Exploration of the binding of DNA binding ligands to<i>Staphylococcal</i>DNA through QM/MM docking and molecular dynamics simulation

Selvaraj, Chandrabose; Nisha, J.; Saipriya, K.; Daisy, P.

doi:10.1080/07391102.2012.706080

Cited by 41 publications

(26 citation statements)

References 29 publications

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“…For identifying the potential of binding site in modeled protein, “Druggability pocket region prediction” protocol was used by sitemap active site prediction module. This prediction has assisted in locating the exact binding site in the homology model of β‐GBP (Vijayalakshmi et al ., ).…”

Section: Methodsmentioning

confidence: 97%

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Interaction investigations of crustacean β‐GBP recognition toward pathogenic microbial cell membrane and stimulate upon prophenoloxidase activation

Sivakamavalli

Selvaraj

Vaseeharan

2014

J of Molecular Recognition

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In invertebrates, crustaceans' immune system consists of pattern recognition receptors (PRRs) instead of immunoglobulin's, which involves in the microbial recognition and initiates the protein-ligand interaction between hosts and pathogens. In the present study, PRRs namely β-1,3 glucan binding protein (β-GBP) from mangrove crab Episesarma tetragonum and its interactions with the pathogens such as bacterial and fungal outer membrane proteins (OMP) were investigated through microbial aggregation and computational interaction studies. Molecular recognition and microbial aggregation results of Episesarma tetragonum β-GBP showed the specific binding affinity toward the fungal β-1,3 glucan molecule when compared to other bacterial ligands. Because of this microbial recognition, prophenoloxidase activity was enhanced and triggers the innate immunity inside the host animal. Our findings disclose the role of β-GBP in molecular recognition, host-pathogen interaction through microbial aggregation, and docking analysis. In vitro results were concurred with the in silico docking, and molecular dynamics simulation analysis. This study would be helpful to understand the molecular mechanism of β-GBP and update the current knowledge on the PRRs of crustaceans.

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Section: Methodsmentioning

confidence: 97%

“…sitemap active site prediction module. This prediction has assisted in locating the exact binding site in the homology model of β-GBP (Vijayalakshmi et al, 2013).…”

Section: Molecular Modeling Environmental Setupmentioning

confidence: 99%

Interaction investigations of crustacean β‐GBP recognition toward pathogenic microbial cell membrane and stimulate upon prophenoloxidase activation

Sivakamavalli

Selvaraj

Vaseeharan

2014

J of Molecular Recognition

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“…By using the Prime, missing residues and the missing loops were filled from the SEQRES records in the PDB file. 29 The requirement of physico-chemical properties in ligands to design the best inhibitor against the protein active site contours were predicted by using SiteMap. Minimization was performed until the average RMSD of the non-hydrogen atoms to reach 0.3 Å.…”

Section: Molecular Modeling Environmental Setupmentioning

confidence: 99%

Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors

2015

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Retroviruses HIV-1 and HTLV-1 are chiefly considered to be the most dangerous pathogens in Homo sapiens. These two viruses have structurally unique protease (PR) enzymes, which are having common function of its replication mechanism. Though HIV PR drugs failed to inhibit HTLV-1 infections, they emphatically emphasise the need for designing new lead compounds against HTLV-1 PR. Therefore, we tried to understand the binding level interactions through the charge environment present in both ligand and protein active sites. The domino effect illustrates that libraries of purvalanol-A are attuned to fill allosteric binding site of HTLV-1 PR through molecular recognition and shows proper binding of ligand pharmacophoric features in receptor contours. Our screening evaluates seven compounds from purvalanol-A libraries, and these compounds' pharmacophore searches for an appropriate place in the binding site and it places well according to respective receptor contour surfaces. Thus our result provides a platform for the progress of more effective compounds, which are better in free energy calculation, molecular docking, ADME and molecular dynamics studies. Finally, this research provided novel chemical scaffolds for HTLV-1 drug discovery.

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“…The charge density was calculated by OPLS-2005 force field on the rRNA receptor. The grid point spacing was defined as 1 Å [19].…”

Section: Prediction Of Binding Pocket Of 40s Ribosomal Rnamentioning

confidence: 99%

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

Ramachandran

Arumugasamy²,

Edayadulla

et al. 2015

J Chem Biol

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The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance.

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Exploration of the binding of DNA binding ligands toStaphylococcalDNA through QM/MM docking and molecular dynamics simulation

Cited by 41 publications

References 29 publications

Interaction investigations of crustacean β‐GBP recognition toward pathogenic microbial cell membrane and stimulate upon prophenoloxidase activation

Interaction investigations of crustacean β‐GBP recognition toward pathogenic microbial cell membrane and stimulate upon prophenoloxidase activation

Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

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