Development of Improved Spectrophotometric Assays for Biocatalytic Silyl Ether Hydrolysis.

Reported herein is the development of assays for the spectrophotometric quantification of biocatalytic silicon-oxygen bond hydrolysis. Central to these assays are a series of chromogenic substrates that release highly absorbing phenoxy anions upon cleavage of the sessile bond. These substrates were tested with silicatein, an enzyme from a marine sponge that is known to catalyse the hydrolysis and condensation of silyl ethers. It was found that, of the substrates tested, tert-butyldimethyl(2-methyl-4-nitrophenoxy)silane provided the best assay performance, as evidenced by the highest ratio of enzyme catalysed reaction rate compared with the background (uncatalysed) reaction. These substrates were also found to be suitable for detailed enzyme kinetics measurements, as demonstrated by their use to determine the Michaelis-Menten kinetic parameters for silicatein.

Polyphenol oxidase mediates (-)-epigallocatechin gallate to inhibit endogenous cathepsin activity in Apostichopus japonicus.

Apostichopus japonicus (A. japonicus) has rich nutritional value and is an important economic crop. Due to its rich endogenous enzyme system, fresh A. japonicus is prone to autolysis during market circulation and storage, resulting in economic losses. In order to alleviate this phenomenon, we investigated the effect of polyphenol oxidase (PPO) mediated (-)-epigallocatechin gallate (EGCG) on the activity and structure of endogenous cathepsin series protein (CEP) from A. japonicus. Research on cathepsin activity showed that PPO mediated EGCG could significantly reduce enzyme activity, resulting in a decrease in enzymatic reaction rate. SDS-PAGE and scanning electron microscopy results showed that PPO mediates EGCG could induce CEP aggregation to form protein aggregates. Various spectral results indicated that EGCG caused changes in the structure of CEP. Meanwhile, the conjugates formed by PPO mediated EGCG had lower thermal stability. In conclusion, PPO mediated EGCG was an effective method to inhibit the endogenous enzyme activity.

Insight into crustacean cathepsins: Structure-evolutionary relationships and functional roles in physiological processes.

Cathepsins belong to a group of proteins that are present in both prokaryotic and eukaryotic organisms and have an extremely high degree of evolutionary conservation. These proteins are functionally active in extracellular environments as soluble enzymatic proteins or attached to plasma membrane receptors. In addition, they occur in cellular secretory vesicles, mitochondria, the cytosol, and within the nuclei of eukaryotic cells. Cathepsins are classified into various groups based on their sequence variations, leading to their structural and functional diversification. The molecular understanding of the physiology of crustaceans has shown that proteases, including cathepsins, are expressed ubiquitously. They also contain one of the central regulatory systems for crustacean reproduction, growth, and immune responses. This review focuses on various aspects of the crustaceans cathepsins and emphasizes their biological roles in different physiological processes such as reproduction, growth, development, and immune responses. We also describe the bioactivity of crustaceans cathepsins. Because of the vital biological roles that cathepsins play as cellular proteases in physiological processes, they have been proposed as potential novel targets for the development of management strategies for the aquaculture industries.

Subnanomolar Cathepsin S Inhibitors with High Selectivity: Optimizing Covalent Reversible α-Fluorovinylsulfones and α-Sulfonates as Potential Immunomodulators in Cancer.

The cysteine protease cathepsin S (CatS) is overexpressed in many tumors. It is known to be involved in tumor progression as well as antigen processing in antigen-presenting cells (APC). Recent evidence suggests that silencing CatS improves the anti-tumor immune response in several cancers. Therefore, CatS is an interesting target to modulate the immune response in these diseases. Here, we present a series of covalent-reversible CatS inhibitors based on the α-fluorovinylsulfone and -sulfonate warheads. We optimized two lead structures by molecular docking approaches, resulting in 22 final compounds which were evaluated in fluorometric enzyme assays for CatS inhibition and for selectivity towards the off-targets CatB and CatL. The most potent inhibitor in the series has subnanomolar affinity (Ki =0.08 nM) and more than 100,000-fold selectivity towards cathepsins B and L. These new reversible and non-cytotoxic inhibitors could serve as interesting leads to develop new immunomodulators in cancer therapy.

A nanoparticle probe for the imaging of autophagic flux in live mice via magnetic resonance and near-infrared fluorescence.

