Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening.

Currently the entire human population is in the midst of a global pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2). This highly pathogenic virus has to date caused >71 million infections and >1.6 million deaths in >180 countries. Several vaccines and drugs are being studied as possible treatments or prophylactics of this viral infection. M3CLpro (coronavirus main cysteine protease) is a promising drug target as it has a significant role in viral replication. Here we use the X-ray crystal structure of M3CLpro in complex with boceprevir to study the dynamic changes of the protease upon ligand binding. The binding free energy was calculated for water molecules at different locations of the binding site, and molecular dynamics (MD) simulations were carried out for the M3CLpro/boceprevir complex, to thoroughly understand the chemical environment of the binding site. Several HCV NS3/4a protease inhibitors were tested in vitro against M3CLpro. Specifically, asunaprevir, narlaprevir, paritaprevir, simeprevir, and telaprevir all showed inhibitory effects on M3CLpro. Molecular docking and MD simulations were then performed to investigate the effects of these ligands on M3CLpro and to provide insights into the chemical environment of the ligand binding site. Our findings and observations are offered to help guide the design of possible potent protease inhibitors and aid in coping with the COVID-19 pandemic.

Glutamine's protection against brain damage in septic rats via increased protein oxygen-N-acetylglucosamine modification.

OBJECTIVE: This study aimed to observe the effect of glutamine (Gln) on brain damage in septic rats and explore its possible mechanism. METHODS: Ninety-three Sprague-Dawley rats were randomly divided into five groups: sham operation group, sepsis group, Gln-treated group, quercetin/Gln-treated group, and alloxan/Gln-treated group. The rats in each group were continuously monitored for mean arterial pressure (MAP) and heart rate changes for 16 h. Neuroreflex scores were measured 24 h after surgery. The water content of the brain tissue was measured. Plasma neuron enolase and cysteine protease-3 were measured using the ELISA. The expression levels of heat shock protein 70 (HSP70) and oxygen-N-acetylglucosamine (O-GlcNAc) were determined by western blot analysis. Finally, the brain tissue was observed via hematoxylin and eosin staining. RESULTS: The brain tissue water content, plasma neuron enolase content, brain tissue cysteine protease-3 content, and nerve reflex score were significantly lower in the Gln-treated group than in the sepsis group (P < 0.05). At the same time, the pathological brain tissue damage in the Gln-treated group was also significantly reduced. It is worth noting that the expression of HSP70 and the protein O-GlcNAc modification levels in the Gln-treated group were significantly elevated than the levels in the sepsis group (P < 0.05), and reversed by pretreatment with the HSP and O-GlcNAc inhibitors quercetion and alloxan. CONCLUSIONS: Gln can attenuate brain damage in rats with sepsis, which may be associated with increased protein O-GlcNAc modification.

Esomeprazole inhibits the lysosomal cysteine protease legumain to prevent cancer metastasis.

Legumain is a newly discovered lysosomal cysteine protease that can cleave asparagine bonds and plays crucial roles in regulating immunity and cancer metastasis. Legumain has been shown to be highly expressed in various solid tumors, within the tumor microenvironment and its levels are directly related to tumor metastasis and poor prognosis. Therefore, legumain presents as a potential cancer therapeutic drug target. In this study, we have identified esomeprazole and omeprazole as novel legumain small molecule inhibitors by screening an FDA approved-drug library. These compounds inhibited enzyme activity of both recombinant and endogenous legumain proteins with esomeprazole displaying the highest inhibitory effect. Further molecular docking analysis also indicated that esomeprazole, the S- form of omeprazole had the most stable binding to legumain protein compared to R-omeprazole. Transwell assay data showed that esomeprazole and omeprazole reduced MDA-MB-231 breast cancer cell invasion without effecting cell viability. Moreover, an in vivo orthotopic transplantation nude mouse model study showed that esomeprazole reduced lung metastasis of MDA-MB-231 breast cancer cells. These results indicated that esomeprazole has the exciting potential to be used in anti-cancer therapy by preventing cancer metastasis via the inhibition of legumain enzyme activity. Graphical abstract.

