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Comprehensive analysis of loops at protein-protein interfaces for macrocycle design

Abstract

Inhibiting protein-protein interactions (PPIs) with synthetic molecules remains a frontier of chemical biology. Many PPIs have been successfully targeted by mimicking α-helices at interfaces, but most PPIs are mediated by nonhelical, nonstrand peptide loops. We sought to comprehensively identify and analyze these loop-mediated PPIs by writing and implementing LoopFinder, a customizable program that can identify loop-mediated PPIs within all of the protein-protein complexes in the Protein Data Bank. Comprehensive analysis of the entire set of 25,005 interface loops revealed common structural motifs and unique features that distinguish loop-mediated PPIs from other PPIs. 'Hot loops', named in analogy to protein hot spots, were identified as loops with favorable properties for mimicry using synthetic molecules. The hot loops and their binding partners represent new and promising PPIs for the development of macrocycle and constrained peptide inhibitors.

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Figure 1: Identification of hot loops.
Figure 2: Visualization of different loop structures observed among the hot loops.
Figure 3: Interface loops use a unique set of amino acids to recognize their binding partners.
Figure 4: Established and new targets for inhibitor design.

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Protein Data Bank

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Acknowledgements

J.G. was supported in part by US National Institutes of Health (NIH)/NIGMS Institutional Research and Academic Career Development Awards grant K12GM074869. T.R.S. was supported in part by Department of Education Graduate Assistance in Areas of National Need grant P200A090303. This work was supported in part by NIH DP2-OD007303 to J.A.K. The authors thank the Tufts Technology Services for research cluster access and R. Scheck for helpful conversations.

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Authors

Contributions

B.A.S. wrote the LoopFinder code. J.G., B.A.S. and J.A.K. performed troubleshooting and debugged and parameterized Loopfinder and Rosetta-based computational alanine scanning. J.G., T.R.S., M.R.E. and J.A.K. analyzed and contextualized data. J.G., T.R.S. and J.A.K. produced figures and tables and wrote the paper.

Corresponding author

Correspondence to Joshua A Kritzer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Results, Supplementary Figures 1–8 and Supplementary Tables 1–6. (PDF 1703 kb)

Supplementary Data Set 1

The entire set of hot loops generated by LoopFinder. (XLSX 307 kb)

Supplementary Data Set 2

The subset of 364 hot loops that do not contain two or more consecutive hot spots. (XLSX 50 kb)

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Gavenonis, J., Sheneman, B., Siegert, T. et al. Comprehensive analysis of loops at protein-protein interfaces for macrocycle design. Nat Chem Biol 10, 716–722 (2014). https://doi.org/10.1038/nchembio.1580

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