Structure-based Virtual Screening Approach for the Discovery of Potent Inhibitors of Aminoglycoside 6'-N-Acetyltransferase Type Ib [AAC(6')-Ib] against K. pneumoniae Infections

Author(s): Reaz Uddin*, Bushra Siraj, Sidra Rafi, Syed Sikander Azam, Abdul Wadood

Journal Name: Letters in Drug Design & Discovery

Volume 17 , Issue 8 , 2020

Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Background: Aminoglycoside 6'-N-acetyltransferase type Ib (AAC(6')-Ib) from Klebsiella pneumoniae is an established drug target and has conferred insensitivity to aminoglycosides. Aminoglycosides are often inactivated by aminoglycoside modifying enzymes encoded by genes present in the chromosome, plasmids, and other genetic elements. The AAC(6′)- Ib is an enzyme of clinical importance found in a wide variety of gram-negative pathogens. The AAC(6′)-Ib enzyme is of interest not only because of its ubiquity but also because of other characteristics e.g., it presents significant microheterogeneity at the N-termini and the aac(6′)-Ib gene is often present in integrons, transposons, plasmids, genomic islands, and other genetic structures. The majority of the reported potent inhibitors against the target are substrate analogs. Therefore, there is a need to develop or discover new scaffolds other than substrate analogs as AAC(6')-Ib inhibitor.

Objective: The objective of this study is to set optimum parameters for the structure-based virtual screening by multiple docking and scoring methods. The multiple scoring of each ligand also incorporates the ‘Induced Fit’ docking effect that helps to build further confidence in the shortlisted compounds. The method eventually is able to predict the potential inhibitors that bind to the active site and can potentially inhibit the activity of the Aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6’)-Ib] from Klebsiella pneumoniae.

Methods: Using the available three-dimensional structure of enzyme AAC(6')-Ib inhibitor complex, a structure-based virtual screening was performed with the hope of prioritizing the promising leads. In order to set up the protocol, 30,000 drug-like molecules were selected from the ChemBridge library. Multiple docking programs, i.e. UCSF DOCK6 and AutoDock Vina have been applied in the current study so that a consensus is developed to the predicted binding modes and thus the docking accuracy. The Amber scores of the Dock6 – a secondary scoring function was also used to perform the ‘Induced Fit’ effect and correspondingly re-rank the compounds.

Results: The top 30 ranked compounds of the most frequent scored were selected from the histogram. The 2D interactions of those 30 compounds were drawn from the Ligplot+ tool. Six of the compounds were prioritized as potential inhibitors as they are representing the maximum number of interactions from the rest of the compounds and also possess the drug-likeness as predicted by the estimated ADMET properties.

Conclusion: This study provided useful insight that the proposed compounds have the potential to bind to the aminoglycoside binding site of AAC(6′)-Ib that may eventually inhibit the Klebsiella pneumoniae. This study has the potential to propose putative new and novel inhibitors against a resistant drug target of Klebsiella pneumoniae.

Keywords: Aminoglycosides, drug resistant, K. pneumoniae, virtual screening, docking, ADMET.

