The structure of viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus as a target against grasserie: docking and molecular dynamics simulations.

The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant sericultural losses because no drugs or therapies are available. In this work, the structure of viral cathepsin BmNPV-Cath was used as a target for virtual screening simulations, aiming to identify potential molecules that could be used to treat the infection. Virtual screening of the Natural Products library from the Zinc Database selected four molecules. Theoretical calculations of ΔGbinding by the molecular mechanics Poisson-Boltzmann surface analysis (MM-PBSA) method indicated that the molecule Zinc12888007 (Bm5) would have high affinity for the enzyme. The in vivo infection models of B. mori caterpillars with BmNPV showed that treatment with a dose of 100 µg Bm5 dissolved in Pluronic-F127 0.02% was able to reduce the mortality of caterpillars in 22.6%, however, it did not impede the liquefaction of dead bodies. Our results suggest a role of BmNPV-Cath in generating a pool of amino acids necessary for viral replication and indicate a mechanism to be exploited in the search for treatments for grasserie disease of the silkworm.

Novel Non-Peptide Inhibitors against SmCL1 of Schistosoma mansoni: In Silico Elucidation, Implications and Evaluation via Knowledge Based Drug Discovery.

Schistosomiasis is a major endemic disease known for excessive mortality and morbidity in developing countries. Because praziquantel is the only drug available for its treatment, the risk of drug resistance emphasizes the need to discover new drugs for this disease. Cathepsin SmCL1 is the critical target for drug design due to its essential role in the digestion of host proteins for growth and development of Schistosoma mansoni. Inhibiting the function of SmCL1 could control the wide spread of infections caused by S. mansoni in humans. With this objective, a homology modeling approach was used to obtain theoretical three-dimensional (3D) structure of SmCL1. In order to find the potential inhibitors of SmCL1, a plethora of in silico techniques were employed to screen non-peptide inhibitors against SmCL1 via structure-based drug discovery protocol. Receiver operating characteristic (ROC) curve analysis and molecular dynamics (MD) simulation were performed on the results of docked protein-ligand complexes to identify top ranking molecules against the modelled 3D structure of SmCL1. MD simulation results suggest the phytochemical Simalikalactone-D as a potential lead against SmCL1, whose pharmacophore model may be useful for future screening of potential drug molecules. To conclude, this is the first report to discuss the virtual screening of non-peptide inhibitors against SmCL1 of S. mansoni, with significant therapeutic potential. Results presented herein provide a valuable contribution to identify the significant leads and further derivatize them to suitable drug candidates for antischistosomal therapy.

On-bead screening of a combinatorial fumaric acid derived peptide library yields antiplasmodial cysteine protease inhibitors with unusual peptide sequences.

A new class of cysteine protease inhibitors based on fumaric acid derived oligopeptides was successfully identified from a high-throughput screening of a solid-phase bound combinatorial library. As target enzymes falcipain and rhodesain were used, which play important roles in the life cycles of the parasites which cause malaria (Plasmodium falciparum) and African sleeping sickness (Trypanosoma brucei rhodesiense). The best inhibitors with unusual amino acid sequences not reported before for this type of enzyme were also fully analyzed in detail in solution. K(i) values in the lower micromolar and even nanomolar region were found. Some inhibitors are even active against plasmodia and show good selectivity relative to other enzymes. Also the mechanism of action was studied and could be shown to be irreversible inhibition.

Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique specificities.

The substrate specificities of papain-like cysteine proteases (clan CA, family C1) papain, bromelain, and human cathepsins L, V, K, S, F, B, and five proteases of parasitic origin were studied using a completely diversified positional scanning synthetic combinatorial library. A bifunctional coumarin fluorophore was used that facilitated synthesis of the library and individual peptide substrates. The library has a total of 160,000 tetrapeptide substrate sequences completely randomizing each of the P1, P2, P3, and P4 positions with 20 amino acids. A microtiter plate assay format permitted a rapid determination of the specificity profile of each enzyme. Individual peptide substrates were then synthesized and tested for a quantitative determination of the specificity of the human cathepsins. Despite the conserved three-dimensional structure and similar substrate specificity of the enzymes studied, distinct amino acid preferences that differentiate each enzyme were identified. The specificities of cathepsins K and S partially match the cleavage site sequences in their physiological substrates. Capitalizing on its unique preference for proline and glycine at the P2 and P3 positions, respectively, selective substrates and a substrate-based inhibitor were developed for cathepsin K. A cluster analysis of the proteases based on the complete specificity profile provided a functional characterization distinct from standard sequence analysis. This approach provides useful information for developing selective chemical probes to study protease-related pathologies and physiologies.

