1
|
Kumar M, Haque MA, Kaur P. Computational and Biophysical Approaches to Identify Cell Wall-Associated Modulators in Salmonella enterica serovar Typhi. Methods Mol Biol 2024; 2727:35-55. [PMID: 37815707 DOI: 10.1007/978-1-0716-3491-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
An increase in the number of antibiotic-resistant bacterial pathogens, in recent times, has posed a great challenge for treating the affected patients. This has paved the way for the development and design of antibiotics against the previously less explored newer targets. Among these, peptidoglycan (PG) biosynthesis serves as a promising target for the design and development of novel drugs. The peptidoglycan cell wall synthesis in bacteria is essential for its viability. The enzyme class, Mur ligases, plays a key role in PG biosynthesis. Therefore, compounds with the ability to inhibit these enzymes (Mur ligase) can serve as potential candidates for developing small modulators. The enzyme, UDP-N-acetyl pyruvyl-glucosamine reductase (MurB), is essential for PG biosynthesis, a crucial part of the bacterial cell wall. The development of novel drugs to treat infections may thus focus on inhibiting MurB function. Understanding the mechanism of action of Mur B is central to developing efficient inhibitors. For the treatment of S. typhi infections, it is also critical to find therapeutic drugs that specifically target MurB. The enzyme Mur B from Salmonella enterica serovar Typhi (stMurB) was expressed and purified for biophysical characterization to gauge the molecular interactions and estimate thermodynamic stability, for determining attributes for possible therapeutic intervention. The thermal melting profile of MurB was monitored by circular dichroism (CD) and validated by performing differential scanning calorimetry (DSC). An in silico virtual screening of various natural inhibitors was conducted with modelled stMurB structure. The three top hits (quercetin, berberine, and scopoletin) obtained from in silico screening were validated for complex stability through molecular dynamics (MD) simulation. Further, fluorescence binding studies were undertaken for the selected natural inhibitors with stMurB alone and with its NADPH-bound form. The natural inhibitors, scopoletin and berberine, displayed lesser binding to stMurB compared to quercetin. Also, a stronger binding affinity was exhibited between quercetin and stMurB compared to NADPH and stMurB. Based on the above two findings, quercetin can be developed as an inhibitor of stMurB enzyme.
Collapse
Affiliation(s)
- Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Md Anzarul Haque
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
2
|
Li Y, Tang X, Yang Z, He J, Ma N, Huang A, Shi Y. BCp12/PLA combination: A novel antibacterial agent targeting Mur family, DNA gyrase and DHFR. Int J Food Microbiol 2023; 406:110370. [PMID: 37678070 DOI: 10.1016/j.ijfoodmicro.2023.110370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
The combination of natural antimicrobial peptide BCp12/phenyllatic acid (BCp12/PLA) presents a more efficient antibacterial effect, but its antibacterial mechanism remains unclear. This study studied the synergistic antibacterial mechanism of BCp12 and PLA against S. aureus. The results demonstrated that the BCp12/PLA combination presented a synergistic antibacterial effect against S. aureus, with a fractional inhibitory concentration of 0.05. Furthermore, flow cytometry and scanning electron microscope analysis revealed that BCp12 and PLA synergistically promoted cell membrane disruption compared with the group treated only with one compound, inducing structural cell damage and cytoplasmic leakage. In addition, fluorescence spectroscopy analysis suggested that BCp12 and PLA synergistically influenced genomic DNA. BCp12 and PLA targeted enzymes related to peptidoglycan and DNA synthesis and interacted by hydrogen bonding and hydrophobic interactions with mur enzymes (murC, murD, murE, murF, and murG), dihydrofolate reductase, and DNA gyrase. Additionally, the combined treatment successfully inhibited microbial reproduction in the storage of pasteurized milk, indicating that the combination of BCp12 and PLA can be used as a new preservative strategy in food systems. Overall, this study could provide potential strategies for preventing and controlling foodborne pathogens.
Collapse
Affiliation(s)
- Yufang Li
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xiaozhao Tang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Zushun Yang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Jinze He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Ni Ma
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
| | - Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
| |
Collapse
|
3
|
Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [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: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
Collapse
Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | | |
Collapse
|
4
|
Frlan R, Hrast M, Gobec S. Inhibition of MurA Enzyme from Escherichia coli by Flavonoids and Their Synthetic Analogues. ACS OMEGA 2023; 8:33006-33016. [PMID: 37720776 PMCID: PMC10500568 DOI: 10.1021/acsomega.3c04813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
MurA catalyzes the first step of peptidoglycan (PG) biosynthesis and is a validated target for the development of new antimicrobial agents. In this study, a library of 49 plant flavonoids and their synthetic derivatives were evaluated for their inhibitory properties against MurA fromEscherichia coli. The compounds were tested with and without preincubation and with the addition of DTT to understand the mechanism of inhibition. Thirteen compounds were identified as reversible, time-dependent inhibitors, with inhibition levels ranging from 480 nM to 57 μM, and ampelopsin as the most potent compound. To investigate the major pharmacophore elements responsible for the activity, 2D-QSAR and docking analyzes were performed. The results showed that the catechol moiety and an additional aromatic system were the most important features contributing to the activity of the compounds. However, most of the compounds did not show antibacterial activity againstE. coli andStaphylococcus aureusstrains, suggesting that their inhibitory activity against MurA may not be strong enough to induce antibacterial effects. Nevertheless, our results suggest that flavonoids are a promising starting point to develop new inhibitors of MurA and show great potential for further steps in drug development.
Collapse
Affiliation(s)
- Rok Frlan
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| |
Collapse
|
5
|
Stefanović C, Hager-Mair FF, Breslmayr E, López-Guzmán A, Lim C, Blaukopf M, Kosma P, Oostenbrink C, Ludwig R, Schäffer C. Molecular modelling and site-directed mutagenesis provide insight into saccharide pyruvylation by the Paenibacillus alvei CsaB enzyme. Sci Rep 2023; 13:13394. [PMID: 37591902 PMCID: PMC10435577 DOI: 10.1038/s41598-023-40072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Pyruvylation is a biologically versatile but mechanistically unexplored saccharide modification. 4,6-Ketal pyruvylated N-acetylmannosamine within bacterial secondary cell wall polymers serves as a cell wall anchoring epitope for proteins possessing a terminal S-layer homology domain trimer. The pyruvyltransferase CsaB from Paenibacillus alvei served as a model to investigate the structural basis of the pyruvyltransfer reaction by a combination of molecular modelling and site-directed mutagenesis together with an enzyme assay using phosphoenolpyruvate (PEP; donor) and synthetic β-D-ManNAc-(1 → 4)-α-D-GlcNAc-diphosphoryl-11-phenoxyundecyl (acceptor). CsaB protein structure modelling was done using Phyre2 and I-Tasser based on the partial crystal structure of the Schizosaccharomyces pombe pyruvyltransferase Pvg1p and by AlphaFold. The models informed the construction of twelve CsaB mutants targeted at plausible PEP and acceptor binding sites and KM and kcat values were determined to evaluate the mutants, indicating the importance of a loop region for catalysis. R148, H308 and K328 were found to be critical to PEP binding and insight into acceptor binding was obtained from an analysis of Y14 and F16 mutants, confirming the modelled binding sites and interactions predicted using Molecular Operating Environment. These data lay the basis for future mechanistic studies of saccharide pyruvylation as a novel target for interference with bacterial cell wall assembly.
Collapse
Affiliation(s)
- Cordula Stefanović
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Fiona F Hager-Mair
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Erik Breslmayr
- Department of Food Science and Technology, Biocatalysis and Biosensing Laboratory, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute for Molecular Modelling and Simulation, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Arturo López-Guzmán
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
- Covirabio GmbH, Brehmstrasse 14a, 1110, Vienna, Austria
| | - Charlie Lim
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Markus Blaukopf
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Paul Kosma
- Department of Chemistry, Institute of Organic Chemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute for Molecular Modelling and Simulation, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria
| | - Roland Ludwig
- Department of Food Science and Technology, Biocatalysis and Biosensing Laboratory, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria
| | - Christina Schäffer
- NanoGlycobiology Research Group, Department of Chemistry, Institute of Biochemistry, Universität für Bodenkultur Wien, Muthgasse 18, 1190, Vienna, Austria.
