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On the active site of mononuclear B1 metallo β-lactamases: a computational study

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Abstract

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called ‘3H’ and ‘DCH’ sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum–classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.

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Notes

  1. A short MD calculation (400 ps) has been run removing the postion restraints on the water molecules after the equilibration, however Wat-H conserves its propensity to exchange its position with other water molecules from the bulk. Then the structure equilibrated with postion restraints was used in the subsequent QM/MM MD.

References

  1. Crowder MW, Spencer J, Vila AJ (2006) Acc Chem Res 39:721–728

    Article  CAS  Google Scholar 

  2. Toney JH, Moloughney JG (2004) Curr Opin Investig Drugs 5:823–826

    CAS  Google Scholar 

  3. Perez-Llarena FJ, Bou G (2009) Curr Med Chem 16:3740–3765

    Article  CAS  Google Scholar 

  4. Simona F, Magistrato A, Dal Peraro M, Cavalli A, Vila AJ, Carloni P (2009) J Biol Chem 284:28164–28171

    Article  CAS  Google Scholar 

  5. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR (2009) Antimicrob Agents Chemother 53:5046–5054

    Article  CAS  Google Scholar 

  6. Carfi A, Pares S, Duee E, Galleni M, Duez C, Frere JM, Dideberg O (1995) EMBO J 14:4914–4921

    CAS  Google Scholar 

  7. Orellano EG, Girardini JE, Cricco JA, Ceccarelli EA, Vila AJ (1998) Biochemistry 37:10173–10180

    Article  CAS  Google Scholar 

  8. Fabiane SM, Sohi MK, Wan T, Payne DJ, Bateson JH, Mitchell T, Sutton BJ (1998) Biochemistry 37:12404–12411

    Article  CAS  Google Scholar 

  9. Bebrone C (2007) Biochem Pharmacol 74:1686–1701

    Article  CAS  Google Scholar 

  10. Bounaga S, Laws AP, Galleni M, Page MI (1998) Biochem J 331:703–711

    CAS  Google Scholar 

  11. Gonzalez JM, Buschiazzo A, Vila AJ (2010) Biochemistry 49:7930–7938

    Article  CAS  Google Scholar 

  12. Llarrull LI, Tioni MF, Vila AJ (2008) J Am Chem Soc 130(47):15842–15851

    Article  CAS  Google Scholar 

  13. Garau G, Lemaire D, Vernet T, Dideberg O, Di Guilmi AM (2005) J Biol Chem 280:28591–28600

    Article  CAS  Google Scholar 

  14. Lisa M-N, Hemmingsen L, Vila AJ (2010) J Biol Chem 285:4570–4577

    Google Scholar 

  15. Moran-Barrio J, Gonzalez JM, Lisa MN, Costello AL, Peraro MD, Carloni P, Bennett B, Tierney DL, Limansky AS, Viale AM, Vila AJ (2007) J Biol Chem 282:18286–18293

    Article  CAS  Google Scholar 

  16. Spencer J, Read J, Sessions RB, Howell S, Blackburn GM, Gamblin SJ (2005) J Am Chem Soc 127:14439–14444

    Article  CAS  Google Scholar 

  17. Tioni MF, Llarrull LI, Poeylaut-Palena AA, Marti MA, Saggu M, Periyannan GR, Mata EG, Bennett B, Murgida DH, Vila AJ (2008) J Am Chem Soc 130:15852–15863

    Article  CAS  Google Scholar 

  18. Gonzalez JM, Medrano Martin FJ, Costello AL, Tierney DL, Vila AJ (2007) J Mol Biol 373:1141–1156

    Article  CAS  Google Scholar 

  19. Tomatis PE, Fabiane SM, Simona F, Carloni P, Sutton BJ, Vila AJ (2008) Proc Natl Acad Sci U S A 105:20605–20610

    Article  CAS  Google Scholar 

  20. Rasia RM, Vila AJ (2004) J Biol Chem 279:26046–26051

    Article  CAS  Google Scholar 

  21. Dal Peraro M, Llarrull LI, Rothlisberger U, Vila AJ, Carloni P (2004) J Am Chem Soc 126:12661–12668

    Article  CAS  Google Scholar 

  22. Dal Peraro M, Vila AJ, Carloni P (2004) Proteins 54:412–423

    Article  CAS  Google Scholar 

  23. Olsen L, Jost S, Adolph H-W, Pettersson I, Hemmingsen L, Jorgensen FS (2006) Bioorg Med Chem 14:2627–2635

    Article  CAS  Google Scholar 

  24. Simona F, Magistrato A, Vera DMA, Garau G, Vila AJ, Carloni P (2007) Proteins 69:595–605

    Article  CAS  Google Scholar 

  25. Wu S, Xu D, Guo H (2010) J Am Chem Soc 132:17986–17988

    Article  CAS  Google Scholar 

  26. Dal Peraro M, Vila AJ, Carloni V (2010) In: Matta F (ed) Quantum biochemistry. New York, USA, pp 605–622

  27. Xu D, Zhou Y, Xie D, Guo H (2005) J Med Chem 48:6679–6689

    Article  CAS  Google Scholar 

  28. Dal Peraro M, Vila AJ, Carloni P (2002) J Biol Inorg Chem 7:704–712

    Article  CAS  Google Scholar 

  29. Magistrato A, DeGrado WF, Laio A, Rothlisberger U, VandeVondele J, Klein ML (2003) J Phys Chem B 107:4182–4188

    Article  CAS  Google Scholar 

  30. Hong R, Magistrato A, Carloni P (2008) J Chem Theory Comput 4:1745–1756

    Article  CAS  Google Scholar 

  31. Becke AD (1988) Phys Rev A 38:3098–3100

    Article  CAS  Google Scholar 

  32. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789

    Article  CAS  Google Scholar 

  33. Becke AD (1993) J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  34. Wang J, Cieplak P, Kollman P (2000) J Comp Chem 21:1049–1074