Vakulenko, S.B.; Mobashery, S. Versatility of aminoglycosides and prospects for their future. Clin. Microbiol. Rev., 2003, 16(3), 430-450.
[] [PMID: 12857776]
Yao, J.D.; Moellering, R.C. In Manual of Clinical Microbiology, 10th ed; American Society of Microbiology, 2011, pp. 1043-1081.
Bakker, E.P. Aminoglycoside and aminocyclitol antibiotics: hygromycin B is an atypical bactericidal compound that exerts effects on cells of Escherichia coli characteristics for bacteriostatic aminocyclitols. J. Gen. Microbiol., 1992, 138(3), 563-569.
[] [PMID: 1375624]
Busse, H-J.; Wöstmann, C.; Bakker, E.P. The bactericidal action of streptomycin: membrane permeabilization caused by the insertion of mistranslated proteins into the cytoplasmic membrane of Escherichia coli and subsequent caging of the antibiotic inside the cells due to degradation of these proteins. J. Gen. Microbiol., 1992, 138(3), 551-561.
[] [PMID: 1375623]
Vicens, Q.; Westhof, E. Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures. Biopolymers, 2003, 70(1), 42-57.
[] [PMID: 12925992]
Magnet, S.; Blanchard, J.S. Molecular insights into aminoglycoside action and resistance. Chem. Rev., 2005, 105(2), 477-498.
[] [PMID: 15700953]
Bonomo, R. A.; Tolmasky, M. enzyme-mediated resistance to antibiotics: mechanisms, dissemination, and prospects for inhibition 2007.
Ramirez, M.S.; Tolmasky, M.E. Aminoglycoside modifying enzymes. Drug Resist. Updat., 2010, 13(6), 151-171.
[] [PMID: 20833577]
Mikkelsen, N.E.; Brännvall, M.; Virtanen, A.; Kirsebom, L.A. Inhibition of RNase P RNA cleavage by aminoglycosides. Proc. Natl. Acad. Sci. USA, 1999, 96(11), 6155-6160.
[] [PMID: 10339557]
Mehta, R.; Champney, W. S. neomycin and paromomycin inhibit 30s ribosomal subunit assembly in staphylococcus aureus. curr. microbiol. 2003, 47(3), 0237--0243.
Belousoff, M.J.; Graham, B.; Spiccia, L.; Tor, Y. Cleavage of RNA oligonucleotides by aminoglycosides. Org. Biomol. Chem., 2009, 7(1), 30-33.
[] [PMID: 19081939]
Boehr, D.D.; Draker, K.A.; Koteva, K.; Bains, M.; Hancock, R.E.; Wright, G.D. Broad-spectrum peptide inhibitors of aminoglycoside antibiotic resistance enzymes. Chem. Biol., 2003, 10(2), 189-196.
[] [PMID: 12618191]
Jana, S.; Deb, J.K. Molecular understanding of aminoglycoside action and resistance. Appl. Microbiol. Biotechnol., 2006, 70(2), 140-150.
[] [PMID: 16391922]
Lin, D.L.; Tran, T.; Adams, C.; Alam, J.Y.; Herron, S.R.; Tolmasky, M.E. Inhibitors of the aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6′)-Ib] identified by in silico molecular docking. Bioorg. Med. Chem. Lett., 2013, 23(20), 5694-5698.
[] [PMID: 24011645]
Warburg, G.; Hidalgo-Grass, C.; Partridge, S.R.; Tolmasky, M.E.; Temper, V.; Moses, A.E.; Block, C.; Strahilevitz, J. A carbapenem-resistant Klebsiella pneumoniae epidemic clone in Jerusalem: sequence type 512 carrying a plasmid encoding aac(6′)-. Ib. J. Antimicrob. Chemother., 2012, 67(4), 898-901.
[] [PMID: 22287232]
Vading, M.; Nauclér, P.; Kalin, M.; Giske, C.G. Invasive infection caused by Klebsiella pneumoniae is a disease affecting patients with high comorbidity and associated with high long-term mortality. PLoS One, 2018, 13(4)e0195258
[] [PMID: 29624618]
Chiem, K.; Fuentes, B.A.; Lin, D.L.; Tran, T.; Jackson, A.; Ramirez, M.S.; Tolmasky, M.E. Inhibition of aminoglycoside 6′-N-acetyltransferase type Ib-mediated amikacin resistance in Klebsiella pneumoniae by zinc and copper pyrithione. Antimicrob. Agents Chemother., 2015, 59(9), 5851-5853.
[] [PMID: 26169410]
Siu, L.K.; Yeh, K-M.; Lin, J-C.; Fung, C-P.; Chang, F-Y. Klebsiella pneumoniae liver abscess: a new invasive syndrome. Lancet Infect. Dis., 2012, 12(11), 881-887.
[] [PMID: 23099082]
Williams, P.; Tomas, J. The pathogenicity of Klebsiella pneumoniae. Rev. Med. Microbiol., 1990, 1, 196-204.
