In silico Studies on Potential Inhibitors of the Penicillin Binding Protein 2B
(PBP2B) of the Resistant G54 and Intermediate-resistant Hungary 19A-6
and SP195 Strains of Streptococcus Pneumoniae

Suvaiyarasan      Suvaithenamudhan; Subbiah      Parthasarathy

doi:10.2174/1570180819666220422111806

Abstract

Background: Mutations in Penicillin Binding Protein 2B (PBP2B) lead to resistance against commercial β-lactam antibiotics among some strains of Streptococcus pneumoniae. In this study, the molecular mechanism of resistance and the alternate strategy for controlling the Penicillin Binding Protein 2B (PBP2B) of resistant G54 and the two intermediate-resistant Hungary19A-6 and SP195 strains of Streptococcus pneumoniae are determined using an in silico approach.

Methods: In this study, we considered four ligand compounds, namely ZINC59376795, ZINC36922620, ZINC39550705, and ZINC36953975 of the ZINC database, identified through high-throughput screening (HTS) study for the resistant strain (5204-PBP2B). Glide XP docking and molecular dynamic simulation studies were performed on the PBP2B of the three resistant strains chosen for this study. The stability analysis was performed with prime-MM/GBSA, and the binding free energy, RMSD, and RMSF were also evaluated.

Results: Out of the four ligands, the ZINC39550705 ligand was found to form a stable complex with PBP2B of all three strains. Furthermore, this ZINC39550705 ligand was observed to form four hydrogen bonds with the PBP2B of all three strains. Molecular dynamics simulations were performed with these four selected ligands and targets. The resulting binding pattern, RMSD, RMSF, and hydrogen bond calculation analyses provide deeper insight into the molecular interactions of these four selected ligands with the PBP2B of the three resistance strains of S. pneumoniae.

Conclusion: The interaction of the selected ligand molecules and PBP2B of the resistant strains of S. pneumoniae revealed that hydroxyl amino acid Thr at position 224, acidic amino acids including Glu at positions 301, 245, and 240, amidic amino acids, Asn at positions 265 and 260, and aliphatic amino acid Gly at the 302 position had a crucial role in the formation of hydrogen bonds with most of the selected ligands that contributed to the stability of the complexes. The molecular dynamics simulation further confirmed that the stability of ligand ZINC39550705–PBP2B of all mutant strains was higher compared to other ligand-protein complexes evaluated in the present study. Selected ligand molecules showed significant properties of the inhibitor to be used against the resistant strains of S. pneumoniae, and the ligand ZINC39550705, in particular, is a potential alternative to commercial β-lactam antibiotics.

Keywords: Penicillin binding protein 2B (PB2BP), β-lactam antibiotics, glide docking, molecular dynamics, Streptococcus pneumonia, wild type R6 strain, resistant strain G54, intermediate resistant Hungary19A-6.

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[1]
O’Brien, K.L.; Wolfson, L.J.; Watt, J.P.; Henkle, E.; Deloria-Knoll, M.; McCall, N.; Lee, E.; Mulholland, K.; Levine, O.S.; Cherian, T. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: Global estimates. Lancet,  2009, 374(9693), 893-902.
 [http://dx.doi.org/10.1016/S0140-6736(09)61204-6] [PMID:  19748398]

[2]
Vollmer, W.; Blanot, D.; de Pedro, M.A. Peptidoglycan structure and architecture. FEMS Microbiol. Rev.,  2008, 32(2), 149-167.
 [http://dx.doi.org/10.1111/j.1574-6976.2007.00094.x] [PMID:  18194336]

[3]
Bentley, S.D.; Aanensen, D.M.; Mavroidi, A.; Saunders, D.; Rabbinowitsch, E.; Collins, M.; Donohoe, K.; Harris, D.; Murphy, L.; Quail, M.A.; Samuel, G.; Skovsted, I.C.; Kaltoft, M.S.; Barrell, B.; Reeves, P.R.; Parkhill, J.; Spratt, B.G. Genetic analysis of the capsular biosynthetic locus from all 90 Pneumococcal serotypes. PLoS Genet.,  2006, 2(3), e31.
 [http://dx.doi.org/10.1371/journal.pgen.0020031] [PMID:  16532061]