Autophagy-the lysosomal degradation of cytoplasmic components via their sequestration into double-membraned autophagosomes-has not been detected non-invasively. Here we show that the flux of autophagosomes can be measured via magnetic resonance imaging or serial near-infrared fluorescence imaging of intravenously injected iron oxide nanoparticles decorated with cathepsin-cleavable arginine-rich peptides functionalized with the near-infrared fluorochrome Cy5.5 (the peptides facilitate the uptake of the nanoparticles by early autophagosomes, and are then cleaved by cathepsins in lysosomes). In the heart tissue of live mice, the nanoparticles enabled quantitative measurements of changes in autophagic flux, upregulated genetically, by ischaemia-reperfusion injury or via starvation, or inhibited via the administration of a chemotherapeutic or the antibiotic bafilomycin. In mice receiving doxorubicin, pre-starvation improved cardiac function and overall survival, suggesting that bursts of increased autophagic flux may have cardioprotective effects during chemotherapy. Autophagy-detecting nanoparticle probes may facilitate the further understanding of the roles of autophagy in disease.

Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide.

Two-dimensional (2D) materials have attracted attention for potential applications in light harvesting, catalysis, and molecular electronics. Mineral proteins involved in hard tissue biogenesis can produce 2D structures with high fidelity by using sustainable production routes. This study shows that a peptide mimic based on the catalytic triad of the marine sponge protein silicatein catalyzes the formation of nanometer thin and stable sheets of silicon dioxide and titanium dioxide.

Cathepsin V: Molecular characteristics and significance in health and disease.

Human cysteine cathepsins form a family of eleven proteases (B, C, F, H, K, L, O, S, V, W, X/Z) that play important roles in a considerable number of biological and pathophysiological processes. Among them, cathepsin V, also known as cathepsin L2, is a lysosomal enzyme, which is mainly expressed in cornea, thymus, heart, brain, and skin. Cathepsin V is a multifunctional endopeptidase that is involved in both the release of antigenic peptides and the maturation of MHC class II molecules and participates in the turnover of elastin fibrils as well in the cleavage of intra- and extra-cellular substrates. Moreover, there is increasing evidence that cathepsin V may contribute to the progression of diverse diseases, due to the dysregulation of its expression and/or its activity. For instance, increased expression of cathepsin V is closely correlated with malignancies (breast cancer, squamous cell carcinoma, or colorectal cancer) as well vascular disorders (atherosclerosis, aortic aneurysm, hypertension) being the most prominent examples. This review aims to shed light on current knowledge on molecular aspects of cathepsin V (genomic organization, protein structure, substrate specificity), its regulation by protein and non-protein inhibitors as well to summarize its expression (tissue and cellular distribution). Then the core biological and pathophysiological roles of cathepsin V will be depicted, raising the question of its interest as a valuable target that can open up pioneering therapeutic avenues.

In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V.

Human cysteine cathepsins are lysosomal proteases, which are involved in different biological processes. Their enzymatic activity can be regulated by glycosaminoglycans (GAGs): long linear periodic negatively charged polysaccharides, which dimeric building blocks consist of uronic acid and hexosamine monosaccharide units. In this study, molecular docking simulations of chondroitin 4-sulfate, chondroitin 6-sulfate, heparin, heparan sulfate, dermatan sulfate and hyaluronic acid of various chain lengths were performed with cathepsins B, L, K, S and V and followed by molecular dynamics-based refinement and binding free energy analysis. We concluded that electrostatics might be a driving force for cathepsin-GAG interactions; indeed as in most of characterised systems, the increase of GAG chain length consequently leads to a more pronounced effect on the strength of cathepsin-GAG interactions. Results also suggest that binding of GAGs at different regions on cathepsins surface affect differently their enzymatic activity and could is dependent on cathepsin and GAG type. Present data contribute to systematic description of cathepsin-GAG interactions, which is helpful in understanding the subtle molecular mechanisms of protease regulation behind their biological functions.

Recruitment of lysosomal cathepsins B, L and D as digestive enzymes in Coleoptera.

