Targeting Proteus mirabilis BAM Complex Proteins for Development of Novel Antibiotics
Authors/Creators
- 1. University of Ghana, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, Accra, Ghana
- 2. University of Ghana, Department of Biochemistry, Cell and Molecular Biology, Legon, Accra, Ghana
- 3. University of Ghana, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, Legon, Accra, Ghana
Description
Urinary tract infections (UTIs) are frequent hospital-acquired infection, with Escherichia coli and Proteus mirabilis accounting for 90% of complicated UTIs. Emergence of multidrug-resistant (MDR) bacteria have complicated the treatment UTIs. P. mirabilis related UTIs has been associated with the production of urinary stones and long-term infections in patients with catheters. P. mirabilis and other uropathogens constitute a largely unexplored pathogen group. The pathogen is resistant to most antibiotics as a result of its impermeable outer membrane (OM). The β-barrel assemble machinery folds and inserts outer membrane proteins; however, there are no antibiotics targeting the OM assemble in clinical use currently. Therefore, this study seeks to identify drugs that will inhibit the activity of P. mirabilis B complex proteins and also determine their effects on P. mirabilis OM biogenesis. This would be achieved by screening approved drugs against the P. mirabilis Bam complex using computer-based in silico screening and cellular-based assays. First, the binding effects of drugs on P. mirabilis B complex proteins will be determined using docking algorithms. The antimicrobial and antivirulence activity of selected drugs from in silico analysis will be screened against MDR P. mirabilis. Finally, the effect of active drug(s) on the OM biogenesis of wild-type P. mirabilis and mutant P. mirabilis will be determined using peptide nucleic acids (PNA). Western lot analysis will be used to determine the abundance of proteins involved in OM biogenesis. Successful completion of this study will lead to the identification of novel antibiotics against MDR P. mirabilis and associated mechanisms while providing the foundation for future research endeavours on other uropathogens.
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References
- Abiola I (2019) Investigating the Mechanisms of Antimicrobial Resistance and Virulence of Bacteria Isolated from Hospital Environments. UgSpace, Accra, 195 pp. [In English]. URL: http://ugspace.ug.edu.gh/handle/123456789/35880
- Armbruster C, Mobley HT, Pearson M (2018) Pathogenesis of Proteus mirabilis Infection. EcoSal Plus 8 (1). https://doi.org/10.1128/ecosalplus.ESP-0009-2017
- Bahrani FK, Mobley HL (1994) Proteus mirabilis MR/P fimbrial operon: genetic organization, nucleotide sequence, and conditions for expression. Journal of Bacteriology 176 (11): 3412‑3419. https://doi.org/10.1128/jb.176.11.3412-3419.1994
- Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports 7 (1). https://doi.org/10.1038/srep42717
- Das B, Moumita S, Ghosh S, Khan MI, Indira D, Jayabalan R, Tripathy S, Mishra A, Balasubramanian P (2018) Biosynthesis of magnesium oxide (MgO) nanoflakes by using leaf extract of Bauhinia purpurea and evaluation of its antibacterial property against Staphylococcus aureus. Materials Science and Engineering: C 91: 436‑444. https://doi.org/10.1016/j.msec.2018.05.059
- Dehbanipour R, Ghalavand Z (2022) Anti-virulence therapeutic strategies against bacterial infections: recent advances. Germs 12 (2): 262‑275. https://doi.org/10.18683/germs.2022.1328
- Delcour A (2009) Outer membrane permeability and antibiotic resistance. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1794 (5): 808‑816. https://doi.org/10.1016/j.bbapap.2008.11.005
- Diederichs K, Ni X, Rollauer S, Botos I, Tan X, King M, Kunji ES, Jiang J, Buchanan S (2020) Structural insight into mitochondrial β-barrel outer membrane protein biogenesis. Nature Communications 11 (1). https://doi.org/10.1038/s41467-020-17144-1
- Flores-Mireles A, Walker J, Caparon M, Hultgren S (2015) Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nature Reviews Microbiology 13 (5): 269‑284. https://doi.org/10.1038/nrmicro3432
- Foxman B (2014) Urinary Tract Infection Syndromes. Infectious Disease Clinics of North America 28 (1): 1‑13. https://doi.org/10.1016/j.idc.2013.09.003