An Irreversible Inhibitor to Probe the Role of Streptococcus pyogenes Cysteine Protease SpeB in Evasion of Host Complement Defenses.

Members of the CA class of cysteine proteases have multifaceted roles in physiology and virulence for many bacteria. Streptococcal pyrogenic exotoxin B (SpeB) is secreted by Streptococcus pyogenes and implicated in the pathogenesis of the bacterium through degradation of key human immune effector proteins. Here, we developed and characterized a clickable inhibitor, 2S-alkyne, based on X-ray crystallographic analysis and structure-activity relationships. Our SpeB probe showed irreversible enzyme inhibition in biochemical assays and labeled endogenous SpeB in cultured S. pyogenes supernatants. Importantly, application of 2S-alkyne decreased S. pyogenes survival in the presence of human neutrophils and supports the role of SpeB-mediated proteolysis as a mechanism to limit complement-mediated host defense. We posit that our SpeB inhibitor will be a useful chemical tool to regulate, label, and quantitate secreted cysteine proteases with SpeB-like activity in complex biological samples and a lead candidate for new therapeutics designed to sensitize S. pyogenes to host immune clearance.

Coumarin as a structural component of substrates and probes for serine and cysteine proteases.

Coumarins represent well-established structures to introduce fluorescence into tool compounds for biochemical investigations. They are valued for their small size, chemical stability and accessibility as well as their tunable photochemical properties. As components of fluorophore/quencher pairs or FRET donor/acceptor pairs, coumarins have frequently been applied in substrate mapping approaches for serine and cysteine proteases. This review also focuses on the incorporation of coumarins into the side chain of amino acids and the exploitation of the resulting fluorescent amino acids for the positional profiling of protease substrates. The protease-inhibiting properties of certain coumarin derivatives and the utilization of coumarin moieties to assemble activity-based probes for serine and cysteine proteases are discussed as well.

Hepatitis E Virus Cysteine Protease Has Papain Like Properties Validated by in silico Modeling and Cell-Free Inhibition Assays.

Hepatitis E virus (HEV) has emerged as a global health concern during the last decade. In spite of a high mortality rate in pregnant women with fulminant hepatitis, no antiviral drugs or licensed vaccine is available in India. HEV-protease is a pivotal enzyme responsible for ORF1 polyprotein processing leading to cleavage of the non-structural enzymes involved in virus replication. HEV-protease region encoding 432-592 amino acids of Genotype-1 was amplified, expressed in Sf21 cells and purified in its native form. The recombinant enzyme was biochemically characterized using SDS-PAGE, Western blotting and Immunofluorescence. The enzyme activity and the inhibition studies were conducted using Zymography, FTC-casein based protease assay and ORF1 polyprotein digestion. To conduct ORF1 digestion assay, the polyprotein, natural substrate of HEV-protease, was expressed in E. coli and purified. Cleavage of 186 kDa ORF1 polyprotein by the recombinant HEV-protease lead to appearance of non-structural proteins viz. Methyltransferase, Protease, Helicase and RNA dependent RNA polymerase which were confirmed through immunoblotting using antibodies generated against specific epitopes of the enzymes. FTC-casein substrate was used for kinetic studies to determine Km and Vmax of the enzyme and also the effect of different metal ions and other protease inhibitors. A 95% inhibition was observed with E-64 which was validated through in silico analysis. The correlation coefficient between inhibition and docking score of Inhibitors was found to have a significant value of r2 = 0.75. The predicted 3D model showed two domain architecture structures similar to Papain like cysteine protease though they differed in arrangements of alpha helices and beta sheets. Hence, we propose that HEV-protease has characteristics of "Papain-like cysteine protease," as determined through structural homology, active site residues and class-specific inhibition. However, conclusive nature of the enzyme remains to be established.

Allosteric Site Inhibitor Disrupting Auto-Processing of Malarial Cysteine Proteases.

