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Rambaher MH, Zdovc I, Glavač NK, Gobec S, Frlan R. Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (-)-epicatechin. J Comput Aided Mol Des 2023; 37:721-733. [PMID: 37796382 PMCID: PMC10618370 DOI: 10.1007/s10822-023-00535-z] [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: 07/12/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
MurC, D, E, and F are ATP-dependent ligases involved in the stepwise assembly of the tetrapeptide stem of forming peptidoglycan. As highly conserved targets found exclusively in bacterial cells, they are of significant interest for antibacterial drug discovery. In this study, we employed a computer-aided molecular design approach to identify potential inhibitors of MurF. A biochemical inhibition assay was conducted, screening twenty-four flavonoids and related compounds against MurC-F, resulting in the identification of quercitrin, myricetin, and (-)-epicatechin as MurF inhibitors with IC50 values of 143 µM, 139 µM, and 92 µM, respectively. Notably, (-)-epicatechin demonstrated mixed type inhibition with ATP and uncompetitive inhibition with D-Ala-D-Ala dipeptide and UM3DAP substrates. Furthermore, in silico analysis using Sitemap and subsequent docking analysis using Glide revealed two plausible binding sites for (-)-epicatechin. The study also investigated the crucial structural features required for activity, with a particular focus on the substitution pattern and hydroxyl group positions, which were found to be important for the activity. The study highlights the significance of computational approaches in targeting essential enzymes involved in bacterial peptidoglycan synthesis.
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Affiliation(s)
- Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Gerbičeva ul. 60, Ljubljana, Slovenia
| | - Nina Kočevar Glavač
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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2
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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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de Oliveira MVD, Furtado RM, da Costa KS, Vakal S, Lima AH. Advances in UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Covalent Inhibition. Front Mol Biosci 2022; 9:889825. [PMID: 35936791 PMCID: PMC9346081 DOI: 10.3389/fmolb.2022.889825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan is a cross-linked polymer responsible for maintaining the bacterial cell wall integrity and morphology in Gram-negative and Gram-positive bacteria. The peptidoglycan pathway consists of the enzymatic reactions held in three steps: cytoplasmic, membrane-associated, and periplasmic. The Mur enzymes (MurA-MurF) are involved in a cytoplasmic stage. The UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme is responsible for transferring the enolpyruvate group from phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine (UNAG) to form UDP-N-acetylglucosamine enolpyruvate (EP-UNAG). Fosfomycin is a natural product analogous to PEP that acts on the MurA target enzyme via binding covalently to the key cysteine residue in the active site. Similar to fosfomycin, other MurA covalent inhibitors have been described with a warhead in their structure that forms a covalent bond with the molecular target. In MurA, the nucleophilic thiolate of Cys115 is pointed as the main group involved in the warhead binding. Thus, in this minireview, we briefly describe the main recent advances in the design of MurA covalent inhibitors.
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Affiliation(s)
| | - Renan Machado Furtado
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Kauê S. da Costa
- Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
| | - Serhii Vakal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Anderson H. Lima,
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4
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El‐Hawary S, Mohammed R, Bahr H, Attia E, El‐Katatny M, Abelyan N, Al‐Sanea M, Moawad A, Abdelmohsen U. Soybean-associated endophytic fungi as potential source for anti-COVID-19 metabolites supported by docking analysis. J Appl Microbiol 2021; 131:1193-1211. [PMID: 33559270 PMCID: PMC8013715 DOI: 10.1111/jam.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/29/2022]
Abstract
AIMS To identify the metabolites produced by the endophytic fungus, Aspergillus terreus and to explore the anti-viral activity of the identified metabolites against the pandemic disease COVID-19 in-silico. METHODS AND RESULTS Herein, we reported the isolation of A. terreus, the endophytic fungus associated with soybean roots, which is then subcultured using OSMAC approach in five different culture media. Analytical analysis of media ethylacetate extracts using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was carried out. Furthermore, the obtained LC-MS data were statistically processed with MetaboAnalyst 4.0. Molecular docking studies were performed for the dereplicated metabolites against COVID-19 main protease (Mpro ). Metabolomic profiling revealed the presence of 18 compounds belonging to different chemical classes. Quinones, polyketides and isocoumarins were the most abundant classes. Multivariate analysis revealed that potato dextrose broth and modified potato dextrose broth are the optimal media for metabolites production. Molecular docking studies declared that the metabolites, Aspergillide B1 and 3a-Hydroxy-3, 5-dihydromonacolin L showed the highest binding energy scores towards COVID-19 main protease (Mpro ) (-9·473) and (-9·386), respectively, and they interact strongly with the catalytic dyad (His41 and Cys145) amino acid residues of Mpro . CONCLUSIONS A combination of metabolomics and in-silico approaches have allowed a shorter route to search for anti-COVID-19 natural products in a shorter time. The dereplicated metabolites, aspergillide B1 and 3α-Hydroxy-3, 5-dihydromonacolin L were found to be potent anti-COVID-19 drug candidates in the molecular docking study. SIGNIFICANCE AND IMPACT OF THE STUDY This study revealed that the endophytic fungus, A. terreus can be considered as a potential source of natural bioactive products. In addition to, the possibility of developing the metabolites, aspergillide B1 and 3α-Hydroxy-3, 5-dihydromonacolin L to be used as phytopharmaceuticals for the management of COVID-19.