The recruitment of the lysosomal cathepsins B (CAB), L (CAL) and D (CAD) as luminal digestive enzymes was investigated in 3 species of beetles. Gene expression was determined by RNA-seq in different regions of the midgut and in the carcasses from the transcriptomes of Dermestes maculatus, Tenebrio molitor and Zabrotes subfasciatus. These data together with phylogenetic analyses, allowed us to identify the sequences of the gene coding for digestive and lysosomal CABs, CADs and CALs in T. molitor and Z. subfasciatus and observe the absence of digestive cathepsins in D. maculatus. Comparisons of structures based on the overall similarity of modelled structures were performed and subsite residues in the lysosomal and digestive CALs were identified by molecular docking. The data showed that S2 subsites are very variable, probably as an adaption to a luminal digestive role. The survey of sequences of the gene coding for cathepsins in the genomes of 13 beetle species from different phylogenetic groups showed that expansion of CAL and CAB genes occurred only in the Cucujiformia clade. Several digestive CABs have a reduced occluding loop, probably to act as digestive enzymes. Pollen-feeding was proposed to be the selective pressure to recruit cathepsins as digestive enzymes in Cucujiformia beetles.

Primary digestive cathepsins L of Tribolium castaneum larvae: Proteomic identification, properties, comparison with human lysosomal cathepsin L.

We previously described the most highly expressed enzymes from the gut of the red flour beetle, Tribolium castaneum, as cathepsins L. In the present study, two C1 family-specific cysteine cathepsin L enzymes from the larval midgut were isolated and identified using MALDI-TOF MS analysis. The isolated T. castaneum cathepsins were characterized according to their specificity against chromogenic and fluorogenic peptide substrates, and the most efficiently hydrolyzed substrate was Z-FR-pNA with Arg in the P1 subsite. The specificity of insect digestive cathepsins was compared with human lysosomal cathepsin L, the well-studied peptidase of the C1 family cathepsins. T. castaneum digestive cathepsins efficiently hydrolyzed substrates with small and uncharged amino acid residues at P1 (Ala, Gln) more than human cathepsin L. In particular, these insect digestive cathepsins cleaved with higher efficiency the analogs of immunogenic peptides of gliadins, which contribute to autoimmune celiac disease in susceptible people, and thus insect enzymes may be useful in enzymatic treatments for this disease. A bioinformatic study supported by the proteomic analysis of the primary structures of the isolated cathepsins was used to compare tertiary models. The phylogenetic analysis of coleopteran and human cathepsins from the L subfamily indicated that insect digestive cathepsins grouped separately from lysosomal cathepsins.

Dano fotoinduzido no sistema endolisossomal: modulação da autofagia e metabolismo de lipídios em células de câncer colorretal / Endo-lysosomal system photodamage: modulation of autophagy and lipid metabolism in colorectal cancer cells

O câncer colorretal (CCR) é o terceiro câncer mais diagnosticado em humanos. O CCR causou mais de 900.000 mortes em 2020 e foi estimado, para o período entre 2020 - 2025, um incremento de 13.5 % no número de casos novos de acordo com a plataforma Web Global Cancer Observatory. A Terapia Fotodinâmica (PDT) é uma alternativa terapêutica promissora. Conhecer as vias de sinalização de morte celular, assim como, as respostas associadas com a resistência ao dano foto-oxidativo, são relevantes para incrementar a eficiência da PDT. Neste trabalho, investigamos como as células de adenocarcinoma colorretal HT 29 respondem ao dano fotoinduzido gerado pelo fotossensibilizador (FS) meso-tetrafenilporfirina dissulfônado (TPPS2a), uma molécula que é ativada pela irradiação com luz em 522 nm. Como esperado, após irradiação (2.1 J cm-2) foi verificado que com o incremento do TPPS2a houve diminuição da viabilidade celular. A concentração do FS escolhida para darmos seguimento ao estudo foi a necessária para reduzir em 30 % a sobrevida celular (DL30; 148 nM). Abordagens moleculares nos permitiram identificar que nas células fotossensibilizadas a redução na maturação da catepsina D (CTSD, 55 %) e da catepsina B (CTSB, 52 %) contribuem com a disfunção endolisossomal. Além disso, comprovamos que as células fotossensibilizadas tiveram, pela menor quantidade de CTSD ativa, o processamento da prosaposina (PSAP) significativamente afetado. Células coletadas após 24 horas de irradiação expressaram 7 vezes mais PSAP do que as amostras dos grupos controle, sugerindo que as reações de oxidação causadas pelo TPPS2a podem ocasionar o acúmulo de glicoesfingolipídios nos endossomos e nos lisossomos, mimetizando o fenótipo observado em doenças de armazenamento lisossomal. Imagens de células HT 29 com expressão estável da proteína LGALS3 fusionada ao marcador EFGP mostraram que, após 24 horas de irradiação, as células não ativaram a lisofagia para remover os endossomos e os lisossomos danificados. A ausência do recrutamento da LGALS3 também apontou que as membranas dos endossomos e dos lisossomos não apresentam rupturas permanentes que permitam a passagem de uma molécula de 26 kDa. Experimentos complementares de análise da expressão proteica dos marcadores autofágicos LC3-II e p62/SQSTM1 (referida como p62) confirmaram o bloqueio do fluxo autofágico nas células fotosenssibilizadas. Pelo envolvimento do sistema endolisossomal no tráfego de membranas e no fluxo de lipídios, o aumento da transcrição da Hidroximetilglutaril-CoA reductase (HMGCR) (≈ 1.6 vezes) uma enzima envolvida na síntese de novo do colesterol - sugeriu que a disfunção dos endossomos e dos lisossomos altera a distribuição de colesterol. Não obstante, para manter a homeostase lipídica nas células fotossensibilizadas este não foi o único mecanismocompensatório acionado, uma vez que houve um incremento sutil; porém, significativo (1.2 vezes) na transcrição da ceramidase ácida (ASAH1). Em conjunto, nossos dados apontam que a fotossensibilização com TPPS2a constitui uma ferramenta promissora para causar dano no sistema endolisossomal, inibindo a autofagia e permitindo o estudo das respostas metabólicas em células expostas a estresse oxidativo

