1
|
Salem ME, Abdelhamid IA, Elwahy AH, Ragheb MA, Alqahtani AS, Zaki ME, Algethami FK, Mahmoud HK. Novel hybrid thiazoles, bis-thiazoles linked to azo-sulfamethoxazole: Synthesis, docking, and antimicrobial activity. Heliyon 2024; 10:e31082. [PMID: 38813143 PMCID: PMC11133767 DOI: 10.1016/j.heliyon.2024.e31082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
The reaction of sulfamethoxazolehydrazonoyl chloride with thiosemicarbazones, bis-thiosemicarbazones, or 4-amino-3-mercapto-1,2,4-triazole in dioxane in the presence of triethylamine as a basic catalyst at reflux resulted in the regioselective synthesis of thiazoles and bis-thiazoles linked to azo-sulfamethoxazole as novel hybrid molecules. The structures of the new compounds were confirmed using a range of spectra. Each compound's antibacterial properties were evaluated using the agar well-diffusion technique, and most of them demonstrated significant potency. In silico investigations revealed that the described compounds had strong interactions with the binding sites of MurE ligase, tyrosyl-tRNA synthetase, and dihydropteroate synthase, demonstrating inhibitory activity.
Collapse
Affiliation(s)
- Mostafa E. Salem
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University(IMSIU), P.O. Box, 90950, Riyadh, 11623, Saudi Arabia
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Ismail A. Abdelhamid
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Ahmed H.M. Elwahy
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Arwa sultan Alqahtani
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University(IMSIU), P.O. Box, 90950, Riyadh, 11623, Saudi Arabia
| | - Magdi E.A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University(IMSIU), P.O. Box, 90950, Riyadh, 11623, Saudi Arabia
| | - Faisal K. Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University(IMSIU), P.O. Box, 90950, Riyadh, 11623, Saudi Arabia
| | - Huda Kamel Mahmoud
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| |
Collapse
|
2
|
Coppinger MN, Laramore K, Popham DL, Stabb EV. A prototrophic suppressor of a Vibrio fischeri D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF). J Bacteriol 2024; 206:e0033323. [PMID: 38411059 PMCID: PMC10955857 DOI: 10.1128/jb.00333-23] [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: 12/08/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in Vibrio fischeri and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic murI racD mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >1011 cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses proB to a gene encoding a putative broad-spectrum racemase of V. fischeri, bsrF. An engineered bsrF allele lacking the putative secretion signal (ΔSS-bsrF) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-bsrF allele similarly suppressed the D-alanine auxotrophy of an alr mutant and restored prototrophy to a murI alr double mutant auxotrophic for both D-ala and D-glu. The ΔSS-bsrF allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in V. fischeri that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance. IMPORTANCE D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in Vibrio fischeri, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.
Collapse
Affiliation(s)
- Macey N. Coppinger
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| | - Kathrin Laramore
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois, Chicago, Illinois, USA
| |
Collapse
|
3
|
Umetsu S, Tsunoda T, Kiyanagi H, Inahashi Y, Nonaka K, Dairi T, Ogasawara Y. Identification of a new oligomycin derivative as a specific inhibitor of the alternative peptidoglycan biosynthetic pathway. J Antibiot (Tokyo) 2024; 77:182-184. [PMID: 38200161 DOI: 10.1038/s41429-023-00693-0] [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] [Received: 07/14/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 01/12/2024]
Abstract
Peptidoglycan is an important macromolecule in bacterial cell walls to maintain cell integrity, and its biosynthetic pathway has been well studied. Recently, we demonstrated that some bacteria such as Xanthomonas oryzae, a pathogen causing bacterial blight of rice, used an alternative pathway for peptidoglycan biosynthesis. In this pathway, MurD2, a MurD homolog, catalyzed the attachment of L-Glu to UDP-MurNAc-L-Ala and MurL, which did not show homology to any known protein, catalyzed epimerization of the terminal L-Glu of the MurD2 product to generate UDP-MurNAc-L-Ala-D-Glu. Because the alternative pathway also operates in some other plant pathogens and opportunistic pathogens, specific inhibitors of the alternative pathway could function as pesticides and antibiotics for these pathogens. In this study, we searched for specific inhibitors of the alternative pathway from metabolites produced by actinomycetes and identified a new oligomycin-class polyketide, which was revealed to inhibit the MurD2 reaction, in culture broth of Micromonospora sp. K18-0097.
Collapse
Affiliation(s)
- Shuhei Umetsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Takeshi Tsunoda
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Haruka Kiyanagi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Yuki Inahashi
- Ōmura Satoshi Memorial Institute, Kitasato University, Minato-ku, Tokyo, 108-8641, Japan
| | - Kenichi Nonaka
- Ōmura Satoshi Memorial Institute, Kitasato University, Minato-ku, Tokyo, 108-8641, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan.
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan.
| |
Collapse
|
4
|
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
|
5
|
Gaur V, Kumar N, Vyas A, Chowdhury D, Singh J, Bera S. Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach. J Biomol Struct Dyn 2023:1-11. [PMID: 38149858 DOI: 10.1080/07391102.2023.2297007] [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: 05/02/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1-S6) displayed a glide score (G-score) within the range of -9.013 to -7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTSE.coli is a common cause of urinary tract infections.E.coli MurD enzyme is a suitable target for drug development.Novel inhibitors against E.coli MurD enzyme were identified.Molecular dynamics studies identified in-silico potential of identified compound.ADMET predictions and Lipinski's rule of five studies showed promising results.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Vinita Gaur
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' University, Udaipur, Rajasthan, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Debabrata Chowdhury
- School of Medicine - Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Joginder Singh
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Surojit Bera
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| |
Collapse
|
6
|
Berdzik N, Koenig H, Mrówczyńska L, Nowak D, Jasiewicz B, Pospieszny T. Synthesis and Hemolytic Activity of Bile Acid-Indole Bioconjugates Linked by Triazole. J Org Chem 2023; 88:16719-16734. [PMID: 38059841 PMCID: PMC10729025 DOI: 10.1021/acs.joc.3c00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
New formyl and acetyl derivatives of bile acid propargyl esters and their bioconjugates with modified gramine molecules have been obtained using the click chemistry method to study their hemolytic potency. The structures of all compounds were confirmed by spectral (1H- and 13C NMR and FT-IR) analysis and mass spectrometry (ESI-MS) as well as PM5 semiempirical methods. According to the results, the structural modification of formyl and acetyl bile acid derivatives, leading to the formation of new propargyl esters and indole bioconjugates, reduces their hemolytic activity. According to molecular docking studies, the tested ligands are highly likely to exhibit a similar affinity, as native ligands, for the active sites of specific protein domains (PDB IDs: 2Q85 and 5V5Z). The obtained results may be helpful for the development of selective bile acid bioconjugates as effective antibacterial, antifungal, or antioxidant agents.
Collapse
Affiliation(s)
- Natalia Berdzik
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Hanna Koenig
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Lucyna Mrówczyńska
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Damian Nowak
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznań, Poland
| | - Beata Jasiewicz
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Tomasz Pospieszny
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| |
Collapse
|
7
|
Hervin V, Roy V, Agrofoglio LA. Antibiotics and Antibiotic Resistance-Mur Ligases as an Antibacterial Target. Molecules 2023; 28:8076. [PMID: 38138566 PMCID: PMC10745416 DOI: 10.3390/molecules28248076] [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: 07/29/2023] [Revised: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The emergence of Multidrug Resistance (MDR) strains of bacteria has accelerated the search for new antibacterials. The specific bacterial peptidoglycan biosynthetic pathway represents opportunities for the development of novel antibacterial agents. Among the enzymes involved, Mur ligases, described herein, and especially the amide ligases MurC-F are key targets for the discovery of multi-inhibitors, as they share common active sites and structural features.