Falcipains are major haemoglobinases of Plasmodium falciparum required for parasite growth and development. They consist of pro- and mature domains that interact via 'hot-spot' interactions and maintain the structural integrity of enzyme in zymogen state. Upon sensing the acidic environment, these interactions dissociate and active enzyme is released. For inhibiting falcipains, several active site inhibitors exist, however, compounds that target via allosteric mechanism remains uncharacterized. Therefore, we designed and synthesized six azapeptide compounds, among which, NA-01 & NA-03 arrested parasite growth by specifically blocking the auto-processing of falcipains. Inhibitors showed high affinity for enzymes in presence of the prodomain without affecting the secondary structure. Binding of NA-03 at the interface induced rigidity in the prodomain preventing structural reorganization. We further reported a histidine-dependent activation of falcipain. Collectively, for the first time we provide a framework for blocking the allosteric site of crucial haemoglobinases of the human malaria parasite. Targeting the allosteric site could provide high selectivity and less vulnerable to drug resistance.

Chikungunya virus inhibition by peptidomimetic inhibitors targeting virus-specific cysteine protease.

Chikungunya virus (CHIKV), a mosquito-borne pathogenic virus that reemerged and caused epidemic in the Indian Ocean island of La Réunion, is a potential public health threat. Currently there is no antiviral drug or vaccine commercially available for the treatment of chikungunya fever, which necessitates the urge for an effective antiviral therapy for chikungunya treatment. In the present study, a FRET based protease assay was used to analyze the proteolytic activity of chikungunya nsP2 protease (CHIKV nsP2pro) - an essential viral enzyme, with fluorogenic substrate peptide. This protease assay was used to assess the inhibitory activity of Pep-I (MMsINC® database ID MMs03131094) and Pep-II (MMsINC® database ID MMs03927237), peptidomimetic compounds identified in a previous study by our group. Both compounds inhibited CHIKV nsP2pro with half maximal inhibition concentration (IC50) values of ∼34 µM and ∼42 µM, respectively. Kinetic studies showed that the inhibition constant (Ki) value is 33.34 ±â€¯2.53 µM for Pep-I and 45.89 ±â€¯4.38 µM for Pep-II. Additionally, these two compounds significantly inhibited CHIKV replication in BHK-21 cells at concentrations much lower than their cytotoxic concentrations. Intriguingly, these compounds did not show inhibitory effect on Sindbis virus. This suggests that Pep-I and Pep-II compounds identified as CHIKV nsP2 substrate peptidomimetics, specifically inhibit CHIKV replication.

Inhibition of Plasmodium falciparum cysteine proteases by the sugarcane cystatin CaneCPI-4.

Malaria is a disease caused by Plasmodium parasites that affects hundreds of millions of people. Plasmodium proteases are involved in invasion, erythrocyte egress and degradation of host proteins. Falcipains are well-studied cysteine peptidases located in P. falciparum food vacuoles that participate in hemoglobin degradation. Cystatins are natural cysteine protease inhibitors that are implicated in a wide range of regulatory processes. Here, we report that a cystatin from sugarcane, CaneCPI-4, is selectively internalized into P. falciparum infected erythrocytes and is not processed by the parasite proteolytic machinery. Furthermore, we demonstrated the inhibition of P. falciparum cysteine proteases by CaneCPI-4, suggesting that it can exert inhibitory functions inside the parasites. The inhibition of the proteolytic activity of parasite cells is specific to this cystatin, as the addition of an anti-CaneCPI-4 antibody completely abolished the inhibition. We extended the studies to recombinant falcipain-2 and falcipain-3 and demonstrated that CaneCPI-4 strongly inhibits these enzymes, with IC50 values of 12nM and 42nM, respectively. We also demonstrated that CaneCPI-4 decreased the hemozoin formation in the parasites, affecting the parasitemia. Taken together, this study identified a natural molecule as a potential antimalarial that specifically targets falcipains and also contributes to a better understanding of macromolecule acquisition by Plasmodium falciparum infected RBCs.

Low virulence potential and in vivo transformation ability in the honey bee venom treated Clinostomum complanatum.