[4]
Hyams, C.; Camberlein, E.; Cohen, J.M.; Bax, K.; Brown, J.S. The Streptococcus pneumoniae capsule inhibits complement activity and neutrophil phagocytosis by multiple mechanisms. Infect. Immun.,  2010, 78(2), 704-715.
 [http://dx.doi.org/10.1128/IAI.00881-09] [PMID:  19948837]

[5]
Contreras-Martel, C.; Dahout-Gonzalez, C.; Martins, A.S.; Kotnik, M.; Dessen, A. PBP active site flexibility as the key mechanism for β-lactam resistance in Pneumococci. J. Mol. Biol.,  2009, 387(4), 899-909.
 [http://dx.doi.org/10.1016/j.jmb.2009.02.024] [PMID:  19233207]

[6]
Hakenbeck, R.; Martin, C.; Dowson, C.; Grebe, T. Penicillinbinding protein 2b of Streptococcus pneumoniae in piperacillinresistant laboratory mutants. J. Bacteriol.,  1994, 176(17), 5574-5577.
 [http://dx.doi.org/10.1128/jb.176.17.5574-5577.1994] [PMID:  8071243]

[7]
Hakenbeck, R.; Kaminski, K.; König, A.; van der Linden, M.; Paik, J.; Reichmann, P.; Zähner, D. Penicillin-binding proteins in beta-lactam-resistant Streptococcus pneumoniae. Microb. Drug Resist.,  1999, 5(2), 91-99.
 [http://dx.doi.org/10.1089/mdr.1999.5.91] [PMID:  10432270]

[8]
Gordon, E.; Mouz, N.; Duée, E.; Dideberg, O. The crystal structure
of the penicillin-binding protein 2X from Streptococcus pneumoniaeand
its acyl-enzyme form: implication in drug resistance
11edited by R. Huber. J. Mol. Biol.,  2000, 299(2), 477-485.

[9]
Dessen, A.; Mouz, N.; Gordon, E.; Hopkins, J.; Dideberg, O. Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: A mosaic framework containing 83 mutations. J. Biol. Chem.,  2001, 276(48), 45106-45112.
 [http://dx.doi.org/10.1074/jbc.M107608200] [PMID:  11553637]

[10]
Nagai, K.; Davies, T.A.; Jacobs, M.R.; Appelbaum, P.C. Effects of amino acid alterations in penicillin-binding proteins (PBPs) 1a, 2b, and 2x on PBP affinities of penicillin, ampicillin, amoxicillin, cefditoren, cefuroxime, cefprozil, and cefaclor in 18 clinical isolates of penicillin-susceptible, -intermediate, and -resistant pneumococci. Antimicrob. Agents Chemother.,  2002, 46(5), 1273-1280.
 [http://dx.doi.org/10.1128/AAC.46.5.1273-1280.2002] [PMID:  11959556]

[11]
Pagliero, E.; Chesnel, L.; Hopkins, J.; Croizé, J.; Dideberg, O.; Vernet, T.; Di Guilmi, A.M. Biochemical characterization of Streptococcus pneumoniae penicillin-binding protein 2b and its implication in β-lactam resistance. Antimicrob. Agents Chemother.,  2004, 48(5), 1848-1855.
 [http://dx.doi.org/10.1128/AAC.48.5.1848-1855.2004] [PMID:  15105143]

[12]
du Plessis, M.; Bingen, E.; Klugman, K.P. Analysis of penicillinbinding protein genes of clinical isolates of Streptococcus pneumoniae with reduced susceptibility to amoxicillin. Antimicrob. Agents Chemother.,  2002, 46(8), 2349-2357.
 [http://dx.doi.org/10.1128/AAC.46.8.2349-2357.2002] [PMID:  12121904]

[13]
Chesnel, L.; Carapito, R.; Croizé, J.; Dideberg, O.; Vernet, T.; Zapun, A. Identical penicillin-binding domains in penicillinbinding proteins of Streptococcus pneumoniae clinical isolates with different levels of β-lactam resistance. Antimicrob. Agents Chemother.,  2005, 49(7), 2895-2902.
 [http://dx.doi.org/10.1128/AAC.49.7.2895-2902.2005] [PMID:  15980366]

