Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions

Brook-Oxidation Reaction of Acylsilanes: General Access to α-Ketoamides and α-Ketothioamides

A novel chemoselective Brook-oxidation reaction of acylsilanes initiated by the carbamoyl anion has been successfully developed for the first time. This method enables the synthesis of diverse α-ketoamides and α-ketothioamides under transition metal-free and strong oxidant-free conditions with high yields and high chemoselectivity. It also demonstrates tolerance toward a wide range of functional groups. The synthetic utility of this process is underscored by its successful application in the synthesis of an orexin receptor antagonist from acylsilane, highlighting its potential for the development of novel therapeutic agents and further exploration in synthetic chemistry.

Progress in Electrochemically Empowered C-O Bond Formation: Unveiling the Pathway of Efficient Green Synthesis

(C-X) bonds (X=C, N, O) are the main backbone for making different skeleton in the organic synthetic transformations. Among all the sustainable techniques, electro-organic synthesis for C-X bond formation is the advanced tool as it offers a greener and more cost-effective approach to chemical reactions by utilizing electrons as reagents. In this review, we want to explore the recent advancements in electrochemical C-O bond formation. The electrochemically driven C-O bond formation represents an emerging and exciting area of research. In this context, electrochemical techniques offers numerous advantages, including higher yields, cost-efficient production, and simplified work-up procedures. This method enables the continuous and consistent formation of C-O bonds in molecules, significantly enhancing overall reaction yields. Furthermore, both intramolecular and intermolecular C-O bond forming reaction provided valuable products of O-containing acyclic/cyclic analogue. Hence, carbonyl (C=O), ether -O-), and ester (-COOR) functionalization in both cyclic/acyclic analogues have been prepared continuously via this innovative pathway. In this context, we want to discuss one-decade electrochemical synthetic pathways of various C-O bond contains functional group in chronological manner. This review focused on all the synthetic aspects including mechanistic path and has also mentioned overall critical finding regarding the C-O bond formation via electrochemical pathways.

Calpain inhibition decreases oxidative stress via mitochondrial regulation in a swine model of chronic myocardial ischemia

INTRODUCTION

Calpain overexpression is implicated in mitochondrial damage leading to tissue oxidative stress and myocardial ischemic injury. The aim of this study was to determine the effects of calpain inhibition (CI) on mitochondrial impairment and oxidative stress in a swine model of chronic myocardial ischemia and metabolic syndrome.

METHODS

Yorkshire swine were fed a high-fat diet for 4 weeks to induce metabolic syndrome then underwent placement of an ameroid constrictor to the left circumflex artery. Three weeks later, animals received: no drug (control, "CON"; n= 7); a low-dose calpain inhibitor (0.12 mg/kg; "LCI", n= 7); or high-dose calpain inhibitor (0.25 mg/kg; "HCI", n=7). Treatment continued for 5 weeks, followed by tissue harvest. Cardiac tissue was assayed for protein carbonyl content, as well as antioxidant and mitochondrial protein expression. Reactive oxygen species (ROS) and mitochondrial respiration was measured in H9c2 cells following exposure to normoxia or hypoxia (1%) for 24 h with or without CI.

RESULTS

In ischemic myocardial tissue, CI was associated with decreased total oxidative stress compared to control. CI was also associated with increased expression of mitochondrial proteins superoxide dismutase 1, SDHA, and pyruvate dehydrogenase compared to control. 100 nM of calpain inhibitor decreased ROS levels and respiration in both normoxic and hypoxic H9c2 cardiomyoblasts.

CONCLUSIONS

In the setting of metabolic syndrome, CI improves oxidative stress in chronically ischemic myocardial tissue. Decreased oxidative stress may be via modulation of mitochondrial proteins involved in free radical scavenging and production.