Collapse
Affiliation(s)
| | - Vincent Roy
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| | - Luigi A. Agrofoglio
- ICOA UMR CNRS 7311, Université d’Orléans et CNRS, Rue de Chartres, 45067 Orléans, France;
| |
Collapse
|
8
|
Hussein M, Allobawi R, Zhao J, Yu H, Neville SL, Wilksch J, Wong LJM, Baker M, McDevitt CA, Rao GG, Li J, Velkov T. Integrated Transcriptomic and Metabolomic Mapping Reveals the Mechanism of Action of Ceftazidime/Avibactam against Pan-Drug-Resistant Klebsiella pneumoniae. ACS Infect Dis 2023; 9:2409-2422. [PMID: 37878861 PMCID: PMC10714405 DOI: 10.1021/acsinfecdis.3c00264] [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: 06/05/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
Here, we employed an integrated metabolomics and transcriptomics approach to investigate the molecular mechanism(s) of action of ceftazidime/avibactam against a pan-drug-resistant K. pneumoniae clinical isolate from a patient with urinary tract infection. Ceftazidime/avibactam induced time-dependent perturbations in the metabolome and transcriptome of the bacterium, mainly at 6 h, with minimal effects at 1 and 3 h. Metabolomics analysis revealed a notable reduction in essential lipids involved in outer membrane glycerolipid biogenesis. This disruption effect extended to peptidoglycan and lipopolysaccharide biosynthetic pathways, including lipid A and O-antigen assembly. Importantly, ceftazidime/avibactam not only affected the final steps of peptidoglycan biosynthesis in the periplasm, a common mechanism of ceftazidime action, but also influenced the synthesis of lipid-linked intermediates and early stages of cytoplasmic peptidoglycan synthesis. Furthermore, ceftazidime/avibactam substantially inhibited central carbon metabolism (e.g., the pentose phosphate pathway and tricarboxylic acid cycle). Consistently, the dysregulation of genes governing these metabolic pathways aligned with the metabolomics findings. Certain metabolomics and transcriptomics signatures associated with ceftazidime resistance were also perturbed. Consistent with the primary target of antibiotic activity, biochemical assays also confirmed the direct impact of ceftazidime/avibactam on peptidoglycan production. This study explored the intricate interactions of ceftazidime and avibactam within bacterial cells, including their impact on cell envelope biogenesis and central carbon metabolism. Our findings revealed the complexities of how ceftazidime/avibactam operates, such as hindering peptidoglycan formation in different cellular compartments. In summary, this study confirms the existing hypotheses about the antibacterial and resistance mechanisms of ceftazidime/avibactam while uncovering novel insights, including its impact on lipopolysaccharide formation.
Collapse
Affiliation(s)
- Maytham Hussein
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Rafah Allobawi
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jinxin Zhao
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Heidi Yu
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie L. Neville
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan Wilksch
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Labell J. M. Wong
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mark Baker
- Discipline
of Biological Sciences, Priority Research Centre in Reproductive Biology,
Faculty of Science and IT, University of
Newcastle, University
Drive, Callaghan, NSW 2308, Australia
| | - Christopher A. McDevitt
- Department
of Microbiology and Immunology, The Peter Doherty Institute for Infection
and Immunity, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Gauri G. Rao
- Division
of Pharmacotherapy and Experimental Therapeutics, Eshelman School
of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7355, United
States
| | - Jian Li
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Velkov
- Monash
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
9
|
Guo J, Xie Z, Ruan W, Tang Q, Qiao D, Zhu W. Thiazole-based analogues as potential antibacterial agents against methicillin-resistant Staphylococcus aureus (MRSA) and their SAR elucidation. Eur J Med Chem 2023; 259:115689. [PMID: 37542993 DOI: 10.1016/j.ejmech.2023.115689] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
In recent years, the overuse of antibiotics has resulted in the emergence of antibiotic resistance, which is a serious global health problem. Methicillin-resistant Staphylococcus aureus (MRSA) is a common and virulent bacterium in clinical practice. Numerous researchers have focused on developing new candidate drugs that are effective, less toxic, and can overcome MRSA resistance. Thiazole derivatives have been found to exhibit antibacterial activity against drug-sensitive and drug-resistant pathogens. By hybridizing thiazole with other antibacterial pharmacophores, it is possible to obtain more effective antibacterial candidate drugs. Thiazole derivatives have shown potential in developing new drugs that can overcome drug resistance, reduce toxicity, and improve pharmacokinetic characteristics. This article reviews the recent progress of thiazole compounds as potential antibacterial compounds and examines the structure-activity relationship (SAR) in various directions. It covers articles published from 2018 to 2023, providing a comprehensive platform to plan and develop new thiazole-based small MRSA growth inhibitors with minimal side effects.
Collapse
Affiliation(s)
- Jiaojiao Guo
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Zhouling Xie
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Wei Ruan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Qidong Tang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Dan Qiao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, 330013, China.
| |
Collapse
|
10
|
Hajdaś G, Kawka A, Koenig H, Kułaga D, Sosnowska K, Mrówczyńska L, Pospieszny T. Click chemistry as a method for the synthesis of steroid bioconjugates of bile acids derivatives and sterols. Steroids 2023; 199:109282. [PMID: 37482327 DOI: 10.1016/j.steroids.2023.109282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Six steroid conjugates of bile acids and sterol derivatives have been synthesized using the click chemistry method. The azide-alkyne Huisgen cycloaddition of the propionyl ester of lithocholic, deoxycholic and cholic acid with azide derivatives of cholesterol and cholestanol gave new bile acid-sterol conjugates linked with a 1,2,3-triazole ring. Previously, sterols were converted to bromoacetate substituted derivatives by reaction with bromoacetic acid bromide in anhydrous dichloromethane. These compounds were then converted to azide derivatives using sodium azide. The propiolic esters of lithocholic, deoxycholic and cholic acids were obtained by reaction with propiolic acid in the presence of p-toluenesulfonic acid. Additionally, two of these steroids: methyl 3α-propynoyloxy-12α-acetoxy-5β-cholane-24-oate and methyl 3α-propynoyloxy-7 α,12α-diacetoxy-5β-cholane-24-oate were also obtained and characterized for the first time. All conjugates were obtained in good yields using an efficient synthesis method. The structures of all conjugates and the four substrates were confirmed by spectral (1H- and 13C NMR, FT-IR) analysis, mass spectrometry (ESI-MS), and PM5 semiempirical methods. The pharmacotherapeutic potential of the synthesized compounds was estimated based on the in silico Prediction of Activity Spectra for Substances (PASS) method. The cytotoxicity of the compounds was in vitro evaluated in a hemolytic assay using human erythrocytes as a cell model. The in silico and in vitro study results indicate that the selected compound possesses an interesting biological activity and can be considered as potential drug design agent. Additionally, molecular docking was performed for the selected conjugate.
Collapse
Affiliation(s)
- Grzegorz Hajdaś
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Anna Kawka
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Hanna Koenig
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland
| | - Damian Kułaga
- Department of Organic Chemistry and Technology, Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24 Street, 31-155 Kraków, Poland
| | - Katarzyna Sosnowska
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Lucyna Mrówczyńska
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Tomasz Pospieszny
- Department of Bioactive Products, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8 Street, 61-614 Poznań, Poland.
| |
Collapse
|
11
|
Harpring M, Cox JV. Plasticity in the cell division processes of obligate intracellular bacteria. Front Cell Infect Microbiol 2023; 13:1205488. [PMID: 37876871 PMCID: PMC10591338 DOI: 10.3389/fcimb.2023.1205488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/07/2023] [Indexed: 10/26/2023] Open
Abstract
Most bacteria divide through a highly conserved process called binary fission, in which there is symmetric growth of daughter cells and the synthesis of peptidoglycan at the mid-cell to enable cytokinesis. During this process, the parental cell replicates its chromosomal DNA and segregates replicated chromosomes into the daughter cells. The mechanisms that regulate binary fission have been extensively studied in several model organisms, including Eschericia coli, Bacillus subtilis, and Caulobacter crescentus. These analyses have revealed that a multi-protein complex called the divisome forms at the mid-cell to enable peptidoglycan synthesis and septation during division. In addition, rod-shaped bacteria form a multi-protein complex called the elongasome that drives sidewall peptidoglycan synthesis necessary for the maintenance of rod shape and the lengthening of the cell prior to division. In adapting to their intracellular niche, the obligate intracellular bacteria discussed here have eliminated one to several of the divisome gene products essential for binary fission in E. coli. In addition, genes that encode components of the elongasome, which were mostly lost as rod-shaped bacteria evolved into coccoid organisms, have been retained during the reductive evolutionary process that some coccoid obligate intracellular bacteria have undergone. Although the precise molecular mechanisms that regulate the division of obligate intracellular bacteria remain undefined, the studies summarized here indicate that obligate intracellular bacteria exhibit remarkable plasticity in their cell division processes.