[14]
Stanhope, M.J.; Lefébure, T.; Walsh, S.L.; Becker, J.A.; Lang, P.; Pavinski Bitar, P.D.; Miller, L.A.; Italia, M.J.; Amrine-Madsen, H. Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development. Infect. Genet. Evol.,  2008, 8(3), 331-339.
 [http://dx.doi.org/10.1016/j.meegid.2008.02.001] [PMID:  18394970]

[15]
Ramalingam, J.; Vennila, J.; Subbiah, P. Computational studies on the resistance of penicillin-binding protein 2B (PBP2B) of wild-type and mutant strains of Streptococcus pneumoniae against β-lactam antibiotics. Chem. Biol. Drug Des.,  2013, 82(3), 275-289.
 [http://dx.doi.org/10.1111/j.1747-0285.2012.01387.x] [PMID:  22448818]

[16]
Sterling, T.; Irwin, J.J. ZINC 15 – ligand discovery for everyone. J. Chem. Inf. Model.,  2015, 55(11), 2324-2337.
 [http://dx.doi.org/10.1021/acs.jcim.5b00559] [PMID:  26479676]

[17]
Irwin, J.J.; Sterling, T.; Mysinger, M.M.; Bolstad, E.S.; Coleman, R.G. ZINC: A free tool to discover chemistry for biology. J. Chem. Inf. Model.,  2012, 52(7), 1757-1768.
 [http://dx.doi.org/10.1021/ci3001277] [PMID:  22587354]

[18]
Suvaithenamudhan, S.; Parthasarathy, S. Structure based virtual screening for the identification of potential inhibitors for penicillin binding protein 2B of the resistant 5204 strain of Streptococcus pneumoniae. Curr. Bioinform.,  2016, 11(1), 66-78.
 [http://dx.doi.org/10.2174/1574893611666151119220500]

[19]
Suvaithenamudhan, S.; Parthasarathy, S. Molecular dynamics simulations of novel potential inhibitors for penicillin binding protein 2b of the resistant 5204 strain of Streptococcus pneumoniae. Curr. Computeraided Drug Des.,  2017, 13(3), 234-248.
 [http://dx.doi.org/10.2174/1573409913666170301120421] [PMID:  28260518]

[20]
Schrödinger,  Release .2020-2: Maestro; Schrödinger, LLC: New York, NY, 2020. 

[21]
Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M.R.; Smith, J.C.; Kasson, P.M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics,  2013, 29(7), 845-854.
 [http://dx.doi.org/10.1093/bioinformatics/btt055] [PMID:  23407358]

[22]
Pruitt, K.; Tatusova, T.; Maglott, D. NCBI reference sequences (Refseq): A curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res.,  2007, 35(Database), D61-D65.

[23]
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res.,  2000, 28(1), 235-242.
 [http://dx.doi.org/10.1093/nar/28.1.235] [PMID:  10592235]

[24]
Sastry, G.M.; Adzhigirey, M.; Day, T.; Annabhimoju, R.; Sherman, W. Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des.,  2013, 27(3), 221-234.
 [http://dx.doi.org/10.1007/s10822-013-9644-8] [PMID:  23579614]

[25]
Shelley, J.C.; Cholleti, A.; Frye, L.L.; Greenwood, J.R.; Timlin, M.R.; Uchimaya, M. Epik: A software program for pK( a ) prediction and protonation state generation for drug-like molecules. J. Comput. Aided Mol. Des.,  2007, 21(12), 681-691.
 [http://dx.doi.org/10.1007/s10822-007-9133-z] [PMID:  17899391]

[26]
Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J.Y.; Wang, L.; Lupyan, D.; Dahlgren, M.K.; Knight, J.L.; Kaus, J.W.; Cerutti, D.S.; Krilov, G.; Jorgensen, W.L.; Abel, R.; Friesner, R.A. OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. J. Chem. Theory Comput.,  2016, 12(1), 281-296.
 [http://dx.doi.org/10.1021/acs.jctc.5b00864] [PMID:  26584231]

[27]
Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J. Chem. Theory Comput.,  2010, 6(5), 1509-1519.
 [http://dx.doi.org/10.1021/ct900587b] [PMID:  26615687]

[28]
Halgren, T.A. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model.,  2009, 49(2), 377-389.
 [http://dx.doi.org/10.1021/ci800324m] [PMID:  19434839]

[29]
Schrödinger, Release 2020-2: LigPrep; Schrödinger, LLC: New York, NY, 2020. 

