Computational and experimental analysis of short peptide motifs for enzyme inhibition

• Published in: PloS one Vol. 12; no. 8; p. e0182847
• Main Authors: Fu, Jinglin, Larini, Luca, Cooper, Anthony J, Whittaker, John W, Ahmed, Azka, Dong, Junhao, Lee, Minyoung, Zhang, Ting
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 15.08.2017; Public Library of Science (PLoS)
• Subjects: Alanine; Amino Acid Motifs; Analysis; beta-Galactosidase - antagonists & inhibitors; Binding Sites; Biology; Biology and Life Sciences; Catalysis; Catalysts; Chemical synthesis; Computation; Computer applications; Computer simulation; Enzyme Activation - drug effects; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Enzymes; Galactosidase; Inhibitory Concentration 50; Ligands; Medical screening; Metabolism; Modulators; Molecular dynamics; Molecular Dynamics Simulation; Mutagenesis; Peptides; Peptides - chemistry; Peptides - pharmacology; Physical Sciences; Physics; Physiological aspects; Protein Binding; Protein Structure, Secondary; Proteins; Research and Analysis Methods; Scanning; Science; Screening; Simulation; Structure; β-Galactosidase; United States; United States > US; New Jersey
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0182847

The metabolism of living systems involves many enzymes that play key roles as catalysts and are essential to biological function. Searching ligands with the ability to modulate enzyme activities is central to diagnosis and therapeutics. Peptides represent a promising class of potential enzyme modulators due to the large chemical diversity, and well-established methods for library synthesis. Peptides and their derivatives are found to play critical roles in modulating enzymes and mediating cellular uptakes, which are increasingly valuable in therapeutics. We present a methodology that uses molecular dynamics (MD) and point-variant screening to identify short peptide motifs that are critical for inhibiting β-galactosidase (β-Gal). MD was used to simulate the conformations of peptides and to suggest short motifs that were most populated in simulated conformations. The function of the simulated motifs was further validated by the experimental point-variant screening as critical segments for inhibiting the enzyme. Based on the validated motifs, we eventually identified a 7-mer short peptide for inhibiting an enzyme with low μM IC50. The advantage of our methodology is the relatively simplified simulation that is informative enough to identify the critical sequence of a peptide inhibitor, with a precision comparable to truncation and alanine scanning experiments. Our combined experimental and computational approach does not rely on a detailed understanding of mechanistic and structural details. The MD simulation suggests the populated motifs that are consistent with the results of the experimental alanine and truncation scanning. This approach appears to be applicable to both natural and artificial peptides. With more discovered short motifs in the future, they could be exploited for modulating biocatalysis, and developing new medicine.