Expression of silicatein in spicules from the Baikalian sponge Lubomirskia baicalensis.

Lake Baikal harbors the largest diversity of sponge species [phylum Porifera] among all freshwater biotopes. The abundantly occurring species Lubomirskia baicalensis was used to study the seasonal silicatein metabolism; the spicules of this species have an unusually thick axial filament, consisting of silicatein, which remains constant in diameter during their growth. In the course of maturation, the size of the silicic acid shell grows, until the final diameter of the spicules of about 8 microm is reached. The seasonal content of silicatein was assessed by use of antibodies raised against silicatein; they stained specifically the axial filaments. In addition we determined, by application of the enzyme-linked immunosorbent assay system, that the proteinaceous content of the spicules, the silicatein, increases from spring to late summer by 8-fold. As molecular markers to quantify the seasonal changes in expression levels of genes coding for proteins/enzymes, the genes for the calumenin-like protein and the kinesin-related protein, were selected. The expression of calumenin-like gene, involved in the intracellular signaling, is highest during September, whereas the expression of the kinesin-related protein does not change during the annual course. These results suggest that the highest metabolic activity of L. baicalensis occurs in late summer (September), in parallel with the highest accumulation of silicatein, a structural protein/enzyme of the spicules.

3,4-disubstituted azetidinones as selective inhibitors of the cysteine protease cathepsin K. Exploring P3 elements for potency and selectivity.

The synthesis of a series of highly potent and selective inhibitors of cathepsin K based on the 3,4-disubstituted azetidin-2-one warhead is reported. A high degree of potency and selectivity was achieved by introducing a basic nitrogen into the distal part of the P3 element of the molecule. Data from kinetic and mass spectrometry experiments are consistent with the interpretation that compounds of this series transiently acylate the sulfhydrile of cathepsin K.

Nonpeptidic, noncovalent inhibitors of the cysteine protease cathepsin S.

The first nonpeptidic, noncovalent inhibitors of the cysteine protease cathepsin S (CatS) are described. Electronic database searching using the program DOCK generated a screening set of potential CatS inhibitors from which two lead structures were identified as promising starting points for a drug discovery effort. Lead optimization afforded potent (IC(50) < 50 nM) and selective inhibitors of CatS demonstrating cellular activity and reversibility of enzyme inhibition.

Cathepsin L1, the major protease involved in liver fluke (Fasciola hepatica) virulence: propetide cleavage sites and autoactivation of the zymogen secreted from gastrodermal cells.

The secretion and activation of the major cathepsin L1 cysteine protease involved in the virulence of the helminth pathogen Fasciola hepatica was investigated. Only the fully processed and active mature enzyme can be detected in medium in which adult F. hepatica are cultured. However, immunocytochemical studies revealed that the inactive procathepsin L1 is packaged in secretory vesicles of epithelial cells that line the parasite gut. These observations suggest that processing and activation of procathepsin L1 occurs following secretion from these cells into the acidic gut lumen. Expression of the 37-kDa procathepsin L1 in Pichia pastoris showed that an intermolecular processing event within a conserved GXNXFXD motif in the propeptide generates an active 30-kDa intermediate form. Further activation of the enzyme was initiated by decreasing the pH to 5.0 and involved the progressive processing of the 37 and 30-kDa forms to other intermediates and finally to a fully mature 24.5 kDa cathepsin L with an additional 1 or 2 amino acids. An active site mutant procathepsin L, constructed by replacing the Cys(26) with Gly(26), failed to autoprocess. However, [Gly(26)]procathepsin L was processed by exogenous wild-type cathepsin L to a mature enzyme plus 10 amino acids attached to the N terminus. This exogenous processing occurred without the formation of a 30-kDa intermediate form. The results indicate that activation of procathepsin L1 by removal of the propeptide can occur by different pathways, and that this takes place within the parasite gut where the protease functions in food digestion and from where it is liberated as an active enzyme for additional extracorporeal roles.

Chelidocystatin, a novel phytocystatin from Chelidonium majus.

