106
Views
0
CrossRef citations to date
0
Altmetric
Rapid Communication

Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach

, ORCID Icon, , , & ORCID Icon
Received 02 May 2023, Accepted 13 Dec 2023, Published online: 27 Dec 2023

References

  • Azam, M. A., & Jupudi, S. (2019). Structure-based virtual screening to identify inhibitors against Staphylococcus aureus MurD enzyme. Structural Chemistry, 30(6), 2123–2133. https://doi.org/10.1007/s11224-019-01330-z
  • Azam, M., Jupudi, S., Saha, N., & Paul, R. (2019). Combining molecular docking and molecular dynamics studies for modelling Staphylococcus aureus MurD inhibitory activity. SAR and QSAR in Environmental Research, 30(1), 1–20. https://doi.org/10.1080/1062936X.2018.1539034
  • Belete, T. M. (2019). Novel targets to develop new antibacterial agents and novel alternatives to antibacterial agents. Human Microbiome Journal, 11, 100052. https://doi.org/10.1016/j.humic.2019.01.001
  • Breindl, A., Beck, B., Clark, T., & Glen, R. C. (1997). Prediction of the n-octanol/water partition coefficient, logP, using a combination of semiempirical MO-calculations and a neural network. Journal of Molecular Modeling, 3(3), 142–155. https://doi.org/10.1007/s008940050027
  • Chakkyarath, V., & Natarajan, J. (2019). Identification of Ideal multi-targeting bioactive compounds against Mur ligases of Enterobacter aerogenes and its binding mechanism in comparison with chemical inhibitors. Interdisciplinary Sciences, Computational Life Sciences, 11(1), 135–144. https://doi.org/10.1007/s12539-017-0261-4
  • Chandrasekaran, B., Abed, S. N., Al-Attraqchi, O., Kuche, K., & Tekade, R. K. (2018). Computer-aided prediction of pharmacokinetic (ADMET) properties. In Editor: Rakesh K. Tekade Dosage form design parameters (pp. 731–755). Elsevier National Institute of Pharmaceutical Education and Research (NIP ER)-Ahmedabad, Gandhinagar, Gujarat, India.
  • Chen, X., Li, H., Tian, L., Li, Q., Luo, J., & Zhang, Y. (2020). Analysis of the physicochemical properties of acaricides based on Lipinski’s rule of five. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 27(9), 1397–1406. https://doi.org/10.1089/cmb.2019.0323
  • Cutinho, P. F., Shankar, R. C., Anand, A., Roy, J., Mehta, C. H., Nayak, U. Y., & Murahari, M. (2020). Hit identification and drug repositioning of potential non-nucleoside reverse transcriptase inhibitors by structure-based approach using computational tools (part II). Journal of Biomolecular Structure & Dynamics, 38(13), 3772–3789. https://doi.org/10.1080/07391102.2019.1663263
  • Dadgostar, P. (2019). Antimicrobial resistance: Implications and costs. Infection and Drug Resistance, 12, 3903–3910. https://doi.org/10.2147/IDR.S234610
  • El Zoeiby, A., Sanschagrin, F., & Levesque, R. C. (2003). Structure and function of the Mur enzymes: Development of novel inhibitors. Molecular Microbiology, 47(1), 1–12. https://doi.org/10.1046/j.1365-2958.2003.03289.x
  • Fan, Y., Unwalla, R., Denny, R. A., Di, L., Kerns, E. H., Diller, D. J., & Humblet, C. (2010). Insights for predicting blood-brain barrier penetration of CNS targeted molecules using QSPR approaches. Journal of Chemical Information and Modeling, 50(6), 1123–1133. https://doi.org/10.1021/ci900384c
  • Fiuza, M., Canova, M. J., Patin, D., Letek, M., Zanella-Cléon, I., Becchi, M., Mateos, L. M., Mengin-Lecreulx, D., Molle, V., & Gil, J. A. (2008). The MurC ligase essential for peptidoglycan biosynthesis is regulated by the serine/threonine protein kinase PknA in Corynebacterium glutamicum. The Journal of Biological Chemistry, 283(52), 36553–36563. https://doi.org/10.1074/jbc.M807175200
  • Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein − ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
  • Garde, S., Chodisetti, P. K., & Reddy, M. (2021). Peptidoglycan: Structure, synthesis, and regulation. EcoSal Plus, 9(2). https://doi.org/10.1128/ecosalplus.ESP-0010-2020
