhesion Lactobacillus strains in the GI tract.
Collapse
Affiliation(s)
- Zhen Wu
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Jing Wu
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Fengxuan Lang
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Zhendong Cai
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Xiaoqun Zeng
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Yuxing Guo
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, PR China
| | - Xiaotao Liu
- Ningbo Dairy Group, Ningbo, 315211, Zhejiang, China
| | - Daodong Pan
- Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China.,National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, PR China
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Leonard AC, Petrie LE, Cox G. Bacterial Anti-adhesives: Inhibition of Staphylococcus aureus Nasal Colonization. ACS Infect Dis 2019; 5:1668-1681. [PMID: 31374164 DOI: 10.1021/acsinfecdis.9b00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacterial adhesion to the skin and mucosa is often a fundamental and early step in host colonization, the establishment of bacterial infections, and pathology. This process is facilitated by adhesins on the surface of the bacterial cell that recognize host cell molecules. Interfering with bacterial host cell adhesion, so-called anti-adhesive therapeutics, offers promise for the development of novel approaches to control bacterial infections. In this review, we focus on the discovery of anti-adhesives targeting the high priority pathogen Staphylococcus aureus. This organism remains a major clinical burden, and S. aureus nasal colonization is associated with poor clinical outcomes. We describe the molecular basis of nasal colonization and highlight potentially efficacious targets for the development of novel nasal decolonization strategies.
Collapse
Affiliation(s)
- Allison C. Leonard
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
| | - Laurenne E. Petrie
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Shi Y, Jiang K, Zheng R, Fu J, Yan L, Gu Q, Zhang Y, Lin F. Design, Microwave‐Assisted Synthesis and in Vitro Antibacterial and Antifungal Activity of 2,5‐Disubstituted Benzimidazole. Chem Biodivers 2019; 16:e1800510. [DOI: 10.1002/cbdv.201800510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Yanpeng Shi
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Kai Jiang
- School of life SciencesJilin University Changchun 130012 P. R. China
| | - Ran Zheng
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Jiaxu Fu
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Liuqing Yan
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Qiang Gu
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Yumin Zhang
- College of ChemistryJilin University Changchun 130012 P. R. China
| | - Feng Lin
- School of life SciencesJilin University Changchun 130012 P. R. China
| |
Collapse
|
29
|
Hou X, Wang M, Wen Y, Ni T, Guan X, Lan L, Zhang N, Zhang A, Yang CG. Quinone skeleton as a new class of irreversible inhibitors against Staphylococcus aureus sortase A. Bioorg Med Chem Lett 2018; 28:1864-1869. [PMID: 29650293 DOI: 10.1016/j.bmcl.2018.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023]
Abstract
Sortase A (SrtA) anchors surface proteins to the cell wall and aids biofilm formation during infection, which functions as a key virulence factor of important Gram-positive pathogens, such as Staphylococcus aureus. At present researchers need a way in which to validate whether or not SrtA is a druggable target alternative to the conventional antibiotic targets in the mechanism. In this study, we performed a high-throughput screening and identified a new class of potential inhibitors of S. aureus SrtA, which are derived from natural products and contain the quinone skeleton. Compound 283 functions as an irreversible inhibitor that covalently alkylates the active site Cys184 of SrtA. NMR analysis confirms the direct interaction of the small-molecule inhibitor towards SrtA protein. The anchoring of protein A (SpA) to the cell wall and the biofilm formation are significantly attenuated when the S. aureus Newman strain is cultured in the presence of inhibitor. Our study indicates that compound 283 could be a potential hit for the development of new anti-virulence agents against S. aureus infections by covalently targeting SrtA.
Collapse
Affiliation(s)
- Xiaochen Hou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Meining Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China
| | - Yi Wen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China
| | - Tengfeng Ni
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China
| | - Xiangna Guan
- Ministry of Education, School of Pharmacy, Fudan University, 826 ZhangHeng Road, Shanghai 201203, China
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China
| | - Naixia Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China.
| | - Ao Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China.
