Computational Analysis and Binding Site Identification of Type III Secretion System ATPase from Pseudomonas aeruginosa

Dash, Raju; Hosen, S. M. Zahid; Sultana, Tasniha; Junaid, Md.; Majumder, Mohuya; Ishat, Ismat Ara; Nasiruddin, Munira

doi:10.1007/s12539-015-0121-z

Cited by 11 publications

(7 citation statements)

References 52 publications

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“…To analyze physiochemical parameters ExPASy’s ProtParam (Gasteiger et al., 2005 ) tool was employed to calculate theoretical pI (Isoelectric point), instability index (II), aliphatic index (AI), grand average of hydropathicity for SARS-CoV-2 M protein. Furthermore, secondary structural properties of the protein were evaluated via self-optimized prediction method with alignment (SOPMA) (Dash et al., 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Structure and dynamics of membrane protein in SARS-CoV-2

Mahtarin

Islam

et al. 2020

Journal of Biomolecular Structure and Dynamics

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Section: Methodsmentioning

confidence: 99%

Structure and dynamics of membrane protein in SARS-CoV-2

Mahtarin

Islam

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…Ramachandran plot for HLA-B*08:01 3D structure generated from PROCHECK states that it has 93.3% residues in most favored core regions, 5.8% residues in additional allowed regions and 0% residues in disallowed regions ( Figure 6). The protein model that has > 90% residues in the core region and allowed is considered to be a high quality model 34 . The quality factor of the model analyzed by ERRAT tool is 97.3684 where a good structure model should have a quality factor > 80.00 35 .…”

Section: Validation Of Predicted Hla Structuresmentioning

confidence: 99%

In Silico screening of T-cell and B-cell Epitopes of Rotavirus VP7 and VP4 proteins for Effective Vaccine Design

Shuvo

Mukharjee

Ahmed

2019

Bangla. J. Microbiol.

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Rotavirus is one of the deadliest causative agents of childhood diarrhea which causes half a million child death across the globe, mostly in developing countries. However, effective vaccine strategies against rotavirus are yet to be established to prevent these unwanted premature deaths. In this regard, in silico vaccine design for rotavirus could be a promising alternative for developing countries due to its efficiency in shortening valuable time and cost. The present study described an epitope-based peptide vaccine design against rotavirus, using a combination of T-cell and B-cell epitope predictions and molecular docking approach. To perform this, sequences of rotavirus VP7 and VP4 proteins were retrieved from the NCBI database and subjected to different bioinformatics tools to predict most immunogenic T-cell and B-cell epitopes. From the identified epitopes, the sequence VMSKRSRSL of VP7 and TQFTDFVSL of VP4 was identified as the most potential epitopes based on their antigenicity, conservancy and interaction with major histocompatability complex I (MHC-I) alleles. Moreover, the peptide VMSKRSRSL interacted with human leukocyte antigen, HLA-B*08:01 and TQFTDFVSL interacted with HLA-A*02:06 with considerable binding energy and affinity score. Combined population coverage for our identified epitopes was found 70.53% and 45.64% for world population and South Asian population respectively. All these results suggest that, the epitopes identified in this study could be a very good vaccine candidate for the strains of rotavirus circulating in Bangladesh. However, as this study is completely dependent on computational prediction algorithms, further in vivo screening is required to come up in a precise conclusion about these epitopes for effective rotavirus vaccination. Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 45-55

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“…The grid box size in AutodockVina was kept at 48.2808, 49.1466, and 52.4875 respectively for X, Y, Z. AutodockVina was implemented through shell script provided by AutodockVina developers. The binding affinity of ligand was monitored in kcal/mol unit for a negative score (Trott and Olson 2010;Dash et al 2016). In order to estimate the accuracy of binding affinity of AutodockVina, MOE-dock module of MOE 2015 software was used for cross-docking analysis.…”

Section: Molecular Docking Analysismentioning

confidence: 99%

Molecular docking and dynamics of Nickel-Schiff base complexes for inhibiting β-lactamase of Mycobacterium tuberculosis

Junaid¹,

Alam²,

Hossain³

et al. 2018

In Silico Pharmacol.

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In recent years, multidrug-resistance has become a primary concern in the treatment and management of tuberculosis, an infectious disease caused by Mycobacterium tuberculosis. In this context, searching new anti-tuberculosis agents particularly targeting the β-lactamase (BlaC) is reported to be promising as this enzyme is one of the key player in the development of multidrug resistance. This study reports the design of some Nickel (Ni) based tetradentate N 2 O 2 Schiff bases, employing density functional theory. All analogs are optimized at B3LYP/SDD level of theory. Dipole moment, electronic energy, enthalpy, Gibbs free energy, HOMO-LUMO gap, and softness of these modified drugs are also investigated. Molecular interactions between designed ligands and BlaC have been analyzed by molecular docking approach, followed by molecular dynamics (MD) simulation. All designed compounds show low HOMO-LUMO gap, while addition of halogen increases the dipole moment of the compounds. Docking and MD simulation investigations reveal that the designed compounds are more potent than standard inhibitor, where Ile117, Pro290, Arg236 and Thr253 residues of BlaC are found to play important role in the ligand binding. Through MD simulation study, the best binding compound is also observed to form stable complex by increasing the protein rigidness. The ADME/T analysis suggests that modified drugs are less toxic and shows an improved pharmacokinetic properties than that of the standard drug. These results further confirm the ability of Ni-directed Schiff bases to bind simultaneously to the active site of BlaC and support them as potential candidates for the future treatment of tuberculosis disease.

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Computational Analysis and Binding Site Identification of Type III Secretion System ATPase from Pseudomonas aeruginosa

Cited by 11 publications

References 52 publications

Structure and dynamics of membrane protein in SARS-CoV-2

Structure and dynamics of membrane protein in SARS-CoV-2

In Silico screening of T-cell and B-cell Epitopes of Rotavirus VP7 and VP4 proteins for Effective Vaccine Design

Molecular docking and dynamics of Nickel-Schiff base complexes for inhibiting β-lactamase of Mycobacterium tuberculosis

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