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. 2022 May 21;15(5):635.
doi: 10.3390/ph15050635.

A Combination of Pharmacophore-Based Virtual Screening, Structure-Based Lead Optimization, and DFT Study for the Identification of VSports - S. epidermidis TcaR Inhibitors

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A Combination of Pharmacophore-Based Virtual Screening, Structure-Based Lead Optimization, and DFT Study for the Identification of S. epidermidis TcaR Inhibitors (VSports在线直播)

"VSports最新版本" Srimai Vuppala et al. Pharmaceuticals (Basel). .

Abstract

The transcriptional regulator (TcaR) enzyme plays an important role in biofilm formation. Prevention of TcaR-DNA complex formation leads to inhibit the biofilm formation is likely to reveal therapeutic ways for the treatment of bacterial infections. To identify the novel ligands for TcaR and to provide a new idea for drug design, two efficient drug design methods, such as pharmacophore modeling and structure-based drug design, were used for virtual screening of database and lead optimization, respectively. Gemifloxacin (FDA-approved drug) was considered to generate the pharmacophore model for virtual screening of the ZINC database, and five hits, namely ZINC77906236, ZINC09550296, ZINC77906466, ZINC09751390, and ZINC01269201, were identified as novel inhibitors of TcaR with better binding energies VSports手机版. Using structure-based drug design, a set of 7a-7p inhibitors of S. epidermidis were considered, and Mol34 was identified with good binding energy and high fitness score with improved pharmacological properties. The active site residues ARG110, ASN20, HIS42, ASN45, ALA38, VAL63, VAL68, ALA24, VAL43, ILE57, and ARG71 are playing a promising role in inhibition process. In addition, we performed DFT simulations of final hits to understand the electronic properties and their significant role in driving the inhibitor to adopt apposite bioactive conformations in the active site. Conclusively, the newly identified and designed hits from both the methods are promising inhibitors of TcaR, which can hinder biofilm formation. .

Keywords: TcaR; bacterial infections; biofilm; drug design; molecular docking V体育安卓版. .

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Illustration of antibiotic treatment of S. epidermidis TcaR preventing the formation of DNA-TcaR complex in ica operon, which leads to inhibition of biofilm formation. The active TcaR can interact with ica operator and prevents the transcription of IcaA. Upon treating with antibiotics, significant conformational changes in the DNA binding domain of TcaR will occur.
Figure 2
Figure 2
Representation of two gemifloxacin pharmacophore models. The green, red, and yellow color interlaces indicate the hydrophobic, negative ion charge, and hydrogen bond acceptor regions, respectively.
Figure 3
Figure 3
Binding mode conformation and molecular interactions of methicillin in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The methicillin is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 4
Figure 4
Binding mode conformation and molecular interactions of gemifloxacin in the active site of S. epidermidis TcaR. The gemifloxacin is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 5
Figure 5
Diagram of the binding mode of methicillin and gemifloxacin (a). Superimposition of hit compound ZINC77906236 on methicillin and gemifloxacin in the active site of TcaR (b). The binding mode of methicillin, gemifloxacin, and hit compound ZINC77906236 (c). The binding mode of methicillin, gemifloxacin, and hit compounds (ZINC77906236, ZINC09550296, ZINC77906466, ZINC09751390, and ZINC01269201) in the active site of TcaR.
Figure 6
Figure 6
Binding mode conformation and molecular interactions of ZINC77906236 in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The hit compound is shown in the ball-stick model, and the key interacting residues are shown as grey sticks. Isodensity plots of HOMO and LUMO and molecular electrostatic potential of hit compound.
Figure 7
Figure 7
Binding mode conformation and molecular interactions of hit compound ZINC09550296 in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The hit compound is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 8
Figure 8
Binding mode conformation and molecular interactions of compound 7a in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The compound 7a is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 9
Figure 9
Binding mode conformation and molecular interactions of compound 7b in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The compound 7b is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 10
Figure 10
Binding mode conformation and molecular interactions of compound 7g in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The compound 7g is shown in the ball-stick model, and the key interacting residues are shown as grey sticks.
Figure 11
Figure 11
Binding mode conformation and molecular interactions of compound Mol34 in the active site of S. epidermidis TcaR. The left and right figures represent the molecular interactions in 3D and 2D, respectively. The hit compound is shown in the ball-stick model, and the key interacting residues are shown as grey sticks. Isodensity plots of HOMO and LUMO and molecular electrostatic potential of hit compound.

References

    1. Uçkay I., Pittet D., Vaudaux P., Sax H., Lew D., Waldvogel F. Foreign body infections due to Staphylococcus epidermidis. Ann. Med. 2009;41:109–119. doi: 10.1080/07853890802337045. - DOI - PubMed
    1. Otto M. Staphylococcus epidermidis—The ‘accidental’ pathogen. Nat. Rev. Microbiol. 2009;7:555–567. doi: 10.1038/nrmicro2182. - "V体育官网" DOI - PMC - PubMed
    1. Rogers K.L., Fey P.D., Rupp M.E. Coagulase—Negative staphylococcal infections. Infect. Dis. Clin. N. Am. 2009;23:73–98. doi: 10.1016/j.idc.2008.10.001. - DOI - PubMed
    1. Costerton J.W., Stewart P.S., Greenberg E.P. Bacterial biofilms: A common cause of persistent infections. Science. 1999;284:1318–1322. doi: 10.1126/science.284.5418.1318. - DOI - PubMed
    1. Dhar Y., Han Y. Current developments in biofilm treatments: Wound and implant infections. Eng. Regen. 2020;1:64–75. doi: 10.1016/j.engreg.2020.07.003. - VSports最新版本 - DOI

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