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 ZuChongZhi Road, Shanghai 201203, China.
| |
Collapse
|
30
|
Luo H, Liang DF, Bao MY, Sun R, Li YY, Li JZ, Wang X, Lu KM, Bao JK. In silico identification of potential inhibitors targeting Streptococcus mutans sortase A. Int J Oral Sci 2018; 9:53-62. [PMID: 28358034 PMCID: PMC5379162 DOI: 10.1038/ijos.2016.58] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2016] [Indexed: 02/08/2023] Open
Abstract
Dental caries is one of the most common chronic diseases and is caused by acid fermentation of bacteria adhered to the teeth. Streptococcus mutans (S. mutans) utilizes sortase A (SrtA) to anchor surface proteins to the cell wall and forms a biofilm to facilitate its adhesion to the tooth surface. Some plant natural products, especially several flavonoids, are effective inhibitors of SrtA. However, given the limited number of inhibitors and the development of drug resistance, the discovery of new inhibitors is urgent. Here, the high-throughput virtual screening approach was performed to identify new potential inhibitors of S. mutans SrtA. Two libraries were used for screening, and nine compounds that had the lowest scores were chosen for further molecular dynamics simulation, binding free energy analysis and absorption, distribution, metabolism, excretion and toxicity (ADMET) properties analysis. The results revealed that several similar compounds composed of benzofuran, thiadiazole and pyrrole, which exhibited good affinities and appropriate pharmacokinetic parameters, were potential inhibitors to impede the catalysis of SrtA. In addition, the carbonyl of these compounds can have a key role in the inhibition mechanism. These findings can provide a new strategy for microbial infection disease therapy.
Collapse
Affiliation(s)
- Hao Luo
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Dan-Feng Liang
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Min-Yue Bao
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Rong Sun
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Yuan-Yuan Li
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Jian-Zong Li
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Xin Wang
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Kai-Min Lu
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China
| | - Jin-Ku Bao
- School of Life Sciences and Key Laboratory of Ministry of Education for Bio-Resources and Bio-Environment, Sichuan University, Chengdu, China.,State Key Laboratory of Biotherapy/Collaborative Innovation Centre for Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
31
|
Chilambi GS, Gao IH, Yoon BK, Park S, Kawakami LM, Ravikumar V, Chan-Park MB, Cho NJ, Bazan GC, Kline KA, Rice SA, Hinks J. Membrane adaptation limitations inEnterococcus faecalisunderlie sensitivity and the inability to develop significant resistance to conjugated oligoelectrolytes. RSC Adv 2018; 8:10284-10293. [PMID: 35540442 PMCID: PMC9078823 DOI: 10.1039/c7ra11823f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/01/2018] [Indexed: 11/21/2022] Open
Abstract
COEs are emerging antimicrobials to combat drug resistant infections and to which bacteria develop only limited resistance.
Collapse
|
32
|
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.
