BBAMEM-82292; No. of pages: 9; 4C: 5, 6, 7 Biochimica et Biophysica Acta xxx (2016) xxx–xxx Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamem Review Therapeutic design of peptide modulators of protein-protein interactions in membranes Tracy A. Stone, Charles M. Deber ⁎ Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada article info abstract Article history: Membrane proteins play the central roles in a variety of cellular processes, ranging from nutrient uptake and sig- Received 21 July 2016 nalling, to cell-cell communication. Their biological functions are directly related to how they fold and assemble; Received in revised form 22 August 2016 defects often lead to disease. Protein–protein interactions (PPIs) within the membrane are therefore of great in- Accepted 24 August 2016 terest as therapeutic targets. Here we review the progress in the application of membrane–insertable peptides for Available online xxxx the disruption or stabilization of membrane–based PPIs. We describe the design and preparation of transmem- Keywords: brane peptide mimics; and of several categories of peptidomimetics used for study, including D-enantiomers, – β fi Peptide non natural amino acids, peptoids, and -peptides. Further aspects of the review describe modi cations to Protein–protein interaction (PPI) membrane–insertable peptides, including lipidation and cyclization via hydrocarbon stapling. These approaches Transmembrane provide a pathway toward the development of metabolically stable, non-toxic, and efficacious peptide modula- Peptidomimetics tors of membrane–based PPIs. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid- Lipidation control of protein activity edited by Dirk Schneider. Hydrocarbon staple © 2016 Elsevier B.V. All rights reserved. Contents 1. Introduction.............................................................. 0 1.1. Protein-proteininteractionsbetweenmembrane-spanninghelices................................... 0 1.2. Developmentoftransmembranepeptidetherapeutics........................................ 0 1.3. Transmembrane peptide modifications............................................... 0 1.4. Peptidomimetics......................................................... 0 1.4.1. Chirality: D-enantiomers.................................................. 0 1.4.2. Side chain alterations: Homo- and α-methyl-aminoacids................................... 0 1.4.3. Backbone alterations: N-methyl amino acids, peptoids, β-aminoacids............................. 0 1.5. Peptidelipidation......................................................... 0 1.6. Peptidecyclization........................................................ 0 2. Conclusions............................................................... 0 Transparencydocument............................................................ 0 Acknowledgements.............................................................. 0 References.................................................................. 0 Abbreviations: PPI, protein–protein interactions; TM, transmembrane; GPCR, G- protein coupled receptor; RTK, receptor tyrosine kinase; TLR, Toll-like receptor; ErbB-2, 1. Introduction EGFR epidermal growth factor receptor; NRP1, neuropilin-1; MPZ, myelin protein zero; gp41, glycoprotein 4; CHAMP, Computed Helical Anti-membrane Protein; Sar, sarcosine; Protein–protein contacts carry out vital roles in mediating protein GpA, glycophorin A; CD3, cluster of differentiation 3; TCRα, T-cell receptor alpha. folding and function. Stabilization or disruption of these interactions is ⁎ Corresponding author at: Division of Molecular Structure & Function, Research therefore of great interest for the modulation of protein function within Institute, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, 686 Bay Street, Toronto M5G 0A4, Ontario, Canada. the cell, marking protein–protein interactions (PPIs) as attractive tar- E-mail address: [email protected] (C.M. Deber). gets for the development of novel therapeutics. The association of http://dx.doi.org/10.1016/j.bbamem.2016.08.013 0005-2736/© 2016 Elsevier B.V. All rights reserved. Please cite this article as: T.A. Stone, C.M. Deber, Therapeutic design of peptide modulators of protein-protein interactions in membranes, Biochim. Biophys. Acta (2016), http://dx.doi.org/10.1016/j.bbamem.2016.08.013 2 T.A. Stone, C.M. Deber / Biochimica et Biophysica Acta xxx (2016) xxx–xxx helical domains mediates many PPIs in both soluble and membrane pro- aromatic residues, which also participate in mediating PPIs within the teins. Such helical domains present specific topological surfaces that can lipid bilayer