The structural clues of substrate recognition by calpain are incompletely understood. In this study, 106 cleavage sites in substrate proteins compiled from the literature have been analyzed to dissect the signal for calpain cleavage and also to enable the design of an ideal calpain substrate and interfere with calpain action via site-directed mutagenesis. In general, our data underline the importance of the primary structure of the substrate around the scissile bond in the recognition process. Significant amino acid preferences were found to extend over 11 residues around the scissile bond, from P(4) to P(7)'. In compliance with earlier data, preferred residues in the P(2) position are Leu, Thr, and Val, and in P(1) Lys, Tyr, and Arg. In position P(1) ', small hydrophilic residues, Ser and to a lesser extent Thr and Ala, occur most often. Pro dominates the region flanking the P(2)-P(1)' segment, i.e. positions P(3) and P(2)'-P(4)'; most notable is its occurrence 5.59 times above chance in P(3)'. Intriguingly, the segment C-terminal to the cleavage site resembles the consensus inhibitory region of calpastatin, the specific inhibitor of the enzyme. Further, the position of the scissile bond correlates with certain sequential attributes, such as secondary structure and PEST score, which, along with the amino acid preferences, suggests that calpain cleaves within rather disordered segments of proteins. The amino acid preferences were confirmed by site-directed mutagenesis of the autolysis sites of Drosophila calpain B; when amino acids at key positions were changed to less preferred ones, autolytic cleavage shifted to other, adjacent sites. Based on these preferences, a new fluorogenic calpain substrate, DABCYLTPLKSPPPSPR-EDANS, was designed and synthesized. In the case of micro- and m-calpain, this substrate is kinetically superior to commercially available ones, and it can be used for the in vivo assessment of the activity of these ubiquitous mammalian calpains.

Cell-penetrating peptides (CPP) are promising tools for the transport of a broad range of compounds into cells. Since the discovery of the first members of this peptide family, many other peptides have been identified; nowadays, dozens of these peptides are known. These peptides sometimes have very different chemical–physical properties, but they have similar drawbacks; e.g., non-specific internalization, fast elimination from the body, intracellular/vesicular entrapment. Although our knowledge regarding the mechanism and structure–activity relationship of internalization is growing, the prediction and design of the cell-penetrating properties are challenging. In this review, we focus on the different modifications of well-known CPPs to avoid their drawbacks, as well as how these modifications may increase their internalization and/or change the mechanism of penetration.

Data reported in this article describe the synthesis of Arg‐rich oligopeptide conjugates of ferrocenecarboxylic acid on solid support with two different strategies and for the first time, the successful preparation of peptide conjugates of ferrocenylacrylic acid in solution. The antitumor effect of conjugates was analyzed by MTT assay in vitro. We demonstrated that ferrocenylacrylic acid possessing an enone (CHCHCO) moiety exhibited remarkable antiproliferative effect against human leukemia cells (HL‐60) in vitro, but its effect was not improved by conjugation with hexa‐ or octaarginines. However, we observed highly increased water‐solubility. In contrast, the results provide evidence that conjugation of ferrocenecarboxylic acid to Arg_n (n = 6, 8) improved not only its water‐solubility, but also antitumor effect on human leukemia cells in vitro. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 88: 108–114, 2007.This article was originally published online as an accepted preprint. The ‘Published Online’ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Introduction: Calpains are intracellular Ca²⁺-dependent cysteine proteases with 15 known members in the enzyme family. They act as regulatory enzymes, their cleavage modifying the function of their substrates. As their substrates have important roles in many physiological processes, adequate function of calpains is mandatory for normal cellular functions. The adverse operation of them is often related to diseases (e.g. neurodegenerative disorders, cancer, type 2 diabetes mellitus, or limb-girdle muscular dystrophy type 2A). Areas covered: Herein, the authors give an overview of calpains, their structure as well as their physiological and pathological functions. The authors further consider the challenges in calpain inhibitor and activator drug discovery and summarize examples of good candidates. New and applicable strategies are also discussed. Expert opinion: Calpain enzymes are attractive targets for inhibitor or activator design and development. The authors believe this area of research is of high potential, although it has many challenges. For one, the selective and targeted inhibition or activation of calpains is needed. Furthermore, uncontrolled calpain activation may cause more serious side effects and so caution is needed when designing novel therapeutics.