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in humans. CRC caused more than 900,000 deaths in 2020 and it was estimated for the period 2020 - 2025, an increase of 13.5 % in the number of new cases according to the Global Cancer Observatory Web platform. Photodynamic Therapy (PDT) is a promising therapeutic alternative. Understandings of cell death signaling pathways as well as the adaptive responses associated with resistance to photo-oxidative damage are relevant to optimize the effectiveness of PDT. For this purpose, in this research, we investigated how HT-29 colorectal adenocarcinoma cells respond to photosensitization reactions generated by TPPS2a, a molecule activated by irradiation with light at 522 nm. PS concentrations displayed increased inhibitory effect on cell viability after irradiation (2.1 J cm-2). The lethal dose selected to photosensibilize cells was the TPPS2a concentration able to reduce 30 % of cell survival (LD30; 148 nM). By molecular methods, we observed a reduction in cathepsin D (CTSD, 55 %) and cathepsin B (CTSB, 52 %) maturation, depletion that may contribute to endo-lysosomal dysfunction in photosensitized cells. It is widely known that endo-lysosomal cathepsins are crucial in protein turnover and degradation. Thus, we focused on the consequence of CTSD reduction. Literature data indicate that CTSD plays a key role in prosaposin (PSAP) processing to the four saposins (SAPs) that are required in glycosphingolipids breakdown. In fact, our results in photosensitized cells showed that, due to the lower amount of active CTSD, PSAP processing was significantly affected. Cells collected after irradiation expressed 7 times more PSAP than cells from the control groups. This data suggest that oxidative photodamage induced by TPPS2a may result in glycosphingolipid-accumulating endosomes and lysosomes, phenotype which mimics lysosomal storage diseases. Furthermore, we monitored by fluorescence microscopy a form of selective autophagy which detects and removes damaged endosomes and lysosomes known as lysophagy. Images of HT-29 cells expressing Galectin 3/LGALS3 fused to EFGP showed that photosensitized cells did not activate lysophagy. The absence of LGALS3 recruitment also indicated that the membranes of endosomes and lysosomes do not present ruptures which allow the passage of proteins with a molecular weight up to at least 26 kDa. Protein expression analysis of the autophagic markers LC3-II and p62/SQSTM1 (referred as p62) confirmed autophagic flux blockade in cells challenged with photoactivated TPPS2a. The endo-lysosomal system plays a key role in membrane trafficking and lipid flux. At the transcriptional level, 1.6-fold increase in gene expression of Hydroxymethylglutaryl-CoA reductase (HMGCR) - an enzyme involved in the synthesis de novo of cholesterol - indicated that endosomes and lysosomes dysfunction alters the distribution of cholesterol in cellschallenged with photoactivated TPPS2a. However, to maintain lipid homeostasis in photosensitized cells, this was not the only compensatory mechanism triggered, since there was a slightly increase (1.2-fold) in the transcription of acid ceramidase (ASAH1). Taken together, our data showed that photosensitization with TPPS2a constitutes a promising tool to damage the endolysosomal system, to inhibit autophagy and to study metabolic responses in cells exposed to oxidative stress

MHC class I antigen cross-presentation mediated by PapMV nanoparticles in human antigen-presenting cells is dependent on autophagy.