The helminth parasites possess great capabilities to adapt themselves within their hosts and also develop strategies to render the commonly used anthelmintics ineffective leading to the development of resistance against these drugs. Besides using anthelmintics the natural products have also been tested for their anti-parasitic effects. Therapeutic efficacy of honey bee venom (HBV) has been tested in various ailments including some protozoal infections but very little is known about its anthelmintic properties. To investigate the anthelmintic effect of HBV the excysted progenetic metacercariae of Clinostomum complanatum, a heamophagic, digenetic trematode with zoonotic potential, infecting a wide variety of hosts, were obtained from Trichogaster fasciatus, a forage fish, which serves as the intermediate host. The metacercarial worms were in vitro incubated in RPMI-1640 medium containing HBV along with the controls which were devoid of HBV for the analysis of worm motility, enzyme activity, polypeptide profile and surface topographical changes. The motility of the worms was significantly reduced in a time dependent manner with an increase in the concentration of HBV. Following incubation of worms the release of cysteine proteases was inhibited in the presence of HBV as revealed by gelatine substrate gel zymography. As well as the polypeptide profile was also significantly influenced, particularly intensity/expression of Mr 19.4 kDa, 24 kDa and 34 kDa was significantly reduced upon HBV treatment. The HBV treatment also inhibited antioxidant enzyme, superoxide dismutase (SOD) and Glutathione-S-transferase (GST) significantly (p < 0.05) in the worms. The scanning electron microscopy of the HBV treated worms revealed tegumental disruptions and erosion of papillae as well as spines showing vacuolation in the tegument. The HBV treated worms also showed a marked decline in the transformation rate when introduced into an experimental host which further reflect the anthelmintic potential of HBV.

Papel das proteases na erosão dentinária / The role of proteases on dental erosion

Na dentina, a matriz orgânica desmineralizada tem um papel protetor contra desafios erosivos subsequentes. Porém, essa camada pode ser degradada por proteases, como as metaloproteinases da matriz (MMPs) e cisteína catepsinas (CCs). Recentemente, o uso de inibidores de proteases da matriz surgiu como uma importante ferramenta preventiva contra a erosão dentinária. Entretanto, o(s) mecanismo(s) exato(s) pelo(s) qual(is) os inibidores de proteases podem prevenir a erosão dentinária, bem como os tipos de proteases mais envolvidas neste processo ainda não são completamente conhecidos. O projeto foi desenvolvido em 2 subprojetos, com os seguintes objetivos: A)Subprojeto 1:Avaliar o papel das proteases na progressão da erosão dentária; B)subprojeto 2: Testar o potencial inibitório do NaF em CCs dentinárias. Para cumprir esses objetivos, foram utilizadas dentina de terceiros molares humanos para a preparação dos espécimes. A)Subprojeto1:Blocos de dentina (4 X 4 x 2 mm) (n=119) foram obtidos de raízes. Os espécimes foram divididos em 7 grupos de acordo com o seu tratamento (E-64, inibidor especifico II de catepsinas B, clorexidina, galardina NaF, placebo) ou sem tratamento, géis foram aplicados uma única vez sobre a superfície e feito o desafio erosivo (90s, 4x por dia por 5 dias) e feita analise perfilométrica. Os espécimes foram incubadas em solução contendo colagenase de Clostridium histolyticum tipo VII por 96hrs e então feita uma segunda analise perfilometrica para se determinar a espessura da MOD. Dois espécimes foram separados para análise de microscopia eletrônica de varredura. B)Subprojeto 2: Palitos de dentina (6 mm X 2 mm X 1 mm) (n=60) foram cortados da porção médio coronária dos dentes e completamente desmineralizados por imersão em EDTA 0,5 M (pH7,4) por 30 dias e lavados em água deionizada sob constante agitação a 4ºC por 72 h. Os espécimes foram divididos em 6 grupos (E-64, NaF e controle negativo, pH 5,5 ou 7,2) e incubados em saliva artificial contendo seus respectivos inibidores por 24 h 7 dias e 21 dias; ao termino de cada período, os espécimes eram pesados para avaliar a perda de massa e analisada a presença de CTX. A)Subprojeto 1: a perda de tecido desmineralizado (m, média± SD) foi: CHX 8,4±1,7b, Gala 8,6±1,9b, IECB 9,6±1,4a, E64 9,9±1,3a, NaF 9,9±1,7a, P 10,9±2,2a, ST 11,0±1,5a. A perda de tecido mineralizado foi: CHX 15,4±2,2b, Gala 16,0±1,8b, IECB 17,6±2,4a, E64 17,6±2,0a, NaF 17,3±2,8a, P 19,1±2,1a, ST 18,9±2,4a. Os inibidores de MMP reduziu significativamente a perda de matriz orgânica e tecido mineralizado em comparação com os outros grupos (p<0,05). Não foi achada diferença significante entre a espessura da matriz orgânica desmineralizada remanescente (p=0,845). B)Subprojeto 2: Na perda de massa houve diferença significante em relação ao inibidor (F=20,047, p<0,0001) e tempo de incubação (F=222,462, p<0,0001) com significante interação entre esses critérios, nos período de menor tempo de incubação, a perda foi similar para todos os grupos testados, no período de maior tempo de incubação, o grupo contendo NaF demostrou os melhores resultados. Na analise de CTX, houve diferença significante em relação aos inibidores (F46,543, p<0,0001), pH (F=14,836, p<0,0004) e tempo de incubação (F=161,438, p<0,0001) com significante interação entre esses critérios, como ocorrido na perda de massa, não houve diferença estatística nos períodos de menor incubação. No período de maior tempo de incubação, mais uma vez o grupo NaF mostrou os melhores resultados. No valor acumulado de CTX, os grupos E64 e controle negativo tiveram os maiores valores de CTX acumulado, o grupo NaF, independente do pH mostrou redução significante em relação aos demais grupos. Após analise dos resultados dos dois subprojetos, podemos indicar que as MMPs são as proteases de maior importância na progressão da erosão dentinária, assim, sua inibição é de maior importância para a redução desta patologia. Mesmo as CCs não exercendo papel direto para a progressão da erosão, elas são efetivas na cascata da ativação de outras proteases, como as próprias MMPs. Com isso, sua inibição também pode ser importante para a redução indireta da progressão da erosão. Neste presente estudo, pudemos comprovar que o NaF tem potencial inibitório sobre as CCs dentinárias, assim, sugerindo um novo inbidor de CCs. Com os resultados deste estudo, podemos afirmar que as MMPs são as principais proteases na progressão da erosão dentinária e que o NaF tem potencial inibitório nas CCs dentinárias.(AU)

