Skip to main content
Log in

Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

Abstract

β-Lactamases are bacterial enzymes conferring resistance to β-lactam antibiotics in clinically-relevant pathogens, and represent relevant drug targets. Recently, the identification of new boronic acids (i.e. RPX7009) paved the way to the clinical application of these molecules as potential drugs. Here, we screened in silico a library of ~1400 boronic acids as potential AmpC β-lactamase inhibitors. Six of the most promising candidates were evaluated in biochemical assays leading to the identification of potent inhibitors of clinically-relevant β-lactamases like AmpC, KPC-2 and CTX-M-15. One of the selected compounds showed nanomolar K i value with the clinically-relevant KPC-2 carbapenemase, while another one exhibited broad spectrum inhibition, being also active on Enterobacter AmpC and the OXA-48 class D carbapenemase.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Drawz SM, Bonomo RA (2010) Three decades of beta-lactamase inhibitors. Clin Microbiol Rev 23(20065329):160–201

    Article  CAS  Google Scholar 

  2. Drawz SM, Papp-Wallace KM, Bonomo RA (2014) New beta-lactamase inhibitors: a therapeutic renaissance in an MDR world. Antimicrob Agents Chemother 58:1835–1846

    Article  Google Scholar 

  3. Farina D, Spyrakis F, Venturelli A, Cross S, Tondi D, Costi MP (2014) Curr Med Chem 21:1405–1434

    Article  CAS  Google Scholar 

  4. Ambler RP (1980) Philos Trans R Soc Lond Ser B Biol Sci 289:321–331

    Article  CAS  Google Scholar 

  5. Prestinaci F, Pezzotti P, Pantosti A (2015) Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health 109:309–318

    Article  Google Scholar 

  6. Livermore DM, Mushtaq S, Warner M, Miossec C, Woodford N (2008) NXL104 combinations versus Enterobacteriaceae with CTX-M extended-spectrum beta-lactamases and carbapenemases. J Antimicrob Chemother 62:1053–1056

    Article  CAS  Google Scholar 

  7. Hirsch EB, Ledesma KR, Chang KT, Schwartz MS, Motyl MR, Tam VH (2012) In vitro activity of MK-7655, a novel beta-lactamase inhibitor, in combination with imipenem against carbapenem-resistant gram-negative bacteria. Antimicrob Agents Chemother 56:3753–3757

    Article  CAS  Google Scholar 

  8. Hecker SJ, Reddy KR, Totrov M, Hirst GC, Lomovskaya O, Griffith DC, King P, Tsivkovski R, Sun D, Sabet M, Tarazi Z, Clifton MC, Atkins K, Raymond A, Potts KT, Abendroth J, Boyer SH, Loutit JS, Morgan EE, Durso S, Dudley MN (2015) Discovery of a cyclic boronic acid beta-lactamase inhibitor (RPX7009) with utility vs class A serine carbapenemases. J Med Chem 58:3682–3692

    Article  CAS  Google Scholar 

  9. Livermore DM, Warner M, Mushtaq S (2013) Activity of MK-7655 combined with imipenem against Enterobacteriaceae and Pseudomonas aeruginosa. J Antimicrob Chemother 68:2286–2290

    CAS  Google Scholar 

  10. https://clinicaltrials.gov/ct2/show/NCT01897779

  11. Weston GS, Blazquez J, Baquero F, Shoichet BK (1998) Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase. J Med Chem 41:4577–4586

    Article  CAS  Google Scholar 

  12. Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP (2014) Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative. J Med Chem 57:5449–5458

    Article  CAS  Google Scholar 

  13. Morandi F, Caselli E, Morandi S, Focia PJ, Blazquez J, Shoichet BK, Prati F (2003) Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc 125:685–695

    Article  CAS  Google Scholar 

  14. Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F (2012) Fragment-guided design of subnanomolar beta-lactamase inhibitors active in vivo. Proc Natl Acad Sci USA 109:17448–17453

    Article  CAS  Google Scholar 

  15. Wang X, Minasov G, Blazquez J, Caselli E, Prati F, Shoichet BK (2003) Recognition and resistance in TEM beta-lactamase. Biochemistry 42:8434–8444

    Article  CAS  Google Scholar 

  16. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J (2014) Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol 10:1066–1072

    Article  CAS  Google Scholar 

  17. Sgrignani J, Novati B, Colombo G, Grazioso G (2015) Covalent docking of selected boron-based serine beta-lactamase inhibitors. J Comput Aided Mol Des 29:441–450

    Article  CAS  Google Scholar 

  18. http://www.sigmaaldrich.com/chemistry/chemistry-services/selected-structure.html. Accessed 18 Apr 2014

  19. Beesley T, Gascoyne N, Knott-Hunziker V, Petursson S, Waley SG, Jaurin B, Grundström T (1983) The inhibition of class C β-lactamases by boronic acids. Biochem J 209:229–233

    Article  CAS  Google Scholar 

  20. Tondi D, Calò S, Shoichet BK, Costi MP (2010) Structural study of phenyl boronic acid derivatives as AmpC β-lactamase inhibitors. Bioorg Med Chem Lett 20:3416–3419