Selective Synthesis of N-[1,3,5]Triazinyl-α-Ketoamides and N-[1,3,5]Triazinyl-Amides from the Reactions of 2-Amine-[1,3,5]Triazines with Ketones

In this study, we report a selective approach for synthesizing N-([1,3,5]triazine-2-yl) α-ketoamides and N-([1,3,5]triazine-2-yl) amides from ketones with 2-amino[1,3,5]triazines through oxidation and oxidative C-C bond cleavage reaction, respectively. The transformation proceeds under mild conditions, provides good functional group tolerance and chemoselectivity, and will serve as a valuable tool for the synthesis of bioactive products.

Electrochemical Radical Reactions of Enol Acetates and Free Alcohols Directly Access to α-Alkoxylated Carbonyl Compounds

The efficient intermolecular alkoxylation reactions of various enol acetates and different alcohols are developed in the electrochemical process for the first time. Enol acetates derived from either aromatic, alkyl, or alicyclic ketones, and abundant free alcohols directly used in this synthetic strategy, make this transformation very valuable in synthesis and application in the future.

One-Pot Synthesis of α-Ketoamides from α-Keto Acids and Amines Using Ynamides as Coupling Reagents

A one-pot strategy for α-keto amide bond formation have been developed by using ynamides as coupling reagents under extremely mild reaction conditions. Diversely structural α-ketoamides were afforded in up to 98% yield for 36 examples. This reaction features advantages such as practical coupling procedure, wide functional group tolerance, and extremely mild conditions and has potential applications in synthetic and medicinal chemistry.

Calpains for dummies: What you need to know about the calpain family

This review was written in memory of our late friend, Dr. Hiroyuki Sorimachi, who, following the steps of his mentor Koichi Suzuki, a pioneer in calpain research, has made tremendous contributions to the field. During his career, Hiro also wrote several reviews on calpain, the last of which, published in 2016, was comprehensive. In this manuscript, we decided to put together a review with the basic information a novice may need to know about calpains. We also tried to avoid similarities with previous reviews and reported the most significant new findings, at the same time highlighting Hiro's contributions to the field. The review will cover a short history of calpain discovery, the presentation of the family, the life of calpain from transcription to activity, human diseases caused by calpain mutations and therapeutic perspectives.

α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment

The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.

Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

Increased calpain activity is linked to neuroinflammation including a heritable retinal disease caused by hyper-activating mutations in the calcium-activated calpain-5 (CAPN5) protease. Although structures for classical calpains are known, the structure of CAPN5, a non-classical calpain, remains undetermined. Here we report the 2.8 Å crystal structure of the human CAPN5 protease core (CAPN5-PC). Compared to classical calpains, CAPN5-PC requires high calcium concentrations for maximal activity. Structure-based phylogenetic analysis and multiple sequence alignment reveal that CAPN5-PC contains three elongated flexible loops compared to its classical counterparts. The presence of a disease-causing mutation (c.799G>A, p.Gly267Ser) on the unique PC2L2 loop reveals a function in this region for regulating enzymatic activity. This mechanism could be transferred to distant calpains, using synthetic calpain hybrids, suggesting an evolutionary mechanism for fine-tuning calpain function by modifying flexible loops. Further, the open (inactive) conformation of CAPN5-PC provides structural insight into CAPN5-specific residues that can guide inhibitor design.

Selective synthesis of aryl thioamides and aryl-α-ketoamides from α-oxocarboxylic acids and tetraalkylthiuram disulfides: an unexpected chemoselectivity from aryl sulfonyl chlorides

Tosyl chloride-controlled generation of thioamides and α-ketoamides via base-promoted decarboxylative reaction of α-oxocarboxylic acids with tetraalkylthiuram disulfides has been established.