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Affiliation(s)
- S.S. El‐Hawary
- Department of Pharmacognosy Faculty of Pharmacy Cairo University Cairo Egypt
| | - R. Mohammed
- Department of Pharmacognosy Faculty of Pharmacy Beni‐Suef University Beni‐Suef Egypt
| | - H.S. Bahr
- Department of Pharmacognosy Faculty of Pharmacy Nahda University Beni‐Suef Egypt
| | - E.Z. Attia
- Department of Pharmacognosy Faculty of Pharmacy Minia University Minia Egypt
| | - M.H. El‐Katatny
- Department of Botany and Microbiology Faculty of Science Minia University Minia Egypt
| | - N. Abelyan
- Institute of Biomedicine and Pharmacy Russian‐Armenian University Yerevan Armenia
- Foundation for Armenian Science and Technology Yerevan Armenia
| | - M.M. Al‐Sanea
- Department of Pharmaceutical Chemistry College of Pharmacy Jouf University Sakaka Saudi Arabia
| | - A.S. Moawad
- Department of Pharmacognosy Faculty of Pharmacy Beni‐Suef University Beni‐Suef Egypt
| | - U.R. Abdelmohsen
- Department of Pharmacognosy Faculty of Pharmacy Minia University Minia Egypt
- Department of Pharmacognosy Faculty of Pharmacy Deraya University New Minia City Minia Egypt
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5
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Kurnia D, Apriyanti E, Soraya C, Satari MH. Antibacterial Flavonoids Against Oral Bacteria of Enterococcus Faecalis ATCC 29212 from Sarang Semut (Myrmecodia pendans) and Its Inhibitor Activity Against Enzyme MurA. Curr Drug Discov Technol 2020; 16:290-296. [PMID: 30152286 DOI: 10.2174/1570163815666180828113920] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/23/2018] [Accepted: 08/16/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND A significant number of antibiotics are known to inhibit peptidoglycan synthesis in the cross-linking stage, while the drug fosfomycin is the only one known to inhibit MurA. Escalated antibiotic resistance has had an impact on the efficacy of fosfomycin, thus demanding the discovery of suitable substitutes with improved potential for MurA inhibition. The aim of this work is to isolate antibacterial compounds from Sarang Semut (Myrmecodia pendans) and to evaluate their antibacterial activity against pathogenic oral bacteria of Enterococcus faecalis ATCC 29212 and inhibitory activity against MurA enzyme. METHODS The antibacterial compounds from Sarang Semut were isolated by a bioactivity-guided separation method with various solvents and combination of column chromatography on normal and reverse phases. The compounds with concentrations of 1000 and 5000 ppm were assessed against E. faecalis ATCC 29212 by agar well diffusion method, with chlorhexidine and fosfomycin being used as positive controls. RESULTS Two antibacterial compounds isolated from Sarang Semut were identified as two new flavonoids derivates of 1 (10 mg) and 2 (4 mg). Both compounds were tested for antibacterial activities against E. faecalis. MIC values of compounds 1 and 2 were 8.15 and 8.05 mm at 1000 ppm and 8.62 and 8.55 mm at 5000 ppm, respectively. MBC values were 156 and 625 ppm for 1 and 625 and 2500 ppm for 2, respectively. In an inhibitory murA enzyme activity assay, compounds 1 and 2 were shown to inhibit the enzyme activity by IC50 values of 21.7 and 151.3 ppm. CONCLUSION The study demonstrated that ethyl acetate fraction of Sarang Semut contained antibacterial flavonoids as active constituents that showed activity against E. faecalis. These results showed the plant's potential in herbal medicine and the development of new antibacterial agent for pathogenic dental caries.