- Department of Bionanosciences, Institute of Biologically Inspired Materials, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria.
| |
Collapse
|
6
|
Qun T, Zhou T, Hao J, Wang C, Zhang K, Xu J, Wang X, Zhou W. Antibacterial activities of anthraquinones: structure-activity relationships and action mechanisms. RSC Med Chem 2023; 14:1446-1471. [PMID: 37593578 PMCID: PMC10429894 DOI: 10.1039/d3md00116d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/24/2023] [Indexed: 08/19/2023] Open
Abstract
With the increasing prevalence of untreatable infections caused by antibiotic-resistant bacteria, the discovery of new drugs from natural products has become a hot research topic. The antibacterial activity of anthraquinones widely distributed in traditional Chinese medicine has attracted much attention. Herein, the structure and activity relationships (SARs) of anthraquinones as bacteriostatic agents are reviewed and elucidated. The substituents of anthraquinone and its derivatives are closely related to their antibacterial activities. The stronger the polarity of anthraquinone substituents is, the more potent the antibacterial effects appear. The presence of hydroxyl groups is not necessary for the antibacterial activity of hydroxyanthraquinone derivatives. Substitution of di-isopentenyl groups can improve the antibacterial activity of anthraquinone derivatives. The rigid plane structure of anthraquinone lowers its water solubility and results in the reduced activity. Meanwhile, the antibacterial mechanisms of anthraquinone and its analogs are explored, mainly including biofilm formation inhibition, destruction of the cell wall, endotoxin inhibition, inhibition of nucleic acid and protein synthesis, and blockage of energy metabolism and other substances.
Collapse
Affiliation(s)
- Tang Qun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
| | - Tiantian Zhou
- School of Chinese Materia Medica, Guangdong Pharmaceutical University 440113 Guangzhou China
| | - Jiongkai Hao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Keyu Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Jing Xu
- Huanghua Agricultural and Rural Development Bureau Bohai New Area 061100 Hebei China
| | - Xiaoyang Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Wen Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| |
Collapse
|
7
|
Lee CG, Cha KH, Kim GC, Im SH, Kwon HK. Exploring probiotic effector molecules and their mode of action in gut-immune interactions. FEMS Microbiol Rev 2023; 47:fuad046. [PMID: 37541953 DOI: 10.1093/femsre/fuad046] [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: 02/13/2023] [Revised: 07/17/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023] Open
Abstract
Probiotics, live microorganisms that confer health benefits when consumed in adequate amounts, have gained significant attention for their potential therapeutic applications. The beneficial effects of probiotics are believed to stem from their ability to enhance intestinal barrier function, inhibit pathogens, increase beneficial gut microbes, and modulate immune responses. However, clinical studies investigating the effectiveness of probiotics have yielded conflicting results, potentially due to the wide variety of probiotic species and strains used, the challenges in controlling the desired number of live microorganisms, and the complex interactions between bioactive substances within probiotics. Bacterial cell wall components, known as effector molecules, play a crucial role in mediating the interaction between probiotics and host receptors, leading to the activation of signaling pathways that contribute to the health-promoting effects. Previous reviews have extensively covered different probiotic effector molecules, highlighting their impact on immune homeostasis. Understanding how each probiotic component modulates immune activity at the molecular level may enable the prediction of immunological outcomes in future clinical studies. In this review, we present a comprehensive overview of the structural and immunological features of probiotic effector molecules, focusing primarily on Lactobacillus and Bifidobacterium. We also discuss current gaps and limitations in the field and propose directions for future research to enhance our understanding of probiotic-mediated immunomodulation.
Collapse
Affiliation(s)
- Choong-Gu Lee
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, 679, Saimdang-ro, Gangneung 25451, Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, 679, Saimdang-ro, Seoul 02792, Korea
- Department of Convergence Medicine, Wonju College of Medicine, Yonsei University, 20, Ilsan-ro, Wonju 26493, Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, 679, Saimdang-ro, Gangneung 25451, Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, 679, Saimdang-ro, Seoul 02792, Korea
- Department of Convergence Medicine, Wonju College of Medicine, Yonsei University, 20, Ilsan-ro, Wonju 26493, Korea
| | - Gi-Cheon Kim
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, and Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul 03722, Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, 77, Cheongam-ro, Pohang 37673, Korea
- Institute for Convergence Research and Education, Yonsei University, 50-1 Yonsei-ro, Seoul 03722, Korea
- ImmunoBiome Inc, Bio Open Innovation Center, 77, Cheongam-ro, Pohang 37673 , Korea
| | - Ho-Keun Kwon
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, and Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul 03722, Korea
| |
Collapse
|
8
|
Jiang Q, Li B, Zhang L, Li T, Hu Q, Li H, Zou W, Hu Z, Huang Q, Zhou R. DivIVA Interacts with the Cell Wall Hydrolase MltG To Regulate Peptidoglycan Synthesis in Streptococcus suis. Microbiol Spectr 2023; 11:e0475022. [PMID: 37212666 PMCID: PMC10269899 DOI: 10.1128/spectrum.04750-22] [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: 11/20/2022] [Accepted: 04/23/2023] [Indexed: 05/23/2023] Open
Abstract
Bacterial morphology is largely determined by the spatial and temporal regulation of peptidoglycan (PG) biosynthesis. Ovococci possess a unique pattern of PG synthesis different from the well studied Bacillus, and the mechanism of the coordination of PG synthesis remains poorly understood. Several regulatory proteins have been identified to be involved in the regulation of ovococcal morphogenesis, among which DivIVA is an important one to regulate PG synthesis in streptococci, while its mechanism is largely unknown. Here, the zoonotic pathogen Streptococcus suis was used to investigate the regulation of DivIVA on PG synthesis. Fluorescent d-amino acid probing and 3D-structured illumination microscopy found that DivIVA deletion caused abortive peripheral PG synthesis, resulting in a decreased aspect ratio. The phosphorylation-depleted mutant (DivIVA3A) cells displayed a longer nascent PG and became longer, whereas the phosphorylation-mimicking mutant (DivIVA3E) cells showed a shorter nascent PG and became shorter, suggesting that DivIVA phosphorylation is involved in regulating peripheral PG synthesis. Several DivIVA-interacting proteins were identified, and the interaction was confirmed between DivIVA and MltG, a cell wall hydrolase essential for cell elongation. DivIVA did not affect the PG hydrolysis activity of MltG, while the phosphorylation state of DivIVA affected its interaction with MltG. MltG was mislocalized in the ΔdivIVA and DivIVA3E cells, and both ΔmltG and DivIVA3E cells formed significantly rounder cells, indicating an important role of DivIVA phosphorylation in regulating PG synthesis through MltG. These findings highlight the regulatory mechanism of PG synthesis and morphogenesis of ovococci. IMPORTANCE The peptidoglycan (PG) biosynthesis pathway provides a rich source of novel antimicrobial drug targets. However, bacterial PG synthesis and its regulation is a very complex process involving dozens of proteins. Moreover, unlike the well studied Bacillus, ovococci undergo unusual PG synthesis with unique mechanisms of coordination. DivIVA is an important regulator of PG synthesis in ovococci, while its exact role in regulating PG synthesis remains poorly understood. In this study, we determined the role of DivIVA in regulating lateral PG synthesis of Streptococcus suis and identified a critical interacting partner, MltG, in which DivIVA influenced the subcellular localizations of MltG through its phosphorylation. Our study characterizes the detailed role of DivIVA in regulating bacterial PG synthesis, which is very helpful for understanding the process of PG synthesis in streptococci.