In the dentine, the demineralized organic matrix has a protector part against the following erosive challenges. Nevertheless, this layer can be degraded by proteases, like the matrix metalloproteinases (MMPS) and cystein cathepsins (CCs). Recently, the use of proteases of the matrix´s inhibitors, emerged as an important preventive tool against the dentinária erosion. However, the exact mechanisms from which the inhibitors of the proteases may prevent the dentin erosion, as much as the kinds of proteases more involved in this process are not completely known yet. Therefore, the general objective of this project was to investigate the part of the two main proteases of the matrix (MMPs and CCs) in the dental erosion. The project was developed in 2 subprojects, with the following objectives: A)Subproject 1: Evaluate the part of the proteases in the progression of the dental erosion; B)subproject 2: To test the NaF inhibitory potencial in the dentin CCs. To accomplish these objectives, human third molar dentin were used for the preparation of the specimens, obtained in the surgery and urgency clinics of FOB-USP (subproject 1) or granted by the University of Oulu (subproject 2). A) Subproject 1: Dentine blocks 4 X 4 X 2 mm) (n=119) were obtained from the roots of the obtained teeth. The specimens were divided in 7 groups according with their treatment. Gels containing inhibitors (E-64, specific cathepsin B inhibitor II, chlorhexidine, galardin NaF, placebo), or without treatment, were produced, applied only one time over the surface and made the erosive challenge (90s, 4x a day for 5 days) and made profilometric analysis. The specimens were incubated in a solution containing collagenase of Clostridium histolyticum type VII for 96 hours and then a second profilometric analysis was made to determine the thickness of the MOD. Two specimens were separated for the electronic microscopy scan analysis. B) Subproject 2: Dentine sticks (6 mm X 2 mm X 1 mm) (n=60) were cut from the medium coronary portion of the teeth and completely demineralized by immersion in EDTA 0,5 M (pH7,4) ifor 30 days and washed in deionized water under constant agitation in 4º C for 72 hours. The specimens were divided in 6 groups (divided by inhibitors: E-64, NaF and negative control, pH 5,5 or 7,2) and incubated in artificial saliva containing their respective inhibitors for 24 hours, 7 days and 21 days; by the end of each period, the specimens were weighted to evaluate the loss of mass and analised the presence of CTX. A)Subproject 1: the loss of demineralized tissue (m, média± SD) was : CHX 8,4±1,7b, Gala 8,6±1,9b, IECB 9,6±1,4a, E64 9,9±1,3a, NaF 9,9±1,7a, P 10,9±2,2a, ST 11,0±1,5a. The loss of demineralized tissue was: CHX 15,4±2,2b, Gala 16,0±1,8b, IECB 17,6±2,4a, E64 17,6±2,0a, NaF 17,3±2,8a, P 19,1±2,1a, ST 18,9±2,4a. The MMP inhibitors reduced significantly the loss of organic matrix and demineralized tissue in comparison with other groups (p<0,05). There was no significant difference found between the thickness of the remaining demineralized organic matrix.(p=0,845). B)Subproject: In the loss of mass, there was a significant difference in relation to the inhibitor (F=20,047, p<0,0001) and incubation time (F=222,462, p<0,0001) with significant interaction between these criteria, in the periods of lesser time of incubation, the loss was similar for all the tested groups, in the period of higher time of incubation, the group containing NaF demonstrated the best results. In the analysis of CTX, there was significant difference in relation the inhibitors (F46,543, p<0,0001), pH (F=14,836, p<0,0004) and time of incubation (F=161,438, p<0,0001)with significant interaction between these criteria, as occurred in the mass loss, there was no statistic difference in the period of lesser incubation. In the period of higher time of incubation, once again, the NaF group demonstrated the best results. The CTX accumulated value, the E64 groups and negative control had the greater accumulated values of CTX, the NaF group, regardlessof the pH, demonstrated significant reduction in relation to the other groups. After the analysisof the results of both subprojects, we can indicate that the MMPs are the proteases of greater importance in the progression of the dentin erosion, thus, its inhibition is of graeter importance for the reduction of this pathology. Even the CCs don´t playing the part directly for the progression of erosion, they are effective in the cascade of the activation of other proteases, like the MMPs themselves. In this manner, its inhibition can also be important for the indirect reduction of the progression of the erosion. In this present study, we can prove that the NaF has inhibiting potential over the dentin CCs, thus, suggesting a new inhibitor of CCs. With the results of this study, we can affirm that the MMPs are the main proteases in the progression of the dentin erosion and that the NaF has inhibiting potential in the dentin CCs.(AU)