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Affiliation(s)
- Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematic and Natural Sciences, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
| | - Eti Apriyanti
- Department of Chemistry, Faculty of Mathematic and Natural Sciences, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
| | - Cut Soraya
- Department of Concervative Dentistry, Faculty of Dentistry, Syiah Kuala Universty, Banda Aceh, Indonesia
| | - Mieke H Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
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6
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Xu W, Chen T, Wang H, Zeng W, Wu Q, Yu K, Xu Y, Zhang X, Zhou T. Molecular Mechanisms and Epidemiology of Fosfomycin Resistance in Staphylococcus aureus Isolated From Patients at a Teaching Hospital in China. Front Microbiol 2020; 11:1290. [PMID: 32670230 PMCID: PMC7332539 DOI: 10.3389/fmicb.2020.01290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a major cause of hospital- and community-acquired infections placing a significant burden on the healthcare system. With the widespread of multidrug-resistant bacteria and the lack of effective antibacterial drugs, fosfomycin has gradually attracted attention as an "old drug." Thus, investigating the resistance mechanisms and epidemiology of fosfomycin-resistant S. aureus is an urgent requirement. In order to investigate the mechanisms of resistance, 11 fosfomycin-resistant S. aureus isolates were analyzed by PCR and sequencing. The genes, including fosA, fosB, fosC, fosD, fosX, and tet38, as well as mutations in murA, glpT, and uhpT were identified. Quantitative real-time PCR (qRT-PCR) was conducted to evaluate the expression of the target enzyme gene murA and the efflux pump gene tet38 under the selection pressure of fosfomycin. Furthermore, multilocus sequence typing (MLST) identified a novel sequence type (ST 5708) of S. aureus strains. However, none of the resistant strains carried fosA, fosB, fosC, fosD, and fosX genes in the current study, and 12 distinct mutations were detected in the uhpT (3), glpT (4), and murA (5) genes. qRT-PCR revealed an elevated expression of the tet38 gene when exposed to increasing concentration of fosfomycin among 8 fosfomycin-resistant S. aureus strains and reference strain ATCC 29213. MLST analysis categorized the 11 strains into 9 STs. Thus, the mutations in the uhpT, glpT, and murA genes might be the primary mechanisms underlying fosfomycin resistance, and the overexpression of efflux pump gene tet38 may play a major role in the fosfomycin resistance in these isolates.
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Affiliation(s)
- Wenya Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tao Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huihui Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weiliang Zeng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Qing Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kaihang Yu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ye Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiucai Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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7
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Mihalovits LM, Ferenczy GG, Keserű GM. Catalytic Mechanism and Covalent Inhibition of UDP- N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials. J Chem Inf Model 2019; 59:5161-5173. [PMID: 31715096 DOI: 10.1021/acs.jcim.9b00691] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) catalyzes the first step in the biosynthesis of the bacterial cell wall. This pathway is essential for the growth of bacteria but missing in mammals, that nominates MurA as an attractive antibacterial target. MurA has a flexible loop whose conformational change is known to be part of the activation mechanism of the enzyme. We have shown that the loop closed conformation makes the proton transfer from Cys115 to His394 possible by a low barrier exothermic process. QM/MM MD simulations revealed that the activated thiolate is able to react with phosphoenolpyruvate (PEP), the natural substrate of MurA. The binding free energy profile of several covalent inhibitors with various warheads reacting with the activated Cys115 was calculated by QM/MM MD simulations and confirmed that reaction barrier heights tend to separate active from inactive compounds. Our results give new insight into the catalytic mechanism and covalent inhibition of MurA and suggest that QM/MM MD simulations are able to support ligand design by providing sensible relative free energy barriers for covalent inhibitors with various warheads reacting with thiolate nucleophiles.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group , Research Centre for Natural Sciences , Magyar tudósok körútja 2 , Budapest 1117 , Hungary
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8