Collapse
Affiliation(s)
- Qinggen Jiang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Boxi Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liangsheng Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tingting Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qiao Hu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Haotian Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenjin Zou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- International Research Centre for Animal Diseases (MOST), Wuhan, China
| |
Collapse
|
9
|
Nguyen HTV, Chen X, Parada C, Luo AC, Shih O, Jeng US, Huang CY, Shih YL, Ma C. Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome. Nat Commun 2023; 14:1903. [PMID: 37019934 PMCID: PMC10076392 DOI: 10.1038/s41467-023-37543-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
The synthesis of the cell-wall peptidoglycan during bacterial cell division is mediated by a multiprotein machine, called the divisome. The essential membrane protein complex of FtsB, FtsL and FtsQ (FtsBLQ) is at the heart of the divisome assembly cascade in Escherichia coli. This complex regulates the transglycosylation and transpeptidation activities of the FtsW-FtsI complex and PBP1b via coordination with FtsN, the trigger for the onset of constriction. Yet the underlying mechanism of FtsBLQ-mediated regulation is largely unknown. Here, we report the full-length structure of the heterotrimeric FtsBLQ complex, which reveals a V-shaped architecture in a tilted orientation. Such a conformation could be strengthened by the transmembrane and the coiled-coil domains of the FtsBL heterodimer, as well as an extended β-sheet of the C-terminal interaction site involving all three proteins. This trimeric structure may also facilitate interactions with other divisome proteins in an allosteric manner. These results lead us to propose a structure-based model that delineates the mechanism of the regulation of peptidoglycan synthases by the FtsBLQ complex.
Collapse
Affiliation(s)
- Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Claudia Parada
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - An-Chi Luo
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30044, Taiwan
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Yu-Ling Shih
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
| |
Collapse
|
10
|
Haque MA, Singh M, Tripathi MK, Ethayathulla AS, Kaur P. Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches. Proteins 2023; 91:363-379. [PMID: 36193975 DOI: 10.1002/prot.26435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 08/02/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
The increase of antibiotic-resistant bacterial pathogens has created challenges in treatment and warranted the design of antibiotics against comparatively less exploited targets. The peptidoglycan (PG) biosynthesis delineates unique pathways for the design and development of a novel class of drugs. Mur ligases are an essential component of bacterial cell wall synthesis that play a pivotal role in PG biosynthesis to maintain internal osmotic pressure and cell shape. Inhibition of these enzymes can interrupt bacterial replication and hence, form attractive targets for drug discovery. In the present work, we focused on the PG biosynthesis pathway enzyme, UDP-N-acetylpyruvylglucosamine reductase, from Salmonella enterica serovar Typhi (stMurB). Biophysical characterization of purified StMurB was performed to gauge the molecular interactions and estimate thermodynamic stability for determination of attributes for possible therapeutic intervention. The thermal melting profile of MurB was monitored by circular dichroism and validated through differential scanning calorimetry experiment. Frequently used chemical denaturants, GdmCl and urea, were employed to study the chemical-induced denaturation of stMurB. In the search for natural compound-based inhibitors, against this important drug target, an in silico virtual screening based investigation was conducted with modeled stMurB structure. The three top hits (quercetin, berberine, and scopoletin) returned were validated for complex stability through molecular dynamics simulation. Further, fluorescence binding studies were undertaken for the selected natural compounds with stMurB alone and with NADPH bound form. The compounds scopoletin and berberine, displayed lesser binding to stMurB whereas quercetin exhibited stronger binding affinity than NADPH. This study suggests that quercetin can be evolved as an inhibitor of stMurB enzyme.
Collapse
Affiliation(s)
- Md Anzarul Haque
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | | | | | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
11
|
Fathalla RK, Fröhner W, Bader CD, Fischer PD, Dahlem C, Chatterjee D, Mathea S, Kiemer AK, Arthanari H, Müller R, Abdel-Halim M, Ducho C, Engel M. Identification and Biochemical Characterization of Pyrrolidinediones as Novel Inhibitors of the Bacterial Enzyme MurA. J Med Chem 2022; 65:14740-14763. [PMID: 36269107 PMCID: PMC9989942 DOI: 10.1021/acs.jmedchem.2c01275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.
Collapse
Affiliation(s)
- Reem K. Fathalla
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Wolfgang Fröhner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Chantal D. Bader
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Patrick D. Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Alexandra K. Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 02215, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 02115, Boston, MA, USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Helmholtz International Lab for Antiinfectives, Campus E8 1, 66123 Saarbrücken, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Matthias Engel
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| |
Collapse
|
12
|
Yoneyama T, Elshamy AI, Yamada J, El-Kashak WA, Kasai Y, Imagawa H, Ban S, Noji M, Umeyama A. Antimicrobial metabolite of Cordyceps tenuipes targeting MurE ligase and histidine kinase via in silico study. Appl Microbiol Biotechnol 2022; 106:6483-6491. [DOI: 10.1007/s00253-022-12176-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/10/2022] [Accepted: 09/07/2022] [Indexed: 11/02/2022]
|
13
|
Grabrijan K, Hrast M, Proj M, Dolšak A, Zdovc I, Imre T, Petri L, Ábrányi-Balogh P, Keserű GM, Gobec S. Covalent inhibitors of bacterial peptidoglycan biosynthesis enzyme MurA with chloroacetamide warhead. Eur J Med Chem 2022; 243:114752. [PMID: 36126388 DOI: 10.1016/j.ejmech.2022.114752] [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: 06/22/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/04/2022]
Abstract
MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) catalyzes the first committed step in the cytoplasmic part of peptidoglycan biosynthesis and is a validated target enzyme for antibacterial drug discovery; the inhibitor fosfomycin has been used clinically for decades. Like fosfomycin, most MurA inhibitors are small heterocyclic compounds that inhibit the enzyme by forming a covalent bond with the active site cysteine. The reactive chloroacetamide group was selected from a series of suitable electrophilic thiol-reactive warheads. The predominantly one-step synthesis led to the construction of the final library of 47 fragment-sized chloroacetamide compounds. Several new E. coli MurA inhibitors were identified, with the most potent compound having an IC50 value in the low micromolar range. The electrophilic reactivity of all chloroacetamide fragments in our library was evaluated by a high-throughput spectrophotometric assay using the reduced Ellman reagent as a surrogate for the cysteine thiol. LC-MS/MS experiments confirmed the covalent binding of the most potent inhibitor to Cys115 of the digested MurA enzyme. The covalent binding was further investigated by a biochemical time-dependent assay and a dilution assay, which confirmed the irreversible and time-dependent mode of action. The efficacy of chloroacetamide derivatives against MurA does not correlate with their thiol reactivity, making the active fragments valuable starting points for fragment-based development of new antibacterial agents targeting MurA.
Collapse
Affiliation(s)
- Katarina Grabrijan
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Ana Dolšak
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Irena Zdovc
- Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia.
| | - Tímea Imre
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary.
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary.
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology, Szt. Gellért tér 4., H-1117, Budapest, Hungary.
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology, Szt. Gellért tér 4., H-1117, Budapest, Hungary.
