Publication Date



Open access

Embargo Period


Degree Type


Degree Name

Doctor of Philosophy (PHD)


Chemistry (Arts and Sciences)

Date of Defense


First Committee Member

Rajeev Prabhakar

Second Committee Member

Orlando Acevedo

Third Committee Member

James Wilson

Fourth Committee Member

Luis Ruiz Pestana


Hydrolysis reaction is involved in a wide range of biological and industrial applications. In our body, phosphoester and peptide hydrolysis are accomplished using specialized enzymes known as phosphoesterases and proteases. These enzymes constitute about 60% of all the enzymes that are used today in textile, food, leather, paper, and ethanol production industries.In this thesis, I have focused on the following three projects; (1) exploring the interactions of various biomolecules (such as enzymes, antimicrobial peptides, DNA, and amyloid β fibrils) with their binding molecules; (2) understanding the mechanism of phosphoester and peptide hydrolysis by glycerophosphodiesterase (GpdQ) and Streptomyces griseus aminopeptidase (SgAP), respectively; and (3) studying the interactions of different host and guest molecules forming supramolecular complexes. In the first project, molecular dynamics (MD) simulations have been performed to study the interactions of GpdQ and SgAP metalloenzymes with their substrates. We have also looked at the DNA binding and cleaving mechanism of an antimicrobial peptide (ClavaninA). Additionally, we have been able to predict the binding sites of the rhenium centered photoluminescence probe on the Aβ peptide. In the second project, DFT calculation has been exploited to study the hydrolytic activity of GpdQ (for cleaving phosphoester bond) and SgAP (for cleaving both peptide and phosphoester bonds). In the third project, we have employed MD simulations to investigate the interactions between host-host and host-guest molecules. In particular, the interactions of host molecules (cucurbiturils and BB4+) and guest molecule (GH22+) have been computed. Additionally, the dynamics of guest molecules encapsulated inside the octa acid host have also been elucidated.


Phosphoester hydrolysis; peptide hydrolysis; amyloids