Collapse
Affiliation(s)
| | - John V. Cox
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
12
|
Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023; 24:518. [PMID: 37667166 PMCID: PMC10478331 DOI: 10.1186/s12864-023-09495-y] [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: 12/14/2022] [Accepted: 06/30/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Safety of probiotic strains that are used in human and animal trials is a prerequisite. Genome based safety assessment of probiotics has gained popularity due its cost efficiency and speed, and even became a part of national regulation on foods containing probiotics in Indonesia. However, reliability of the safety assessment based only on a full genome sequence is not clear. Here, for the first time, we sequenced, assembled, and analysed the genome of the probiotic strain Lactiplantibacillus plantarum IS-10506, that was isolated from dadih, a traditional fermented buffalo milk. The strain has already been used as a probiotic for more than a decade, and in several clinical trials proven to be completely safe. METHODS The genome of the probiotic strain L. plantarum IS-10506 was sequenced using Nanopore sequencing technology, assembled, annotated and screened for potential harmful (PH) and beneficial genomic features. The presence of the PH features was assessed from general annotation, as well as with the use of specialised tools. In addition, PH regions in the genome were compared to all other probiotic and non-probiotic L. plantarum strains available in the NCBI RefSeq database. RESULTS For the first time, a high-quality complete genome of L. plantarum IS-10506 was obtained, and an extensive search for PH and a beneficial signature was performed. We discovered a number of PH features within the genome of L. plantarum IS-10506 based on the general annotation, including various antibiotic resistant genes (AMR); however, with a few exceptions, bioinformatics tools specifically developed for AMR detection did not confirm their presence. We further demonstrated the presence of the detected PH genes across multiple L. plantarum strains, including probiotics, and overall high genetic similarities between strains. CONCLUSION The genome of L. plantarum IS-10506 is predicted to have several PH features. However, the strain has been utilized as a probiotic for over a decade in several clinical trials without any adverse effects, even in immunocompromised children with HIV infection and undernourished children. This implies the presence of PH feature signatures within the probiotic genome does not necessarily indicate their manifestation during administration. Importantly, specialized tools for the search of PH features were found more robust and should be preferred over manual searches in a general annotation.
Collapse
Affiliation(s)
- Alexander Umanets
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands
| | - Ingrid S Surono
- Food Technology Department, Faculty of Engineering, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, Villafloraweg 1, Venlo, 5928 SZ, the Netherlands.
| |
Collapse
|
13
|
Cho H. Assembly of Bacterial Surface Glycopolymers as an Antibiotic Target. J Microbiol 2023; 61:359-367. [PMID: 36951963 DOI: 10.1007/s12275-023-00032-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/24/2023]
Abstract
Bacterial cells are covered with various glycopolymers such as peptidoglycan (PG), lipopolysaccharides (LPS), teichoic acids, and capsules. Among these glycopolymers, PG assembly is the target of some of our most effective antibiotics, consistent with its essentiality and uniqueness to bacterial cells. Biosynthesis of other surface glycopolymers have also been acknowledged as potential targets for developing therapies to control bacterial infections, because of their importance for bacterial survival in the host environment. Moreover, biosynthesis of most surface glycopolymers are closely related to PG assembly because the same lipid carrier is shared for glycopolymer syntheses. In this review, I provide an overview of PG assembly and antibiotics that target this pathway. Then, I discuss the implications of a common lipid carrier being used for assembly of PG and other surface glycopolymers in antibiotic development.
Collapse
Affiliation(s)
- Hongbaek Cho
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
14
|
de Oliveira Rossini N, Dos Santos Silva C, Vinicius Bertacine Dias M. The crystal structure of Mycobacterium thermoresistibile MurE ligase reveals the binding mode of the substrate m-diaminopimelate. J Struct Biol 2023; 215:107957. [PMID: 36944394 DOI: 10.1016/j.jsb.2023.107957] [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: 11/02/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
The cytoplasmatic biosynthesis of the stem peptide from the peptidoglycan in bacteria involves six steps, which have the role of three ATP-dependent Mur ligases that incorporate three consecutive amino acids to a substrate precursor. MurE is the last Mur ligase to incorporate a free amino acid. Although the structure of MurE from Mycobacterium tuberculosis (MtbMurE) was determined at 3.0Å, the binding mode of (meso-Diaminopimelate) m-DAP and the effect of substrate absence is unknown. Herein, we show the structure of MurE from M. thermoresistibile (MthMurE) in complex with ADP and m-DAP at 1.4 Å resolution. The analysis of the structure indicates key conformational changes that the substrate UDP-MurNAc-L-Ala-D-Glu (UAG) and the free amino acid m-DAP cause on the MthMurE conformation. We observed several movements of domains or loop regions that displace their position in order to perform enzymatic catalysis. Since MthMurE has a high similarity to MtbMurE, this enzyme could also guide strategies for structure-based antimicrobial discovery to fight against tuberculosis or other mycobacterial infections. Synopsis Structural characterization of Mycobacterium thermoresistibile MurE at 1.45Å resolution in complex with ADP and m-DAP shows novel conformational changes when compared to other MurE structures in complex with different ligands.
Collapse
Affiliation(s)
- Nicolas de Oliveira Rossini
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo. Av. Prof Lineu Prestes, 1374, CEP 05508-000, São Paulo, SP. Brazil
| | - Catharina Dos Santos Silva
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo. Av. Prof Lineu Prestes, 1374, CEP 05508-000, São Paulo, SP. Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo. Av. Prof Lineu Prestes, 1374, CEP 05508-000, São Paulo, SP. Brazil; Department of Chemistry. The University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
15
|
Hu J, Chen L, Li G, Pan Y, Lu Y, Chen J, Xiong W, Zeng Z. Prevalence and genetic characteristics of fosB-positive Staphylococcus aureus in duck farms in Guangdong, China in 2020. J Antimicrob Chemother 2023; 78:802-809. [PMID: 36691844 DOI: 10.1093/jac/dkad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES To investigate the epidemiology of fosB-positive Staphylococcus aureus in waterfowl farms in the Pearl River tributaries in Guangdong Province, China in 2020. METHODS A total of 63 S. aureus were recovered from 315 samples collected from six duck farms and one goose farm. PFGE, WGS and analysis were performed on 19 fosB-positive S. aureus. RESULTS The fosfomycin resistance rate of the strains was as high as 52.4% (33/63), and 30.1% (19/63) of the strains carried fosB. Resistance gene prediction results showed that duck farm environment-derived strains contained the oxazolidinone drug resistance gene optrA. All fosB-positive S. aureus were MRSA and most of them were MDR, mainly ST9-t899 and ST164-t899. PFGE showed that fosB-positive S. aureus from humans and ducks could be clustered into the same clade. In addition, core-genome SNP analysis showed that clonal transmission of S. aureus occurred between humans and water. Pan-genome analysis showed that S. aureus had an open pangenome. The fosB gene was located on 2610-2615 bp plasmids, which all contained a broad host-range plasmid replication protein family 13. Small plasmids carrying the fosB gene could be found in different multilocus STs of S. aureus. CONCLUSIONS This study indicated that duck farms in Guangdong, China could be an important reservoir of fosB-positive S. aureus. The spread of drug-resistant bacteria in waterfowl farms requires further monitoring.