Nanoparticles made of the coat protein of papaya mosaic virus (PapMV) and a single-strand RNA were previously shown to be an efficient antigen presentation system for the trigger of cellular immunity. Engineering of PapMV nano with a cytotoxic T lymphocyte epitope was previously shown activating specific T lymphocytes through a proteasome-independent major histocompatibility complex class I (MHC-I) cross-presentation. In this study, we provide new insights into the mechanism of the MHC-I cross-presentation mediated by PapMV nanoparticles. We demonstrate that PapMV nanoparticles do not require the transporter associated with antigen presentation (TAP), but rather depend on lysosome acidification and cathepsin S protease activity for presentation of the T cell epitope. We have also linked the induction of autophagy with this vacuolar MHC-I cross-presentation process. Interestingly, autophagy is induced in antigen-presenting cells after PapMV nanoparticles exposure and inhibition of autophagy reduce MHC-I cross-presentation. This study demonstrates that autophagy is associated with TAP- and proteasome-independent MHC-I cross-presentation. A deeper understanding of the autophagy-dependent MHC-I cross-presentation will be useful in designing vaccination platforms that aim to trigger an efficient cytotoxic T lymphocyte response.

Procathepsin V Is Secreted in a TSH Regulated Manner from Human Thyroid Epithelial Cells and Is Accessible to an Activity-Based Probe.

The significance of cysteine cathepsins for the liberation of thyroid hormones from the precursor thyroglobulin was previously shown by in vivo and in vitro studies. Cathepsin L is most important for thyroglobulin processing in mice. The present study aims at specifying the possible contribution of its closest relative, cysteine cathepsin L2/V, to thyroid function. Immunofluorescence analysis on normal human thyroid tissue revealed its predominant localization at the apical plasma membrane of thyrocytes and within the follicle lumen, indicating the secretion of cathepsin V and extracellular tasks rather than its acting within endo-lysosomes. To explore the trafficking pathways of cathepsin V in more detail, a chimeric protein consisting of human cathepsin V tagged with green fluorescent protein (GFP) was stably expressed in the Nthy-ori 3-1 thyroid epithelial cell line. Colocalization studies with compartment-specific markers and analyses of post-translational modifications revealed that the chimeric protein was sorted into the lumen of the endoplasmic reticulum and subsequently transported to the Golgi apparatus, while being N-glycosylated. Immunoblotting showed that the chimeric protein reached endo-lysosomes and it became secreted from the transduced cells. Astonishingly, thyroid stimulating hormone (TSH)-induced secretion of GFP-tagged cathepsin V occurred as the proform, suggesting that TSH upregulates its transport to the plasma membrane before it reaches endo-lysosomes for maturation. The proform of cathepsin V was found to be reactive with the activity-based probe DCG-04, suggesting that it possesses catalytic activity. We propose that TSH-stimulated secretion of procathepsin V is the default pathway in the thyroid to enable its contribution to thyroglobulin processing by extracellular means.

Design and expression of polytopic construct of cathepsin-L1, SAP-2 and FhTP16.5 proteins of Fasciola hepatica.

The enzyme-linked immunosorbent assay (ELISA) technique can play an important role in the early detection of fascioliasis. However, they have some diagnostic limitations, including cross-reaction with other helminths. It seems that the combination of recombinant parasite proteins as antigen can reduce these problems. Hence, the present study was aimed to design and confirm the antigenic recombinant multi-epitope (rMEP) construct of three protein epitopes (linear and conformational B-cell epitopes) of the parasite using immunoinformatic tools. For this purpose, the tertiary structures of Fasciola hepatica cathepsin-L1, saposin-like protein 2 and 16.5-kDa tegument-associated protein were predicted using the I-TASSER server. Validation of the modelled structures was performed by Ramachandran plots. The antigenic epitopes of the proteins were achieved by analysing the features of the IEDB server. The synthesized gene was cloned into the pET-22b (+) expression vector and transformed into the Escherichia coli BL21. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to verify and analyse the expression of the rMEP protein. Western blotting was utilized to confirm rMEP protein immunogenicity in two forms, one using an anti-His tag antibody and the other with human pooled sera samples (fascioliasis, non-fascioliasis and negative control sera). Our results demonstrated that the rMEP designed for the three proteins of F. hepatica was highly antigenic, and immune-detection techniques confirmed the antigen specificity. In conclusion, the presented antigenic multi-epitope may be very helpful to develop serodiagnostic kits such as indirect ELISA to evaluate the proper diagnosis of fascioliasis in humans and ruminants.