Collapse
|
33
|
Kempson J, Ovalle D, Guo J, Wrobleski ST, Lin S, Spergel SH, Duan JJW, Jiang B, Lu Z, Das J, Yang BV, Hynes J, Wu H, Tokarski J, Sack JS, Khan J, Schieven G, Blatt Y, Chaudhry C, Salter-Cid LM, Fura A, Barrish JC, Carter PH, Pitts WJ. Discovery of highly potent, selective, covalent inhibitors of JAK3. Bioorg Med Chem Lett 2017; 27:4622-4625. [DOI: 10.1016/j.bmcl.2017.09.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Viani F, Rossi B, Panzeri W, Merlini L, Martorana AM, Polissi A, Galante YM. Synthesis and anti-bacterial activity of a library of 1,2-benzisothiazol-3(2H)-one (BIT) derivatives amenable of crosslinking to polysaccharides. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.02.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
36
|
van Harten RM, Willems RJL, Martin NI, Hendrickx APA. Multidrug-Resistant Enterococcal Infections: New Compounds, Novel Antimicrobial Therapies? Trends Microbiol 2017; 25:467-479. [PMID: 28209400 DOI: 10.1016/j.tim.2017.01.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 02/08/2023]
Abstract
Over the past two decades infections due to antibiotic-resistant bacteria have escalated world-wide, affecting patient morbidity, mortality, and health care costs. Among these bacteria, Enterococcus faecium and Enterococcus faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections because of intrinsic and acquired resistance to a plethora of antibiotics. In recent years, a number of novel antimicrobial compound classes have been discovered and developed that target Gram-positive bacteria, including E. faecium and E. faecalis. These new antibacterial agents include teixobactin (targeting lipid II and lipid III), lipopeptides derived from nisin (targeting lipid II), dimeric vancomycin analogues (targeting lipid II), sortase transpeptidase inhibitors (targeting the sortase enzyme), alanine racemase inhibitors, lipoteichoic acid synthesis inhibitors (targeting LtaS), various oxazolidinones (targeting the bacterial ribosome), and tarocins (interfering with teichoic acid biosynthesis). The targets of these novel compounds and mode of action make them very promising for further antimicrobial drug development and future treatment of Gram-positive bacterial infections. Here we review current knowledge of the most favorable anti-enterococcal compounds along with their implicated modes of action and efficacy in animal models to project their possible future use in the clinical setting.
Collapse
Affiliation(s)
- Roel M van Harten
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
| |
Collapse
|
37
|
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.
Collapse
|
38
|
Chen JL, Wang X, Yang F, Cao C, Otting G, Su XC. 3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:13744-13748. [DOI: 10.1002/anie.201606223] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/15/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Gottfried Otting
- Research School of Chemistry; Australian National University; Canberra ACT 2601 Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| |
Collapse
|
39
|
Chen JL, Wang X, Yang F, Cao C, Otting G, Su XC. 3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Gottfried Otting
- Research School of Chemistry; Australian National University; Canberra ACT 2601 Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| |
Collapse
|
40
|
Zheng Y, Tsuji G, Opoku-Temeng C, Sintim HO. Inhibition of P. aeruginosa c-di-GMP phosphodiesterase RocR and swarming motility by a benzoisothiazolinone derivative. Chem Sci 2016; 7:6238-6244. [PMID: 30034764 PMCID: PMC6024209 DOI: 10.1039/c6sc02103d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/15/2016] [Indexed: 01/18/2023] Open
Abstract
Various important cellular processes in bacteria are controlled by c-di-GMP, such as motility, biofilm formation and virulence factors production. C-di-GMP is synthesized from two molecules of GTP by diguanylate cyclases (DGCs) and its actions are terminated by EAL or HD-GYP domain phosphodiesterases (PDEs), which hydrolyze c-di-GMP to linear pGpG or GMP. Thus far the majority of efforts have been dedicated to the development of inhibitors of DGCs but not PDEs. This is probably because the old view was that inhibiting any c-di-GMP PDE would lead to biofilm formation, an undesirable phenotype. Recent data however suggest that some PDEs only change the localized (not global) concentration of c-di-GMP to increase bacterial virulence and do not affect biofilm formation. A challenge therefore is to be able to develop selective PDE inhibitors that inhibit virulence-associated PDEs but not inhibit PDEs that regulate bacterial biofilm formation. Using high throughput docking experiments to screen a library of 250 000 commercially available compounds against E. coli YahA (also called PdeL), a benzoisothiazolinone derivative was found to bind to the c-di-GMP binding site of YahA with favorable energetics. Paradoxically the in silico identified inhibitor (a benzoisothiazolinone derivative) did not inhibit the hydrolysis of c-di-GMP by YahA, the model PDE that was used in the docking, but instead inhibited RocR, which is a PDE from the opportunistic pathogen P. aeruginosa (PA). RocR promotes bacterial virulence but not biofilm dispersal, making it an ideal PDE to target for anti-virulence purposes. This newly identified RocR ligand displayed some selectivity and did not inhibit other P. aeruginosa PDEs, such as DipA, PvrR and PA4108. DipA, PvrR and PA4108 are key enzymes that reduce global c-di-GMP concentration and promote biofilm dispersal; therefore the identification of an inhibitor of a PA PDE, such as RocR, that does not inhibit major PDEs that modulate global c-di-GMP is an important step towards the development of selective c-di-GMP PDEs that could have interesting biomedical applications. The identified RocR ligand could also inhibit P. aeruginosa (PAO1) swarming but not swimming or biofilm formation. Rhamnolipid production was decreased, explaining the inhibition of swarming.