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Liang H, Zhou G, Ge Y, D'Ambrosio EA, Eidem TM, Blanchard C, Shehatou C, Chatare VK, Dunman PM, Valentine AM, Voelz VA, Grimes CL, Andrade RB. Elucidating the inhibition of peptidoglycan biosynthesis in Staphylococcus aureus by albocycline, a macrolactone isolated from Streptomyces maizeus. Bioorg Med Chem 2018; 26:3453-3460. [PMID: 29805074 PMCID: PMC6008248 DOI: 10.1016/j.bmc.2018.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/02/2018] [Accepted: 05/12/2018] [Indexed: 02/01/2023]
Abstract
Antibiotic resistance is a serious threat to global public health, and methicillin-resistant Staphylococcus aureus (MRSA) is a poignant example. The macrolactone natural product albocycline, derived from various Streptomyces strains, was recently identified as a promising antibiotic candidate for the treatment of both MRSA and vancomycin-resistant S. aureus (VRSA), which is another clinically relevant and antibiotic resistant strain. Moreover, it was hypothesized that albocycline's antimicrobial activity was derived from the inhibition of peptidoglycan (i.e., bacterial cell wall) biosynthesis. Herein, preliminary mechanistic studies are performed to test the hypothesis that albocycline inhibits MurA, the enzyme that catalyzes the first step of peptidoglycan biosynthesis, using a combination of biological assays alongside molecular modeling and simulation studies. Computational modeling suggests albocycline exists as two conformations in solution, and computational docking of these conformations to an ensemble of simulated receptor structures correctly predicted preferential binding to S. aureus MurA-the enzyme that catalyzes the first step of peptidoglycan biosynthesis-over Escherichia coli (E. coli) MurA. Albocycline isolated from the producing organism (Streptomyces maizeus) weakly inhibited S. aureus MurA (IC50 of 480 μM) but did not inhibit E. coli MurA. The antimicrobial activity of albocycline against resistant S. aureus strains was superior to that of vancomycin, preferentially inhibiting Gram-positive organisms. Albocycline was not toxic to human HepG2 cells in MTT assays. While these studies demonstrate that albocycline is a promising lead candidate against resistant S. aureus, taken together they suggest that MurA is not the primary target, and further work is necessary to identify the major biological target.
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Affiliation(s)
- Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Guangfeng Zhou
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Elizabeth A D'Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Tess M Eidem
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Catlyn Blanchard
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Cindy Shehatou
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Vijay K Chatare
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Ann M Valentine
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States.
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9
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Ferguson LB, Ozburn AR, Ponomarev I, Metten P, Reilly M, Crabbe JC, Harris RA, Mayfield RD. Genome-Wide Expression Profiles Drive Discovery of Novel Compounds that Reduce Binge Drinking in Mice. Neuropsychopharmacology 2018; 43:1257-1266. [PMID: 29251283 PMCID: PMC5916369 DOI: 10.1038/npp.2017.301] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/06/2017] [Accepted: 11/24/2017] [Indexed: 12/18/2022]
Abstract
Transcriptome-based drug discovery has identified new treatments for some complex diseases, but has not been applied to alcohol use disorder (AUD) or other psychiatric diseases, where there is a critical need for improved pharmacotherapies. High Drinking in the Dark (HDID-1) mice are a genetic model of AUD risk that have been selectively bred (from the HS/Npt line) to achieve intoxicating blood alcohol levels (BALs) after binge-like drinking. We compared brain gene expression of HDID-1 and HS/Npt mice, to determine a molecular signature for genetic risk for high intensity, binge-like drinking. Using multiple computational methods, we queried LINCS-L1000 (Library of Integrated Network-Based Cellular Signatures), a database containing gene expression signatures of thousands of compounds, to predict candidate drugs with the greatest potential to decrease alcohol consumption. Our analyses predicted novel compounds for testing, many with anti-inflammatory properties, providing further support for a neuroimmune mechanism of excessive alcohol drinking. We validated the top 2 candidates in vivo as a proof-of-concept. Terreic acid (a Bruton's tyrosine kinase inhibitor) and pergolide (a dopamine and serotonin receptor agonist) robustly reduced alcohol intake and BALs in HDID-1 mice, providing the first evidence for transcriptome-based drug discovery to target an addiction trait. Effective drug treatments for many psychiatric diseases are lacking, and the emerging tools and approaches outlined here offer researchers studying complex diseases renewed opportunities to discover new or repurpose existing compounds and expedite treatment options.