Collapse
Affiliation(s)
- Jianxin Hu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Lin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Guihua Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Yixing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Jin Chen
- National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
16
|
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
|
17
|
Anti-Tuberculosis Mur Inhibitors: Structural Insights and the Way Ahead for Development of Novel Agents. Pharmaceuticals (Basel) 2023; 16:ph16030377. [PMID: 36986477 PMCID: PMC10058398 DOI: 10.3390/ph16030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Mur enzymes serve as critical molecular devices for the synthesis of UDP-MurNAc-pentapeptide, the main building block of bacterial peptidoglycan polymer. These enzymes have been extensively studied for bacterial pathogens such as Escherichia coli and Staphylococcus aureus. Various selective and mixed Mur inhibitors have been designed and synthesized in the past few years. However, this class of enzymes remains relatively unexplored for Mycobacterium tuberculosis (Mtb), and thus offers a promising approach for drug design to overcome the challenges of battling this global pandemic. This review aims to explore the potential of Mur enzymes of Mtb by systematically scrutinizing the structural aspects of various reported bacterial inhibitors and implications concerning their activity. Diverse chemical scaffolds such as thiazolidinones, pyrazole, thiazole, etc., as well as natural compounds and repurposed compounds, have been reviewed to understand their in silico interactions with the receptor or their enzyme inhibition potential. The structural diversity and wide array of substituents indicate the scope of the research into developing varied analogs and providing valuable information for the purpose of modifying reported inhibitors of other multidrug-resistant microorganisms. Therefore, this provides an opportunity to expand the arsenal against Mtb and overcome multidrug-resistant tuberculosis.
Collapse
|
18
|
Kawka A, Hajdaś G, Kułaga D, Koenig H, Kowalczyk I, Pospieszny T. Molecular structure, spectral and theoretical study of new type bile acid–sterol conjugates linked via 1,2,3-triazole ring. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
19
|
Tiwari H, Raina D, Gupta M, Barik MR, Khan IA, Khan F, Nargotra A. Identification of novel MurA inhibitors using in silico approach, their validation and elucidation of mode of inhibition. J Biomol Struct Dyn 2023; 41:457-468. [PMID: 34866550 DOI: 10.1080/07391102.2021.2007793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an important enzyme involved in the first cytosolic step of bacterial cell wall synthesis. In this study a combination of ligand based and structure based in silico virtual screening methods were utilised for screening of more than 50,000 drug-like compounds from CSIR-IIIM in-house compound library in order to identify potent inhibitors of MurA. The identified hits were validated in vitro under various incubation conditions using Malachite green phosphate assay, and two potent hits viz 3772-9534 and D396-0012 were identified. Among these hits, compound 3772-9534 showed significant changes in the activity values in different assay conditions. The MD simulation study of 3772-9534 suggested a novel binding site in MurA enzyme, independent of the two-substrate binding sites. Binding of inhibitors at the allosteric site induces conformational changes in the enzyme, which leads to inhibition of enzymatic activity. Overall, the study offers new insight for targeting MurA, which may promote the discovery of novel MurA allosteric site inhibitors.
Collapse
Affiliation(s)
- Harshita Tiwari
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Diksha Raina
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Monika Gupta
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Manas Ranjan Barik
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Inshad Ali Khan
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Department of Microbiology, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Farrah Khan
- Clinical Microbiology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Amit Nargotra
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
20
|
Shoaib M, Shehzadi I, Asif MU, Shen Y, Ni J. Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii. Front Mol Biosci 2023; 10:1183073. [PMID: 37152898 PMCID: PMC10160657 DOI: 10.3389/fmolb.2023.1183073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii infections have become a major public health concern globally. Inhibition of its essential MurF protein has been proposed as a potential target for broad-spectrum drugs. This study aimed to evaluate the potential of a novel ecological niche of 374 fungus-growing termite associated Natural Products (NPs). The molecular docking and computational pharmacokinetics screened four compounds, i.e., Termstrin B, Fridamycin A, Maduralactomycin A, and Natalenamide C, as potential compounds that have higher binding affinities and favourable protein-ligand interactions. The compound Maduralactomycin A induced more stability based on its lowest average RMSD value (2.31 Å) and low standard deviation (0.35) supported by the consistent flexibility and β-factor during the protein's time-dependent motion. While hydrogen bond analysis indicated that Termstrin B has formed the strongest intra-protein interaction, solvent accessibility was in good agreement with Maduralactomycin A compactness. Maduralactomycin A has the strongest binding energy among all the compounds (-348.48 kcal/mol) followed by Termstrin B (-321.19 kcal/mol). Since these findings suggest Maduralactomycin A and Termstrin B as promising candidates for inhibition of MurF protein, the favourable binding energies of Maduralactomycin A make it a more important compound to warrant further investigation. However, experimental validation using animal models and clinical trials is recommended before reaching any final conclusions.
Collapse
Affiliation(s)
- Muhammad Shoaib
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | | | | | - Yulong Shen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
| |
Collapse
|
21
|
Nirwan S, Chahal V, Kakkar R. A comparative study of different docking methodologies to assess the protein-ligand interaction for the E. coli MurB enzyme. J Biomol Struct Dyn 2022; 40:11229-11238. [PMID: 34323658 DOI: 10.1080/07391102.2021.1957019] [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] [Indexed: 10/20/2022]
Abstract
We have investigated the active site of E. coli MurB using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The docking of three novel series of 4-thiazolidinone derivatives has been performed using two methods: rigid docking and flexible docking (Induced Fit Docking: IFD). The results have been compared to understand the conformational aspects of the enzyme. The docking results from rigid docking show that the ligands with highly negative ΔGbind have poor docking scores. In addition, the value of the regression coefficient (R) obtained on correlating the ΔGbind and the experimental pMIC values is insignificant. On keeping the protein flexible, there is a remarkable improvement in both the docking score and ΔGbind, along with a good value of R (0.64). Two important residues, Tyr254 and Try190 are found to be highly displaced during the flexible docking and hence their role in effective ligand binding has been confirmed. Thus, comparing the two methodologies, IFD has emerged as the more appropriate one for studying the E. coli MurB enzyme. To further substantiate the findings, MD studies over a time period of 20 ns have been performed on the IFD-LIII j and Rigid/XP-LIII j complexes and the results shows the former complex to be more stable, with lower average RMSD and higher average ΔGbind.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sonam Nirwan
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Varun Chahal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| |
Collapse
|
22
|
Iram D, Kindarle UA, Sansi MS, Meena S, Puniya AK, Vij S. Peptidomics-based identification of an antimicrobial peptide derived from goat milk fermented by Lactobacillus rhamnosus (C25). J Food Biochem 2022; 46:e14450. [PMID: 36226982 DOI: 10.1111/jfbc.14450] [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: 06/17/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 01/14/2023]
Abstract
Antimicrobial peptides (AMPs) are emerging as promising novel drug applicants. In the present study, goat milk was fermented using Lactobacillus rhamnosus C25 to generate bioactive peptides (BAPs). The peptide fractions generated were separated using ultrafiltration membranes with molecular weight cut-offs of 3, 5, and 10 kDa, and their antimicrobial activity toward Gram-positive and Gram-negative bacteria was investigated. Isolated AMPs were characterized using RP-HPLC and identified by LC-MS/MS. A total of 569 sequences of peptides were identified by mass spectrometry. Out of the 569, 36 were predicted as AMPs, 21 were predicted as cationic, and out of 21, 6 AMPs were helical peptides. In silico analysis indicated that the majority of peptides were antimicrobial and cationic in nature, an important factor for peptide interaction with the negative charge membrane of bacteria. The results showed that the peptides of <5 kDa exhibited maximum antibacterial activity against E. faecalis, E. coli, and S. typhi. Further, molecular docking was used to evaluate the potent MurD ligase inhibitors. On the basis of ligand binding energy, six predicted AMPs were selected and then analyzed by AutoDock tools. Among the six AMPs, peptides IGHFKLIFSLLRV (-7.5 kcal/mol) and KSFCPAPVAPPPPT (-7.6 kcal/mol), were predicted as a high-potent antimicrobial. Based on these findings, in silico investigations reveal that proteins of goat milk are a potential source of AMPs. This is for the first time that the antimicrobial peptides produced by Lactobacillus rhamnosus (C25) fermentation of goat milk have been identified via LC-MS/MS and predicted as AMPs, cationic charges, helical structure in nature, and potent MurD ligase inhibitors. These peptides can be synthesized and improved for use as antimicrobial agents. PRACTICAL APPLICATIONS: Goat milk is considered a high-quality source of milk protein. According to this study, goat milk protein is a potential source of AMPs, Fermentation can yield goat milk-derived peptides with a broad antibacterial activity spectrum at a low cost. The approach described here could be beneficial in that the significant AMPs can be synthesized and used in the pharmaceutical and food industries.
