Exploring the binding potential of carbon nanotubes and fullerene towards major drug targets of multidrug resistant bacterial pathogens and their utility as novel therapeutic agents

Skariyachan, Sinosh; Garka, Shruthi

doi:10.1016/b978-0-12-813691-1.00001-4

Cited by 11 publications

(6 citation statements)

References 110 publications

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“…This method is used to generate a previously unknown protein structure by "fitting" its sequence (target) into a known structure (template), with a certain degree of sequence homology (at least 30%) between the target and template (Sensoy et al, 2017). It is accurate for making structural models of proteins (Skariyachan and Garka, 2018). ACE2's 3D structure prediction uses the Swiss-Model webserver to obtain accurate modeling.…”

Section: Results and Discussion Homology Modeling Using Swiss Modelmentioning

confidence: 99%

Homology modeling and mutation prediction of ACE2 from COVID-19

et al. 2021

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SARS-CoV-2 has become a pandemic in the world. The virus binds to the Angiotensin-Converting Enzyme 2 (ACE2) receptor, which is found in epithelial cells such as in the lungs, to generate the pathology of COVID-19. It is essential to analyze the characteristics of ACE2 in understanding the development of the disease and study potential new drugs. The analysis was carried out using computer simulations to speed up protein analysis that utilized Artificial Intelligence technology, databases, and big data. Homology modeling is a method to exhibit homologous of protein families, hence the model and arrangement of protein sequences modeled are established. This research aims to determine the possibility of mutations in ACE2 by performing the mutation prediction. The result shows reliable homologous modeling with the score of GA341, MPQS, Z-DOPE, and TSVMod NO35 were 1; 1.28252; -0.47; and 0.793, respectively. Moreover, Gene Ontology (GO) analysis describes that ACE2 has a molecular transport function in cells while there are no mutations found occurred in ACE2 analyzed using SIFT and PROVEAN.

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Section: Results and Discussion Homology Modeling Using Swiss Modelmentioning

confidence: 99%

Homology modeling and mutation prediction of ACE2 from COVID-19

et al. 2021

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“…We used comparative homology modeling instead of experimental NMR and X-ray crystallography. Comparative homology modeling is considered as a highly favorable option because of its capability for function prediction as well as its application in different research fields (e.g., 3D structure prediction, mutagenesis analysis, and disulfide bridge analysis) [46,47]. We predicted 3D structures for all four IROMPs and validated them.…”

Section: Discussionmentioning

confidence: 96%

In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis

Rahman¹,

Biswas²,

Biswas

et al. 2020

Applied Sciences

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Neisseria meningitidis is a commensal pathogen that causes infectious cerebrospinal disease in people of all ages. The multivariate role of six disease-causing polysaccharide serotypes is found to play a crucial role in developing vaccines (or general treatment strategies) to treat this emerging pathogen. Iron is a crucial transition metal for N. meningitidis. Proteomic analysis data could be valuable for vaccine design. Here, we conduct a comparative study using computational bioinformatic tools to identify the most effective iron-regulated outer membrane proteins (OMPs) as immunogenic targets for a potential vaccine against N. meningitidis. The basic properties of N. meningitidis OMPs are explored for flexibility, solubility, hydrophilicity, beta-turns, and overall antigenic probability. Results of our study suggest that iron-regulated OMPs are flexible and soluble in water with high densities of conformational B-cell epitopes. As such, they can be recommended as a novel candidate for a vaccine against N. meningitidis both in vitro and in vivo.

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“…arabiensis was not available, it was elected to employ the use of homology modelling [ 40 ]. This approach involved four successive steps: (i) target amino acid sequence identification, (ii) template identification, (iii) sequence alignment between target and template, and (iv) model building and optimization [ 41 , 42 ]. Homology modelling is considered the most accurate in silico approach to generate 3D models of proteins [ 42 ], however, certain minimum requirements had to be met.…”

Section: Methodsmentioning

confidence: 99%

The in silico and in vitro analysis of donepezil derivatives for Anopheles acetylcholinesterase inhibition

Rants’o

Greunen²,

Westhuizen³

et al. 2022

PLoS ONE

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Current studies on Anopheles anticholinesterase insecticides are focusing on identifying agents with high selectivity towards Anopheles over mammalian targets. Acetylcholinesterase (AChE) from electric eel is often used as the bioequivalent enzyme to study ligands designed for activity and inhibition in human. In this study, previously identified derivatives of a potent AChE, donepezil, that have exhibited low activity on electric eel AChE were assessed for potential AChE-based larvicidal effects on four African malaria vectors; An. funestus, An. arabiensis, An. gambiae and An. coluzzii. This led to the identification of four larvicidal agents with a lead molecule, 1-benzyl-N-(thiazol-2-yl) piperidine-4-carboxamide 2 showing selectivity for An. arabiensis as a larvicidal AChE agent. Differential activities of this molecule on An. arabiensis and electric eel AChE targets were studied through molecular modelling. Homology modelling was used to generate a three-dimensional structure of the An. arabiensis AChE for this binding assay. The conformation of this molecule and corresponding interactions with the AChE catalytic site was markedly different between the two targets. Assessment of the differences between the AChE binding sites from electric eel, human and Anopheles revealed that the electric eel and human AChE proteins were very similar. In contrast, Anopheles AChE had a smaller cysteine residue in place of bulky phenylalanine group at the entrance to the catalytic site, and a smaller aspartic acid residue at the base of the active site gorge, in place of the bulky tyrosine residues. Results from this study suggest that this difference affects the ligand orientation and corresponding interactions at the catalytic site. The lead molecule 2 also formed more favourable interactions with An. arabiensis AChE model than other Anopheles AChE targets, possibly explaining the observed selectivity among other assessed Anopheles species. This study suggests that 1-benzyl-N-(thiazol-2-yl) piperidine-4-carboxamide 2 may be a lead compound for designing novel insecticides against Anopheles vectors with reduced toxic potential on humans.

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Exploring the binding potential of carbon nanotubes and fullerene towards major drug targets of multidrug resistant bacterial pathogens and their utility as novel therapeutic agents

Cited by 11 publications

References 110 publications

Homology modeling and mutation prediction of ACE2 from COVID-19

Homology modeling and mutation prediction of ACE2 from COVID-19

In Silico Analysis of the Antigenic Properties of Iron-Regulated Proteins against Neisseria meningitidis

The in silico and in vitro analysis of donepezil derivatives for Anopheles acetylcholinesterase inhibition

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