The cAMP/PKA Pathway Inhibits Beta-amyloid Peptide Release from Human Platelets

The main component of Alzheimer's disease (AD) is the amyloid-beta peptide (Aβ), the brain of these patients is characterized by deposits in the parenchyma and cerebral blood vessels known as cerebral amyloid angiopathy (CAA). On the other hand, the platelets are the major source of the Aβ peptide in circulation and once secreted can activate the platelets and endothelial cells producing the secretion of several inflammatory mediators that finally end up unchaining the CAA and later AD. In the present study we demonstrate that cAMP/PKA pathway plays key roles in the regulation of calpain activation and secretion of Aβ in human platelets. We confirmed that inhibition of platelet functionality occurred when platelets were incubated with forskolin (molecule that rapidly increased cAMP levels). In this sense we found that platelets pre-incubated with forskolin (20 μM) present a complete inhibition of calpain activity and this effect is reversed using an inhibitor of protein kinase A. Consequentially, when platelets were inhibited by forskolin a reduction in the processing of the APP with the consequent decrease in the Aβ peptide secretion was observed. Therefore our study provides novel insight in relation to the mechanism of processing and release of the Aβ peptide from human platelets.

Insertion sequence 1 from calpain-3 is functional in calpain-2 as an internal propeptide

Calpains are intracellular, calcium-activated cysteine proteases. Calpain-3 is abundant in skeletal muscle, where its mutation-induced loss of function causes limb-girdle muscular dystrophy type 2A. Unlike the small subunit-containing calpain-1 and -2, the calpain-3 isoform homodimerizes through pairing of its C-terminal penta-EF-hand domain. It also has two unique insertion sequences (ISs) not found in the other calpains: IS1 within calpain-3's protease core and IS2 just prior to the penta-EF-hand domain. Production of either native or recombinant full-length calpain-3 to characterize the function of these ISs is challenging. Therefore, here we used recombinant rat calpain-2 as a stable surrogate and inserted IS1 into its equivalent position in the protease core. As it does in calpain-3, IS1 occupied the catalytic cleft and restricted the enzyme's access to substrate and inhibitors. Following activation by Ca²⁺, IS1 was rapidly cleaved by intramolecular autolysis, permitting the enzyme to freely accept substrate and inhibitors. The surrogate remained functional until extensive intermolecular autoproteolysis inactivated the enzyme, as is typical of calpain-2. Although the small-molecule inhibitors E-64 and leupeptin limited intermolecular autolysis of the surrogate, they did not block the initial intramolecular cleavage of IS1, establishing its role as a propeptide. Surprisingly, the large-molecule calpain inhibitor, calpastatin, completely blocked enzyme activity, even with IS1 intact. We suggest that calpastatin is large enough to oust IS1 from the catalytic cleft and take its place. We propose an explanation for why calpastatin can inhibit calpain-2 bearing the IS1 insertion but cannot inhibit WT calpain-3.

A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay

Mutations that activate the protease calpain-5 (CAPN5) cause a nonsyndromic adult-onset autoinflammatory eye disease characterized by uveitis, altered synaptic signaling, retinal degeneration, neovascularization, and intraocular fibrosis. We describe a pediatric patient with severe inflammatory vitreoretinopathy accompanied by hearing loss and developmental delay associated with a novel, de novo CAPN5 missense mutation (c.865C>T, p.Arg289Trp) that shows greater hyperactivation of the calpain protease, indicating a genotype–phenotype correlation that links mutation severity to proteolytic activity and the possibility of earlier onset syndromic disease with auditory and neurological abnormalities.

Calpain-2 as a therapeutic target for acute neuronal injury

INTRODUCTION

Calpains represent a family of neutral, calcium-dependent proteases, which modify the function of their target proteins by partial truncation. These proteases have been implicated in numerous cell functions, including cell division, proliferation, migration, and death. In the CNS, where calpain-1 and calpain-2 are the main calpain isoforms, their activation has been linked to synaptic plasticity as well as to neurodegeneration. This review will focus on the role of calpain-2 in acute neuronal injury and discuss the possibility of developing selective calpain-2 inhibitors for therapeutic purposes. Areas covered: This review covers the literature showing how calpain-2 is implicated in neuronal death in a number of pathological conditions. The possibility of developing new selective calpain-2 inhibitors for treating these conditions is discussed. Expert opinion: As evidence accumulates that calpain-2 activation participates in acute neuronal injury, there is interest in developing therapeutic approaches using selective calpain-2 inhibitors. Recent data indicate the potential use of such inhibitors in various pathologies associated with acute neuronal death. The possibility of extending the use of such inhibitors to more chronic forms of neurodegeneration is discussed.

Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?

Reversible covalent inhibitors have many clinical advantages over noncovalent or irreversible covalent drugs. However, apart from selecting a warhead, substantial efforts in design and synthesis are needed to optimize noncovalent interactions to improve target-selective binding. Computational prediction of binding affinity for reversible covalent inhibitors presents a unique challenge since the binding process consists of multiple steps, which are not necessarily independent of each other. In this study, we lay out the relation between relative binding free energy and the overall reversible covalent binding affinity using a two-state binding model. To prove the concept, we employed free energy perturbation (FEP) coupled with λ-exchange molecular dynamics method to calculate the binding free energy of a series of α-ketoamide analogues relative to a common warhead scaffold, in both noncovalent and covalent binding states, and for two highly homologous proteases, calpain-1 and calpain-2. We conclude that covalent binding state alone, in general, can be used to predict reversible covalent binding selectivity. However, exceptions may exist. Therefore, we also discuss the conditions under which the noncovalent binding step is no longer negligible and propose to combine the relative FEP calculations with a single QM/MM calculation of warhead to predict the binding affinity and binding kinetics. Our FEP calculations also revealed that covalent and noncovalent binding states of an inhibitor do not necessarily exhibit the same selectivity. Thus, investigating both binding states, as well as the kinetics will provide extremely useful information for optimizing reversible covalent inhibitors.

One pot synthesis of α-ketoamides from ethylarenes and amines: a metal free difunctionalization strategy

One-pot and metal free synthesis of α-ketoamides has been described through in situ generation of aryl ketones from easily available ethylarenes followed by amidation with various amines. This multiple oxidation protocol involves catalytic I₂-pyridine-TBHP (t-butyl hydroperoxide) mediated oxidative benzylic carbonylation and sequential NaI-TBHP mediated oxidative amidation without using any solvent.

Calpain inhibition modulates glycogen synthase kinase 3β pathways in ischemic myocardium: A proteomic and mechanistic analysis

BACKGROUND

Calpain inhibition has an enhancing effect on myocardial perfusion and improves myocardial density by inhibiting glycogen synthase kinase 3β (GSK-3β) and up-regulating downstream signaling pathways, including the insulin/PI3K and WNT/β-catenin pathways, in a pig model of chronic myocardial ischemia in the setting of metabolic syndrome.

METHODS

Pigs were fed a high-fat diet for 4 weeks, then underwent placement of an ameroid constrictor to the left circumflex artery. Three weeks later, the animals received no drug (high-cholesterol controls [HCC]), a high-dose calpain inhibitor (HCI), a low-dose calpain inhibitor (LCI), or a GSK-3β inhibitor (GSK-3βI). The diets and drug regimens were continued for 5 weeks and the myocardial tissue was harvested.

RESULTS

Calpain and GSK-3β inhibition caused an increase in myocardial perfusion ratios at rest and during pacing compared with controls. Pigs in the LCI and HCI groups had increased vessel density in the ischemic myocardium, and pigs in the GSK-3βI group had increased vessel density in the ischemic and nonischemic myocardium compared with the HCC group. Calpain inhibition modulates proteins involved in the insulin/PI3K and WNT/β-catenin pathways. Quantitative proteomics revealed that calpain and GSK-3β inhibition significantly modulated the expression of proteins enriched in cytoskeletal regulation, metabolism, respiration, and calcium-binding pathways.

CONCLUSIONS

In the setting of metabolic syndrome, calpain or GSK-3β inhibition increases vessel density in both ischemic and nonischemic myocardial tissue. Calpain inhibition may exert these effects through the inhibition of GSK-3β and up-regulation of downstream signaling pathways, including the insulin/PI3K and WNT/β-catenin pathways.

