Non-β-Lactam Allosteric Inhibitors Target Methicillin-Resistant Staphylococcus aureus: An In Silico Drug Discovery Study

Abstract

Penicillin-binding proteins (PBPs) catalyze the final stages for peptidoglycan cell-wall bio-synthesis. Mutations in the PBP2a subunit can attenuate β-lactam antibiotic activity, resulting in unimpeded cell-wall formation and methicillin-resistant Staphylococcus aureus (MRSA). A double mutation in PBP2a (i.e., N146K and E150K) is resistant to β-lactam inhibitors; however, (E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl) benzoic acid (QNZ), a heterocyclic antibiotic devoid of a β-lactam ring, interacts non-covalently with PBP2a allosteric site and inhibits PBP enzymatic activity. In the search for novel inhibitors that target this PBP2a allosteric site in acidic medium, an in silico screening was performed. Chemical databases including eMolecules, ChEMBL, and ChEBI were virtually screened for candidate inhibitors with a physicochemical similarity to QNZ. PBP2a binding affinities from the screening were calculated based on molecular docking with co-crystallized ligand QNZ serving as a reference. Molecular minimization calculations were performed for inhibitors with docking scores lower than QNZ (calc. −8.3 kcal/mol) followed by combined MD simulations and MM-GBSA binding energy calculations. Compounds eMol26313223 and eMol26314565 exhibited promising inhibitor activities based on binding affinities (ΔGbinding) that were twice that of QNZ (−38.5, −34.5, and −15.4 kcal/mol, respectively). Structural and energetic analyses over a 50 ns MD simulation revealed high stability for the inhibitors when complexed with the double mutated PBP2a. The pharmacokinetic properties of the two inhibitors were predicted using an in silico ADMET analysis. Calculated binding affinities hold promise for eMol26313223 and eMol26314565 as allosteric inhibitors of PBP2a in acidic medium and establish that further in vitro and in vivo inhibition experimentation is warranted.

Methicillin-Resistant Staphylococcus aureus: Docking-Based Virtual Screening and Molecular Dynamics Simulations to Identify Potential Penicillin-Binding Protein 2a Inhibitors from Natural Flavonoids

“…As such, we also evaluated the binding affinity of our top-ranked PBP2a active site inhibitors including kaempferol 3-rutinoside-7-sophoroside and rutin to the allosteric site of PBP2a. We used the same protein Ibrahim et al [ 9 ] used in their study (PDB ID: 4CJN; chain B). Interestingly, kaempferol 3-rutinoside-7-sophoroside and rutin exhibited high binding affinity to the PBP2a allosteric site with the Δ G binding values of −14.35 and −9.68 kcal/mol, respectively.…”

“…This study considered the best SauPBP2a active site inhibitors to evaluate their binding affinity to the enzyme's allosteric site. The grid box options at this stage followed the settings of the study by Ibrahim et al [ 9 ]: X -dimension: 52; Y -dimension: 52; Z -dimension: 52; X -center: 9.658; Y -center: −1.662; Z -center: −70.269; spacing: 0.375 Å.…”

“…Thus, PBP2a in S. aureus (SauPBP2a) has been considered a potential target for developing specific inhibitors to combat MRSA, which will be accelerated by analyzing the three-dimensional structure of the SauPBP2a active site [ 8 ]. Furthermore, the allosteric site of SauPBP2a has also been considered for negative regulation of the enzyme's activity [ 9 ].…”

Synthesis, X-ray diffraction analysis, quantum chemical studies and α-amylase inhibition of probenecid derived S-alkylphthalimide-oxadiazole-benzenesulfonamide hybrids

“…The technical specifics of the utilised molecular docking computations are elucidated in Ref. 60–64 . In concise, the resolved three-dimensional (3 D) crystal structure of α -amylase (PDB ID: 1OSE 65 ) in complex with acarbose is downloaded from RCSB PDB and opted for docking computations.…”

NS3 helicase inhibitory potential of the marine sponge Spongia irregularis

“…31 The details of the utilized MD simulations are elucidated in ref. 32–35 . In the MD simulations, AMBER force field 14SB and general AMBER force field (GAFF2) were employed to characterize the HCV targets and the investigated inhibitors, respectively.…”