Covalent docking of selected boron-based serine beta-lactamase inhibitors

Journal of Computer-Aided Molecular Design

Volumn 29, Issue 5, 2015, Pages 441-450

  Sgrignani, Jacopo ^b,c   Novati, Beatrice ^a   Colombo, Giorgio ^b   Grazioso, Giovanni ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b CNR   (Italy)

^c Institute of Research in Biomedicine   (Switzerland)

Author keywords

AmpC; Beta lactamase; Boronic acids; Docking; GOLD5.2; Inhibitors

Indexed keywords

AMINO ACIDS; ANTIBIOTICS; BACTERIA; BINDING ENERGY; BORON; LIGANDS; MOLECULES;

AMPC; BETA-LACTAMASE; BORONIC ACID; DOCKING; GOLD5.2; HYDROLYTIC ENZYME; INHIBITOR; LACTAMASES; WATER MOLECULE; Β-LACTAMASE;

ENZYMES;

BETA LACTAMASE; BETA LACTAMASE INHIBITOR; BORON; SERINE;

CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MOLECULAR DOCKING;

BETA-LACTAMASE INHIBITORS; BETA-LACTAMASES; BORON; HUMANS; MOLECULAR DOCKING SIMULATION; MOLECULAR STRUCTURE; SERINE;

EID: 84940007738     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-015-9834-7     Document Type: Article

References (53)