  • Gaur, V., & Bera, S. (2022). 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, 3, 100137. https://doi.org/10.1016/j.crphar.2022.100137
  • Gegnas, L. D., Waddell, S. T., Chabin, R. M., Reddy, S., & Wong, K. K. (1998). Inhibitors of the bacterial cell wall biosynthesis enzyme Mur D. Bioorganic & Medicinal Chemistry Letters, 8(13), 1643–1648. https://doi.org/10.1016/S0960-894X(98)00285-6
  • Gobec, S., Urleb, U., Auger, G., & Blanot, D. (2001). Synthesis and biochemical evaluation of some novel N-acyl phosphono-and phosphinoalanine derivatives as potential inhibitors of the D-glutamic acid-adding enzyme. Die Pharmazie, 56(4), 295–297. https://doi.org/10.1002/chin.200127170
  • Haque, M. A., Singh, M., Tripathi, M. K., Ethayathulla, A. S., & Kaur, P. (2022). Identification of natural small molecule modulators of MurB from Salmonella enterica serovar Typhi Ty2 strain using computational and biophysical approaches. Proteins, 91(3), 363–379. https://doi.org/10.1002/prot.26435
  • Hernández, S. B., Dörr, T., Waldor, M. K., & Cava, F. (2020). Modulation of peptidoglycan synthesis by recycled cell wall tetrapeptides. Cell Reports, 31(4), 107578. https://doi.org/10.1016/j.celrep.2020.107578
  • Hrast, M., Rožman, K., Ogris, I., Škedelj, V., Patin, D., Sova, M., Barreteau, H., Gobec, S., Grdadolnik, S. G., & Zega, A. (2019). Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent Mur ligases. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 1010–1017. https://doi.org/10.1080/14756366.2019.1608981
  • Husain, A., Bhutani, M., Parveen, S., Khan, S. A., Ahmad, A., & Iqbal, M. A. (2021). Synthesis, in vitro cytotoxicity, ADME, and molecular docking studies of benzimidazole‐bearing furanone derivatives. Journal of the Chinese Chemical Society, 68(2), 362–373. https://doi.org/10.1002/jccs.202000130
  • Jacob, R. B., Andersen, T., & McDougal, O. M. (2012). Accessible high-throughput virtual screening molecular docking software for students and educators. PLoS Computational Biology, 8(5), e1002499. https://doi.org/10.1371/journal.pcbi.1002499
  • Jorgensen, W. L., & Duffy, E. M. (2002). Prediction of drug solubility from structure. Advanced Drug Delivery Reviews, 54(3), 355–366. https://doi.org/10.1016/S0169-409X(02)00008-X
  • Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
  • Kahler, C. M., Sarkar-Tyson, M., Kibble, E. A., Stubbs, K. A., & Vrielink, A. (2018). Enzyme targets for drug design of new anti-virulence therapeutics. Current Opinion in Structural Biology, 53, 140–150. https://doi.org/10.1016/j.sbi.2018.08.010
  • Kapetanovic, I. (2008). Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach. Chemico-Biological Interactions, 171(2), 165–176. https://doi.org/10.1016/j.cbi.2006.12.006
  • Kouidmi, I., Levesque, R. C., & Paradis‐Bleau, C. (2014). The biology of Mur ligases as an antibacterial target. Molecular Microbiology, 94(2), 242–253. https://doi.org/10.1111/mmi.12758
  • Kumar, N., Hendriks, B. S., Janes, K. A., de Graaf, D., & Lauffenburger, D. A. (2006). Applying computational modeling to drug discovery and development. Drug Discovery Today, 11(17–18), 806–811. https://doi.org/10.1016/j.drudis.2006.07.010
  • Kurnia, D., Hutabarat, G. S., Windaryanti, D., Herlina, T., Herdiyati, Y., & Satari, M. H. (2020). Potential allylpyrocatechol derivatives as antibacterial agent against oral pathogen of S. sanguinis ATCC 10,556 and as inhibitor of MurA enzymes: In vitro and in silico study. Drug Design, Development and Therapy, 14, 2977–2985. https://doi.org/10.2147/DDDT.S255269
  • Lin, W.-H., Wang, M.-C., Liu, P.-Y., Chen, P.-S., Wen, L.-L., Teng, C.-H., & Kao, C.-Y. (2022). Escherichia coli urinary tract infections: Host age-related differences in bacterial virulence factors and antimicrobial susceptibility. Wei Mian yu Gan Ran za Zhi [Journal of Microbiology, Immunology, and Infection], 55(2), 249–256. https://doi.org/10.1016/j.jmii.2021.04.001