The role of human in the loop: lessons from D3R challenge 4.

The rapid development of new machine learning techniques led to significant progress in the area of computer-aided drug design. However, despite the enormous predictive power of new methods, they lack explainability and are often used as black boxes. The most important decisions in drug discovery are still made by human experts who rely on intuitions and simplified representation of the field. We used D3R Grand Challenge 4 to model contributions of human experts during the prediction of the structure of protein-ligand complexes, and prediction of binding affinities for series of ligands in the context of absence or abundance of experimental data. We demonstrated that human decisions have a series of biases: a tendency to focus on easily identifiable protein-ligand interactions such as hydrogen bonds, and neglect for a more distributed and complex electrostatic interactions and solvation effects. While these biases still allow human experts to compete with blind algorithms in some areas, the underutilization of the information leads to significantly worse performance in data-rich tasks such as binding affinity prediction.

Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks.

Enzymes are catalysts in biochemical reactions that, by definition, increase rates of reactions without being altered or destroyed. However, when that enzyme is a protease, a subclass of enzymes that hydrolyze other proteins, and that protease is in a multiprotease system, protease-as-substrate dynamics must be included, challenging assumptions of enzyme inertness, shifting kinetic predictions of that system. Protease-on-protease inactivating hydrolysis can alter predicted protease concentrations used to determine pharmaceutical dosing strategies. Cysteine cathepsins are proteases capable of cathepsin cannibalism, where one cathepsin hydrolyzes another with substrate present, and misunderstanding of these dynamics may cause miscalculations of multiple proteases working in one proteolytic network of interactions occurring in a defined compartment. Once rates for individual protease-on-protease binding and catalysis are determined, proteolytic network dynamics can be explored using computational models of cooperative/competitive degradation by multiple proteases in one system, while simultaneously incorporating substrate cleavage. During parameter optimization, it was revealed that additional distraction reactions, where inactivated proteases become competitive inhibitors to remaining, active proteases, occurred, introducing another network reaction node. Taken together, improved predictions of substrate degradation in a multiple protease network were achieved after including reaction terms of autodigestion, inactivation, cannibalism, and distraction, altering kinetic considerations from other enzymatic systems, since enzyme can be lost to proteolytic degradation. We compiled and encoded these dynamics into an online platform (https://plattlab.shinyapps.io/catKLS/) for individual users to test hypotheses of specific perturbations to multiple cathepsins, substrates, and inhibitors, and predict shifts in proteolytic network reactions and system dynamics.

Cyclopalladated compounds containing 2,6-lutidine: Synthesis, spectral and biological studies.

Bridge splitting reactions between [Pd(C2,N-dmba)(µ-X)]2 (dmba = N,N-dimethylbenzylamine; X = Cl, I, N3, NCO) and 2,6-lutidine (lut) in the 1:2 molar ratio at room temperature afforded cyclopalladated compounds of general formulae [Pd(C2,N-dmba)(X)(lut)] {X = Cl- (1), I-(2), NNN-(3), NCO-(4)}, which were characterized by elemental analyses and infrared (IR), 1H NMR spectroscopy. The molecular structures of all synthesized palladacycles have been solved by single-crystal X-ray crystallography. The cytotoxicity of the cyclopalladated compounds has been evaluated against a panel of murine {mammary carcinoma (4T1) and melanoma (B16F10-Nex2)} and human {melanoma (A2058, SK-MEL-110 and SK-MEL-5) tumor cell lines. All complexes were about 10 to 100-fold more active than cisplatin, depending on the tested tumor cell line. For comparison purposes, the cytotoxic effects of 1-4 towards human lung fibroblasts (MRC-5) have also been tested. The late apoptosis-inducing properties of 1-4 compounds in SK-MEL-5 cells were verified 24 h incubation using annexin V-Fluorescein isothiocyanate (FITC)/propidium iodide (PI). The binding properties of the model compound 1 on human serum albumin (HSA) and calf thymus DNA (ct-DNA) have been studied using circular dichroism and fluorescence spectroscopy. Docking simulations have been carried out to gain more information about the interaction of the palladacycle and HSA. The ability of compounds 1-4 to inhibit the activity of cathepsin B and L has also been investigated in this work.

