Fuchs JE, Wellenzohn B, Weskamp N, Liedl KR. Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications.
J Chem Inf Model 2015;
55:2315-23. [PMID:
26501781 PMCID:
PMC4658635 DOI:
10.1021/acs.jcim.5b00476]
[Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Biopharmaceuticals hold great promise
for the future of drug discovery.
Nevertheless, rational drug design strategies are mainly focused on
the discovery of small synthetic molecules. Herein we present matched
peptides, an innovative analysis technique for biological data related
to peptide and protein sequences. It represents an extension of matched
molecular pair analysis toward macromolecular sequence data and allows
quantitative predictions of the effect of single amino acid substitutions
on the basis of statistical data on known transformations. We demonstrate
the application of matched peptides to a data set of major histocompatibility
complex class II peptide ligands and discuss the trends captured with
respect to classical quantitative structure–activity relationship
approaches as well as structural aspects of the investigated protein–peptide
interface. We expect our novel readily interpretable tool at the interface
of cheminformatics and bioinformatics to support the rational design
of biopharmaceuticals and give directions for further development
of the presented methodology.
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