Insights into the antibiotic resistance and inhibition mechanism of aminoglycoside phosphotransferase from Bacillus cereus: In silico and in vitro perspective

Abstract

Because of the lack of structural studies on aminoglycoside phosphotransferase (APH) from prevalent volatile human pathogen Bacillus cereus, aminoglycoside resistance therapeutics research remains elusive. Hence, in this computational study, we have performed homology modeling, molecular docking, molecular dynamics (MD), and principal component analysis studies on APH from B. cereus. The structure of APH was predicted by homology modeling using MODELLER 9v12 and validated for its stereochemical qualities. Sequence analysis study of the template (Protein Data Bank ID: 3TDW) and APH from B. cereus sensu lato group showed exact matching of active-site residues. The mechanism of substrate and inhibitor binding to APH was studied using molecular docking, which identified GTP as the more preferred substrate, whereas ZINC71575479 as the most effective inhibitor. The active-site residues, ARG41, TYR90, ASP195, and ASP215 at nucleotide triphosphate-binding cavity of APH were found to be involved in binding with substrate and inhibitor. Molecular dynamics simulation study of APH in apo form and bound form confirmed the stability and effective binding of GTP and ZINC71575479 in a dynamic state. Molecular mechanics Poisson-Boltzmann surface area calculations revealed energetic contributions of active-site residues of APH in binding with GTP and ZINC71575479. The principal component analysis revealed the internal global motion of APH in apo and complex form. Furthermore, experimental studies on APH from B. cereus ATCC 10876 validated the in silico findings for its inhibition. Thus, this study provides more information on structure-function relationships of APH from B. cereus and open avenues for designing effective strategies to overcome antibiotic resistance.

<p>Knockdown Of Long Non-Coding RNA TP73-AS1 Inhibited Cell Proliferation And Metastasis Through Wnt/β-Catenin Pathway In Lung Adenocarcinoma</p>

“…LncRNA antisense RNA to TP73 gene (TP73-AS1) is located on human chromosomal band 1p36.32 32 and identified as an oncogenic RNA in breast cancer, esophagus cancer, glioma, hepatocellular carcinoma and lung cancer. 16,17,19,33,34 Nevertheless, more detailed functional effects and associated molecular regulatory mechanism of lncRNA TP73-AS1 in lung adenocarcinoma remain largely to be explored.…”

“…15 Previous studies reported that TP73-AS1 was closely associated with tumor progression and poor prognosis in esophageal squamous cell carcinoma, breast cancer, brain glioma, gastric cancer and hepatocellular carcinoma. [16][17][18][19][20][21][22][23] These reports demonstrated that lncRNA TP73-AS1 acted as one oncogene in the tumorigenesis of cancer. Unfortunately, the biological function and underlying mechanism of lncRNA TP73-AS1 in lung adenocarcinoma are rarely explored and more researches are needed to be clarified.…”

Antibiotic resistance and inhibition mechanism of novel aminoglycoside phosphotransferase APH(5) from B. subtilis subsp. subtilis strain RK

“…This inhibitor was selected based on our earlier results obtained through virtual screening, molecular docking, molecular dynamics simulation, and binding free energy calculation study performed on one of the known APH [16]. In vitro enzymatic inhibition of purified APH by virtually screened inhibitor was studied using coupled spectrophotometric assay [28,29]. The components of the reaction mixture for coupled spectrophotmetric assay were same as described earlier [28].…”

“…The components of the reaction mixture for coupled spectrophotmetric assay were same as described earlier [28]. For inhibition study of APH, an extra cuvette was used comprising all components like earlier study [28,29] along with virtually screened inhibitor. The monitoring of the reaction was carried out by detection of oxidation of NADH at 340 nm spectrophotometrically.…”

<p>The association between omentin and diabetes: a systematic review and meta-analysis of observational studies</p>

“…These adipokines could control carbohydrate and lipid metabolism and appear to play a vital role in the pathogenesis of insulin resistance, diabetes, inflammation, atherosclerosis, and vascular endothelial dysfunction. [4][5][6][7][8][9][10] Identification of a novel adipokine associated with diabetes might provide new opportunities for clinicians for early diagnosis and better management of diabetes and its related complications. Omentin (intelectin, intestinal lactoferrin receptor, endothelin lectin HL-1, galactofuranosebinding lectin) is a novel fat depot-specific adipokine identified by Yang et al, in 2003 from a visceral omental adipose tissue cDNA library.…”