Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions

Andrew M Watkins; Richard Bonneau; Paramjit S Arora

doi:10.1007/978-1-4939-6798-8_17

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions

Methods Mol Biol. 2017:1561:291-307. doi: 10.1007/978-1-4939-6798-8_17.

Authors

Andrew M Watkins¹, Richard Bonneau^{2

3}, Paramjit S Arora⁴

Affiliations

¹ Department of Chemistry, New York University, New York, NY, USA.
² Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
³ Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
⁴ Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA. arora@nyu.edu.

PMID: 28236245
DOI: 10.1007/978-1-4939-6798-8_17

Abstract

We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.

Keywords: Computational design; Inhibitor design; Peptidomimetics; Protein–protein interactions.

MeSH terms

Binding Sites
Humans
Models, Molecular
Peptide Fragments / chemistry*
Peptide Fragments / metabolism*
Peptidomimetics / pharmacology*
Protein Binding
Protein Conformation
Protein Interaction Maps / drug effects*
Proteins / chemistry
Proteins / metabolism*
Software*

Substances

Peptide Fragments
Peptidomimetics
Proteins