[30]
Friesner, R.A.; Murphy, R.B.; Repasky, M.P.; Frye, L.L.; Greenwood, J.R.; Halgren, T.A.; Sanschagrin, P.C.; Mainz, D.T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem.,  2006, 49(21), 6177-6196.
 [http://dx.doi.org/10.1021/jm051256o] [PMID:  17034125]

[31]
Jacobson, M.P.; Pincus, D.L.; Rapp, C.S.; Day, T.J.; Honig, B.; Shaw, D.E.; Friesner, R.A. A hierarchical approach to all-atom protein loop prediction. Proteins,  2004, 55(2), 351-367.
 [http://dx.doi.org/10.1002/prot.10613] [PMID:  15048827]

[32]
Mobley, D.L.; Dill, K.A. Binding of small-molecule ligands to proteins: “what you see” is not always “what you get”. Structure,  2009, 17(4), 489-498.
 [http://dx.doi.org/10.1016/j.str.2009.02.010] [PMID:  19368882]

[33]
Jakubík, J.; Randáková, A.; Doležal, V. On homology modeling of the M₂ muscarinic acetylcholine receptor subtype. J. Comput. Aided Mol. Des.,  2013, 27(6), 525-538.
 [http://dx.doi.org/10.1007/s10822-013-9660-8] [PMID:  23812908]

[34]
Das, D.; Koh, Y.; Tojo, Y.; Ghosh, A.K.; Mitsuya, H. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J. Chem. Inf. Model.,  2009, 49(12), 2851-2862.
 [http://dx.doi.org/10.1021/ci900320p] [PMID:  19928916]

[35]
Oostenbrink, C.; Villa, A.; Mark, A.E.; van Gunsteren, W.F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem.,  2004, 25(13), 1656-1676.
 [http://dx.doi.org/10.1002/jcc.20090] [PMID:  15264259]

[36]
Van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Hünenberger, P.H.; Krüger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular simulation: The GROMOS96 manual and user guide; Verlag der Fachvereine: Zürich, 1996, pp. 1-1024.

[37]
Schüttelkopf, A.W.; van Aalten, D.M. PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr.,  2004, 60(Pt 8), 1355-1363.
 [http://dx.doi.org/10.1107/S0907444904011679] [PMID:  15272157]

[38]
Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Hermans, J. Interaction models for water in relation to protein hydration. Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981, pp. 331-342.
 [http://dx.doi.org/10.1007/978-94-015-7658-1_21]

[39]
Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. A smooth particle mesh ewald method. J. Chem. Phys.,  1995, 103(19), 8577-8593.
 [http://dx.doi.org/10.1063/1.470117]

[40]
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N⋅Log (N) method for Ewald sums in large systems. J. Chem. Phys.,  1993, 98(12), 10089-10092.
 [http://dx.doi.org/10.1063/1.464397]

[41]
Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem.,  1997, 18(12), 1463-1472.
 [http://dx.doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H]

[42]
Pernot, L.; Chesnel, L.; Le Gouellec, A.; Croizé, J.; Vernet, T.; Dideberg, O.; Dessen, A. A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to β-lactam antibiotics. J. Biol. Chem.,  2004, 279(16), 16463-16470.
 [http://dx.doi.org/10.1074/jbc.M313492200] [PMID:  14734544]

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DOI https://dx.doi.org/10.2174/1570180819666220422111806	Print ISSN 1570-1808
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In silico Studies on Potential Inhibitors of the Penicillin Binding Protein 2B (PBP2B) of the Resistant G54 and Intermediate-resistant Hungary 19A-6 and SP195 Strains of Streptococcus Pneumoniae

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