    Article  CAS  Google Scholar 

  35. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25:1157–1174

    Article  CAS  Google Scholar 

  36. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein LM (1983) J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  37. Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) J Phys Chem 97:10269–10280

    Article  CAS  Google Scholar 

  38. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Laham A, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian 03, Revision C.02

  39. Diaz N, Suarez D, Merz KM (2001) J Am Chem Soc 123:9867–9879

    Article  CAS  Google Scholar 

  40. Suarez D, Diaz N, Merz KM (2002) J Comput Chem 23(16):1587–1600

    Article  CAS  Google Scholar 

  41. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts BP, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2010) AMBER 11. University of California, San Francisco

    Google Scholar 

  42. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comp Phys 23:327–341

    Article  CAS  Google Scholar 

  43. Garau G, Bebrone C, Anne C, Galleni M, Frere J-M, Dideberg O (2005) J Mol Biol 345:785–795

    Article  CAS  Google Scholar 

  44. Suarez D, Merz KM (2001) J Am Chem Soc 123:3759–3770

    Article  CAS  Google Scholar 

  45. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9, University of California. University of California, San Francisco, San Francisco

    Google Scholar 

  46. VandeVondele J, Krack M, Mohamed F, Parrinello M, Chassain T, Hutter J (2005) Comput Phys Commun 167:103–128

    Article  CAS  Google Scholar 

  47. Laino T, Mohamed F, Laio A, Parrinello M (2005) J Chem Theory Comput 1:1176–1184

    Article  CAS  Google Scholar 

  48. Laino T, Mohamed F, Laio A, Parrinello M (2006) J Chem Theory Comput 2:1370–1378

    Article  CAS  Google Scholar 

  49. Goedecker S, Teter M, Hutter J (1996) Phys Rev B 54:1703–1710

    Article  CAS  Google Scholar 

  50. Hartwigsen C, Goedecker S, Hutter J (1998) Phys Rev B 58:3641–3662

    Article  CAS  Google Scholar 

  51. Hoover WG (1985) Phys Rev A 31:1695–1697

    Article  Google Scholar 

  52. Shao J, Tanner SW, Thompson N, Cheatham TE (2007) J Chem Theory Comput 3:2312–2334

    Article  CAS  Google Scholar 

  53. Xu D, Xie D, Guo H (2006) J Biol Chem 281:8740–8747

    Article  CAS  Google Scholar 

  54. Fonseca F, Bromley EHC, Saavedra MJ, Correia A, Spencer J (2011) J Mol Biol 411:951–959

    Article  CAS  Google Scholar 

  55. Spiegel K, Magistrato A (2006) Org Biomol Chem 4:2507–2517

    Article  CAS  Google Scholar 

  56. Sgrignani J, Magistrato A (2012) J Phys Chem B 116:2259–2268

    Article  CAS  Google Scholar 

  57. Llarrull LI, Fabiane SM, Kowalski JM, Bennett B, Sutton BJ, Vila AJ (2007) J Biol Chem 282:18276–18285

    Article  CAS  Google Scholar 

  58. Tomatis PE, Rasia RM, Segovia L, Vila AJ (2005) Proc Natl Acad Sci USA 102:13761–13766

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work has been supported in part by the FIRB project Contract RBLA032ZM7, by the EC contract SPINE II n° 031220 and by grants from HHMI (Howard Hughes Medical Instituteand ANPCyT (Agencia Nacional de Promoción Científica y Tecnológica) to AJV. AJV is a fellow of the John Simon Guggenheim Foundation and an HHMI International Research Scholar. Access to the computational resources supplied by CASPUR and by CINECA is gratefully acknowledged.

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Author notes

  1. Jacopo Sgrignani

    Present address: CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy

Authors and Affiliations

  1. CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy

    Jacopo Sgrignani & Roberta Pierattelli

  2. CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy

    Alessandra Magistrato

  3. Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne—EPFL, 1015, Lausanne, Switzerland

    Matteo Dal Peraro

  4. Instituto de Biología Molecular y Celular de Rosario (IBR); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, S2002LRK, Rosario, Argentina

    Alejandro J. Vila

  5. Computational Biophysics, German Research School for Simulation Sciences, 52425, Jülich, Germany

    Paolo Carloni

  6. Institute for Advanced Simulation, Forschungszentrum Jülich, 52425, Jülich, Germany

    Paolo Carloni

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  1. Jacopo Sgrignani
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Correspondence to Alessandra Magistrato or Roberta Pierattelli.

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Paolo Carloni: Joint venture of RWTH Aachen University and Forschungszentrum Jülich, Germany.

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Sgrignani, J., Magistrato, A., Dal Peraro, M. et al. On the active site of mononuclear B1 metallo β-lactamases: a computational study. J Comput Aided Mol Des 26, 425–435 (2012). https://doi.org/10.1007/s10822-012-9571-0

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