Interaction of Proteins with small Molecules and Peptides
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
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| Title |
Interaction of Proteins with small Molecules and Peptides
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| Creator |
Pal, Uttam
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| Subject |
Structural Biology & Bioinformatics
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| Description |
Understanding the molecular interaction of proteins with small molecules and peptides is essential in drug discovery. This thesis explores the importance of
protein small molecule interactions in biology and its implications in rational drug development. Using combined theoretical and experimental chemistry, author
tried to device new approaches or build upon the existing tools to study the interactions of proteins with small molecules and peptides. New algorithm has been developed based on the existing molecular docking methods to improve the specificity in docking prediction and reduce the false positive results (hits) in virtual high throughput screening. In recent years allosteric drugs have gained much
attention because of the specificity it can achieve due to the evolutionarily diverse binding sites on the target proteins. The author developed a pattern based
approach using molecular docking tools to detect the allosteric binding sites on structured protein targets and analyzed the druggability of these allosteric binding
sites. Detections of binding sites in the intrinsically disordered proteins was also explored using the sequence based analysis tools. Statistical distribution of binding
sites in a library of disordered proteins was characterized. A fluorescent probe molecule has been developed to study the microenvironment of protein binding
sites, which showed increased quantum yield, anisotropy and higher energy emission upon binding to a hydrophobic site of the target protein. Author studied even deeper into the finer details of molecular interactions such as the hydrogen
bonding and its strength on model system (alcohol amine complexes) using isotope labeling, solution state nuclear magnetic resonance spectroscopy and quantum mechanics with implications in protein small molecule interactions.
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| Date |
2016-02-22
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| Type |
Thesis
NonPeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/2550/1/Thesis_Uttam_Pal.pdf
Pal, Uttam (2016) Interaction of Proteins with small Molecules and Peptides. PhD thesis, J U . |
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| Relation |
http://www.eprints.iicb.res.in/2550/
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