A novel form of ficin from Ficus carica latex: Purification and characterization.

A novel ficin form, named ficin E, was purified from fig tree latex by a combination of cation-exchange chromatography on SP-Sepharose Fast Flow, Thiopropyl Sepharose 4B and fplc-gel filtration chromatography. The new ficin appeared not to be sensitive to thiol derivatization by a polyethylene glycol derivative, allowing its purification. The protease is homogeneous according to PAGE, SDS-PAGE, mass spectrometry, N-terminal micro-sequencing analyses and E-64 active site titration. N-terminal sequencing of the first ten residues has shown high identity with the other known ficin (iso)forms. The molecular weight was found to be (24,294±10)Da by mass spectrometry, a lower value than the apparent molecular weight observed on SDS-PAGE, around 27 kDa. Far-UV CD data revealed a secondary structure content of 22% α-helix and 26% ß-sheet. The protein is not glycosylated as shown by carbohydrate analysis. pH and temperature measurements indicated maxima activity at pH 6.0 and 50 °C, respectively. Preliminary pH stability analyses have shown that the protease conserved its compact structure in slightly acidic, neutral and alkaline media but at acidic pH (<3), the formation of some relaxed or molten state was evidenced by 8-anilino-1-naphtalenesulfonic acid binding characteristics. Comparison with the known ficins A, B, C, D1 and D2 (iso)forms revealed that ficin E showed activity profile that looked like ficin A against two chromogenic substrates while it resembled ficins D1 and D2 against three fluorogenic substrates. Enzymatic activity of ficin E was not affected by Mg(2+), Ca(2+) and Mn(2+) at a concentration up to 10mM. However, the activity was completely suppressed by Zn(2+) at a concentration of 1mM. Inhibitory activity measurements clearly identified the enzyme as a cysteine protease, being unaffected by synthetic (Pefabloc SC, benzamidine) and by natural proteinaceous (aprotinin) serine proteases inhibitors, by aspartic proteases inhibitors (pepstatin A) and by metallo-proteases inhibitors (EDTA, EGTA). Surprisingly, it was well affected by the metallo-protease inhibitor o-phenanthroline. The enzymatic activity was however completely blocked by cysteine proteases inhibitors (E-64, iodoacetamide), by thiol-blocking compounds (HgCl2) and by cysteine/serine proteases inhibitors (TLCK and TPCK). This is a novel ficin form according to peptide mass fingerprint analysis, specific amidase activity, SDS-PAGE and PAGE electrophoretic mobility, N-terminal sequencing and unproneness to thiol pegylation.