Characterization of cathepsin S exosites that govern its elastolytic activity.

We have previously determined that the elastolytic activities of cathepsins (Cat) K and V require two exosites sharing the same structural localization on both enzymes. The structural features involved in the elastolytic activity of CatS have not yet been identified. We first mutated the analogous CatK and V putative exosites of CatS into the elastolytically inactive CatL counterparts. The modification of the exosite 1 did not affect the elastase activity of CatS whilst mutation of the Y118 of exosite 2 decreased the cleavage of elastin by ∼70% without affecting the degradation of other macromolecular substrates (gelatin, thyroglobulin). T06, an ectosteric inhibitor that disrupt the elastolytic activity of CatK, blocked ∼80% of the elastolytic activity of CatS without blocking the cleavage of gelatin and thyroglobulin. Docking studies showed that T06 preferentially interacts with a binding site located on the Right domain of the enzyme, outside of the active site. The structural examination of this binding site showed that the loop spanning the L174N175G176K177 residues of CatS is considerably different from that of CatL. Mutation of this loop into the CatL-like equivalent decreased elastin degradation by ∼70% and adding the Y118 mutation brought down the loss of elastolysis to ∼80%. In addition, the Y118 mutation selectively reduced the cleavage of the basement membrane component laminin by ∼50%. In summary, our data show that the degradation of elastin by CatS requires two exosites where one of them is distinct from those of CatK and V whilst the cleavage of laminin requires only one exosite.

MathDL: mathematical deep learning for D3R Grand Challenge 4.

We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranking and free energy estimation for Cathepsin S (CatS). We have developed advanced mathematics, namely differential geometry, algebraic graph, and/or algebraic topology, to accurately and efficiently encode high dimensional physical/chemical interactions into scalable low-dimensional rotational and translational invariant representations. These representations are integrated with deep learning models, such as generative adversarial networks (GAN) and convolutional neural networks (CNN) for pose prediction and energy evaluation, respectively. Overall, our MathDL models achieved the top place in pose prediction for BACE ligands in Stage 1a. Moreover, our submissions obtained the highest Spearman correlation coefficient on the affinity ranking of 460 CatS compounds, and the smallest centered root mean square error on the free energy set of 39 CatS molecules. It is worthy to mention that our method on docking pose predictions has significantly improved from our previous ones.

Schistosoma mansoni cathepsin D1: Biochemical and biophysical characterization of the recombinant enzyme expressed in HEK293T cells.

Schistosomes express a variety of aspartyl proteases (APs) with distinct roles in the helminth pathophysiology, among which degradation of host haemoglobin is key, since it is the main amino acid source for these parasites. A cathepsin D-like AP from Schistosoma mansoni (SmCD1) has been used as a model enzyme for vaccine and drug development studies in schistosomes and yet a reliable expression system for readily producing the recombinant enzyme in high yield has not been reported. To contribute to further advancing the knowledge about this valuable antischistosomal target, we developed a transient expression system in HEK 293T mammalian cells and performed a biochemical and biophysical characterization of the recombinant enzyme (rSmCD1). It was possible to express a recombinant C-terminal truncated form of SmCD1 (rSmCD1ΔCT) and purify it with high yield (16 mg/L) from the culture supernatant. When analysed by Size-Exclusion Chromatography and multi-angle laser light scattering, rSmCD1ΔCT behaved as a dimer at neutral pH, which is unusual for cathepsins D, turning into a monomer after acidification of the medium. Through analytical ultrancentrifugation, the dimer was confirmed for free rSmCD1ΔCT in solution as well as stabilization of the monomer during interaction with pepstatin. The mammalian cell expression system used here was able to produce rSmCD1ΔCT with high yields allowing for the first time the characterization of important kinetic parameters as well as initial description of its biophysical properties.