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| |
Collapse
|
14
|
Haubrich BA, Nayyab S, Gallati M, Hernandez J, Williams C, Whitman A, Zimmerman T, Li Q, Chen Y, Zhou CZ, Basu A, Reid CW. Inhibition of Streptococcus pneumoniae growth by masarimycin. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35467499 DOI: 10.1099/mic.0.001182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Despite renewed interest, development of chemical biology methods to study peptidoglycan metabolism has lagged in comparison to the glycobiology field in general. To address this, a panel of diamides were screened against the Gram-positive bacterium Streptococcus pneumoniae to identify inhibitors of bacterial growth. The screen identified the diamide masarimycin as a bacteriostatic inhibitor of S. pneumoniae growth with an MIC of 8 µM. The diamide inhibited detergent-induced autolysis in a concentration-dependent manner, indicating perturbation of peptidoglycan degradation as the mode-of-action. Cell based screening of masarimycin against a panel of autolysin mutants, identified a higher MIC against a ΔlytB strain lacking an endo-N-acetylglucosaminidase involved in cell division. Subsequent biochemical and phenotypic analyses suggested that the higher MIC was due to an indirect interaction with LytB. Further analysis of changes to the cell surface in masarimycin treated cells identified the overexpression of several moonlighting proteins, including elongation factor Tu which is implicated in regulating cell shape. Checkerboard assays using masarimycin in concert with additional antibiotics identified an antagonistic relationship with the cell wall targeting antibiotic fosfomycin, which further supports a cell wall mode-of-action.
Collapse
Affiliation(s)
- Brad A Haubrich
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA.,Department of Basic Sciences, Touro University Nevada, College of Osteopathic Medicine, Henderson, NV 89014, USA
| | - Saman Nayyab
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA.,Amherst Department of Molecular and Cellular Biology, University of Massachusetts, 230 Stockbridge Rd Amherst, MA, USA
| | - Mika Gallati
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Jazmeen Hernandez
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Caroline Williams
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Andrew Whitman
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| | - Tahl Zimmerman
- Department of Family and Consumer Sciences, North Carolina A&T State University, Greensboro, NC, USA
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Amit Basu
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Christopher W Reid
- Center for Health and Behavioral Sciences, Department of Science and Technology, Bryant University, 1150 Douglas Pike, Smithfield, RI 02917, USA
| |
Collapse
|
15
|
Xiao W, Satoh Y, Ogasawara Y, Dairi T. Biosynthetic Gene Cluster of linaridin Peptides Contain Epimerase Gene. Chembiochem 2022; 23:e202100705. [PMID: 35460155 DOI: 10.1002/cbic.202100705] [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: 12/23/2021] [Revised: 03/24/2022] [Indexed: 11/10/2022]
Abstract
Salinipeptins belong to the type-A linaridin class of ribosomally synthesized and post-translationally modified peptides (RiPPs) comprising 22 amino acid residues with multiple D-amino acids. Although chirality of other type-A linaridins, such as grisemycin and cypemycin, has not been reported, the biosynthetic gene clusters of type-A linaridins have identical gene organization. Here, we report heterologous expression of grisemycin biosynthetic gene cluster ( grm ) and show that grisemycin contained multiple D-amino acids, similar to salinipeptins. The heterologous expression experiments also confirmed involvement of a novel peptide epimerase in grisemycin biosynthesis. Gene-deletion experiments indicated that grmL , a sole gene with unknown function, was indispensable for grisemycin production. We also show that the presence of D-amino acids is likely a common feature of linaridin natural products by analyzing two other type-A linaridin clusters.
Collapse
Affiliation(s)
- Wanlu Xiao
- Hokkaido University: Hokkaido Daigaku, Graduate School of Chemical Sciences and Engineering, JAPAN
| | - Yasuharu Satoh
- Hokkaido University: Hokkaido Daigaku, Graduate School of Engineering, JAPAN
| | - Yasushi Ogasawara
- Hokkaido University: Hokkaido Daigaku, Graduate School of Engineering, N13 W8, Kita-ku, 060-8628, Sapporo, JAPAN
| | - Tohru Dairi
- Hokkaido University, Graduate School of Engineering, N 13 W 8, Kita, 060-8628, Sapporo, JAPAN
| |
Collapse
|
16
|
Raina D, Kumar C, Kumar V, Khan IA, Saran S. Potential Inhibitors Targeting Escherichia coli UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): An Overview. Indian J Microbiol 2022; 62:11-22. [PMID: 35068599 PMCID: PMC8758813 DOI: 10.1007/s12088-021-00988-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges that is escalating and affecting humanity across the globe. To overcome this increasing burden of resistance, discovering novel hits by targeting the enzymes involved in peptidoglycan (murein) biosynthesis has always been considered better in antimicrobial drug discovery. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme has been identified as essential for Escherichia coli survival and catalyzes the early-stage step in bacterial cell wall synthesis. The present article gives a brief overview of the role of enzymes in peptidoglycan synthesis and MurA enzyme (previously known as MurZ in E. coli), in particular, including its structural and active site features. This review also provides an insight into the current knowledge of the reported MurA inhibitors, their mechanism of action and drawbacks of these hits that hinder their clinical trials, which would be helpful for synthesis and discovering potent molecules. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12088-021-00988-6.
Collapse
Affiliation(s)
- Diksha Raina
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Chetan Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India ,Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India
| | - Vinod Kumar
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Inshad Ali Khan
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan 305817 India
| | - Saurabh Saran
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| |
Collapse
|
17
|
Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
Collapse
|
18
|
Acebrón-García-de-Eulate M, Mayol-Llinàs J, Holland MTO, Kim SY, Brown KP, Marchetti C, Hess J, Di Pietro O, Mendes V, Abell C, Floto RA, Coyne AG, Blundell TL. Discovery of Novel Inhibitors of Uridine Diphosphate- N-Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa, an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients. J Med Chem 2022; 65:2149-2173. [PMID: 35080396 PMCID: PMC7614804 DOI: 10.1021/acs.jmedchem.1c01684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is of major concern for cystic fibrosis patients where this infection can be fatal. With the emergence of drug-resistant strains, there is an urgent need to develop novel antibiotics against P. aeruginosa. MurB is a promising target for novel antibiotic development as it is involved in the cell wall biosynthesis. MurB has been shown to be essential in P. aeruginosa, and importantly, no MurB homologue exists in eukaryotic cells. A fragment-based drug discovery approach was used to target Pa MurB. This led to the identification of a number of fragments, which were shown to bind to MurB. One fragment, a phenylpyrazole scaffold, was shown by ITC to bind with an affinity of Kd = 2.88 mM (LE 0.23). Using a structure guided approach, different substitutions were synthesized and the initial fragment was optimized to obtain a small molecule with Kd = 3.57 μM (LE 0.35).
Collapse
Affiliation(s)
| | - Joan Mayol-Llinàs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Matthew T O Holland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Chiara Marchetti
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeannine Hess
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ornella Di Pietro
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| |
Collapse
|
19
|
Global Proteomic Analysis of Listeria monocytogenes' Response to Linalool. Foods 2021; 10:foods10102449. [PMID: 34681498 PMCID: PMC8535586 DOI: 10.3390/foods10102449] [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: 08/30/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
Listeria monocytogenes (LM) is one of the most serious foodborne pathogens. Listeriosis, the disease caused by LM infection, has drawn attention worldwide because of its high hospitalization and mortality rates. Linalool is a vital constituent found in many essential oils; our previous studies have proved that linalool exhibits strong anti-Listeria activity. In this study, iTRAQ-based quantitative proteomics analysis was performed to explore the response of LM exposed to linalool, and to unravel the mode of action and drug targets of linalool against LM. A total of 445 differentially expressed proteins (DEPs) were screened out, including 211 up-regulated and 234 down-regulated proteins which participated in different biological functions and pathways. Thirty-one significantly enriched gene ontology (GO) functional categories were obtained, including 12 categories in “Biological Process”, 10 categories in “Cell Component”, and 9 categories in “Molecular Function”. Sixty significantly enriched biological pathways were classified, including 6 pathways in “Cell Process”, 6 pathways in “Environmental Information Processing”, 3 pathways in “Human Disease”, 40 pathways in “Metabolism”, and 2 pathways in “Organic System”. GO and Kyoto Encyclopedia of Genes (KEGG) enrichment analysis together with flow cytometry data implied that cell membranes, cell walls, nucleoids, and ribosomes might be the targets of linalool against LM. Our study provides good evidence for the proteomic analysis of bacteria, especially LM, exposed to antibacterial agents. Further, those drug targets discovered by proteomic analysis can provide theoretical support for the development of new drugs against LM.