- Gentle I, Burri L, Lithgow T (2005) Molecular architecture and function of the Omp85 family of proteins. Molecular Microbiology 58 (5): 1216‑1225. https://doi.org/10.1111/j.1365-2958.2005.04906.x
- Girlich D, Bonnin R, Dortet L, Naas T (2020) Genetics of Acquired Antibiotic Resistance Genes in Proteus spp. Frontiers in Microbiology 11 https://doi.org/10.3389/fmicb.2020.00256
- Good L, Awasthi SK, Dryselius R, Larsson O, Nielsen P (2001) Bactericidal antisense effects of peptide–PNA conjugates. Nature Biotechnology 19 (4): 360‑364. https://doi.org/10.1038/86753
- Gurung AB, Bhattacharjee A, Ali MA (2016) Exploring the physicochemical profile and the binding patterns of selected novel anticancer Himalayan plant derived active compounds with macromolecular targets. Informatics in Medicine Unlocked 5: 1‑14. https://doi.org/10.1016/j.imu.2016.09.004
- Hart E, Mitchell A, Konovalova A, Grabowicz M, Sheng J, Han X, Rodriguez-Rivera F, Schwaid A, Malinverni J, Balibar C, Bodea S, Si Q, Wang H, Homsher M, Painter R, Ogawa A, Sutterlin H, Roemer T, Black T, Rothman D, Walker S, Silhavy T (2019) A small-molecule inhibitor of BamA impervious to efflux and the outer membrane permeability barrier. Proceedings of the National Academy of Sciences 116 (43): 21748‑21757. https://doi.org/10.1073/pnas.1912345116
- Hazan R, Que Y, Maura D, Rahme LG (2012) A method for high throughput determination of viable bacteria cell counts in 96-well plates. BMC Microbiology 12 (1). https://doi.org/10.1186/1471-2180-12-259
- Imai Y, Meyer K, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan Z, Kaur H, Wu R, Mateus A, Typas A, Savitski M, Espinoza J, O'Rourke A, Nelson K, Hiller S, Noinaj N, Schäberle T, D'Onofrio A, Lewis K (2019) A new antibiotic selectively kills Gram-negative pathogens. Nature 576 (7787): 459‑464. https://doi.org/10.1038/s41586-019-1791-1
- Kielkopf C, Bauer W, Urbatsch I (2020) Bradford Assay for Determining Protein Concentration. Cold Spring Harbor Protocols 2020 (4). https://doi.org/10.1101/pdb.prot102269
- Kim K, Aulakh S, Paetzel M (2012) The bacterial outer membrane β-barrel assembly machinery. Protein Science 21 (6): 751‑768. https://doi.org/10.1002/pro.2069
- Knowles T, Scott-Tucker A, Overduin M, Henderson I (2009) Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nature Reviews Microbiology 7 (3): 206‑214. https://doi.org/10.1038/nrmicro2069
- Lehman K, Grabowicz M (2019) Countering Gram-Negative Antibiotic Resistance: Recent Progress in Disrupting the Outer Membrane with Novel Therapeutics. Antibiotics 8 (4). https://doi.org/10.3390/antibiotics8040163
- Levison M, Kaye D (2013) Treatment of Complicated Urinary Tract Infections With an Emphasis on Drug-Resistant Gram-Negative Uropathogens. Current Infectious Disease Reports 15 (2): 109‑115. https://doi.org/10.1007/s11908-013-0315-7
- Lichtenberger P, Hooton T (2008) Complicated urinary tract infections. Current Infectious Disease Reports 10 (6): 499‑504. https://doi.org/10.1007/s11908-008-0081-0
- Livak K, Schmittgen T (2001) Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods 25 (4): 402‑408. https://doi.org/10.1006/meth.2001.1262
- Li Y, Zhu X, Zhang J, Lin Y, You X, Chen M, Wang Y, Zhu N, Si S (2020) Identification of a Compound That Inhibits the Growth of Gram-Negative Bacteria by Blocking BamA–BamD Interaction. Frontiers in Microbiology 11 https://doi.org/10.3389/fmicb.2020.01252
- Mahmood T, Yang P (2012) Western blot: technique, theory, and trouble shooting. North American journal of medical sciences 4 (9): 429‑34. https://doi.org/10.4103/1947-2714.100998
- Mata C, Miró E, Rivera A, Mirelis B, Coll P, Navarro F (2010) Prevalence of acquired AmpC β-lactamases in Enterobacteriaceae lacking inducible chromosomal ampC genes at a Spanish hospital from 1999 to 2007. Clinical Microbiology and Infection 16 (5): 472‑476. https://doi.org/10.1111/j.1469-0691.2009.02864.x
- Norsworthy A, Pearson M (2017) From Catheter to Kidney Stone: The Uropathogenic Lifestyle of Proteus mirabilis. Trends in Microbiology 25 (4): 304‑315. https://doi.org/10.1016/j.tim.2016.11.015
- O'Hara CM, Brenner F, Miller JM (2000) Classification, Identification, and Clinical Significance of Proteus , Providencia , and Morganella. Clinical Microbiology Reviews 13 (4): 534‑546. https://doi.org/10.1128/CMR.13.4.534