  • Major, J. (1998). Challenges and opportunities in high throughput screening: Implications for new technologies. SLAS Discovery, 3(1), 13–17. https://doi.org/10.1177/108705719800300102.
  • Mayr, L. M., & Bojanic, D. (2009). Novel trends in high-throughput screening. Current Opinion in Pharmacology, 9(5), 580–588. https://doi.org/10.1016/j.coph.2009.08.004
  • Miyachiro, M. M., Granato, D., Trindade, D. M., Ebel, C., Paes Leme, A. F., & Dessen, A. (2019). Complex formation between Mur enzymes from Streptococcus pneumoniae. Biochemistry, 58(30), 3314–3324. https://doi.org/10.1021/acs.biochem.9b00277
  • Naclerio, G. A., & Sintim, H. O. (2020). Multiple ways to kill bacteria via inhibiting novel cell wall or membrane targets. Future Medicinal Chemistry, 12(13), 1253–1279. https://doi.org/10.4155/fmc-2020-0046
  • Perdih, A., Hrast, M., Barreteau, H., Gobec, S., Wolber, G., & Solmajer, T. (2014). Benzene-1, 3-dicarboxylic acid 2, 5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC–MurF). Bioorganic & Medicinal Chemistry, 22(15), 4124–4134. https://doi.org/10.1016/j.bmc.2014.05.058
  • Perdih, A., Kotnik, M., Hodoscek, M., & Solmajer, T. (2007). Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD. Proteins, 68(1), 243–254. https://doi.org/10.1002/prot.21374
  • Pereira, D., & Williams, J. (2007). Origin and evolution of high throughput screening. British Journal of Pharmacology, 152(1), 53–61. https://doi.org/10.1038/sj.bjp.0707373
  • Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
  • Simba, S. M., Omwenga, E. O., & Musyoki, S. K. (2022). Prevalence of E. coli as a causative agent of urinary tract infections and its drug susceptibility patterns among pregnant mothers seeking medicare at Kisii teaching and referral hospital, Kenya. International Journal of Community Medicine and Public Health, 9(3), 1161. https://doi.org/10.18203/2394-6040.ijcmph20220671
  • Šink, R., Barreteau, H., Patin, D., Mengin-Lecreulx, D., Gobec, S., & Blanot, D. (2013). MurD enzymes: Some recent developments. Biomolecular Concepts, 4(6), 539–556. https://doi.org/10.1515/bmc-2013-0024
  • Smith, C. A. (2006). Structure, function and dynamics in the Mur family of bacterial cell wall ligases. Journal of Molecular Biology, 362(4), 640–655. https://doi.org/10.1016/j.jmb.2006.07.066
  • Sova, M., Kovac, A., Turk, S., Hrast, M., Blanot, D., & Gobec, S. (2009). Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF. Bioorganic Chemistry, 37(6), 217–222. https://doi.org/10.1016/j.bioorg.2009.09.001
  • Strancar, K., Blanot, D., & Gobec, S. (2006). Design, synthesis and structure–activity relationships of new phosphinate inhibitors of MurD. Bioorganic & Medicinal Chemistry Letters, 16(2), 343–348. https://doi.org/10.1016/j.bmcl.2005.09.086
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Wang, H., Jin, K., Wang, C., Guo, X., Chen, Z., & Tao, J. (2019). Effect of fiber surface functionalization on shear behavior at carbon fiber/epoxy interface through molecular dynamics analysis. Composites Part A: Applied Science and Manufacturing, 126, 105611. https://doi.org/10.1016/j.compositesa.2019.105611
  • Zhang, F., Graham, J., Zhai, T., Liu, Y., & Huang, Z. (2022). Discovery of MurA inhibitors as novel antimicrobials through an integrated computational and experimental approach. Antibiotics, 11(4), 528. https://doi.org/10.3390/antibiotics11040528
  • Zhang, M.-Q., & Wilkinson, B. (2007). Drug discovery beyond the ‘rule-of-five. Current Opinion in Biotechnology, 18(6), 478–488. https://doi.org/10.1016/j.copbio.2007.10.005
  • Zsila, F., Bikadi, Z., Malik, D., Hari, P., Pechan, I., Berces, A., & Hazai, E. (2011). Evaluation of drug–human serum albumin binding interactions with support vector machine aided online automated docking. Bioinformatics, 27(13), 1806–1813. https://doi.org/10.1093/bioinformatics/btr284

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.