Collapse
|
20
|
Qin Y, Xu L, Teng Y, Wang Y, Ma P. Discovery of novel antibacterial agents: Recent developments in D-alanyl-D-alanine ligase inhibitors. Chem Biol Drug Des 2021; 98:305-322. [PMID: 34047462 DOI: 10.1111/cbdd.13899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 01/14/2023]
Abstract
Bacterial infections can cause serious problems that threaten public health over a long period of time. Moreover, the continuous emergence of drug-resistant bacteria necessitates the development of novel antibacterial agents. D-alanyl-D-alanine ligase (Ddl) is an indispensable adenosine triphosphate-dependent bacterial enzyme involved in the biosynthesis of peptidoglycan precursor, which catalyzes the ligation of two D-alanine molecules into one D-alanyl-D-alanine dipeptide. This dipeptide is an essential component of the intracellular peptidoglycan precursor, uridine diphospho-N-acetylmuramic acid (UDP-MurNAc)-pentapeptide, that maintains the integrity of the bacterial cell wall by cross-linking the peptidoglycan chain, and is crucial for the survival of pathogens. Consequently, Ddl is expected to be a promising target for the development of antibacterial agents. In this review, we present a brief introduction regarding the structure and function of Ddl, as well as an overview of the various Ddl inhibitors currently being used as antibacterial agents, specifically highlighting their inhibitory activities, structure-activity relationships and mechanisms of action.
Collapse
Affiliation(s)
- Yinhui Qin
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Linlin Xu
- Department of Pharmacy, Taian City Central Hospital, Taian, China
| | - Yuetai Teng
- Department of Pharmacy, Jinan Vocational College of Nursing, Jinan, China
| | - Yinhu Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Peizhi Ma
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| |
Collapse
|
21
|
Shinde Y, Ahmad I, Surana S, Patel H. The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall. Eur J Med Chem 2021; 222:113568. [PMID: 34118719 DOI: 10.1016/j.ejmech.2021.113568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023]
Abstract
TUBERCULOSIS: (TB) transmitted by Mycobacterium tuberculosis (Mtb) is one of the top 10 causes of death globally. Currently, the widespread occurrence of resistance toward Mtb strains is becoming a significant concern to public health. This scenario exaggerated the need for the discovery of novel targets and their inhibitors. Targeting the "Mtb cell wall peptidoglycan synthesis" is an attractive strategy to overcome drug resistance. Mur enzymes (MurA-MurF) play essential roles in the peptidoglycan synthesis by catalyzing the ligation of key amino acid residues to the stem peptide. These enzymes are unique and confined to the eubacteria and are absent in humans, representing potential targets for anti-tubercular drug discovery. Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme. In light of these findings in the current review, we have discussed the recent advances in medicinal chemistry of Mtb Mur enzymes (MurA-MurF) and their inhibitors, offering attractive multi-targeted strategies to combat the problem of drug-resistant in M. tuberculosis.
Collapse
Affiliation(s)
- Yashodeep Shinde
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India.
| |
Collapse
|
22
|
Black KA, Duan L, Mandyoli L, Selbach BP, Xu W, Ehrt S, Sacchettini JC, Rhee KY. Metabolic bifunctionality of Rv0812 couples folate and peptidoglycan biosynthesis in Mycobacterium tuberculosis. J Exp Med 2021; 218:212052. [PMID: 33950161 PMCID: PMC8105722 DOI: 10.1084/jem.20191957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/16/2021] [Accepted: 03/30/2021] [Indexed: 11/04/2022] Open
Abstract
Comparative sequence analysis has enabled the annotation of millions of genes from organisms across the evolutionary tree. However, this approach has inherently biased the annotation of phylogenetically ubiquitous, rather than species-specific, functions. The ecologically unusual pathogen Mycobacterium tuberculosis (Mtb) has evolved in humans as its sole reservoir and emerged as the leading bacterial cause of death worldwide. However, the physiological factors that define Mtb’s pathogenicity are poorly understood. Here, we report the structure and function of a protein that is required for optimal in vitro fitness and bears homology to two distinct enzymes, Rv0812. Despite diversification of related orthologues into biochemically distinct enzyme families, rv0812 encodes a single active site with aminodeoxychorismate lyase and D–amino acid transaminase activities. The mutual exclusivity of substrate occupancy in this active site mediates coupling between nucleic acid and cell wall biosynthesis, prioritizing PABA over D-Ala/D-Glu biosynthesis. This bifunctionality reveals a novel, enzymatically encoded fail-safe mechanism that may help Mtb and other bacteria couple replication and division.
Collapse
Affiliation(s)
| | - Lijun Duan
- Texas A&M University, College Station, TX
| | | | | | | | | | | | | |
Collapse
|
23
|
Design, synthesis and molecular modelling of phenoxyacetohydrazide derivatives as Staphylococcus aureus MurD inhibitors. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
24
|
Shiraishi T, Kuzuyama T. Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products. Biosci Biotechnol Biochem 2021; 85:42-52. [PMID: 33577658 DOI: 10.1093/bbb/zbaa052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Phosphonates are organophosphorus compounds possessing a characteristic C-P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C-P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.
Collapse
Affiliation(s)
- Taro Shiraishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
25
|
Shaku M, Ealand C, Kana BD. Cell Surface Biosynthesis and Remodeling Pathways in Mycobacteria Reveal New Drug Targets. Front Cell Infect Microbiol 2020; 10:603382. [PMID: 33282752 PMCID: PMC7688586 DOI: 10.3389/fcimb.2020.603382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/20/2020] [Indexed: 12/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains the leading cause of death from an infectious bacterium and is responsible for 1.8 million deaths annually. The emergence of drug resistance, together with the need for a shorter more effective regimen, has prompted the drive to identify novel therapeutics with the bacterial cell surface emerging as a tractable area for drug development. Mtb assembles a unique, waxy, and complex cell envelope comprised of the mycolyl-arabinogalactan-peptidoglycan complex and an outer capsule like layer, which are collectively essential for growth and pathogenicity while serving as an inherent barrier against antibiotics. A detailed understanding of the biosynthetic pathways required to assemble the polymers that comprise the cell surface will enable the identification of novel drug targets as these structures provide a diversity of biochemical reactions that can be targeted. Herein, we provide an overview of recently described mycobacterial cell wall targeting compounds, novel drug combinations and their modes of action. We anticipate that this summary will enable prioritization of the best pathways to target and triage of the most promising molecules to progress for clinical assessment.
Collapse
Affiliation(s)
- Moagi Shaku
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher Ealand
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Bavesh D Kana
- National Health Laboratory Service, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
26
|
Azam MA, Manoj VCV. An explorative study on diarylquinoline-based inhibitor targeting Enterococcus faecium MurF. Struct Chem 2020. [DOI: 10.1007/s11224-020-01622-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
27
|
Mokbel SA, Fathalla RK, El-Sharkawy LY, Abadi AH, Engel M, Abdel-Halim M. Synthesis of novel 1,2-diarylpyrazolidin-3-one-based compounds and their evaluation as broad spectrum antibacterial agents. Bioorg Chem 2020; 99:103759. [PMID: 32220665 DOI: 10.1016/j.bioorg.2020.103759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/13/2020] [Indexed: 11/16/2022]
Abstract
There is a continuous need to develop new antibacterial agents with non-traditional mechanisms to combat the nonstop emerging resistance to most of the antibiotics used in clinical settings. We identified novel pyrazolidinone derivatives as antibacterial hits in an in-house library screening and synthesized several derivatives in order to improve the potency and increase the polarity of the discovered hit compounds. The oxime derivative 24 exhibited promising antibacterial activity against E. coli TolC, B. subtilis and S. aureus with MIC values of 4, 10 and 20 µg/mL, respectively. The new lead compound 24 was found to exhibit a weak dual inhibitory activity against both the E. coli MurA and MurB enzymes with IC50 values of 88.1 and 79.5 µM, respectively, which could partially explain its antibacterial effect. A comparison with the previously reported, structurally related pyrazolidinediones suggested that the oxime functionality at position 4 enhanced the activity against MurA and recovered the activity against the MurB enzyme. Compound 24 can serve as a lead for further development of novel and safe antibiotics with potential broad spectrum activity.
