Date of Award


Degree Type


Degree Name

Master of Science (MS)


Biomedical and Chemical Engineering


Shikha Nangia

Second Advisor

Arindam Chakraborty


AMP;Antimicrobial;Medical Implant;Molecular Dynamics;Peptoid

Subject Categories

Chemical Engineering | Engineering


Peptoids are peptidomimetics, in which the side chains are carried by the backbone nitrogen atoms instead of the alpha carbon, resulting in N-substituted glycine repeat units. The cationic peptoids have antimicrobial properties and can be sequestered into anionic hydrogels as coatings on implantable devices to prevent infection. In a recent study, our lab investigated the self-assembly of short peptoids with 6 to 12 repeat units. We showed that peptoids can cluster into large aggregates or remain as individual molecules depending on the net charge and nature of the sidechains. This study also demonstrated that the complexation of peptoids with microgels depends on the size of peptoid clusters; small clusters of 2-4 peptoids load into microgels more effectively and show higher antimicrobial activity than larger or smaller clusters. In this work, I focused on identifying optimal peptoids with seven repeat units using a combination of three building blocks—NLys, Nspe, and Nspe(p-Br). The goal is to optimize the peptoid sequence that forms small clusters, has a nonzero positive charge to be loaded into anionic microgels, and is antimicrobial. I used a computational approach to build the molecular structure of 52 unique peptoids with a +2 charge. I examined the self-assembly properties of all 52 peptides using molecular dynamics simulations. The results showed high sensitivity to the molecular structure of the peptoids, particularly to the number of the NLys, Nspe, and Nspe(p-Br) repeat units in the 7-mer. A peptoid with three Nspe(p-Br) formed larger clusters than the peptoid with two such repeats because the presence of Br resulted in higher hydrophobicity. Moreover, increasing the net charge from 2 to 3 by adding more NLys, decreased clustering. Although more work needs to be performed to explore the entire design space of 37= 2187 possible peptoids, this work provides insights to optimize the peptoid with the desired clustering and, consequently, the desired antimicrobial activity


Open Access

Available for download on Sunday, June 21, 2026