1. Drawz SM, Bonomo RA (2010) Three decades of beta-lactamase inhibitors. Clin Microbiol Rev 23(20065329):160-201
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
3. Farina D, Spyrakis F, Venturelli A, Cross S, Tondi D, Costi MP (2014) The inhibition of extended spectrum β-lactamases: hits and leads. Curr Med Chem 21:1405-1434
4. Ambler RP (1980) The structure of beta-lactamases. Philos Trans R Soc Lond B Biol Sci 289:321-331
5. Sgrignani J, Magistrato A, Dal Peraro M, Vila AJ, Carloni P, Pierattelli R (2012) On the active site of mononuclear B1 metallo-lactamases: a computational study. J Comput Aided Mol Des 26:425-435
6. Dal Peraro M, Carloni P (2010) Catalytic mechanism of metallo β-lactamases: insights from calculations and experiments. In: Matta F (ed) Quantum biochemistry. Wiley-VCH Verlag GmbH & Co. KGaA, New York, pp 605-622
7. Page MI, Badarau A (2008) The mechanisms of catalysis by metallo beta-lactamases. Bioinorg Chem Appl. doi: 10.1155/2008/576297
8. Simona F, Magistrato A, Dal Peraro M, Cavalli A, Vila AJ, Carloni P (2009) Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme. J Biol Chem 284:28164-28171
9. Dal Peraro M, Vila AJ, Carloni P, Klein ML (2007) Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. J Am Chem Soc 129:2808-2816
10. Kiener PA, Waley SG (1978) Reversible inhibitors of penicillinases. Biochem J 169:197-204
11. Goldstein EJ, Citron DM, Tyrrell KL, Merriam CV (2013) In vitro activity of Biapenem plus RPX7009, a carbapenem combined with a serine beta-lactamase inhibitor, against anaerobic bacteria. Antimicrob Agents Chemother 57:2620-2630
12. Warren GL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49:5912-5931
13. Coupez B, Lewis RA (2006) Docking and scoring - theoretically easy, practically impossible? Curr Med Chem 13:2995-3003
14. Weill N, Therrien E, Campagna-Slater V, Moitessier N (2013) Methods for docking small molecules to macromolecules: a user's perspective. 1. Theory Curr Pharm Des 20:3338-3359
15. Ouyang X, Zhou S, Ge Z, Li R, Kwoh CK (2013) CovalentDock Cloud: a web server for automated covalent docking. Nucl Acids Res 41(Web Server issue):W329-W332. doi: 10.1093/nar/gkt406
16. Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E (2014) Docking covalent inhibitors: a parameter free approach to pose prediction and scoring. J Chem Inf Model 54:1932-1940
17. 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
18. Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245:43-53
19. Sgrignani J, Bonaccini C, Grazioso G, Chioccioli M, Cavalli A, Gratteri P (2009) Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. J Comput Chem 30:2443-2454
20. Lexa KW, Carlson HA (2012) Protein flexibility in docking and surface mapping. Q Rev Biophys 45:301-343
21. Roberts BC, Mancera RL (2008) Ligand-protein docking with water molecules. J Chem Inf Model 48:397-408
22. Kumar A, Zhang KYJ (2013) Investigation on the effect of key water molecules on docking performance in CSARdock exercise. J Chem Inf Model 53:1880-1892
23. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič 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
24. Knight JDR, Hamelberg D, McCammon JA, Kothary R (2009) The role of conserved water molecules in the catalytic domain of protein kinases. Proteins 76:527-535
25. Powers RA, Blazquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK (1999) The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase. Protein Sci 8:2330-2337
26. Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK (2001) Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases. Chem Biol 8:17-31
27. Tondi D, Powers RA, Caselli E, Negri MC, Blázquez J, Costi MP, Shoichet BK (2001) Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase. Chem Biol 8:593-611
28. Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK (2001) Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design. Biochemistry 40:9207-9214
29. Powers RA, Shoichet BK (2002) Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem 45:3222-3234
30. Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK (2006) The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 128:2970-2976
31. Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F (2008) Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem 16:1195-1205
32. Tondi D, Calo S, Shoichet BK, Costi MP (2010) Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett 20:3416-3419
33. Eidam O, Romagnoli C, Caselli E, Babaoglu K, Pohlhaus DT, Karpiak J, Bonnet R, Shoichet BK, Prati F (2010) Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as beta-lactamase inhibitors. J Med Chem 53:7852-7863
34. 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
35. Frisch MJ, Trucks GW, Schlegel HB, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JJA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, revision A.02. Gaussian Inc., Wallingford, CT
36. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098
37. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648-5652
38. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comp Chem 30:2785-2791
39. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comp Chem 31:455-461
40. Ouyang X, Zhou S, Su CTT, Ge Z, Li R, Kwoh CK (2013) CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints. J Comp Chem 34:326-336
41. Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW (2007) Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 50:726-741
42. Clark M, Cramer RD, Van Opdenbosch N (1989) Validation of the general purpose tripos 5.2 force field. J Comp Chem 10:982-1012
43. Verdonk ML, Chessari G, Cole JC, Hartshorn MJ, Murray CW, Nissink JW, Taylor RD, Taylor R (2005) Modeling water molecules in protein-ligand docking using GOLD. J Med Chem 48:6504-6515
44. Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Walker C, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2012) Amber 12. University of California, San Francisco
45. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
46. For occupancy definition see http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui
47. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593
48. Berendsen HJC, Postma JPM, Van Gunsteren WF, Dinola A, Haak JR (1984) J Chem Phys 81:3684
49. de Beer SBA, Vermeulen NPE, Oostenbrink C (2010) The role of water molecules in computational drug design. Curr Top Med Chem 10:55-66
50. De Vivo M (2011) Bridging quantum mechanics and structure-based drug design. Front Biosci 16:1619-1633
51. Sgrignani J, Magistrato A (2013) First-principles modeling of biological systems and structure-based drug-design. Curr Comput Aided Drug Des 9:15-34
52. Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E (2014) Docking covalent inhibitors: a parameter free approach to pose prediction and scoring. J Chem Inf Mod 54:1932-1940
53. Toledo Warshaviak D, Golan G, Borrelli KW, Zhu K, Kalid O (2014) Structure-based virtual screening approach for discovery of covalently bound ligands. J Chem Inf Mod 54:1941-1950