Collapse
Affiliation(s)
- Salma A Mokbel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Reem K Fathalla
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Lina Y El-Sharkawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; Division of Pharmacy & Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PT, UK
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany.
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt.
| |
Collapse
|
28
|
Soni AS, Vacariu CM, Chen JY, Tanner ME. Synthesis of a meso-Oxa-Diaminopimelic Acid Containing Peptidoglycan Pentapeptide and Coupling to the GlcNAc- anhydro-MurNAc Disaccharide. Org Lett 2020; 22:2313-2317. [PMID: 32133861 DOI: 10.1021/acs.orglett.0c00505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The syntheses of peptidoglycan (PG)-derived peptides containing meso-diaminopimelic acid (meso-Dap) are typically quite lengthy due to the need to prepare orthogonally protected meso-Dap. In this work, the preparation of the PG pentapeptide containing the isosteric analog meso-oxa-Dap is described. The synthesis relies on the ring opening of a peptide embedded aziridine via the attack of a serine residue. The pentapeptide was attached to a GlcNAc-anhydro-MurNAc disaccharide, to produce a putative substrate for the AmpG pore protein.
Collapse
Affiliation(s)
- Arvind S Soni
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Condarache M Vacariu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jeff Y Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
29
|
Jupudi S, Azam MA, Wadhwani A. Synthesis, molecular docking, binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors. J Recept Signal Transduct Res 2020; 39:283-293. [PMID: 31538846 DOI: 10.1080/10799893.2019.1663538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC50 value of 13.37 μM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30 ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.
Collapse
Affiliation(s)
- Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , India
| | - Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy , Ooty , India
| | - Ashish Wadhwani
- Department of Biotechnology, JSS College of Pharmacy , Ooty , India
| |
Collapse
|
30
|
Chen X, Wong CH, Ma C. Targeting the Bacterial Transglycosylase: Antibiotic Development from a Structural Perspective. ACS Infect Dis 2019; 5:1493-1504. [PMID: 31283163 DOI: 10.1021/acsinfecdis.9b00118] [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] [Indexed: 01/03/2023]
Abstract
One of the major threats to human life nowadays is widespread antibiotic resistance. Antibiotics are used to treat bacterial infections by targeting their essential pathways, such as the biosynthesis of bacterial cell walls. Bacterial transglycosylase, particularly glycosyltransferase family 51 (GT51), is one critical player in the cell wall biosynthesis and has long been known as a promising yet challenging target for antibiotic development. Here, we review the structural studies of this protein and summarize recent progress in developing its specific inhibitors, including synthetic substrate analogs and novel compounds identified from high-throughput screens. A detailed analysis of the protein-ligand interface has also provided us with valuable insights into the future antibiotic development against the bacterial transglycosylase.
Collapse
Affiliation(s)
- Xiaorui Chen
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Che Ma
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| |
Collapse
|
31
|
Díaz-Sáez L, Torrie LS, McElroy SP, Gray D, Hunter WN. Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. FEBS J 2019; 286:4509-4524. [PMID: 31260169 PMCID: PMC6899670 DOI: 10.1111/febs.14976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023]
Abstract
Burkholderia pseudomallei is a serious, difficult to treat Gram‐negative pathogen and an increase in the occurrence of drug‐resistant strains has been detected. We have directed efforts to identify and to evaluate potential drug targets relevant to treatment of infection by B. pseudomallei. We have selected and characterised the essential enzyme d‐alanine‐d‐alanine ligase (BpDdl), required for the ATP‐assisted biosynthesis of a peptidoglycan precursor. A recombinant supply of protein supported high‐resolution crystallographic and biophysical studies with ligands (AMP and AMP+d‐Ala‐d‐Ala), and comparisons with orthologues enzymes suggest a ligand‐induced conformational change occurring that might be relevant to the catalytic cycle. The detailed biochemical characterisation of the enzyme, development and optimisation of ligand binding assays supported the search for novel inhibitors by screening of selected compound libraries. In a similar manner to that observed previously in other studies, we note a paucity of hits that are worth follow‐up and then in combination with a computational analysis of the active site, we conclude that this ligase represents a difficult target for drug discovery. Nevertheless, our reagents, protocols and data can underpin future efforts exploiting more diverse chemical libraries and structure‐based approaches.
Collapse
Affiliation(s)
- Laura Díaz-Sáez
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, UK
| | - Leah S Torrie
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, UK
| | - Stuart P McElroy
- European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - David Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, UK
| | - William N Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, UK
| |
Collapse
|
32
|
Patel B, Ryan P, Makwana V, Zunk M, Rudrawar S, Grant G. Caprazamycins: Promising lead structures acting on a novel antibacterial target MraY. Eur J Med Chem 2019; 171:462-474. [DOI: 10.1016/j.ejmech.2019.01.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/29/2022]
|
33
|
Soni AS, Lin CSH, Murphy MEP, Tanner ME. Peptides Containing meso-Oxa-Diaminopimelic Acid as Substrates for the Cell-Shape-Determining Proteases Csd6 and Pgp2. Chembiochem 2019; 20:1591-1598. [PMID: 30746833 DOI: 10.1002/cbic.201900011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 12/17/2022]
Abstract
The enzymes Csd6 and Pgp2 are peptidoglycan (PG) proteases found in the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, respectively. These enzymes are involved in the trimming of non-crosslinked PG sidechains and catalyze the cleavage of the bond between meso-diaminopimelic acid (meso-Dap) and d-alanine, thus converting a PG tetrapeptide into a PG tripeptide. They are known to be cell-shape-determining enzymes, because deletion of the corresponding genes results in mutant strains that have lost the normal helical phenotype and instead possess a straight-rod morphology. In this work, we report two approaches directed towards the synthesis of the tripeptide substrate Ac-iso-d-Glu-meso-oxa-Dap-d-Ala, which serves as a mimic of the terminus of an non-crosslinked PG tetrapeptide substrate. The isosteric analogue meso-oxa-Dap was utilized in place of meso-Dap to simplify the synthetic procedure. The more efficient synthesis involved ring opening of a peptide-embedded aziridine by a serine-based nucleophile. A branched tetrapeptide was also prepared as a mimic of the terminus of a crosslinked PG tetrapeptide. We used MS analysis to demonstrate that the tripeptide serves as a substrate for both Csd6 and Pgp2 and that the branched tetrapeptide serves as a substrate for Pgp2, albeit at a significantly slower rate.
Collapse
Affiliation(s)
- Arvind S Soni
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Chang Sheng-Huei Lin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| |
Collapse
|
34
|
Kwiatkowska-Semrau K, Wojciechowski M, Gabriel I, Crucho S, Milewski S. Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1181-1189. [DOI: 10.1016/j.bbapap.2018.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/15/2018] [Indexed: 02/02/2023]
|
35
|
Wang X, Krasnova L, Wu KB, Wu WS, Cheng TJ, Wong CH. Towards new antibiotics targeting bacterial transglycosylase: Synthesis of a Lipid II analog as stable transition-state mimic inhibitor. Bioorg Med Chem Lett 2018; 28:2708-2712. [PMID: 29602680 PMCID: PMC6182773 DOI: 10.1016/j.bmcl.2018.03.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Described here is the asymmetric synthesis of iminosugar 2b, a Lipid II analog, designed to mimic the transition state of transglycosylation catalyzed by the bacterial transglycosylase. The high density of functional groups, together with a rich stereochemistry, represents an extraordinary challenge for chemical synthesis. The key 2,6-anti- stereochemistry of the iminosugar ring was established through an iridium-catalyzed asymmetric allylic amination. The developed synthetic route is suitable for the synthesis of focused libraries to enable the structure-activity relationship study and late-stage modification of iminosugar scaffold with variable lipid, peptide and sugar substituents. Compound 2b showed 70% inhibition of transglycosylase from Acinetobacter baumannii, providing a basis for further improvement.
