Explication of interactions between HMGCR isoform 2 and various statins through In silico modeling and docking

Karthik, M. V. K.; Deepak, M.V.K.N. Satya; Shukla, Pratyoosh

doi:10.1016/j.compbiomed.2011.11.003

Cited by 8 publications

(2 citation statements)

References 32 publications

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“…In this study, details about the structure and residues involved in binding of squalene epoxidase of T. rubrum are provided. Figure 1 shows the schematic representation of the work flow presented in this study and have also reported about the perceptive enzyme substrate interactions which are also helpful in understanding the role of enzymes [17,18]. Despite the fact that few studies proposed the activity of terbinafine against squalene epoxidase, the 3D structure and binding activities of squalene epoxidase were not elaborated.…”

Section: Introductionmentioning

confidence: 93%

In Silico Analog Design for Terbinafine Against Trichophyton rubrum: A Preliminary Study

2015

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The diseases caused by dermatophytes are common among several other infections which cause serious threat to human health. It is evident that enzyme squalene epoxidase is responsible for prolonged dermatophyte infection and it is appealing to note that this enzyme is also responsible for fatty acid synthesis in these groups of fungi. In the present study, terbinafine drug which targets enzyme squalene epoxidase has been explored to design its various novel analogues. The present study suggests that many more prominent drug analogues could be constituted which may be crucial towards designing new drug candidates. In the present study, we have designed a series of such analogues viz. [(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)(naphthalen-1-ylmethyl)amine, N-[8-({[(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)amino}methyl)naphthalen-1-yl]-2-(sulfoamino) acetamide, {[4-(dihydroxyamino)-8-({[(2E)-6,6-dimethylhept-2-en-4-yn-1-yl](methyl)amino}methyl)naphthalen-1-yl]sulfanyl}methanol and (R)-{[4-({[(2E,6R)-6,7-dimethyloct-2-en-4-yn-1-yl](methyl)amino}methyl)-5-[(hydroxysulfamoyl)amino]naphthalen-1-yl]amino}sulfinic acid. Moreover, further by molecular docking approach the binding between enzyme and designed analogues was further analysed. The present preliminary report suggested a considerably good docking interaction score of -338.75 kcal/mol between terbinafine and squalene epoxidase from Trichophyton rubrum. This preliminary study implies that few designed candidate ligands can be effectual towards the activity of this enzyme and can play crucial role in pathogenesis control of T. rubrum.

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Section: Introductionmentioning

confidence: 93%

In Silico Analog Design for Terbinafine Against Trichophyton rubrum: A Preliminary Study

2015

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“…Furthermore, various genetic modifications which involve the introduction of desired genes may also have a constructive impact in the probiotic field (Gupta and Shukla, 2015). There are many reports on molecular docking of enzymes, which gives good insights of various protein interactions and their effective binding patterns (Singh and Shukla, 2011, 2014; Singh et al, 2011, 2016; Karthik et al, 2012; Baweja et al, 2015, 2016). …”

Section: Introductionmentioning

confidence: 99%

Catalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from L. plantarum RYPR1 and Its Prebiotic Utilization

Yadav¹,

Singh²,

Puniya³

et al. 2017

Front. Microbiol.

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Prebiotics are the non-digestible carbohydrate, which passes through the small intestine into unmetabolized form, reaches the large intestine and undergoes fermentation by the colonic bacteria thus; prebiotics stimulate the growth of probiotic bacteria. Further, bile salt hydrolase (BSH) is an enzyme that catalyses the deconjugation of bile salt, so it has enormous potential toward utilizing such capability of Lactobacillus plantarum RYPR1 toward detoxifying through BSH enzyme activity. In the present study, six isolates of Lactobacillus were evaluated for the co-aggregation assay and the isolate Lactobacillus plantarum RYPR1 was further selected for studies of prebiotic utilization, catalytic interactions and molecular docking. The prebiotic utilization ability was assessed by using commercially available prebiotics lactulose, inulin, xylitol, raffinose, and oligofructose P95. The results obtained revealed that RYPR1 is able to utilize these probiotics, maximum with lactulose by showing an increase in viable cell count (7.33 ± 0.02 to 8.18 ± 0.08). In addition, the molecular docking of BSH from Lactobacillus plantarum RYPR1 was performed which revealed the binding energy –4.42 and 7.03 KJ/mol. This proves a considerably good interactions among BSH and its substrates like Taurocholic acid (–4.42 KJ/mol) and Glycocholic acid (–7.03 KJ/mol). These results from this study establishes that Lactobacillus plantarum RYPR1 possesses good probiotic effects so it could be used for such applications. Further, molecular dynamics simulations were used to analyze the dynamic stability of the of modeled protein to stabilize it for further protein ligand docking and it was observed that residues Asn12, Ile8, and Leu6 were interacting among BSH and its substrates, i.e., Taurocholic acid and Lys88 and Asp126 were interacting with Glycocholic acid. These residues were interacting when the docking was carried out with stabilized BSH protein structure, thus, these residues may have a vital role in stabilizing the binding of the ligands with the protein.

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Enzyme Technology, Functional Proteomics, and Systems Biology Toward Unraveling Molecular Basis for Functionality and Interactions in Biotechnological Processes

Singh

Shukla

2016

Frontier Discoveries and Innovations in Interdisciplinary Microbiology

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Explication of interactions between HMGCR isoform 2 and various statins through In silico modeling and docking

Cited by 8 publications

References 32 publications

In Silico Analog Design for Terbinafine Against Trichophyton rubrum: A Preliminary Study

In Silico Analog Design for Terbinafine Against Trichophyton rubrum: A Preliminary Study

Catalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from L. plantarum RYPR1 and Its Prebiotic Utilization

Enzyme Technology, Functional Proteomics, and Systems Biology Toward Unraveling Molecular Basis for Functionality and Interactions in Biotechnological Processes

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