Labby, K.J.; Garneau-Tsodikova, S. Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections. Future Med. Chem., 2013, 5(11), 1285-1309.
[] [PMID: 23859208]
Gao, F.; Yan, X.; Baettig, O.M.; Berghuis, A.M.; Auclair, K. Regio- and chemoselective 6′-N-derivatization of aminoglycosides: bisubstrate inhibitors as probes to study aminoglycoside 6′-N-acetyltransferases. Angew. Chem. Int. Ed. Engl., 2005, 44(42), 6859-6862.
[] [PMID: 16206301]
Gao, F.; Yan, X.; Shakya, T.; Baettig, O.M.; Ait-Mohand-Brunet, S.; Berghuis, A.M.; Wright, G.D.; Auclair, K. Synthesis and structure-activity relationships of truncated bisubstrate inhibitors of aminoglycoside 6′-N-acetyltransferases. J. Med. Chem., 2006, 49(17), 5273-5281.
[] [PMID: 16913716]
Williams, J.W.; Northrop, D.B. Synthesis of a tight-binding, multisubstrate analog inhibitor of gentamicin acetyltransferase I. J. Antibiot. (Tokyo), 1979, 32(11), 1147-1154.
[] [PMID: 393684]
Li, Y.; Green, K.D.; Johnson, B.R.; Garneau-Tsodikova, S. Inhibition of aminoglycoside acetyltransferase resistance enzymes by metal salts. Antimicrob. Agents Chemother., 2015, 00885-00815.
Chiem, K.; Hue, F.; Magallon, J.; Tolmasky, M.E. Inhibition of aminoglycoside 6′-N-acetyltransferase type Ib-mediated amikacin resistance by zinc complexed with clioquinol, an ionophore active against tumors and neurodegenerative diseases. Int. J. Antimicrob. Agents, 2018, 51(2), 271-273.
[] [PMID: 28782708]
Tran, T.; Chiem, K.; Jani, S.; Arivett, B.A.; Lin, D.L.; Lad, R.; Jimenez, V.; Farone, M.B.; Debevec, G.; Santos, R.; Giulianotti, M.; Pinilla, C.; Tolmasky, M.E. Identification of a small molecule inhibitor of the aminoglycoside 6′-N-acetyltransferase type Ib [AAC(6′)-Ib] using mixture-based combinatorial libraries. Int. J. Antimicrob. Agents, 2018, 51(5), 752-761.
[] [PMID: 29410367]
Lombès, T.; Bégis, G.; Maurice, F.; Turcaud, S.; Lecourt, T.; Dardel, F.; Micouin, L. NMR-guided fragment-based approach for the design of AAC(6′)-Ib ligands. ChemBioChem, 2008, 9(9), 1368-1371.
[] [PMID: 18464231]
Soler Bistué, A.J.; Martín, F.A.; Vozza, N.; Ha, H.; Joaquín, J.C.; Zorreguieta, A.; Tolmasky, M.E. Inhibition of aac(6′)-Ib-mediated amikacin resistance by nuclease-resistant external guide sequences in bacteria. Proc. Natl. Acad. Sci. USA, 2009, 106(32), 13230-13235.
[] [PMID: 19666539]
Garzan, A.; Willby, M.J.; Green, K.D.; Gajadeera, C.S.; Hou, C.; Tsodikov, O.V.; Posey, J.E.; Garneau-Tsodikova, S. Sulfonamide-based inhibitors of aminoglycoside acetyltransferase Eis abolish resistance to kanamycin in Mycobacterium tuberculosis. J. Med. Chem., 2016, 59(23), 10619-10628.
[] [PMID: 27933949]
Sanchez, G.V.; Master, R.N.; Clark, R.B.; Fyyaz, M.; Duvvuri, P.; Ekta, G.; Bordon, J. Klebsiella pneumoniae antimicrobial drug resistance, United States, 1998-2010. Emerg. Infect. Dis., 2013, 19(1), 133-136.
[] [PMID: 23260464]
Meng, X-Y.; Zhang, H-X.; Mezei, M.; Cui, M. Molecular docking: a powerful approach for structure-based drug discovery. Curr. Comput. Aided Drug Des., 2011, 7(2), 146-157.
[] [PMID: 21534921]
Houston, D.R.; Walkinshaw, M.D. Consensus docking: improving the reliability of docking in a virtual screening context. J. Chem. Inf. Model., 2013, 53(2), 384-390.
[] [PMID: 23351099]
Berry, M.; Fielding, B.; Gamieldien, J. Practical Considerations in Virtual Screening and Molecular emerging trends in 156 computer science and applied computing , 2015; pp. 487-502.
Vetting, M.W.; Park, C.H.; Hegde, S.S.; Jacoby, G.A.; Hooper, D.C.; Blanchard, J.S. Mechanistic and structural analysis of aminoglycoside N-acetyltransferase AAC(6′)-Ib and its bifunctional, fluoroquinolone-active AAC(6′)-Ib-cr variant. Biochemistry, 2008, 47(37), 9825-9835.
[] [PMID: 18710261]
Bernstein, F.C.; Koetzle, T.F.; Williams, G.J.; Meyer, E.F., Jr; Brice, M.D.; Rodgers, J.R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem., 1977, 80(2), 319-324.
