Protein surface recognition and proteomimetics: mimics of protein surface structure and function Steven Fletcher and Andrew D Hamilton Due to their key roles in a number of biological processes, protein–protein interactions are attractive and important targets, typically involving areas greater than 6 nm 2 . The disruption of such interactions remains a challenging feat but, in recent years, there has been considerable progress in the design of proteomimetics: molecules that mimic the structure and function of extended regions of protein surfaces. In particular, porphyrins, calixarenes, a-helical mimetics and small molecules have successfully modulated significant protein–protein interactions, including those involved in cancer and HIV. Addresses Department of Chemistry, Yale University, CT 06520-8107, USA Corresponding author: Hamilton, Andrew D (andrew.hamilton@yale.edu) Current Opinion in Chemical Biology 2005, 9:1–7 This review comes from a themed issue on Model systems Edited by Paolo Scrimin and Lars Baltzer 1367-5931/$ – see front matter # 2005 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cbpa.2005.10.006 Introduction Protein–protein interactions play key roles in several bio- logical processes, such as cell proliferation, growth and differentiation, and these interactions are therefore attrac- tive targets for the chemical biologist [1]. However, the disruption of protein–protein interactions remains a diffi- cult challenge, primarily because of the large interfacial area required for specific recognition (typically > 6 nm 2 is buried during a protein–protein interaction), as well as the unique topological distribution of charged, polar and hydrophobic residues on the protein surface. Nonetheless, there have been many studies reporting some success in this field [2–5]. In this review, we focus on recent advances of protein recognition by compounds that mimic protein surface structure and function: proteomimetics. Porphyrins, peptidocalixarenes and metal-based systems Observing that cytochrome c (cyt c) interacts with its redox partners (e.g. cytochrome c oxidase) predominantly through a hydrophobic patch that is surrounded by invar- iant Arg and Lys residues, Hamilton et al. designed tetracarboxyphenylporphyrin derivatives bearing anionic side chains to complement the distribution of function- ality on the protein surface. The authors have successfully prepared low nanomolar binders of cyt c (K i = 20 nM) [6], which can be improved to subnanomolar binders by extending the hydrophobic core scaffold of tetraphenyl- porphyin (diameter = 15.5 A ˚ ) to the wider 24.0 A ˚ tetra- biphenylporphyrin scaffold and by increasing the number of peripheral anionic groups from 8 to 16 (K i = 0.67 nM, Figure 1a) [7]. Furthermore, some of these anionic por- phyrins have been shown to denature cyt c through binding-induced disruption of tertiary and secondary structure [8,9], thereby leading to accelerated proteolytic degradation [10  ]. Trauner and co-workers have similarly described the use of porphyrins to match the symmetry of the homotetra- meric human K v 1.3 potassium channel [11]. A large variety of potassium channel inhibitors have been iden- tified, although all bind the pore region of the protein and do not take advantage of its inherent fourfold symmetry. Trauner et al. proposed that the molecular architecture provided by tetracarboxyphenylporphyrin derivatives could also allow for pore binding by the central porphyrin scaffold. Moreover, its four peripheral acids could be derivatized with cationic groups simultaneously project- ing towards highly conserved Asp or Glu ‘hot spot’ residues in each of the channel subunits, leading to a strong polyvalency effect. Indeed, the authors demon- strated, by competitive binding studies, that their cationic porphyrins strongly interact, in the nanomolar range, with the potassium channel, and, as determined by electro- physiological measurements, significantly reduce the cur- rent through the channel (Figure 1b). Further work in this area may lead to novel therapeutic agents against diseases such as diabetes and epilepsy. In a popular area of research [12,13] there have been recent reports on protein surface recognition by peptido- calixarenes. Cunsolo et al. have designed basic amino acid calix[8]arene receptors that behave as competitive inhi- bitors of recombinant human tryptase, probably binding the intended region of Asp residues near the active sites of the tetrameric protein [14]. Neri et al. recently demon- strated the surface recognition of transglutaminase by their peptidocalix[4]arene diversomers (isomers compris- ing the same components that are arranged in different orders) [15]. Again, competition assays suggest their inhi- bitors bind to a surface area of the protein (‘hot spot’) other than the enzyme active site, exerting their inhibi- tory effects either by causing a conformational change in COCHBI 296 www.sciencedirect.com Current Opinion in Chemical Biology 2005, 9:1–7