Molecular dynamics simulation of the complex PBP-2x with drug cefuroxime to explore the drug resistance mechanism of Streptococcus suis R61

Abstract

Drug resistance of Streptococcus suis strains is a worldwide problem for both humans and pigs. Previous studies have noted that penicillin-binding protein (PBPs) mutation is one important cause of β-lactam antibiotic resistance. In this study, we used the molecular dynamics (MD) method to study the interaction differences between cefuroxime (CES) and PBP2x within two newly sequenced Streptococcus suis: drug-sensitive strain A7, and drug-resistant strain R61. The MM-PBSA results proved that the drug bound much more tightly to PBP2x in A7 (PBP2x-A7) than to PBP2x in R61 (PBP2x-R61). This is consistent with the evidently different resistances of the two strains to cefuroxime. Hydrogen bond analysis indicated that PBP2x-A7 preferred to bind to cefuroxime rather than to PBP2x-R61. Three stable hydrogen bonds were formed by the drug and PBP2x-A7, while only one unstable bond existed between the drug and PBP2x-R61. Further, we found that the Gln569, Tyr594, and Gly596 residues were the key mutant residues contributing directly to the different binding by pair wise energy decomposition comparison. By investigating the binding mode of the drug, we found that mutant residues Ala320, Gln553, and Thr595 indirectly affected the final phenomenon by topological conformation alteration. Above all, our results revealed some details about the specific interaction between the two PBP2x proteins and the drug cefuroxime. To some degree, this explained the drug resistance mechanism of Streptococcus suis and as a result could be helpful for further drug design or improvement.

Figure 1. Sequence alignment between PBP2x-R61 (R61), PBP2x-A7 (A7), and the template protein (PDB code 1QMF).

Figure 2. Ramachandran plot of modeled PBP2x-R61 and PBP2x-A7.

The most favored regions are red. Additionally allowed, generously allowed, and disallowed regions are indicated as yellow, light yellow, and white, respectively.

Figure 3. Comparison of PBP2x-R61 and PBP2x-A7.

(A) The superimposition of initial structures of the complex between PBP2x-R61 (white color) and PBP2x-A7 (cyan color) with the drug (green color). (B) The structure of the cefuroxime drug.

Figure 4. RMSD values for PBP2x-R61-CES and PBP2x-A7-CES relative to the starting structure during MD simulation.

(A) The whole backbone atoms. (B) The drug molecule.

Figure 5. Relative decomposed energies of the corresponding residues between PBP2x-R61-CES and PBP2x-A7-CES.

The ovals characterize the two active site areas and the blocks mark the three essential mutated residues.

Figure 6. The distance variation of the five hydrogen bonds during MD simulation.

(A) for PBP2x-R61-CES. (B) for PBP2x-A7-CES. Bond 1: Ser396 O - CES O7; Bond 2: Gly350 N - CES O3; Bond 3: Thr351 OG1 - CES N2; Bond 4:Thr351 OG1 - CES O5; and Bond 5: Thr351 N - CES O5.

Figure 7. LIGPLOT representation of cefuroxime (CES) binding to PBP2x-R61 and PBP2x-A7.

Ligand, protein, and hydrogen bonds are in thick blue, thick brown, and broken green lines, respectively. Residues involved in hydrophobic contact are associated with a curved comb. (A) Open form of cefuroxime (CES) bound to PBP2x-R61. (B) Open form of cefuroxime (CES) bound to PBP2x-A7.