Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Pharmaceutical and Chemical Sciences

First Advisor

Bhaskara R. Jasti

First Committee Member

Xiaoling Li

Second Committee Member

Jerry Tsai

Third Committee Member

Xin Guo

Fourth Committee Member

John Livesey


Structure based computational peptide design methods have gained significant interest in recent years with the availability of structural insights of protein-protein interactions obtained from the crystal structures. Most of these approaches design new peptide ligands by connecting the crucial amino acid residues from the protein interface and are generally not based on any predicted receptor-ligand interaction. In this work, a peptide design method based on the Knob-Socket model was used to identify the specific ligand residues packing into the receptor interface. This method enables rational peptide ligand design by predicting amino acid residues that will fit best at the binding site of the receptor protein. Specific peptide ligands for the model receptor CD13 that are overexpressed in several cancer types were designed in this study. From the initial library of designed peptides, three potential candidates were selected based on simulated energies in the CD13 binding site using the programs Molecular Operating Environment (MOE) and AutoDock Vina. In the CD13 enzymatic activity inhibition assay, the three identified peptides exhibited 2.7 to 7.4 times lower IC50 values (GYPAY, 227 µM; GFPAY, 463 µM; GYPAVYLF, 170 µM) when compared to the known peptide ligand CNGRC(C1-C5) (1260 µM). The binding affinities of the peptides (GYPAY, Ki = 54.0 µM; GFPAY, Ki = 74.3 µM; GYPAVYLF, Ki = 38.8 µM) were 10 to 20 times higher than that of CNGRC (C1-C5) (Ki = 773 µM). The double reciprocal plots from the steady state enzyme kinetic assays confirmed the binding of the peptides to the intended active site of CD13. The cell binding and confocal microscopy assays showed that the designed peptides selectively bind to the CD13 on cell surface. The designed peptide-drug conjugates (PDCs) showed lower in vitro cytotoxicity and slightly better in vivo antitumor efficacy as compared to a model drug MMAE. However, the PDCs contributed to much lower weight loss in mice indicating lower side effects in vivo.

This study demonstrated the feasibility of a Knob-Socket based rational design of novel peptides ligands in improving the identification of specific binding in comparison to the labor intensive current methods.





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