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Wagdy RA, Abutaleb NS, Fathalla RK, Elgammal Y, Weck S, Pal R, Fischer PD, Ducho C, Abadi AH, N Seleem M, Engel M, Abdel-Halim M. Discovery of 1,2-diaryl-3-oxopyrazolidin-4-carboxamides as a new class of MurA enzyme inhibitors and characterization of their antibacterial activity. Eur J Med Chem 2023; 261:115789. [PMID: 37717380 DOI: 10.1016/j.ejmech.2023.115789] [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: 04/13/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/19/2023]
Abstract
The cytoplasmic steps of peptidoglycan synthesis represent an important targeted pathway for development of new antibiotics. Herein, we report the synthesis of novel 3-oxopyrazolidin-4-carboxamide derivatives with variable amide side chains as potential antibacterial agents targeting MurA enzyme, the first committed enzyme in these cytosolic steps. Compounds 15 (isoindoline-1,3-dione-5-yl), 16 (4-(1H-pyrazol-4-yl)phenyl), 20 (5-cyanothiazol-2-yl), 21 and 31 (5-nitrothiazol-2-yl derivatives) exhibited the most potent MurA inhibition, with IC50 values of 9.8-12.2 μM. Compounds 15, 16 and 21 showed equipotent inhibition of the C115D MurA mutant developed by fosfomycin-resistant Escherichia coli. NMR binding studies revealed that some of the MurA residues targeted by 15 also interacted with fosfomycin, but not all, indicating an overlapping but not identical binding site. The antibacterial activity of the compounds against E. coli ΔtolC suggests that inhibition of MurA accounts for the observed effect on bacterial growth, considering that a few potent MurA inhibitors could not penetrate the bacterial outer membrane and were therefore inactive as proven by the bacterial cell uptake assay. The most promising compounds were also evaluated against a panel of Gram-positive bacteria. Remarkably, compounds 21 and 31 (MurA IC50 = 9.8 and 10.2 μM respectively) exhibited a potent activity against Clostridioides difficile strains with MIC values ranging from 0.125 to 1 μg/mL, and were also shown to be bactericidal with MBC values between 0.25 and 1 μg/mL. Furthermore, both compounds were shown to have a limited activity against human normal intestinal flora and showed high safety towards human colon cells (Caco-2) in vitro. The thiolactone derivative (compound 5) exhibited an interesting broad spectrum antibacterial activity despite its weak MurA inhibition. Altogether, the presented series provides a promising class of antibiotics that merits further investigation.
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Affiliation(s)
- Reem A Wagdy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Reem K Fathalla
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Yehia Elgammal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Stefanie Weck
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Rusha Pal
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Patrick D Fischer
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Christian Ducho
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA; Center for One Health Research, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123, Saarbrücken, Germany.
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
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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.
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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
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3
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Jiang D, Ma P. Canagliflozin, characterized as a HDAC6 inhibitor, inhibits gastric cancer metastasis. Front Oncol 2022; 12:1057455. [DOI: 10.3389/fonc.2022.1057455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer is a common gastrointestinal cancer. Survival outcome for patients with the recurrence or metastasis remains poor due to the lack of effective targeting drugs. The mechanisms of non-histone acetylation modifications are key epigenetic regulations that participate in various biological processes. HDAC6 is mostly located in the cytoplasm to deacetylate non-histone substrates, which has been identified as a critical promoter of many oncogenic pathways in cancers, including gastric cancer. Nevertheless, its inhibitor has not been applied in gastric cancer clinically. In this study, we identified canagliflozin as an active HDAC6-targeted inhibitor from FDA-approved Drug Library by enzymatic assay. The strong affinity of the compounds with HDAC6 was further verified by surface plasmon resonance (SPR) and cellular thermal shift assay (CETSA). In addition, molecular docking showed that canagliflozin could bind to the active pocket of HDAC6 and form interactions with key residues. Further experiments revealed that canagliflozin could effectively inhibit the migration and epithelial-mesenchymal-transition (EMT) of gastric cancer cells in vitro and in vivo. These results reveal a novel finding that canagliflozin has the potential to be an effective agent in inhibiting gastric cancer metastasis.
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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: 15] [Impact Index Per Article: 7.5] [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.
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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,
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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.
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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.
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6
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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.
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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
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Funes Chabán M, Hrast M, Frlan R, Graikioti DG, Athanassopoulos CM, Carpinella MC. Inhibition of MurA Enzyme from Escherichia coli and Staphylococcus aureus by Diterpenes from Lepechinia meyenii and Their Synthetic Analogs. Antibiotics (Basel) 2021; 10:1535. [PMID: 34943747 PMCID: PMC8698320 DOI: 10.3390/antibiotics10121535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022] Open
Abstract
Enzymes MurA and MurF, involved in bacterial cell wall synthesis, have been validated as targets for the discovery of novel antibiotics. A panel of plant-origin antibacterial diterpenes and synthetic analogs derived therefrom were investigated for their inhibitory properties on these enzymes from Escherichia coli and Staphylococcus aureus. Six compounds were proven to be effective for inhibiting MurA from both bacteria, with IC50 values ranging from 1.1 to 25.1 µM. To further mechanistically investigate the nature of binding and to explain the activity, these compounds were docked into the active site of MurA from E. coli. The aromatic ring of the active compounds showed a T-shaped π-π interaction with the phenyl ring of Phe328, and at least one hydrogen bond was formed between the hydroxy groups and Arg120 and/or Arg91. The results disclosed here establish new chemical scaffolds for the development of novel entities targeting MurA as potential antibiotics to combat the threat of pathogenic bacteria, particularly resistant strains.
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Affiliation(s)
- Macarena Funes Chabán
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, Universidad Católica de Córdoba, Córdoba 5016, Argentina;
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.H.); (R.F.)
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.H.); (R.F.)
| | - Dafni G. Graikioti
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece; (D.G.G.); (C.M.A.)
| | - Constantinos M. Athanassopoulos
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504 Patras, Greece; (D.G.G.); (C.M.A.)
| | - María Cecilia Carpinella
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, Universidad Católica de Córdoba, Córdoba 5016, Argentina;
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