Calpain research for drug discovery: challenges and potential

Calpains are a family of proteases that were scientifically recognized earlier than proteasomes and caspases, but remain enigmatic. However, they are known to participate in a multitude of physiological and pathological processes, performing 'limited proteolysis' whereby they do not destroy but rather modulate the functions of their substrates. Calpains are therefore referred to as 'modulator proteases'. Multidisciplinary research on calpains has begun to elucidate their involvement in pathophysiological mechanisms. Therapeutic strategies targeting malfunctions of calpains have been developed, driven primarily by improvements in the specificity and bioavailability of calpain inhibitors. Here, we review the calpain superfamily and calpain-related disorders, and discuss emerging calpain-targeted therapeutic strategies.

Cu(i)-Functionalized SBA-16: an efficient catalyst for the synthesis of α-ketoamides under moderate conditions

An efficient catalyst based on the cage-like mesoporous material SBA-16 as the support and Cu(i) as active sites has been successfully prepared. The catalyst demonstrated high catalytic activity (up to 88%) in the direct oxidative synthesis of α-ketoamides between acetophenone and piperidine, employing O2 from open air as the oxidant without other additives. A heterogeneous catalyst was applied in this reaction for the first time, and the catalyst could be easily separated from the reaction system by filtration and reused several times without a significant loss of activity.

Copper–TEMPO-catalyzed synthesis of α-ketoamides via tandem sp3C–H aerobic oxidation and amination of phenethyl alcohol derivatives

The first synthesis of α-ketoamides from phenethyl alcohol derivatives, simple and readily available substrates, was achieved.

A two-step continuous synthesis of α-ketoamides and α-amino ketones from 2° benzylic alcohols using hydrogen peroxide as an economic and benign oxidant

A practical two-step flow synthesis of α-ketoamides and α-amino ketones via direct oxidative coupling between 2° benzylic alcohols and amines was developed.

Mechanism of action of thalassospiramides, a new class of calpain inhibitors

Thalassospiramides comprise a large family of lipopeptide natural products produced by Thalassospira and Tistrella marine bacteria. Here we provide further evidence of their nanomolar inhibitory activity against the human calpain 1 protease. Analysis of structure-activity relationship data supported our hypothesis that the rigid 12-membered ring containing an α,β-unsaturated carbonyl moiety is the pharmacologically active functional group, in contrast to classic electrophilic “warheads” in known calpain inhibitors. Using a combination of chemical modifications, mass spectrometric techniques, site-directed mutagenesis, and molecular modeling, we show the covalent binding of thalassospiramide's α,β-unsaturated carbonyl moiety to the thiol group of calpain's catalytic Cys115 residue by a Michael 1,4-addition reaction. As nanomolar calpain inhibitors with promising selectivity and low toxicity from natural sources are rare, we consider thalassospiramides as promising drug leads.

In silico affinity profiling of neuroactive polyphenols for post-traumatic calpain inactivation: a molecular docking and atomistic simulation sensitivity analysis

Calcium-activated nonlysosomal neutral proteases, calpains, are believed to be early mediators of neuronal damage associated with neuron death and axonal degeneration after traumatic neural injuries. In this study, a library of biologically active small molecular weight calpain inhibitors was used for model validation and inhibition site recognition. Subsequently, two natural neuroactive polyphenols, curcumin and quercetin, were tested for their sensitivity and activity towards calpain's proteolytic sequence and compared with the known calpain inhibitors via detailed molecular mechanics (MM), molecular dynamics (MD), and docking simulations. The MM and MD energy profiles (SJA6017 < AK275 < AK295 < PD151746 < quercetin < leupeptin < PD150606 < curcumin < ALLN < ALLM < MDL-28170 < calpeptin) and the docking analysis (AK275 < AK295 < PD151746 < ALLN < PD150606 < curcumin < leupeptin < quercetin < calpeptin < SJA6017 < MDL-28170 < ALLM) demonstrated that polyphenols conferred comparable calpain inhibition profiling. The modeling paradigm used in this study provides the first detailed account of corroboration of enzyme inhibition efficacy of calpain inhibitors and the respective calpain-calpain inhibitor molecular complexes' energetic landscape and in addition stimulates the polyphenol bioactive paradigm for post-SCI intervention with implications reaching to experimental in vitro, in cyto, and in vivo studies.