Collapse
Affiliation(s)
- Xiaolei Wang
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Larissa Krasnova
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Kevin Binchia Wu
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Wei-Shen Wu
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Ting-Jen Cheng
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Chi-Huey Wong
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA; Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan.
| |
Collapse
|
36
|
Ogasawara Y, Dairi T. Peptide Epimerization Machineries Found in Microorganisms. Front Microbiol 2018; 9:156. [PMID: 29467749 PMCID: PMC5808125 DOI: 10.3389/fmicb.2018.00156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
D-Amino acid residues have been identified in peptides from a variety of eukaryotes and prokaryotes. In microorganisms, UDP-N-acetylmuramic acid pentapeptide (UDP-MurNAc-L-Ala-D-Glu-meso-diaminopimelate-D-Ala-D-Ala), a unit of peptidoglycan, is a representative. During its biosynthesis, D-Ala and D-Glu are generally supplied by racemases from the corresponding isomers. However, we recently identified a unique unidirectional L-Glu epimerase catalyzing the epimerization of the terminal L-Glu of UDP-MurNAc-L-Ala-L-Glu. Several such enzymes, introducing D-amino acid resides into peptides via epimerization, have been reported to date. This includes a L-Ala-D/L-Glu epimerase, which is possibly used during peptidoglycan degradation. In bacterial primary metabolisms, to the best of our knowledge, these two machineries are the only examples of peptide epimerization. However, a variety of peptides containing D-amino acid residues have been isolated from microorganisms as secondary metabolites. Their biosynthetic mechanisms have been studied and three different peptide epimerization machineries have been reported. The first is non-ribosomal peptide synthetase (NRPS). Excellent studies with dissected modules of gramicidin synthetase and tyrocidine synthetase revealed the reactions of the epimerization domains embedded in the enzymes. The obtained information is still utilized to predict epimerization domains in uncharacterized NRPSs. The second includes the biosynthetic enzymes of lantibiotics, which are ribosome-dependently supplied peptide antibiotics containing polycyclic thioether amino acids (lanthionines). A mechanism for the formation of the D-Ala moiety in lanthionine by two enzymes, dehydratases catalyzing the conversion of L-Ser into dehydroalanine and enzymes catalyzing nucleophilic attack of the thiol of cysteine into dehydroalanine, was clarified. Similarly, the formation of a D-Ala residue by reduction of the dehydroalanine residue was also reported. The last type of machinery includes radical-S-adenosylmethionine (rSAM)-dependent enzymes, which catalyze a variety of radical-mediated chemical transformations. In the biosynthesis of polytheonamide, a marine sponge-derived and ribosome-dependently supplied peptide composed of 48 amino acids, a rSAM enzyme (PoyD) is responsible for unidirectional epimerizations of multiple different amino acids in the precursor peptide. In this review, we briefly summarize the discovery and current mechanistic understanding of these peptide epimerization enzymes.
Collapse
Affiliation(s)
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
| |
Collapse
|
37
|
Stiers KM, Xu J, Lee Y, Addison ZR, Van Doren SR, Beamer LJ. Phosphorylation-Dependent Effects on the Structural Flexibility of Phosphoglucosamine Mutase from Bacillus anthracis. ACS OMEGA 2017; 2:8445-8452. [PMID: 31457382 PMCID: PMC6645435 DOI: 10.1021/acsomega.7b01490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/16/2017] [Indexed: 06/09/2023]
Abstract
Phosphoglucosamine mutase (PNGM) is an evolutionarily conserved bacterial enzyme in the peptidoglycan biosynthetic pathway, catalyzing the reversible conversion between glucosamine 1- and 6-phosphate. Previous structural studies of PNGM from the pathogen Bacillus anthracis revealed its dimeric assembly and highlighted the rotational mobility of its C-terminal domain. Recent studies of two other enzymes in the same superfamily have demonstrated the long-range effects on the conformational flexibility associated with phosphorylation of the conserved, active site phosphoserine involved in phosphoryl transfer. Building on this work, we use a combination of experimental and computational studies to show that the active, phosphorylated version of B. anthracis PNGM has decreased flexibility relative to its inactive, dephosphorylated state. Limited proteolysis reveals an enhanced and accelerated cleavage of the dephosphorylated enzyme. 15N transverse relaxation-optimized NMR spectra corroborate a conformational adjustment with broadening and shifts of peaks relative to the phospho-enzyme. Electrostatic calculations indicate that residues in the mobile, C-terminal domain are linked to the phosphoserine by lines of attraction that are absent in the dephosphorylated enzyme. Phosphorylation-dependent changes in protein flexibility appear linked with the conformational change and enzyme mechanism in PNGM, establishing this as a conserved theme in multiple subgroups of the diverse α-d-phosphohexomutase superfamily.
Collapse
|
38
|
Stiers KM, Muenks AG, Beamer LJ. Biology, Mechanism, and Structure of Enzymes in the α-d-Phosphohexomutase Superfamily. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:265-304. [PMID: 28683921 PMCID: PMC5802415 DOI: 10.1016/bs.apcsb.2017.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these enzymes have recently benefitted from biophysical characterization, including X-ray crystallography, NMR, and hydrogen-deuterium exchange studies. This work has provided new insights into the unique catalytic mechanism of the superfamily, shed light on the molecular determinants of ligand recognition, and revealed the evolutionary conservation of conformational flexibility. Novel associations with inherited metabolic disease and the pathogenesis of bacterial infections have emerged, spurring renewed interest in the long-appreciated functional roles of these enzymes.
Collapse
Affiliation(s)
| | | | - Lesa J Beamer
- University of Missouri, Columbia, MO, United States.
| |
Collapse
|
39
|
Mehla K, Ramana J. Tapping into Salmonella typhimurium LT2 genome in a quest to explore its therapeutic arsenal: A metabolic network modeling approach. Biomed Pharmacother 2016; 86:57-66. [PMID: 27939520 DOI: 10.1016/j.biopha.2016.11.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/27/2016] [Indexed: 01/17/2023] Open
Abstract
S. typhimurium, the classical broad-host-range serovar is a widely distributed cause of food-borne illness. Escalating antibiotic resistance and potential of conjugal transmission to other pathogens attributable to its broad spectrum host specificities have aided S. typhimurium to emerge as a global health threat. To keep pace with ever evolving bacterial defenses, there is dire need to restock the antibiotic pipeline. Genome scale metabolic reconstructions present immense possibilities to decipher physiological properties of an organism using constraint-based methods The systems-level approaches of genome scale metabolic networks interrogation open up new avenues of drug target identification against deadly infectious diseases. We performed flux balance analysis and minimization of metabolic adjustment studies of genome scale reconstruction model of S. typhimurium targeted at identifying large number of metabolites with a potential to be utilized as therapeutic drug targets. These constraint based approaches initially predict a set of genes indispensable to bacterial survival by performing gene knockout studies which are then prioritized through a multistep process. Metabolites involved in l-rhamnose biosynthesis, peptidoglycan biosynthesis, fatty acid biosynthesis, and folate biosynthesis pathways were prioritized as candidate drug targets. This study provides a general therapeutic approach which can be effectively applied to other pathogens as well.