[] [PMID: 923582]
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol., 1990, 215(3), 403-410.
[] [PMID: 2231712]
Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 2006, 22(2), 195-201.
[] [PMID: 16301204]
Volkamer, A.; Kuhn, D.; Rippmann, F.; Rarey, M. DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics, 2012, 28(15), 2074-2075.
[] [PMID: 22628523]
Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem., 2004, 25(13), 1605-1612.
[] [PMID: 15264254]
Shi, Z.; Chen, J.; Guo, X.; Cheng, L.; Guo, X.; Yu, T. In silico identification of potent small molecule inhibitors targeting epidermal growth factor receptor 1. J. Cancer Res. Ther., 2018, 14(1), 18-23.
[] [PMID: 29516953]
Trott, O.; Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2010, 31(2), 455-461.
[PMID: 19499576]
Lang, P.T.; Brozell, S.R.; Mukherjee, S.; Pettersen, E.F.; Meng, E.C.; Thomas, V.; Rizzo, R.C.; Case, D.A.; James, T.L.; Kuntz, I.D. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA, 2009, 15(6), 1219-1230.
[] [PMID: 19369428]
Jakalian, A.; Bush, B.L.; Jack, D.B.; Bayly, C.I. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method. J. Comput. Chem., 2000, 21(2), 132-146.
Jakalian, A.; Jack, D.B.; Bayly, C.I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem., 2002, 23(16), 1623-1641.
[] [PMID: 12395429]
Mazumder, D.; Case, D.A. Abstracts of Papers of the American Chemical Society; AMER CHEMICAL SOC 1155 16TH ST, NW. WASHINGTON, DC, 2007, 233, 20.
Tetko, I.V.; Gasteiger, J.; Todeschini, R.; Mauri, A.; Livingstone, D.; Ertl, P.; Palyulin, V.A.; Radchenko, E.V.; Zefirov, N.S.; Makarenko, A.S.; Tanchuk, V.Y.; Prokopenko, V.V. Virtual computational chemistry laboratory--design and description. J. Comput. Aided Mol. Des., 2005, 19(6), 453-463.
[] [PMID: 16231203]
Laskowski, R.A.; Swindells, M.B. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 2011, 51(10), 2778-2786.
[] [PMID: 21919503]
Lavecchia, A.; Di Giovanni, C. Virtual screening strategies in drug discovery: a critical review. Curr. Med. Chem., 2013, 20(23), 2839-2860.
[] [PMID: 23651302]
Benod, C.; Carlsson, J.; Uthayaruban, R.; Hwang, P.; Irwin, J.J.; Doak, A.K.; Shoichet, B.K.; Sablin, E.P.; Fletterick, R.J. Structure-based discovery of antagonists of nuclear receptor LRH-1. J. Biol. Chem., 2013, 288(27), 19830-19844.
[] [PMID: 23667258]
Cheng, T.; Li, Q.; Zhou, Z.; Wang, Y.; Bryant, S.H. Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J., 2012, 14(1), 133-141.
[] [PMID: 22281989]
Andricopulo, A.D.; Salum, L.B.; Abraham, D.J. Structure-based drug design strategies in medicinal chemistry. Curr. Top. Med. Chem., 2009, 9(9), 771-790.
[] [PMID: 19754394]
Wolf, E.; Vassilev, A.; Makino, Y.; Sali, A.; Nakatani, Y.; Burley, S.K. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell, 1998, 94(4), 439-449.
[] [PMID: 9727487]
Dyda, F.; Klein, D.C.; Hickman, A.B. GCN5-related N-acetyltransferases: a structural overview. Annu. Rev. Biophys. Biomol. Struct., 2000, 29(1), 81-103.
[] [PMID: 10940244]
Vetting, M.W.; S de Carvalho, L.P.; Yu, M.; Hegde, S.S.; Magnet, S.; Roderick, S.L.; Blanchard, J.S. Structure and functions of the GNAT superfamily of acetyltransferases. Arch. Biochem. Biophys., 2005, 433(1), 212-226.
[] [PMID: 15581578]
Soler Bistué, A.J.; Birshan, D.; Tomaras, A.P.; Dandekar, M.; Tran, T.; Newmark, J.; Bui, D.; Gupta, N.; Hernandez, K.; Sarno, R.; Zorreguieta, A.; Actis, L.A.; Tolmasky, M.E. Klebsiella pneumoniae multiresistance plasmid pMET1: similarity with the Yersinia pestis plasmid pCRY and integrative conjugative elements. PLoS One, 2008, 3(3)e1800
[] [PMID: 18350140]

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2020
Page: [1027 - 1035]
Pages: 9
DOI: 10.2174/1570180817666200108095912
Price: $65

Article Metrics

PDF: 16