An updated patent review of calpain inhibitors (2012 - 2014)

INTRODUCTION

Calpain is a family of cysteine proteases found in eukaryotes and a few bacteria. There is considerable interest in the search for calpain inhibitors because the enzyme has been implicated in several diseases including ocular disorders, neurodegenerative disorders, metabolic disorders and cancer.

AREAS COVERED

An overview of calpain inhibitors disclosed between 2012 and 2014 is presented. Among these are epoxysuccinates, dipeptide imaging agents, macrocyclic inhibitors, α-helical peptidomimetic inhibitors, carboxamides, 5-azolones and α-mercaptoacrylates. Additionally, preclinical studies of calpain inhibitors in pathologies such blood disorders, ocular disorders, neurological disorders and muscle disorders are discussed.

EXPERT OPINION

Major advances made in calpain inhibitor research between 2012 and 2014 include: i) the discovery of cytosolic-stable carboxamide calpain inhibitors; ii) synthesis of epoxysuccinates with excellent bioavailability; iii) disclosure of the X-ray crystal structures of novel α-mercaptoacrylates bound to the pentaEF hand region from human calpain; and iv) disclosure of calpain inhibitors as anti-sickling agents. Several calpain inhibitors were reported but limited effort was directed towards the discovery of calpain isoform selective agents, which continues to dampen the therapeutic potential of calpain inhibitors.

Understanding the interaction determinants of CAPN1 inhibition by CAST4 from bovines using molecular modeling techniques

HCV-induced CAPN activation and its effects on virus-infected cells in a host-immune system have been studied recently. It has been shown that the HCV-nonstructural 5A protein acts as both an inducer and a substrate for host CAPN protease; it participates in suppressing the TNF-α-induced apoptosis response and downstream IFN-induced antiviral processes. However, little is known regarding the disturbance of antiviral responses generated by bovine CAPN activation by BVDV, which is a surrogate model of HCV and is one of the most destructive diseases leading to great economic losses in cattle herds worldwide. This is also thought to be associated with the effects of either small CAPN inhibitors or the natural inhibitor CAST. They mainly bind to the binding site of CAPN substrate proteins and competitively inhibit the binding of the enzyme substrates to possibly defend against the two viruses (HCV and BVDV) for anti-viral immunity. To devise a new stratagem to discover lead candidates for an anti-BVDV drug, we first attempted to understand the bovine CAPN-CAST interaction sites and the interaction constraints of local binding architectures, were well reflected in the geometry between the pharmacophore features and its shape constraints identified using our modeled bovine CAPN1/CAST4 complex structures. We propose a computer-aided molecular design of an anti-BVDV drug as a mimetic CAST inhibitor to develop a rule-based screening function for adjusting the puzzle of relationship between bovine CAPN1 and the BVDV nonstructural proteins from all of the data obtained in the study.

Metal-free in situ sp3, sp2, and sp C–H functionalization and oxidative cross coupling with benzamidines hydrochloride: a promising approach for the synthesis of α-ketoimides

A new metal-free tandem protocol for the synthesis of α-ketoimides via sp³, sp², and sp C–H functionalization followed by oxidative cross coupling with benzamidines hydrochloride using catalytic iodine with TBHP in DMSO has been developed.