    Article  CAS  Google Scholar 

  21. Dubus A, Normark S, Kania M, Page MG (1995) Role of asparagine 152 in catalysis of beta-lactam hydrolysis by Escherichia coli AmpC beta-lactamase studied by site-directed mutagenesis. Biochemistry 34:7757–7764

    Article  CAS  Google Scholar 

  22. Powers RA, Shoichet BK (2002) Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem 45:3222–3234

    Article  CAS  Google Scholar 

  23. McKinney DC, Zhou F, Eyermann CJ, Ferguson AD, Prince DB, Breen J, Giacobbe RA, Lahiri S, Verheijen JC (2015) 4,5-disubstituted 6-aryloxy-1,3-dihydrobenzo[c][1, 2]oxaboroles are broad-spectrum serine β-lactamase inhibitors. ACS Infect Dis 1:310–316

    Article  CAS  Google Scholar 

  24. Ruble JF, Lefurgy ST, Cornish VW, Powers RA (2012) Structural analysis of the Asn152Gly mutant of P99 cephalosporinase. Acta Crystallogr D 68:1189–1193

    Article  CAS  Google Scholar 

  25. Ke W, Bethel CR, Papp-Wallace KM, Pagadala SR, Nottingham M, Fernandez D, Buynak JD, Bonomo RA, van den Akker F (2012) Crystal structures of KPC-2 beta-lactamase in complex with 3-nitrophenyl boronic acid and the penam sulfone PSR-3-226. Antimicrob Agents Chemother 56:2713–2718

    Article  CAS  Google Scholar 

  26. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727–748

    Article  CAS  Google Scholar 

  27. Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WT, Mortenson PN, Murray CW (2007) Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 50:726–741

    Article  CAS  Google Scholar 

  28. Clark M, Cramer RD, Van Opdenbosch N (1989) Validation of the general purpose tripos 5.2 force field. J Comput Chem 10:982–1012

    Article  CAS  Google Scholar 

  29. Korb O, Stutzle T, Exner TE (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Mod 49:84–96

    Article  CAS  Google Scholar 

  30. Johnson SC (1967) Hierarchical clustering schemes. Psychometrika 32:241–254

    Article  CAS  Google Scholar 

  31. Borgianni L, Vandenameele J, Matagne A, Bini L, Bonomo RA, Frère JM, Rossolini GM, Docquier JD (2010) Mutational analysis of VIM-2 reveals an essential determinant for metallo-beta-lactamase stability and folding. Antimicrob Agents Chemother 54:3197–3204

    Article  CAS  Google Scholar 

  32. De Luca F, Benvenuti M, Carboni F, Pozzi C, Rossolini GM, Mangani S, Docquier JD (2011) Evolution to carbapenem-hydrolyzing activity in noncarbapenemase class D β-lactamase OXA-10 by rational protein design. Proc Natl Acad Sci USA 108:18424–18429

    Article  Google Scholar 

  33. De Luca F, Rossolini GM, Docquier JD (2015) In: ASM Press (ed) 55th Interscience conference on antimicrobial agents and chemotherapy, ICAAC/ICC 2015. Washington DC, San Diego, CA

  34. Docquier JD, Calderone V, De Luca F, Benvenuti M, Giuliani F, Bellucci L, Tafi A, Nordmann P, Botta M, Rossolini GM, Mangani S (2009) Crystal structure of the OXA-48 beta-lactamase reveals mechanistic diversity among class D carbapenemases. Chem Biol 16:540–547

    Article  CAS  Google Scholar 

  35. Lahiri SD, Mangani S, Durand-Reville T, Benvenuti M, De Luca F, Sanyal G, Docquier JD (2013) Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC β-lactamases. Antimicrob Agents Chemother 57:2496–2505

    Article  CAS  Google Scholar 

  36. Docquier JD, Pantanella F, Giuliani F, Thaller MC, Amicosante G, Galleni M, Frere JM, Bush K, Rossolini GM (2002) CAU-1, a subclass B3 metallo-beta-lactamase of low substrate affinity encoded by an ortholog present in the Caulobacter crescentus chromosome. Antimicrob Agents Chemother 46:1823–1830

    Article  CAS  Google Scholar 

  37. Docquier JD, Lamotte-Brasseur J, Galleni M, Amicosante G, Frere JM, Rossolini GM (2003) On functional and structural heterogeneity of VIM-type metallo-beta-lactamases. J Antimicrob Chemother 51:257–266

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We kindly acknowledge Prof. Brian K. Shoichet for the availability to test our compounds. GC acknowledges Grant IG15420 from AIRC. We acknowledge the CINECA and the Regione Lombardia award under the LISA initiative, for the availability of high performance computing resources and support.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Giorgio Colombo or Giovanni Grazioso.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 3677 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sgrignani, J., De Luca, F., Torosyan, H. et al. Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors. J Comput Aided Mol Des 30, 851–861 (2016). https://doi.org/10.1007/s10822-016-9962-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-016-9962-8

Keywords

Navigation