- Pecoraro C, Carbone D, Parrino B, Cascioferro S, Diana P (2023) Recent Developments in the Inhibition of Bacterial Adhesion as Promising Anti-Virulence Strategy. International Journal of Molecular Sciences 24 (5). https://doi.org/10.3390/ijms24054872
- Psonis J, Chahales P, Henderson N, Rigel N, Hoffman P, Thanassi D (2019) The small molecule nitazoxanide selectively disrupts BAM-mediated folding of the outer membrane usher protein. Journal of Biological Chemistry 294 (39): 14357‑14369. https://doi.org/10.1074/jbc.ra119.009616
- Ricci D, Silhavy T (2019) Outer Membrane Protein Insertion by the β-barrel Assembly Machine. In: M. Sandkvist ECaPC (Ed.) Protein Secretion in Bacteria. [ISBN 978-1-68367-044-5 978-1-68367-027-8]. https://doi.org/10.1128/9781683670285.ch8
- Rosa SV, Santos W (2020) Clinical trials on drug repositioning for COVID-19 treatment. Revista Panamericana de Salud Pública 44 https://doi.org/10.26633/rpsp.2020.40
- Rudrapal M, J. Khairnar S, G. Jadhav A (2020) Drug Repurposing (DR): An Emerging Approach in Drug Discovery. In: Badria F (Ed.) Drug Repurposing - Hypothesis, Molecular Aspects and Therapeutic Applications. [ISBN 978-1-83968-520-0 978-1-83968-521-7]. https://doi.org/10.5772/intechopen.93193
- Sander T, Freyss J, Von Korff M, Rufener C (2015) DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. Journal of Chemical Information and Modeling 55 (2): 460‑473. https://doi.org/10.1021/ci500588j
- Schaffer J, Pearson M (2016) Proteus mirabilis and Urinary Tract Infections. In: Matthew A. Mulvey DKAES (Ed.) Urinary Tract Infections. [ISBN 978-1-68367-065-0 978-1-55581-739-8]. https://doi.org/10.1128/9781555817404.ch17
- Shrivastava S, Shrivastava P, Ramasamy J (2018) World health organization releases global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. Journal of Medical Society 32 (1). https://doi.org/10.4103/jms.jms_25_17
- Stamm W, Norrby SR (2001a) Urinary Tract Infections: Disease Panorama and Challenges. The Journal of Infectious Diseases 183 (s1). https://doi.org/10.1086/318850
- Stamm W, Norrby SR (2001b) Urinary Tract Infections: Disease Panorama and Challenges. The Journal of Infectious Diseases 183 https://doi.org/10.1086/318850
- Talevi A (2018) Drug repositioning: current approaches and their implications in the precision medicine era. Expert Review of Precision Medicine and Drug Development 3 (1): 49‑61. https://doi.org/10.1080/23808993.2018.1424535
- Torzewska A, Rozalski A (2014) Inhibition of crystallization caused by Proteus mirabilis during the development of infectious urolithiasis by various phenolic substances. Microbiological Research 169 (7-8): 579‑584. https://doi.org/10.1016/j.micres.2013.09.020
- Turanli B, Grøtli M, Boren J, Nielsen J, Uhlen M, Arga K, Mardinoglu A (2018) Drug Repositioning for Effective Prostate Cancer Treatment. Frontiers in Physiology 9 https://doi.org/10.3389/fphys.2018.00500
- Vaca D, Thibau A, Schütz M, Kraiczy P, Happonen L, Malmström J, Kempf VJ (2019) Interaction with the host: the role of fibronectin and extracellular matrix proteins in the adhesion of Gram-negative bacteria. Medical Microbiology and Immunology 209 (3): 277‑299. https://doi.org/10.1007/s00430-019-00644-3
- Wang X, Peterson J, Bernstein H (2021) Bacterial Outer Membrane Proteins Are Targeted to the Bam Complex by Two Parallel Mechanisms. mBio 12 (3). https://doi.org/10.1128/mBio.00597-21
- Wiegand I, Hilpert K, Hancock REW (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nature Protocols 3 (2): 163‑175. https://doi.org/10.1038/nprot.2007.521
- Wu T, Malinverni J, Ruiz N, Kim S, Silhavy T, Kahne D (2005a) Identification of a Multicomponent Complex Required for Outer Membrane Biogenesis in Escherichia coli. Cell 121 (2): 235‑245. https://doi.org/10.1016/j.cell.2005.02.015
- Wu T, Malinverni J, Ruiz N, Kim S, Silhavy T, Kahne D (2005b) Identification of a Multicomponent Complex Required for Outer Membrane Biogenesis in Escherichia coli. Cell 121 (2): 235‑245. https://doi.org/10.1016/j.cell.2005.02.015
- Xue H, Li J, Xie H, Wang Y (2018) Review of Drug Repositioning Approaches and Resources. International Journal of Biological Sciences 14 (10): 1232‑1244. https://doi.org/10.7150/ijbs.24612