Collapse
Affiliation(s)
- Kusum Mehla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN 173234 Himachal Pradesh, India
| | - Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN 173234 Himachal Pradesh, India.
| |
Collapse
|
40
|
Koppermann S, Ducho C. Natural Products at Work: Structural Insights into Inhibition of the Bacterial Membrane Protein MraY. Angew Chem Int Ed Engl 2016; 55:11722-4. [DOI: 10.1002/anie.201606396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
41
|
Koppermann S, Ducho C. Naturstoffe bei der Arbeit: strukturelle Einblicke in die Inhibition des bakteriellen Membranproteins MraY. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stefan Koppermann
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| | - Christian Ducho
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| |
Collapse
|
42
|
Wiegmann D, Koppermann S, Wirth M, Niro G, Leyerer K, Ducho C. Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents. Beilstein J Org Chem 2016; 12:769-795. [PMID: 27340469 PMCID: PMC4902027 DOI: 10.3762/bjoc.12.77] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/23/2022] Open
Abstract
Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure-activity relationship (SAR) studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.
Collapse
Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Marius Wirth
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Kristin Leyerer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| |
Collapse
|
43
|
Liu Y, Frirdich E, Taylor JA, Chan ACK, Blair KM, Vermeulen J, Ha R, Murphy MEP, Salama NR, Gaynor EC, Tanner ME. A Bacterial Cell Shape-Determining Inhibitor. ACS Chem Biol 2016; 11:981-91. [PMID: 26735022 DOI: 10.1021/acschembio.5b01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials against these human pathogens.
Collapse
Affiliation(s)
- Yanjie Liu
- Contribution
from the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Emilisa Frirdich
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jennifer A. Taylor
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Department
of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | - Anson C. K. Chan
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kris M. Blair
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Program
in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, United States
| | - Jenny Vermeulen
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Reuben Ha
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nina R. Salama
- Division
of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
- Department
of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195, United States
- Program
in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, United States
| | - Erin C. Gaynor
- Department
of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin E. Tanner
- Contribution
from the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
44
|
Hsu CH, Schelwies M, Enck S, Huang LY, Huang SH, Chang YF, Cheng TJR, Cheng WC, Wong CH. Iminosugar C-glycoside analogues of α-D-GlcNAc-1-phosphate: synthesis and bacterial transglycosylase inhibition. J Org Chem 2014; 79:8629-37. [PMID: 25137529 PMCID: PMC4168788 DOI: 10.1021/jo501340s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
We
herein describe the first synthesis of iminosugar C-glycosides
of α-d-GlcNAc-1-phosphate in 10 steps starting from
unprotected d-GlcNAc. A diastereoselective intramolecular
iodoamination–cyclization as the key step was employed to construct
the central piperidine ring of the iminosugar and the C-glycosidic
structure of α-d-GlcNAc. Finally, the iminosugar phosphonate
and its elongated phosphate analogue were accessed. These phosphorus-containing
iminosugars were coupled efficiently with lipophilic monophosphates
to give lipid-linked pyrophosphate derivatives, which are lipid II
mimetics endowed with potent inhibitory properties toward bacterial
transglycosylases (TGase).
Collapse
Affiliation(s)
- Che-Hsiung Hsu
- Genomics Research Center, Academica Sinica , Taipei 115, Taiwan
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Hrast M, Sosič I, Sink R, Gobec S. Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F. Bioorg Chem 2014; 55:2-15. [PMID: 24755374 DOI: 10.1016/j.bioorg.2014.03.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 01/12/2023]
Abstract
The widespread emergence of resistant bacterial strains is becoming a serious threat to public health. This thus signifies the need for the development of new antibacterial agents with novel mechanisms of action. Continuous efforts in the design of novel antibacterials remain one of the biggest challenges in drug development. In this respect, the Mur enzymes, MurA-F, that are involved in the formation of UDP-N-acetylmuramyl-pentapeptide can be genuinely considered as promising antibacterial targets. This review provides an in-depth insight into the recent developments in the field of inhibitors of the MurA-F enzymes. Special attention is also given to compounds that act as multiple inhibitors of two, three or more of the Mur enzymes. Moreover, the reasons for the lack of preclinically successful inhibitors and the challenges to overcome these hurdles in the next years are also debated.
Collapse
Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Roman Sink
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
| |
Collapse
|
46
|
Hrast M, Anderluh M, Knez D, Randall CP, Barreteau H, O'Neill AJ, Blanot D, Gobec S. Design, synthesis and evaluation of second generation MurF inhibitors based on a cyanothiophene scaffold. Eur J Med Chem 2014; 73:83-96. [DOI: 10.1016/j.ejmech.2013.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 11/29/2022]
|
47
|
Characterization of mycobacterial UDP-N-acetylglucosamine enolpyruvyle transferase (MurA). Res Microbiol 2014; 165:91-101. [PMID: 24463011 DOI: 10.1016/j.resmic.2014.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
The mycobacterial peptidoglycan has structure and biosynthetic pathways to similar those of other bacteria. UDP-N-acetylglucosamine enolpyruvyle transferase (MurA) catalyzes the first reaction in the biosynthesis of peptidoglycan. The MurA enzyme has been identified from various bacterial species, but the in-depth biochemical properties of mycobacterial MurA have not been characterized. In this study, both Mycobacterium tuberculosis MurA protein and Mycobacterium smegmatis MurA protein were overexpressed in Escherichia coli and purified by affinity chromatography. MurA activity was detected by HPLC. A colorimetric assay of MurA activity was also developed and the kinetic properties of Mtb MurA and Msm MurA were determined using this colorimetric assay. A conditional murA gene knockout strain was constructed by DNA homologous recombination. The disruption of murA in the genome of M. smegmatis led to loss of viability at a non-permissive temperature. Drastic morphological and structural alterations in the M. smegmatis murA knockout strain were observed by scanning electron microscopy and transmission electron microscopy. These results demonstrated that murA was an essential gene for growth of M. smegmatis. Therefore, MurA is a potential target for developing new anti-tuberculosis drugs.
Collapse
|
48
|
|
49
|
Salem M, Seidelin JB, Rogler G, Nielsen OH. Muramyl dipeptide responsive pathways in Crohn's disease: from NOD2 and beyond. Cell Mol Life Sci 2013; 70:3391-404. [PMID: 23275943 PMCID: PMC11113952 DOI: 10.1007/s00018-012-1246-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 12/15/2022]
Abstract
Crohn's disease (CD) is one of main disease entities under the umbrella term chronic inflammatory bowel disease. The etiology of CD involves alterations in genetic, microbiological, and immunological factors. This review is devoted to the role of the bacterial wall compound muramyl dipeptide (MDP) for the activation of inflammatory pathways involved in the pathogenesis of CD. The importance of this molecule is underscored by the fact that (1) MDP, which is found in most Gram-negative and -positive bacteria, is able to trigger several immunological responses in the intestinal system, and (2) that alterations in several mediators of the MDP response including-but not restricted to-nucleotide oligomerization domain 2 (NOD2) are associated with CD. The normalization of MDP signaling is one of several important factors that influence the intestinal inflammatory response, a fact which emphasizes the pathogenic importance of MDP signaling for the pathogenesis of CD. The important aspects of NOD2 and non-NOD2 mediated effects of MDP for the development of CD are highlighted, as well as how alterations in these pathways might translate into the development of new therapeutic strategies.
Collapse
Affiliation(s)
- Mohammad Salem
- Department of Gastroenterology D, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark
| | - Jakob Benedict Seidelin
- Department of Gastroenterology D, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark
- Department of Internal Medicine, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, Zürich University Hospital, Zurich, Switzerland
| | - Ole Haagen Nielsen
- Department of Gastroenterology D, Medical Section, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark
| |
Collapse
|
50
|
Sukhithasri V, Nisha N, Biswas L, Anil Kumar V, Biswas R. Innate immune recognition of microbial cell wall components and microbial strategies to evade such recognitions. Microbiol Res 2013; 168:396-406. [DOI: 10.1016/j.micres.2013.02.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 02/08/2013] [Accepted: 02/09/2013] [Indexed: 01/19/2023]
|