Greater celandine (Chelidonium majus L.) has traditional uses in European and Chinese herbal medicine. In the plant sap significant inhibitory activity against papain was observed. A cysteine proteinase inhibitor, named chelidocystatin, was isolated from the plant using papain Sepharose affinity chromatography followed by gel filtration and ion-exchange chromatography. Chelidocystatin showed a M(r) of 10,000 on SDS-PAGE with the pI of 9.3, and was a strong inhibitor of cathepsin L (Ki = 5.6 x 10(-11) M), papain (Ki = 1.1 x 10(-10) M) and cathepsin H (Ki = 7.5 x 10(-9) M). The complete amino acid sequence of the protein was obtained with N-terminal sequencing and sequencing of the peptides after digestion of the protein. Moreover, a major part of the sequence was verified by molecular cloning. The conserved glycine residue at the N-terminal region and the QVVAG motif, which are both believed to be involved in the inhibitory activity, indicate that it is a member of the cystatin superfamily. The amino acid sequence of chelidocystatin shows a high degree of homology with cysteine proteinase inhibitors belonging to the phytocystatin group, especially with the recently described carrot and sunflower phytocystatins with which it shares 57% and 54% homology, respectively.

Lysine-based structure responsible for selective mannose phosphorylation of cathepsin D and cathepsin L defines a common structural motif for lysosomal enzyme targeting.

Previous studies have shown that lysine residues on the surface of cathepsins and other lysosomal proteins are a shared component of the recognition structure involved in mannose phosphorylation. In this study, the involvement of specific lysine residues in mannose phosphorylation of cathepsin D was explored by site-directed mutagenesis. Mutation of two lysine residues in the mature portion of the protein, Lys-203 and Lys-293, cooperated to inhibit mannose phosphorylation by 70%. Other positively charged residues could not substitute for lysine at these positions, and comparison of thermal denaturation curves for the wild type and mutant proteins indicated that the inhibition could not be explained by alterations in protein folding. Structural comparisons of the two lysine residues with those required for phosphorylation of cathepsin L, using models generated from recently acquired crystal structures, revealed several relevant similarities. On both molecules, the lysine residues were positioned approximately 34 A apart (34.06 A for cathepsin D and 33.80 A for cathepsin L). When the lysine pairs were superimposed, N-linked glycosylation sites on the two proteins were found to be oriented so that oligosaccharides extending out from the sites could share a common region of space. Further similarities in the local environments of the critical lysines were also observed. These results provide details for a common lysosomal targeting structure based on a specific arrangement of lysine residues with respect to each other and to glycosylation sites on the surface of lysosomal proteins.

Molecular cloning and sequencing of two cDNAs encoding cathepsin L-related cysteine proteinases in the nervous system and in the stomach of the Norway lobster (Nephrops norvegicus).

Two cathepsin L-related cysteine proteinase molecular clones were isolated from cDNA libraries of mRNA from the eyestalk nervous system and the stomach of Nephrops norvegicus and sequenced. The cDNA from nervous system was first obtained by screening an eyestalk cDNA library with an oligonucleotide whose sequence derived from the amino acid sequence of a peptide isolated previously and subsequently with the 5' end of the longest cDNA probe thus obtained. Several clones were isolated and analysed: one of these clones contains the complete cDNA (NCP1:AC = X80989). It encodes a preproenzyme of 324 amino acid residues, and a putative mature enzyme of 217 residues. Only one variant (with one amino acid change) was identified. The screening of the stomach cDNA library was carried out with a cDNA probe corresponding to the 5' terminal region of the nervous system cysteine proteinase cDNA previously obtained. A near full-length cDNA (NCP2:AC = X80990) was isolated. The sequence for mature stomach cathepsin L-related cysteine proteinase is 215 residues long. Nervous system cathepsin L-like NCP1 is very similar to the American lobster cysteine proteinase LCP1 (81% identity) and the stomach cathepsin L-related NCP2 is very similar to cysteine protease LCP3 (82% identity). Moreover, comparison of the two Nephrops norvegicus cathepsin L-related cysteine proteinases revealed only 68% identity.

Monomeric human cathepsin E.

Cathepsin E is a homodimer, consisting of two monomers linked by an inter-molecular disulphide bond. The cysteine residue involved is located near to the N-terminus of the mature proteinase. By mutating this residue to alanine, a monomeric form of human cathepsin E was engineered and purified. The activity of the resultant enzyme was not altered significantly (in terms of its ability to hydrolyse two chromogenic peptide substrates; and its susceptibility to inhibition by pepstatin). However, the stability of the mutant enzyme to alkaline pH and to temperature was markedly reduced.