Collapse
Affiliation(s)
- Daraksha Iram
- Antimicrobial Peptides, Biofunctional Probiotics & Peptidomics Laboratory, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Uday Arun Kindarle
- Antimicrobial Peptides, Biofunctional Probiotics & Peptidomics Laboratory, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Manish Singh Sansi
- Biofunctional Peptidomics & Metabolic Syndrome Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Sunita Meena
- Biofunctional Peptidomics & Metabolic Syndrome Laboratory, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Anil Kumar Puniya
- Anaerobic Microbial Fermentation Laboratory, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Shilpa Vij
- Antimicrobial Peptides, Biofunctional Probiotics & Peptidomics Laboratory, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| |
Collapse
|
23
|
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
|
24
|
Gaur V, Bera S. Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100137. [PMID: 36568273 PMCID: PMC9780078 DOI: 10.1016/j.crphar.2022.100137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/09/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The rapid emergence of antibiotic resistance among various bacterial pathogens has been one of the major concerns of health organizations across the world. In this context, for the development of novel inhibitors against antibiotic-resistant bacterial pathogens, UDP-N-Acetylmuramoyl-L-Alanine-D-Glutamate Ligase (MurD) enzyme represents one of the most apposite targets. Body The present review focuses on updated advancements on MurD-targeted inhibitors in recent years along with genetic regulation, structural and functional characteristics of the MurD enzyme from various bacterial pathogens. A concise account of various crystal structures of MurD enzyme, submitted into Protein Data Bank is also discussed. Discussion MurD, an ATP dependent cytoplasmic enzyme is an important target for drug discovery. The genetic organization of MurD enzyme is well elucidated and many crystal structures of MurD enzyme are submitted into Protein Data bank. Various inhibitors against MurD enzyme have been developed so far with an increase in the use of in-silico methods in the recent past. But cell permeability barriers and conformational changes of MurD enzyme during catalytic reaction need to be addressed for effective drug development. So, a combination of in-silico methods along with experimental work is proposed to counter the catalytic machinery of MurD enzyme.
Collapse
Key Words
- Antibiotic resistance
- HTS, High Throughput Screening
- In-silico
- MD, Molecular Dynamics
- MIC, Minimum Inhibitory Concentration
- MurD
- PDB, Protein Data Bank
- PEP, Phosphoenolpyruvate
- PG, Peptidoglycan
- Peptidoglycan
- SAR, Structural Activity Relationship
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-Mpp, UDP-N-acetylmuramylpentapeptide
- UDP-MurNAc, UDP-N-acetylmuramicacid
- UMA, UDP N-acetylmuramoyl-l-alanine
- UNAG, UDP- N-acetylglucosamine
Collapse
|
25
|
Memili A, Kutchy N, Braimah OA, Morenikeji OB. Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci. Vet World 2022; 15:2407-2413. [DOI: 10.14202/vetworld.2022.2407-2413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis.
Materials and Methods: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro.
Results: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium.
Conclusion: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.
Collapse
Affiliation(s)
- Aylin Memili
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Naseer Kutchy
- Department of Anatomy, Physiology, Pharmacology, School of Veterinary Medicine, St. George's University, Grenada, West Indies
| | - Olubumi A. Braimah
- Division of Biological Health Sciences, University of Pittsburgh, Bradford, Pennsylvania, United States
| | - Olanrewaju B. Morenikeji
- Division of Biological Health Sciences, University of Pittsburgh, Bradford, Pennsylvania, United States
| |
Collapse
|
26
|
Zhou J, Cai Y, Liu Y, An H, Deng K, Ashraf MA, Zou L, Wang J. Breaking down the cell wall: Still an attractive antibacterial strategy. Front Microbiol 2022; 13:952633. [PMID: 36212892 PMCID: PMC9544107 DOI: 10.3389/fmicb.2022.952633] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
Collapse
Affiliation(s)
- Jingxuan Zhou
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yi Cai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Ying Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Kaihong Deng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Muhammad Awais Ashraf
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- *Correspondence: Jun Wang,
| |
Collapse
|
27
|
Subedi BP, Schofield LR, Carbone V, Wolf M, Martin WF, Ronimus RS, Sutherland-Smith AJ. Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178458 DOI: 10.1099/mic.0.001235] [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
Archaea have diverse cell wall types, yet none are identical to bacterial peptidoglycan (murein). Methanogens Methanobacteria and Methanopyrus possess cell walls of pseudomurein, a structural analogue of murein. Pseudomurein differs from murein in containing the unique archaeal sugar N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, β-1,3 glycosidic bonds in place of β-1,4 bonds and only l-amino acids in the peptide cross-links. We have determined crystal structures of methanogen pseudomurein peptide ligases (termed pMurE) from Methanothermus fervidus (Mfer762) and Methanothermobacter thermautotrophicus (Mth734) that are structurally most closely related to bacterial MurE peptide ligases. The homology of the archaeal pMurE and bacterial MurE enzymes is clear both in the overall structure and at the level of each of the three domains. In addition, we identified two UDP-binding sites in Mfer762 pMurE, one at the exterior surface of the interface of the N-terminal and middle domains, and a second site at an inner surface continuous with the highly conserved interface of the three domains. Residues involved in ATP binding in MurE are conserved in pMurE, suggesting that a similar ATP-binding pocket is present at the interface of the middle and the C-terminal domains of pMurE. The presence of pMurE ligases in members of the Methanobacteriales and Methanopyrales, that are structurally related to bacterial MurE ligases, supports the idea that the biosynthetic origins of archaeal pseudomurein and bacterial peptidoglycan cell walls are evolutionarily related.
Collapse
Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand.,Present address: Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Linley R Schofield
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Vincenzo Carbone
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Maximilian Wolf
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,Present address: Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ron S Ronimus
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | | |
Collapse
|
28
|
Selected heterocycles for the development of pyrophosphate mimics. Future Med Chem 2022; 14:1219-1222. [PMID: 35861044 DOI: 10.4155/fmc-2022-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
29
|
Raina D, Khan FG, Tiwari H, Sangwan PL, Nargotra A, Kumar V, Khan IA, Saran S. Boswellic acids, as novel inhibitor targeting peptidoglycan biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) in Escherichia coli. Arch Microbiol 2022; 204:472. [PMID: 35819545 DOI: 10.1007/s00203-022-03066-7] [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: 04/05/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an essential cytosolic enzyme in the biosynthesis of peptidoglycan. It becomes a potential bacterial target for screening promising antibacterial compounds as it is associated with the early phases of peptidoglycan production. MurA enzyme is conserved and necessary for bacterial viability with no mammalian homolog, which is a well-proven therapeutic research target. The present study reports the natural compounds from Boswellia serrata targeting the MurA enzyme. The identified inhibitors against MurA Escherichia coli (E. coli): β-boswellic acid (IC50 33.65 µM), Acetyl-β-boswellic acid (IC50 30.17 µM), and Acetyl-11-keto-β-boswellic acid (IC50 37.67 µM). Inhibitors showed a fourfold decrease in IC50 values on pre-incubation with substrate-UDP-N-acetyl-glucosamine (UDP-GlcNAc). Mode-of-inhibition studies revealed their uncompetitive nature with both the substrates. Although these boswellic acids have been explored for their pharmacological potential, this is the first study reporting these compounds' E. coli MurA inhibiting potential.