Collapse
Affiliation(s)
- Yue Zheng
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
- Graduate Program in Biochemistry , University of Maryland , College Park , MD 20742 , USA
| | - Genichiro Tsuji
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
| | - Clement Opoku-Temeng
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
- Graduate Program in Biochemistry , University of Maryland , College Park , MD 20742 , USA
| | - Herman O Sintim
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
| |
Collapse
|
41
|
Synthesis, biological evaluation and molecular docking of 2-phenyl-benzo[d]oxazole-7-carboxamide derivatives as potential Staphylococcus aureus Sortase A inhibitors. Bioorg Med Chem Lett 2016; 26:4081-5. [PMID: 27400889 DOI: 10.1016/j.bmcl.2016.06.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/09/2016] [Accepted: 06/25/2016] [Indexed: 11/20/2022]
Abstract
A series of novel 2-phenyl-benzo[d]oxazole-7-carboxamide derivatives were designed, synthesized and evaluated for their in vitro inhibitory activities against Staphylococcus aureus Sortase A with known Sortase A inhibitor pHMB as positive compound (IC50=130μM). Most compounds exhibited excellent inhibitory activity (IC50=19.8-184.2μM). Structure-activity relationship studies demonstrated that substitution at 7-position and 2-position of benzoxazole had great influence on the activities. Specifically, the substituent at 7-position is indispensable for inhibitory activity. The molecular docking studies revealed the i-butyl amide group went towards the β6/β7 loop-β8 substructure of the protein and the benzoxazole core lied in a hydrophobic pocket composed of Ala118, Val166, Val168, Val169 and Ile182, shaping the whole molecule into a L-shape mode to be recognized by Sortase A.
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
A new class of phenylhydrazinylidene derivatives as inhibitors of Staphylococcus aureus biofilm formation. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1535-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
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
| |
Collapse
|
46
|
Bradshaw WJ, Davies AH, Chambers CJ, Roberts AK, Shone CC, Acharya KR. Molecular features of the sortase enzyme family. FEBS J 2015; 282:2097-114. [PMID: 25845800 DOI: 10.1111/febs.13288] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/13/2015] [Accepted: 03/28/2015] [Indexed: 01/31/2023]
Abstract
Bacteria possess complex and varying cell walls with many surface exposed proteins. Sortases are responsible for the covalent attachment of specific proteins to the peptidoglycan of the cell wall of Gram-positive bacteria. Sortase A of Staphylococcus aureus, which is seen as the archetypal sortase, has been shown to be essential for pathogenesis and has therefore received much attention as a potential target for novel therapeutics. Being widely present in Gram-positive bacteria, it is likely that other Gram-positive pathogens also require sortases for their pathogenesis. Sortases have also been shown to be of significant use in a range of industrial applications. We review current knowledge of the sortase family in terms of their structures, functions and mechanisms and summarize work towards their use as antibacterial targets and microbiological tools.