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Affiliation(s)
- Laura B Ferguson
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - Angela R Ozburn
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Igor Ponomarev
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - Pamela Metten
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Matthew Reilly
- Division of Neuroscience and Behavior, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - R Adron Harris
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Dayne Mayfield
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
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10
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Skariyachan S, Manjunath M, Bachappanavar N. Screening of potential lead molecules against prioritised targets of multi-drug-resistant-Acinetobacter baumannii - insights from molecular docking, molecular dynamic simulations and in vitro assays. J Biomol Struct Dyn 2018. [PMID: 29529934 DOI: 10.1080/07391102.2018.1451387] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acinetobacter baumannii, an opportunistic pathogen, has become multi-drug resistant (MDR) to major classes of antibacterial and poses grave threat to public health. The current study focused to screen novel phytotherapeutics against prioritised targets of Acinetobacter baumannii by computational investigation. Fourteen potential drug targets were screened based on their functional role in various biosynthetic pathways and the 3D structures of 9 targets were retrieved from Protein Data Bank and others were computationally predicted. By extensive literature survey, 104 molecules from 48 herbal sources were screened and subjected to virtual screening. Ten clinical isolates of A. baumannii were tested for antibiotic susceptibility towards clinafloxacin, imipenem and polymyxin-E. Computational screening suggested that Ajmalicine ((19α)-16, 17-didehydro-19-methyloxayohimban-16-carboxylic acid methyl ester from Rauwolfia serpentina), Strictamin (Akuammilan-17-oic acid methyl ester from Alstonia scholaris) and Limonin (7, 16-dioxo-7, 16-dideoxylimondiol from Citrus sps) exhibited promising binding towards multiple drug targets of A. baumannii in comparison with the binding between standard drugs and their targets. Limonin displayed promising binding potential (binding energy -9.8 kcal/mol) towards diaminopimelate epimerase (DapF) and UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA). Ajmalicine and Strictamin demonstrated good binding potential (-9.5, -8.5 kcal/mol, respectively) towards MurA and shikimate dehydrogenase (-7.8 kcal/mol). Molecular dynamic simulations further validated the docking results. In vitro assay suggested that the tested isolates exhibited resistance to clinafloxacin, imipenem and polymyxin-E and the herbal preparations (crude extract) demonstrated a significant antibacterial potential (p ≤ .05). The study suggests that the aforementioned lead candidates and targets can be used for structure-based drug screening towards MDR A. baumannii.
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Affiliation(s)
- Sinosh Skariyachan
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
| | - Meghna Manjunath
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
| | - Nikhil Bachappanavar
- a Department of Biotechnology Engineering , Dayananda Sagar Institutions , Bengaluru 560 078 , Karnataka , India.,b Visvesvaraya Technological University , Belagavi , India
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Rožman K, Lešnik S, Brus B, Hrast M, Sova M, Patin D, Barreteau H, Konc J, Janežič D, Gobec S. Discovery of new MurA inhibitors using induced-fit simulation and docking. Bioorg Med Chem Lett 2017; 27:944-949. [DOI: 10.1016/j.bmcl.2016.12.082] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/26/2016] [Accepted: 12/29/2016] [Indexed: 11/15/2022]
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12
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Sharma R, Lambu MR, Jamwal U, Rani C, Chib R, Wazir P, Mukherjee D, Chaubey A, Khan IA. Escherichia coli N-Acetylglucosamine-1-Phosphate-Uridyltransferase/Glucosamine-1-Phosphate-Acetyltransferase (GlmU) Inhibitory Activity of Terreic Acid Isolated from Aspergillus terreus. ACTA ACUST UNITED AC 2016; 21:342-53. [PMID: 26762501 DOI: 10.1177/1087057115625308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022]
Abstract
Secondary metabolite of Aspergillus terreus, terreic acid, is a reported potent antibacterial that was identified more than 60 years ago, but its cellular target(s) are still unknown. Here we screen its activity against the acetyltransferase domain of a bifunctional enzyme, Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). An absorbance-based assay was used to screen terreic acid against the acetyltransferase activity of E. coli GlmU. Terreic acid was found to inhibit the acetyltransferase domain of E. coli GlmU with an IC50 of 44.24 ± 1.85 µM. Mode of inhibition studies revealed that terreic acid was competitive with AcCoA and uncompetitive with GlcN-1-P. It also exhibited concentration-dependent killing of E. coli ATCC 25922 up to 4× minimum inhibitory concentration and inhibited the growth of biofilms generated by E. coli. Characterization of resistant mutants established mutation in the acetyltransferase domain of GlmU. Terreic acid was also found to be metabolically stable in the in vitro incubations with rat liver microsome in the presence of a NADPH regenerating system. The studies reported here suggest that terreic acid is a potent antimicrobial agent and support that E. coli GlmU acetyltransferase is a molecular target of terreic acid, resulting in its antibacterial activity.