Collapse
Affiliation(s)
- Diksha Raina
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Fermentation 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
| | - Farrah Gul Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Harshita Tiwari
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Payare L Sangwan
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Amit Nargotra
- Discovery Informatics, NPMC Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002, India
| | - Vinod Kumar
- Fermentation 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
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India.
| | - Saurabh Saran
- Fermentation 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
|
30
|
Zheng Y, Zhang J, Meisner J, Li W, Luo Y, Wei F, Wen L. Cofactor-Driven Cascade Reactions Enable the Efficient Preparation of Sugar Nucleotides. Angew Chem Int Ed Engl 2022; 61:e202115696. [PMID: 35212445 DOI: 10.1002/anie.202115696] [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: 11/17/2021] [Indexed: 12/14/2022]
Abstract
Glycosylation is catalyzed by glycosyltransferases using sugar nucleotides or occasionally lipid-linked phosphosugars as donors. However, only very few common sugar nucleotides that occur in humans can be obtained readily, while the majority of sugar nucleotides that exist in bacteria, plants, archaea, or viruses cannot be synthesized in sufficient quantities by either enzymatic or chemical synthesis. The limited availability of such rare sugar nucleotides is one of the major obstacles that has greatly hampered progress in glycoscience. Herein we describe a general cofactor-driven cascade conversion strategy for the efficient synthesis of sugar nucleotides. The described strategy allows the large-scale preparation of rare sugar nucleotides from common sugars in high yields and without the need for tedious purification processes.
Collapse
Affiliation(s)
- Yuan Zheng
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiabin Zhang
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China
| | | | - Wanjin Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yawen Luo
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangyu Wei
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
31
|
Heliawati L, Lestari S, Hasanah U, Ajiati D, Kurnia D. Phytochemical Profile of Antibacterial Agents from Red Betel Leaf (Piper crocatum Ruiz and Pav) against Bacteria in Dental Caries. Molecules 2022; 27:molecules27092861. [PMID: 35566225 PMCID: PMC9101570 DOI: 10.3390/molecules27092861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 12/23/2022] Open
Abstract
Based on data from The Global Burden of Disease Study in 2016, dental and oral health problems, especially dental caries, are a disease experienced by almost half of the world’s population (3.58 billion people). One of the main causes of dental caries is the pathogenesis of Streptococcus mutans. Prevention can be achieved by controlling S. mutans using an antibacterial agent. The most commonly used antibacterial for the treatment of dental caries is chlorhexidine. However, long-term use of chlorhexidine has been reported to cause resistance and some side effects. Therefore, the discovery of a natural antibacterial agent is an urgent need. A natural antibacterial agent that can be used are herbal medicines derived from medicinal plants. Piper crocatum Ruiz and Pav has the potential to be used as a natural antibacterial agent for treating dental and oral health problems. Several studies reported that the leaves of P. crocatum Ruiz and Pav contain secondary metabolites such as essential oils, flavonoids, alkaloids, terpenoids, tannins, and phenolic compounds that are active against S. mutans. This review summarizes some information about P. crocatum Ruiz and Pav, various isolation methods, bioactivity, S. mutans bacteria that cause dental caries, biofilm formation mechanism, antibacterial properties, and the antibacterial mechanism of secondary metabolites in P. crocatum Ruiz and Pav.
Collapse
Affiliation(s)
- Leny Heliawati
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
- Correspondence: ; Tel.: +62-8521-615-0330
| | - Seftiana Lestari
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
| | - Uswatun Hasanah
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
| | - Dwipa Ajiati
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia; (D.A.); (D.K.)
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia; (D.A.); (D.K.)
| |
Collapse
|
32
|
Kumar S, Mollo A, Kahne D, Ruiz N. The Bacterial Cell Wall: From Lipid II Flipping to Polymerization. Chem Rev 2022; 122:8884-8910. [PMID: 35274942 PMCID: PMC9098691 DOI: 10.1021/acs.chemrev.1c00773] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The peptidoglycan (PG) cell wall is an extra-cytoplasmic glycopeptide polymeric structure that protects bacteria from osmotic lysis and determines cellular shape. Since the cell wall surrounds the cytoplasmic membrane, bacteria must add new material to the PG matrix during cell elongation and division. The lipid-linked precursor for PG biogenesis, Lipid II, is synthesized in the inner leaflet of the cytoplasmic membrane and is subsequently translocated across the bilayer so that the PG building block can be polymerized and cross-linked by complex multiprotein machines. This review focuses on major discoveries that have significantly changed our understanding of PG biogenesis in the past decade. In particular, we highlight progress made toward understanding the translocation of Lipid II across the cytoplasmic membrane by the MurJ flippase, as well as the recent discovery of a novel class of PG polymerases, the SEDS (shape, elongation, division, and sporulation) glycosyltransferases RodA and FtsW. Since PG biogenesis is an effective target of antibiotics, these recent developments may lead to the discovery of much-needed new classes of antibiotics to fight bacterial resistance.
Collapse
Affiliation(s)
- Sujeet Kumar
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aurelio Mollo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
33
|
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
|
34
|
Wen L, Zheng Y, Zhang J, Meisner J, Li W, Luo Y, Wei F. Cofactor‐Driven Cascade Reactions Enable the Efficient Preparation of Sugar Nucleotides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Liuqing Wen
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Chemistry 501 Haike Road 30303 shanghai CHINA
| | - Yuan Zheng
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Carbohydrate-based drug research center CHINA
| | - Jiabinq Zhang
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Carbohydrate-based drug research center CHINA
| | | | - Wanjin Li
- Shanghai Institute of Materia Medica Chinese Academy of Sciences carbohydrate-based drug research center CHINA
| | - Yawen Luo
- Shanghai Institute of Materia Medica Chinese Academy of Sciences cArbohydrate-based drug research center CHINA
| | - Fangyu Wei
- Shanghai Institute of Materia Medica Chinese Academy of Sciences carbohydrate-based drug research center CHINA
| |
Collapse
|
35
|
Abstract
Biosynthesis of many important polysaccharides (including peptidoglycan, lipopolysaccharide, and N-linked glycans) necessitates the transport of lipid-linked oligosaccharides (LLO) across membranes from their cytosolic site of synthesis to their sites of utilization. Much of our current understanding of LLO transport comes from genetic, biochemical, and structural studies of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily protein MurJ, which flips the peptidoglycan precursor lipid II. MurJ plays a pivotal role in bacterial cell wall synthesis and is an emerging antibiotic target. Here, we review the mechanism of LLO flipping by MurJ, including the structural basis for lipid II flipping and ion coupling. We then discuss inhibition of MurJ by antibacterials, including humimycins and the phage M lysis protein, as well as how studies on MurJ could provide insight into other flippases, both within and beyond the MOP superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Alvin C Y Kuk
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA; .,Current affiliation: Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA;
| |
Collapse
|
36
|
Golla VK, Piselli C, Kleinekathöfer U, Benz R. Permeation of Fosfomycin through the Phosphate-Specific Channels OprP and OprO of Pseudomonas aeruginosa. J Phys Chem B 2022; 126:1388-1403. [PMID: 35138863 DOI: 10.1021/acs.jpcb.1c08696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen responsible for many nosocomial infections. It is quite resistant to various antibiotics, caused by the absence of general diffusion pores in the outer membrane. Instead, it contains many substrate-specific channels. Among them are the two phosphate- and pyrophosphate-specific porins OprP and OprO. Phosphonic acid antibiotics such as fosfomycin and fosmidomycin seem to be good candidates for using these channels to enter P. aeruginosa bacteria. Here, we investigated the permeation of fosfomycin through OprP and OprO using electrophysiology and molecular dynamics (MD) simulations. The results were compared to those of the fosmidomycin translocation, for which additional MD simulations were performed. In the electrophysiological approach, we noticed a higher binding affinity of fosfomycin than of fosmidomycin to OprP and OprO. In MD simulations, the ladder of arginine residues and the cluster of lysine residues play an important role in the permeation of fosfomycin through the OprP and OprO channels. Molecular details on the permeation of fosfomycin through OprP and OprO channels were derived from MD simulations and compared to those of fosmidomycin translocation. In summary, this study demonstrates that the selectivity of membrane channels can be employed to improve the permeation of antibiotics into Gram-negative bacteria and especially into resistant P. aeruginosa strains.