Anti-trypanosomal activities and structural chemical properties of selected compound classes.

Potent compounds do not necessarily make the best drugs in the market. Consequently, with the aim to describe tools that may be fundamental for refining the screening of candidates for animal and preclinical studies and further development, molecules of different structural classes synthesized within the frame of a broad screening platform were evaluated for their trypanocidal activities, cytotoxicities against murine macrophages J774.1 and selectivity indices, as well as for their ligand efficiencies and structural chemical properties. To advance into their modes of action, we also describe the morphological and ultrastructural changes exerted by selected members of each compound class on the parasite Trypanosoma brucei. Our data suggest that the potential organelles targeted are either the flagellar pocket (compound 77, N-Arylpyridinium salt; 15, amino acid derivative with piperazine moieties), the endoplasmic reticulum membrane systems (37, bisquaternary bisnaphthalimide; 77, N-Arylpyridinium salt; 68, piperidine derivative), or mitochondria and kinetoplasts (88, N-Arylpyridinium salt; 68, piperidine derivative). Amino acid derivatives with fumaric acid and piperazine moieties (4, 15) weakly inhibiting cysteine proteases seem to preferentially target acidic compartments. Our results suggest that ligand efficiency indices may be helpful to learn about the relationship between potency and chemical characteristics of the compounds. Interestingly, the correlations found between the physico-chemical parameters of the selected compounds and those of commercial molecules that target specific organelles indicate that our rationale might be helpful to drive compound design toward high activities and acceptable pharmacokinetic properties for all compound families.

Effects of acid etching and adhesive treatments on host-derived cysteine cathepsin activity in dentin.

PURPOSE: To analyze the effects of different processes during bonding on endogenous cysteine cathepsin activity in dentin. MATERIALS AND METHODS: Dentin powder, prepared from extracted human third molars, was divided into 10 groups. Two lots of dentin powder were used to detect the effects of the procedure of protein extraction on endogenous cathepsin activity. The others were used to study effects of different acid-etching or adhesive treatments on enzyme activity. Concentrations of 37% phosphoric acid or 10% phosphoric acid, two etch-and-rinse adhesive systems, and two self-etching adhesive systems were used as dentin powder treatments. The untreated mineralized dentin powder was set as the control. After treatment, the proteins of each group were extracted. The total cathepsin activity in the extracts of each group was monitored with a fluorescence reader. RESULTS: In the control group, there were no significant differences in cathepsin activity between the protein extract before EDTA treatment and the protein extract after EDTA treatment (p > 0.05). The cathepsin activities of the three different extracts in the 37% phosphoric acid-treated group were different from each other (p < 0.05). The two acid-etching groups and two etch-and-rinse groups showed significant enzyme activity reduction vs the control group (p < 0.05). There were no significant differences between those four groups (p > 0.05). Treating the dentin powder with any of the two self-etching adhesives resulted in an increase in cathepsin activity (p < 0.05). CONCLUSIONS: The activity of cysteine cathepsins can be detected in dentin powder. Treatment with EDTA during protein extraction exerted an influence on cathepsin activity. Acid etching or etch-and-rinse adhesive systems may reduce the activity of endogenous cathepsins in dentin. Self-etching adhesive systems may increase the enzyme activity.