through inter-helical hydrogen bonds, polar–polar, and ar- readily be mimicked using a variety of biochemical techniques [1]. omatic–aromatic interactions [12–15]. While both small molecules and short protein domains (peptides and While some membrane-embedded domains serve the simple func- peptidomimetics) have been applied to the targeting of soluble helical tion of anchoring cytosolic or extracellular domains to the bilayer, PPIs with great success [2], targeting membrane-embedded PPIs has many TM domains are directly involved in protein function, forming proven challenging. Compared to their soluble counterparts, few drugs conduits through the membrane for molecule transport or undergoing target PPIs within the membrane, a problem that undoubtedly arises intramolecular conformational changes and/or intermolecular oligo- from the unique environment membrane proteins must fold and func- merization to transmit a signal. The TM domains of eukaryotic mem- tion within. Small molecule approaches have been utilized with limited brane proteins are commonly α-helical (with the exception of β- success, held back by limited membrane permeability and low barrel proteins found in the mitochondrial outer membrane), spanning specificity. The large, extended surface of most PPIs (N800 Å2), renders the bilayer through an average of 20–24 amino acids [16]. These the use of larger scaffolds and protein mimetics more effective than membrane-embedded domains are predominantly hydrophobic in na- small molecules [3]. ture [16], allowing for favourable interactions with surrounding apolar Despite the barrier presented by the lipid bilayer, membrane pro- lipid acyl chains. Nevertheless, polar and charged amino acids are teins remain important drug targets. Membrane proteins provide the found within TM domains, where these ‘unfavourable’ amino acids communication link between the extracellular world and the inside of carry out important functional roles in the linings of pore and channels the cell, carrying out critical cellular functions involved in nutrient and as well as initiating helix-helix contacts. Membrane protein folding is waste transport, cell-cell recognition, and signal transduction. These further complicated by the complex environment of the lipid bilayer. proteins constitute ca. 30% of human protein encoding genes [4] and Not only is the membrane composed of lipids varying in head group, represent ca. 60% of all human drug targets [5]. The importance of mem- tail length and saturation, but the membrane is also protein-dense. brane proteins in maintaining cellular homeostasis is clear, many dis- Competition for helix interactions between neighbouring helices and ease states arising from the improper folding, function or localization lipid molecules makes the adoption of appropriate helix-helix and of these proteins. Many cancers, neurological, metabolic and immune helix-lipid contacts very intricate. disorders and can be attributed to the faulty function of membrane Lipid interactions also play important roles in protein folding and olig- proteins [6]. omerization. Membrane proteins present irregular surfaces and both Membrane-embedded receptors and transporters collectively repre- polar and apolar atoms to surrounding lipid, resulting unfavourable sent the largest group of human drug targets, with GPCRs being the lipid–proteinandrestrictiononlipid–lipid interactions, can drive TM do- most abundant (ca. 36% of all drug targets), followed by ligand and volt- mains to self-associate in a manner mediated by the motifs mentioned age gated channels and receptor tyrosine kinases [5]. Notably, all of above. Particularly, small–small motifs produce a cavity or ‘hole’ on a these membrane proteins either contain several transmembrane (TM) TM helix face that may only favorably be occupied by the bulky ‘knobs’ strands and/or undergo some degree of oligomerization. As examples, of a complementary TM domains [17,18]. GPCRs are seven-TM proteins and their function can be modulated The high frequency with which TM domains associate through van through oligomerization [7]; ligand and voltage gated channels general- der Waals interactions, mediated by a limited number of motifs, ly have more than one TM domain and exist as oligomers [8];andrecep- both simplifies and convolutes the development of de novo inhibitor/ tor tyrosine kinases, while containing only a single TM domain, must stabilizing compounds. Table 1 details examples of membrane proteins dimerize to function [9]. Thus, protein–protein interactions play essen- that utilize the common small–small motif to oligomerize and diseases tial roles not only in