Collapse
Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| |
Collapse
|
37
|
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: 32] [Impact Index Per Article: 16.0] [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
|
38
|
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: 2] [Impact Index Per Article: 1.0] [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
|
39
|
Azam MA, Singh A. Molecular insight into the binding mode of thieno[3,2-c]pyrazol-3-ols with Streptococcus pneumoniae MurF enzyme by combined molecular modeling approach. Struct Chem 2022. [DOI: 10.1007/s11224-021-01866-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
40
|
Privalsky TM, Soohoo AM, Wang J, Walsh CT, Wright GD, Gordon EM, Gray NS, Khosla C. Prospects for Antibacterial Discovery and Development. J Am Chem Soc 2021; 143:21127-21142. [PMID: 34860516 PMCID: PMC8855840 DOI: 10.1021/jacs.1c10200] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rising prevalence of multidrug-resistant bacteria is an urgent health crisis that can only be countered through renewed investment in the discovery and development of antibiotics. There is no panacea for the antibacterial resistance crisis; instead, a multifaceted approach is called for. In this Perspective we make the case that, in the face of evolving clinical needs and enabling technologies, numerous validated antibacterial targets and associated lead molecules deserve a second look. At the same time, many worthy targets lack good leads despite harboring druggable active sites. Creative and inspired techniques buoy discovery efforts; while soil screening efforts frequently lead to antibiotic rediscovery, researchers have found success searching for new antibiotic leads by studying underexplored ecological niches or by leveraging the abundance of available data from genome mining efforts. The judicious use of "polypharmacology" (i.e., the ability of a drug to alter the activities of multiple targets) can also provide new opportunities, as can the continued search for inhibitors of resistance enzymes with the capacity to breathe new life into old antibiotics. We conclude by highlighting available pharmacoeconomic models for antibacterial discovery and development while making the case for new ones.
Collapse
Affiliation(s)
- Thomas M. Privalsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Alexander M. Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 United States
| | - Christopher T. Walsh
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric M. Gordon
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Nathanael S. Gray
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Corresponding Author: Correspondence to
| |
Collapse
|
41
|
Nowak MG, Skwarecki AS, Milewska MJ. Amino Acid Based Antimicrobial Agents - Synthesis and Properties. ChemMedChem 2021; 16:3513-3544. [PMID: 34596961 PMCID: PMC9293202 DOI: 10.1002/cmdc.202100503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/02/2021] [Indexed: 12/20/2022]
Abstract
Structures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are effective enzyme inhibitors, as structural mimics of tetrahedral transition state intermediates. Synthesis of amino acid antimicrobials is a particular challenge, especially in terms of the need for enantioselective methods, including the asymmetric synthesis. All these issues are addressed in this review, summing up the current state‐of‐the‐art and presenting perspectives fur further progress.
Collapse
Affiliation(s)
- Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| |
Collapse
|
42
|
Zheng X, Zheng T, Liao Y, Luo L. Identification of Potential Inhibitors of MurD Enzyme of Staphylococcus aureus from a Marine Natural Product Library. Molecules 2021; 26:molecules26216426. [PMID: 34770835 PMCID: PMC8587310 DOI: 10.3390/molecules26216426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that can cause fatal bacterial infections. MurD catalyzes the formation of peptide bond between UDP-N-acetylehyl-l-alanine and d-glutamic acid, which plays an important role in the synthesis of peptidoglycan and the formation of cell wall by S. aureus. Because S. aureus is resistant to most existing antibiotics, it is necessary to develop new inhibitors. In this study, Schrodinger 11.5 Prime homology modeling was selected to prepare the protein model of MurD enzyme, and its structure was optimized. We used a virtual screening program and similarity screening to screen 47163 compounds from three marine natural product libraries to explore new inhibitors of S. aureus. ADME provides analysis of the physicochemical properties of the best performing compounds during the screening process. To determine the stability of the docking effect, a 100 ns molecular dynamics was performed to verify how tightly the compound was bound to the protein. By docking analysis and molecular dynamics analysis, both 46604 and 46608 have strong interaction with the docking pocket, have good pharmacological properties, and maintain stable conformation with the target protein, so they have a chance to become drugs for S. aureus. Through virtual screening, similarity screening, ADME study and molecular dynamics simulation, 46604 and 46608 were selected as potential drug candidates for S. aureus.
Collapse
Affiliation(s)
- Xiaoqi Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Tongyu Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524023, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
- Correspondence:
| |
Collapse
|
43
|
Canarini A, Schmidt H, Fuchslueger L, Martin V, Herbold CW, Zezula D, Gündler P, Hasibeder R, Jecmenica M, Bahn M, Richter A. Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community. Nat Commun 2021; 12:5308. [PMID: 34489463 PMCID: PMC8421443 DOI: 10.1038/s41467-021-25675-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events. Legacies of past ecological disturbances are expected but challenging to demonstrate. Here the authors report a 10-year field experiment in a mountain grassland that shows ecological memory of soil microbial community and functioning in response to recurrent drought.
Collapse
Affiliation(s)
- Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Victoria Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - David Zezula
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Philipp Gündler
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Roland Hasibeder
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Marina Jecmenica
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| |
Collapse
|
44
|
El Khalfi B, Addoum B, Harrati S, Elmakssoudi A, Soukri A. Synthesis, in silico studies and antibacterial assessment of α-amino phosphonates derivatives. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.03.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The widespread of multi-resistant strains due to the lack of specific treatment and the propagation of infectious diseases requires all resources to remedy this scourge. This study is therefore aimed to assess the antibacterial activity of four synthetic α-Aminophosphonate 4(a-d). Methods: Firstly, α-Aminophosphonate has been synthesized and characterized, then molecular docking of these compounds 4(a-d) into the active binding site of Escherichia coli MurB enzyme (PDB Id: 1MBT) was performed to gain a comprehensive understanding of their biological activity. These compounds have been subjected to in vitro antibacterial screening against three multi-resistant strains E. coli, S. aureus, and L. monocytogenes. These compounds showed crucial antibacterial behavior against all studied strains. Thus, their docking estimation supported the in vitro results and showed that the 4c derivative has considerable binding energy towards the active site of Escherichia coli MurB. These findings provide critical information for the exploration of α-amino phosphonates as novel antibacterial agents.