Collapse
Affiliation(s)
- William J Bradshaw
- Department of Biology and Biochemistry, University of Bath, UK.,Public Health England, Porton Down, Salisbury, UK
| | | | - Christopher J Chambers
- Department of Biology and Biochemistry, University of Bath, UK.,Public Health England, Porton Down, Salisbury, UK
| | | | | | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
| |
Collapse
|
47
|
Quercitrin, an inhibitor of Sortase A, interferes with the adhesion of Staphylococcal aureus. Molecules 2015; 20:6533-43. [PMID: 25871372 PMCID: PMC6272417 DOI: 10.3390/molecules20046533] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 11/16/2022] Open
Abstract
Sortase A (SrtA) is a cysteine transpeptidase of most Gram-positive bacteria that is responsible for the anchorage of many surface protein virulence factors to the cell wall layer. SrtA mutants are unable to display surface proteins and are defective in the establishment of infections without affecting microbial viability. In this study, we report that quercitrin (QEN), a natural compound that does not affect Staphylococcus aureus growth, can inhibit the catalytic activity of SrtA in fibrinogen (Fg) cell-clumping and immobilized fibronectin (Fn) adhesion assays. Molecular dynamics simulations and mutagenesis assays suggest that QEN binds to the binding sites of the SrtA G167A and V193A mutants. These findings indicate that QEN is a potential lead compound for the development of new anti-virulence agents against S. aureus infections.
Collapse
|
48
|
Chen WN, Kuppan KV, Lee MD, Jaudzems K, Huber T, Otting G. O-tert-Butyltyrosine, an NMR tag for high-molecular-weight systems and measurements of submicromolar ligand binding affinities. J Am Chem Soc 2015; 137:4581-6. [PMID: 25789794 DOI: 10.1021/jacs.5b01918] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O-tert-Butyltyrosine (Tby) is an unnatural amino acid that can be site-specifically incorporated into proteins using established orthogonal aminoacyl-tRNA synthetase/tRNA systems. Here we show that the tert-butyl group presents an outstanding NMR tag that can readily be observed in one-dimensional (1)H NMR spectra without any isotope labeling. Owing to rapid bond rotations and the chemical equivalence of the protons of a solvent-exposed tert-butyl group from Tby, the singlet resonance from the tert-butyl group generates an easily detectable narrow signal in a spectral region with limited overlap with other methyl resonances. The potential of the tert-butyl (1)H NMR signal in protein research is illustrated by the observation and assignment of two resonances in the Bacillus stearothermophilus DnaB hexamer (320 kDa), demonstrating that this protein preferentially assumes a 3-fold rather than 6-fold symmetry in solution, and by the quantitative measurement of the submicromolar dissociation constant Kd (0.2 μM) of the complex between glutamate and the Escherichia coli aspartate/glutamate binding protein (DEBP, 32 kDa). The outstanding signal height of the (1)H NMR signal of the Tby tert-butyl group allows Kd measurements using less concentrated protein solutions than usual, providing access to Kd values 1 order of magnitude lower than established NMR methods that employ direct protein detection for Kd measurements.
Collapse
Affiliation(s)
- Wan-Na Chen
- †Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Kekini Vahini Kuppan
- †Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael David Lee
- ‡Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
| | | | - Thomas Huber
- †Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- †Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
49
|
Guo Y, Cai S, Gu G, Guo Z, Long Z. Recent progress in the development of sortase A inhibitors as novel anti-bacterial virulence agents. RSC Adv 2015. [DOI: 10.1039/c5ra07568h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent progress in the development of sortase A inhibitors as novel anti-virulence drugs for antibacterial therapy has been reviewed.
Collapse
Affiliation(s)
- Yuchuan Guo
- National Glycoengineering Research Center
- Shandong University
- Jinan
- China
| | - Shuihong Cai
- Qidong Dongyue Pharmaceutical Company
- Qidong
- China
| | - Guofeng Gu
- National Glycoengineering Research Center
- Shandong University
- Jinan
- China
| | - Zhongwu Guo
- National Glycoengineering Research Center
- Shandong University
- Jinan
- China
- Qidong Dongyue Pharmaceutical Company
| | | |
Collapse
|