New tripeptide-based macrocyclic calpain inhibitors formed by N-alkylation of histidine

Two new series of 15-membered macrocyclic peptidomimetics, in which the P1 and P3 residues of the peptide backbone are linked by a bridge containing a 1,4-disubstituted 1H-imidazole, are reported. The structure with an aldehyde at the C-terminus and the imidazole at P3, i.e., 4c, shows significant inhibitory activity against calpain 2, with an IC(50) value of 238 nM. The macrocyclic aldehyde with the imidazole at the alternative P1 position, i.e., 5c, is significantly less active. The relative activities are linked to the ability of the component macrocycles to mimic a β-strand geometry that is known to favor active-site binding. This ability is defined by conformational searches and docking studies with calpain.

Structure-function relationships in calpains

Calpains are a family of complex multi-domain intracellular enzymes that share a calcium-dependent cysteine protease core. These are not degradative enzymes, but instead carry out limited cleavage of target proteins in response to calcium signalling. Selective cutting of cytoskeletal proteins to facilitate cell migration is one such function. The two most abundant and extensively studied members of this family in mammals, calpains 1 and 2, are heterodimers of an isoform-specific 80 kDa large subunit and a common 28 kDa small subunit. Structures of calpain-2, both Ca2+-free and bound to calpastatin in the activated Ca2+-bound state, have provided a wealth of information about the enzyme's structure-function relationships and activation. The main association between the subunits is the pairing of their C-terminal penta-EF-hand domains through extensive intimate hydrophobic contacts. A lesser contact is made between the N-terminal anchor helix of the large subunit and the penta-EF-hand domain of the small subunit. Up to ten Ca2+ ions are co-operatively bound during activation. The anchor helix is released and individual domains change their positions relative to each other to properly align the active site. Because calpains 1 and 2 require ~30 and ~350 μM Ca2+ ions for half-maximal activation respectively, it has long been argued that autoproteolysis, subunit dissociation, post-translational modifications or auxiliary proteins are needed to activate the enzymes in the cell, where Ca2+ levels are in the nanomolar range. In the absence of robust support for these mechanisms, it is possible that under normal conditions calpains are transiently activated by high Ca2+ concentrations in the microenvironment of a Ca2+ influx, and then return to an inactive state ready for reactivation.

Development of α-helical calpain probes by mimicking a natural protein-protein interaction

We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening 24 commercially available cross-linkers for successful cysteine alkylation in a model peptide sequence. The effects of cross-linking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid cross-linkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs will be useful for future investigation of calpains, while the cross-linking technique will enable exploration of other protein-protein interactions.

Peptidyl alpha-ketoamides with nucleobases, methylpiperazine, and dimethylaminoalkyl substituents as calpain inhibitors

A series of peptidyl alpha-ketoamides with the general structure Cbz-L-Leu-D,L-AA-CONH-R were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II, and cathepsin B. Nucleobases, methylpiperazine, and dimethylaminoalkyl groups were incorporated into the primed region of the inhibitors to generate compounds that potentially cross the blood-brain barrier. Two of these compounds (Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-adenin-9-yl and Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-(4-methylpiperazin-1-yl) have been shown to have useful concentrations in the brain in animals. The best inhibitor for calpain I was Cbz-Leu-D,L-Abu-CONH-(CH(2))(3)-2-methoxyadenin-9-yl (K(i) = 23 nM), and the best inhibitor for calpain II was Cbz-Leu-D,L-Phe-CONH-(CH(2))(3)-adenin-9-yl (K(i) = 68 nM). On the basis of the crystal structure obtained with heterocyclic peptidyl alpha-ketoamides, we have improved inhibitor potency by introducing a small hydrophobic group on the adenine ring. These inhibitors have good potential to be used in the treatment of neurodegenerative diseases.

Passerini reaction-amine deprotection-acyl migration peptide assembly: efficient formal synthesis of cyclotheonamide C

A short, convergent, formal total synthesis of cyclotheonamide C is described. The key linear pentapeptide intermediate is assembled at the same time as the elaboration of the alpha-hydroxyhomoarginine (H-hArg) residue via a three-component Passerini reaction-amine deprotection-O,N-acyl migration strategy.