Collapse
Affiliation(s)
- Bouchra El Khalfi
- Laboratory of Physiopathology, Genetics, Molecular and Biotechnology (PGMB), Department of Biology, Faculty of Sciences Aïn Chock, Research Center of Health and Biotechnology, Hassan II University of Casablanca, B.P 5366 Maarif, Casablanca, Morocco
| | - Boutaina Addoum
- Laboratory of Physiopathology, Genetics, Molecular and Biotechnology (PGMB), Department of Biology, Faculty of Sciences Aïn Chock, Research Center of Health and Biotechnology, Hassan II University of Casablanca, B.P 5366 Maarif, Casablanca, Morocco
| | - Suhayla Harrati
- Laboratory of Physiopathology, Genetics, Molecular and Biotechnology (PGMB), Department of Biology, Faculty of Sciences Aïn Chock, Research Center of Health and Biotechnology, Hassan II University of Casablanca, B.P 5366 Maarif, Casablanca, Morocco
| | - Abdelhakim Elmakssoudi
- Laboratory of Organic Synthesis, Extraction, and Valorization, Department of Chemistry, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, B.P 5366 Maarif, Casablanca, Morocco
| | - Abdelaziz Soukri
- Laboratory of Physiopathology, Genetics, Molecular and Biotechnology (PGMB), Department of Biology, Faculty of Sciences Aïn Chock, Research Center of Health and Biotechnology, Hassan II University of Casablanca, B.P 5366 Maarif, Casablanca, Morocco
| |
Collapse
|
45
|
Ogasawara Y, Dairi T. Discovery of an alternative pathway of peptidoglycan biosynthesis: A new target for pathway specific inhibitors. J Ind Microbiol Biotechnol 2021; 48:6296644. [PMID: 34114638 PMCID: PMC8788868 DOI: 10.1093/jimb/kuab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022]
Abstract
Peptidoglycan in bacterial cell walls is a biopolymer consisting of sugars and amino acids and plays important role in maintaining cell integrity from the environment. Its biosynthesis is a major target for antibiotics and the genes and enzymes involved in the biosynthetic pathway have been well studied. However, we recently identified an alternative pathway in the early stage of peptidoglycan biosynthesis in Xanthomonas oryzae, a plant pathogen causing bacterial blight disease of rice. The distribution of the alternative pathway is limited to relatively few bacterial genera that contain many pathogenic species, including Xylella and Stenotrophomonas, besides Xanthomonas. Thus, the alternative pathway is an attractive target for the development of narrow spectrum antibiotics specific to pathogens. In this minireview, we summarize the discovery of the alternative pathway and identification of its specific inhibitors.
Collapse
Affiliation(s)
- Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13 & W8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13 & W8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| |
Collapse
|
46
|
In Silico Molecular Analysis and Docking of Potent Antimicrobial Peptides Against MurE Enzyme of Methicillin Resistant Staphylococcus Aureus. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
47
|
Boulhissa I, Chikhi A, Bensegueni A, Ghattas MA, Mokrani EH, Alrawashdeh S, Obaid DEE. Investigation of New Inhibitors of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) by Virtual Screening with Antibacterial Assessment. Curr Comput Aided Drug Des 2021; 17:214-224. [PMID: 32053077 DOI: 10.2174/1573409916666200213124929] [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] [Received: 10/11/2019] [Revised: 01/02/2020] [Accepted: 01/13/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Considering the interesting role in the peptidoglycan biosynthesis pathway, the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase is an attractive target to develop new antibacterial agents. It catalyzes the first key step of this pathway and its inhibition leads to bacterial cell death. Fosfomycin is known as the natural inhibitor of MurA. OBJECTIVE The study aimed to introduce new inhibitors of MurA by virtual screening of different chemical compounds libraries, and test the best scored "virtual hits" against three pathogenic bacteria: Escherichia coli, Bacillus subtilis and Staphylococcus aureus. METHODS A virtual screening of the structural analogues of fosfomycin downloaded from the Pub- Chem database was performed. Moreover, French National Chemical Library and ZINC database were also utilized to identify new structures different from fosfomycin. FlexX was the software used for this study. The antibacterial testing was divided into two methods: disk diffusion and broth dilution. RESULTS A set of virtual hits was found to have better energy score than that of fosfomycin, seven of them were tested in vitro. In addition, the disk diffusion method explored four compounds that exhibited antibacterial activity: CID-21680357 (fosfomycin analogue), AB-00005001, ZINC04658565, and ZINC901335. The testing was continued by broth dilution method for both compounds CID-21680357 and ZINC901335 to determine their minimum inhibitory concentrations, and ZINC901335 had the best value with 457μg/ml against Staphylococcus aureus. CONCLUSION Four compounds were found and proven in silico and in vitro to have antibacterial activity, namely CID-21680357, AB-00005001, ZINC04658565, and ZINC901335.
Collapse
Affiliation(s)
- Ilham Boulhissa
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
| | - El H Mokrani
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, Algeria
| | - Sara Alrawashdeh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
| | - Dana E E Obaid
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, United Arab Emirates
| |
Collapse
|
48
|
Screening of compound library identifies novel inhibitors against the MurA enzyme of Escherichia coli. Appl Microbiol Biotechnol 2021; 105:3611-3623. [PMID: 33860835 DOI: 10.1007/s00253-021-11272-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 11/27/2022]
Abstract
Bacterial cell has always been an attractive target for anti-infective drug discovery. MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) enzyme of Escherichia coli (E.coli) is crucial for peptidoglycan biosynthetic pathway, as it is involved in the early stages of bacterial cell wall biosynthesis. In the present study we aim to identify novel chemical structures targeting the MurA enzyme. For screening purpose, we used in silico approach (pharmacophore based strategy) for 52,026 library compounds (Chembridge, Chemdiv and in house synthetics) which resulted in identification of 50 compounds. These compounds were screened in vitro against MurA enzyme and release of inorganic phosphate (Pi) was estimated. Two compounds (IN00152 and IN00156) were found to inhibit MurA enzyme > 70% in primary screening and IC50 of 14.03 to 32.30 μM respectively. These two hits were further evaluated for their mode of inhibition studies and whole-cell activity where we observed 2-4 folds increase in activity in presence of Permeabilizer EDTA (Ethylenediaminetetraacetic acid). Combination studies were also performed with known antibiotics in presence of EDTA. Hits are reported for the first time against this target and our report also support the use of OM permeabilizer in combination with antibacterial compounds to address the permeability and efficacy issue. These lead hits can be further optimized for drug discovery. KEY POINTS: • Emerging Gram negative resistant strains is a matter of concern. • Need for new screening strategies to cope with drying up antibiotics pipeline. • Outer membrane permeabilizers could be useful to improve potency of molecules to reach its target.
Collapse
|
49
|
Kumari M, Subbarao N. Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening. J Biomol Struct Dyn 2021; 40:8185-8196. [PMID: 33826470 DOI: 10.1080/07391102.2021.1908913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current therapeutic strategies for several diseases, including Mycobacterium tuberculosis infection, have evolved from an initial single-target treatment to a multitarget one. A multitarget antitubercular drugs targeting different mycobacterial proteins are more effective at suppressing bacterial growth. In this study, a high throughput virtual screening was performed to identify hits to the potential antitubercular multitarget: murA, murB, murC, murD, murE, murF, murG and murI from M. tuberculosis that is involved in peptidoglycan biosynthesis. In the virtual screening, we were docked 56,400 compounds of the ChEMBL antimycobacterial library and re-scored and identified the top 10 ranked compounds as antitubercular drug candidates. Further, the best common docked complex CHEMBL446262 was subjected to molecular dynamics simulation to understand the molecule's stability in the presence of an active site environment. After that, we have calculated binding free energy the top-ranked docked complexes using the MM/PBSA method. These ligands exhibited the highest binding affinity; find out novel drug-likeness might show the M. tuberculosis effect's inhibitor by interacting with multitarget Mur enzymes. New antitubercular therapies that include multitarget drugs may have higher efficacy than single-target medicines and provide a more straightforward antitubercular therapy regimen.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
50
|
Hrast M, Frlan R, Knez D, Zdovc I, Barreteau H, Gobec S. Mur ligases inhibitors with azastilbene scaffold: Expanding the structure-activity relationship. Bioorg Med Chem Lett 2021; 40:127966. [PMID: 33744441 DOI: 10.1016/j.bmcl.2021.127966] [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] [Received: 01/15/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance represents one of the biggest public health challenges in the last few years. Mur ligases (MurC-MurF) are involved in the synthesis of UDP-N-acetylmuramyl-pentapeptide, the main building block of bacterial peptidoglycan polymer. They are essential for the survival of bacteria and therefore important antibacterial targets. We report herein the synthesis and structure-activity relationships of Mur ligases inhibitors with an azastilbene scaffold. Several compounds showed promising inhibitory potencies against multiple ligases and one compound also possessed moderate antibacterial activity. These results represent a solid ground for further development and optimization of structurally novel antimicrobial agents to combat the rising bacterial resistance.
Collapse
Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, SI-1000 Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|