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Affiliation(s)
- Rashmi Sharma
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
| | - Mallikharjuna Rao Lambu
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Natural Products Chemistry: Microbes, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, India
| | - Urmila Jamwal
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Chitra Rani
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India
| | - Priya Wazir
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Natural Products Chemistry: Microbes, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, India
| | - Asha Chaubey
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, India Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, India
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13
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Sharma R, Rani C, Mehra R, Nargotra A, Chib R, Rajput VS, Kumar S, Singh S, Sharma PR, Khan IA. Identification and characterization of novel small molecule inhibitors of the acetyltransferase activity of Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). Appl Microbiol Biotechnol 2015; 100:3071-85. [PMID: 26563552 DOI: 10.1007/s00253-015-7123-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/19/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
Abstract
This study aims at identifying novel chemical scaffolds as inhibitors specific to the acetyltransferase domain of a bifunctional enzyme, Escherichia coli GlmU, involved in the cell wall biosynthesis of Gram-negative organisms. A two-pronged approach was used to screen a 50,000 small-molecule library. Using the first approach, the library was in silico screened by docking the library against acetyltransferase domain of E. coli GlmU studies. In the second approach, complete library was screened against Escherichia coli ATCC 25922 to identify the whole cell active compounds. Active compounds from both the screens were screened in a colorimetric absorbance-based assay to identify inhibitors of acetyltransferase domain of E. coli GlmU which resulted in the identification of 1 inhibitor out of 56 hits identified by in silico screening and 4 inhibitors out of 35 whole cell active compounds on Gram-negative bacteria with the most potent inhibitor showing IC50 of 1.40 ± 0.69 μM. Mode of inhibition studies revealed these inhibitors to be competitive with AcCoA and uncompetitive with GlcN-1-P. These selected inhibitors were also tested for their antibacterial and cytotoxic activities. Compounds 5175178 and 5215319 exhibited antibacterial activity that co-related with GlmU inhibition. These compounds, therefore, represent novel chemical scaffolds targeting acetyltransferase activity of E. coli GlmU.
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Affiliation(s)
- Rashmi Sharma
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Chitra Rani
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Vikrant S Rajput
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sunil Kumar
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Samsher Singh
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Parduman R Sharma
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi, 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Inshad A Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India. .,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
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14
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Hrast M, Sosič I, Sink R, Gobec S. Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F. Bioorg Chem 2014; 55:2-15. [PMID: 24755374 DOI: 10.1016/j.bioorg.2014.03.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 01/12/2023]
Abstract
The widespread emergence of resistant bacterial strains is becoming a serious threat to public health. This thus signifies the need for the development of new antibacterial agents with novel mechanisms of action. Continuous efforts in the design of novel antibacterials remain one of the biggest challenges in drug development. In this respect, the Mur enzymes, MurA-F, that are involved in the formation of UDP-N-acetylmuramyl-pentapeptide can be genuinely considered as promising antibacterial targets. This review provides an in-depth insight into the recent developments in the field of inhibitors of the MurA-F enzymes. Special attention is also given to compounds that act as multiple inhibitors of two, three or more of the Mur enzymes. Moreover, the reasons for the lack of preclinically successful inhibitors and the challenges to overcome these hurdles in the next years are also debated.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Roman Sink
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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