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      Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein–Protein Interactions

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          Abstract

          Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.

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          An empirical framework for binary interactome mapping

          Kavitha Venkatesan, Jean-François Rual, Alexei Vazquez … (2009)
          Several attempts have been made at systematically mapping protein-protein interaction, or “interactome” networks. However, it remains difficult to assess the quality and coverage of existing datasets. We describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human are superior in precision to literature-curated interactions supported by only a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains ~130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the human genome project, estimates of protein interaction data quality and interactome size are critical to establish the magnitude of the task of comprehensive human interactome mapping and to illuminate a path towards this goal.
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            Advances in chemical protein modification.

            Omar Boutureira, Gonçalo J L Bernardes (2015)
            Article 0 comments Cited 249 times – based on 0 reviews     Review now
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              The atomic structure of protein-protein recognition sites.

              L. Lo Conte, C Chothia, J Janin (1999)
              The non-covalent assembly of proteins that fold separately is central to many biological processes, and differs from the permanent macromolecular assembly of protein subunits in oligomeric proteins. We performed an analysis of the atomic structure of the recognition sites seen in 75 protein-protein complexes of known three-dimensional structure: 24 protease-inhibitor, 19 antibody-antigen and 32 other complexes, including nine enzyme-inhibitor and 11 that are involved in signal transduction.The size of the recognition site is related to the conformational changes that occur upon association. Of the 75 complexes, 52 have "standard-size" interfaces in which the total area buried by the components in the recognition site is 1600 (+/-400) A2. In these complexes, association involves only small changes of conformation. Twenty complexes have "large" interfaces burying 2000 to 4660 A2, and large conformational changes are seen to occur in those cases where we can compare the structure of complexed and free components. The average interface has approximately the same non-polar character as the protein surface as a whole, and carries somewhat fewer charged groups. However, some interfaces are significantly more polar and others more non-polar than the average. Of the atoms that lose accessibility upon association, half make contacts across the interface and one-third become fully inaccessible to the solvent. In the latter case, the Voronoi volume was calculated and compared with that of atoms buried inside proteins. The ratio of the two volumes was 1.01 (+/-0.03) in all but 11 complexes, which shows that atoms buried at protein-protein interfaces are close-packed like the protein interior. This conclusion could be extended to the majority of interface atoms by including solvent positions determined in high-resolution X-ray structures in the calculation of Voronoi volumes. Thus, water molecules contribute to the close-packing of atoms that insure complementarity between the two protein surfaces, as well as providing polar interactions between the two proteins. Copyright 1999 Academic Press.
              Article 0 comments Cited 248 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Molecules
                Journal ID (iso-abbrev): Molecules
                Journal ID (publisher-id): molecules
                Title: Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry
                Publisher: MDPI
                ISSN (Electronic): 1420-3049
                Publication date (Electronic): 19 April 2018
                Publication date Collection: April 2018
                Volume: 23
                Issue: 4
                Electronic Location Identifier: 959
                Affiliations
                Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; nsr32@ 123456cam.ac.uk
                Author notes
                [* ]Correspondence: spring@ 123456ch.cam.ac.uk ; Tel.: +44-1223-336498
                Author information
                https://orcid.org/0000-0001-5519-9158
                https://orcid.org/0000-0001-7355-2824
                Article
                Publisher ID: molecules-23-00959
                DOI: 10.3390/molecules23040959
                PMC ID: 6017787
                PubMed ID: 29671834
                SO-VID: 39ad7ea7-3056-49ba-8eb3-d5787cb8753f
                Copyright © © 2018 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 27 March 2018
                Date accepted : 18 April 2018
                Categories
                Subject: Review

                Keywords: protein–protein interactions,peptidomimetics,proteomimetics,macrocycles,stapled peptides
                Data availability:
                Keywords: protein–protein interactions, peptidomimetics, proteomimetics, macrocycles, stapled peptides

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