Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases

Leucine-Rich, Potent Anti-Bacterial Protein against Vibrio cholerae, Staphylococcus aureus from Solanum trilobatum Leaves

A 24 kDa leucine-rich protein from ion exchange fractions of Solanum trilobatum, which has anti-bacterial activity against both the Gram-negative Vibrio cholerae and Gram-positive Staphylococcus aureus bacteria has been purified. In this study, mass spectrometry analysis identified the leucine richness and found a luminal binding protein (LBP). Circular dichroism suggests that the protein was predominantly composed of α- helical contents of its secondary structure. Scanning electron microscopy visualized the characteristics and morphological and structural changes in LBP-treated bacterium. Further in vitro studies confirmed that mannose-, trehalose- and raffinose-treated LBP completely inhibited the hemagglutination ability towards rat red blood cells. Altogether, these studies suggest that LBP could bind to sugar moieties which are abundantly distributed on bacterial surface which are essential for maintaining the structural integrity of bacteria. Considering that Solanum triolbatum is a well-known medicinal and edible plant, in order to shed light on its ancient usage in this work, an efficient anti-microbial protein was isolated, characterized and its in vitro functional study against human pathogenic bacteria was evaluated.

Understanding the binding mechanism of succinic acid against phospholipase A2 from bee venom

Phospholipase A₂ (PLA₂ ) is responsible for the release of fatty acids from glycerophospholipids. PLA₂ is commonly found in mammalian tissues. It is also found in venom from different animals ranging from insects, arachnid, and snakes. The release of arachidonic acid in large amount results in inflammation and pain. Identification of compounds that can inhibit the activity of PLA₂ is of large scientific and medicinal interest as these compounds can act as antidotes toward snake bites and bee stings. Among the different compounds that have been tested for inhibition of PLA₂ , a secondary metabolite succinic acid is identified to inhibit PLA₂ activity. The inhibition was analyzed using an in vitro PLA₂ inhibition assay and isothermal titration calorimetry (ITC) studies. The molecular mechanism of the mode of inhibition was studied using molecular docking and simulation studies.

Inhibitory effect of edible natural compounds with di- and tri-carboxyl moiety on endogenous protease inducing disassembly and degradation of myofibrils from grass carp (Ctenopharyngodon idella)

Inhibition of endogenous protease is a rapid and feasible approach to control the proteolysis proceeding of post mortem fish flesh. In the present study, the in vitro inhibitory effects of common edible di- and tri-carboxylic acids and salts on endogenous proteolytic activities as well as myofibrillar disassembly and degradation mediated by crude enzyme of grass carp muscle were investigated. The results showed that among the compounds tested, maleic acid, fumaric acid, tartaric acid and malic acid were the most effective inhibitor for cathepsin B, L and calpain, with IC₅₀ ranging from 7.76 to 30.13 mM, from 32.38 to 65.12 mM, from 1.06 to 6.76 mM, respectively. Also, relatively lower Ki (ranging from 1.04 to 43.21 mM) of these compounds were found towards cathepsin B, L and calpain. Incubation of myofibrillar protein with crude enzyme in the presence of di- and tri-carboxylic compounds could remarkably suppress the dissociation and degradation of myosin heavy chain (MHC), and ameliorate the loss of heat shock protein (HSP) in myofibrils, with tartaric acid and fumaric acid proved more effective than other compounds, possibly implicating their application as potential and efficient inhibitors for quality control of fish muscle products.

Crystal structure of Leishmania mexicana cysteine protease B in complex with a high-affinity azadipeptide nitrile inhibitor

Leishmania mexicana is an obligate intracellular protozoan parasite that causes the cutaneous form of leishmaniasis affecting South America and Mexico. The cysteine protease LmCPB is essential for the virulence of the parasite and therefore, it is an appealing target for antiparasitic therapy. A library of nitrile-based cysteine protease inhibitors was screened against LmCPB to develop a treatment of cutaneous leishmaniasis. Several compounds are sufficiently high-affinity LmCPB inhibitors to serve both as starting points for drug discovery projects and as probes for target validation. A 1.4 Å X ray crystal structure, the first to be reported for LmCPB, was determined for the complex of this enzyme covalently bound to an azadipeptide nitrile ligand. Mapping the structure-activity relationships for LmCPB inhibition revealed superadditive effects for two pairs of structural transformations. Therefore, this work advances our understanding of azadipeptidyl and dipeptidyl nitrile structure-activity relationships for LmCPB structure-based inhibitor design. We also tested the same series of inhibitors on related cysteine proteases cathepsin L and Trypanosoma cruzi cruzain. The modulation of these mammalian and protozoan proteases represents a new framework for targeting papain-like cysteine proteases.