An access to aza-Freidinger lactams and E-locked analogs.

Freidinger lactams, possessing a peptide bond configuration locked to Z, are important key elements of conformationally restricted peptidomimetics. In the present work, the C(α)H(i+1) unit has been replaced by N, leading to novel aza-Freidinger lactams. A synthesis to corresponding building blocks and their E-locked analogs is introduced. The versatile buildings blocks reported here are expected to serve as useful elements in peptide synthesis.

Tooth bleaching increases dentinal protease activity.

Hydrogen peroxide is an oxidative agent commonly used for dental bleaching procedures. The structural and biochemical responses of enamel, dentin, and pulp tissues to the in vivo bleaching of human (n = 20) premolars were investigated in this study. Atomic force microscopy (AFM) was used to observe enamel nanostructure. The chemical composition of enamel and dentin was analyzed by infrared spectroscopy (FTIR). The enzymatic activities of dental cathepsin B and matrix metalloproteinases (MMPs) were monitored with fluorogenic substrates. The amount of collagen in dentin was measured by emission of collagen autofluorescence with confocal fluorescence microscopy. The presence of Reactive Oxygen Species (ROS) in the pulp was evaluated with a fluorogenic 2',7'-dichlorodihydrofluorescein diacetate (DCFDA) probe. Vital bleaching of teeth significantly altered all tested parameters: AFM images revealed a corrosion of surface enamel nanostructure; FTIR analysis showed a loss of carbonate and proteins from enamel and dentin, along with an increase in the proteolytic activity of cathepsin-B and MMPs; and there was a reduction in the autofluorescence of collagen and an increase in both cathepsin-B activity and ROS in pulp tissues. Together, these results indicate that 35% hydrogen peroxide used in clinical bleaching protocols dramatically alters the structural and biochemical properties of dental hard and soft pulp tissue.

A novel transglutaminase substrate from Streptomyces mobaraensis inhibiting papain-like cysteine proteases.

Transglutaminase from Streptomyces mobaraensis is an enzyme of unknown function that cross-links proteins to high molecular weight aggregates. Previously, we characterized two intrinsic transglutaminase substrates with inactivating activities against subtilisin and dispase. This report now describes a novel substrate that inhibits papain, bromelain, and trypsin. Papain was the most sensitive protease; thus, the protein was designated Streptomyces papain inhibitor (SPI). To avoid transglutaminase-mediated glutamine deamidation during culture, SPI was produced by Streptomyces mobaraensis at various growth temperatures. The best results were achieved by culturing for 30-50 h at 42 degrees C, which yielded high SPI concentrations and negligibly small amounts of mature transglutaminase. Transglutaminasespecific biotinylation displayed largely unmodified glutamine and lysine residues. In contrast, purified SPI from the 28 degrees C culture lost the potential to be cross-linked, but exhibited higher inhibitory activity as indicated by a significantly lower Ki (60 nM vs. 140 nM). Despite similarities in molecular mass (12 kDa) and high thermostability, SPI exhibits clear differences in comparison with all members of the wellknown family of Streptomyces subtilisin inhibitors. The neutral protein (pI of 7.3) shares sequence homology with a putative protein from Streptomyces lavendulae, whose conformation is most likely stabilized by two disulfide bridges. However, cysteine residues are not localized in the typical regions of subtilisin inhibitors. SPI and the formerly characterized dispase-inactivating substrate are unique proteins of distinct Streptomycetes such as Streptomyces mobaraensis. Along with the subtilisin inhibitory protein, they could play a crucial role in the defense of vulnerable protein layers that are solidified by transglutaminase.

Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors.

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted on a series (39 molecules) of peptidyl vinyl sulfone derivatives as potential Plasmodium Falciparum cysteine proteases inhibitors. Two different methods of alignment were employed: (i) a receptor-docked alignment derived from the structure-based docking algorithm GOLD and (ii) a ligand-based alignment using the structure of one of the ligands derived from a crystal structure from the PDB databank. The best predictions were obtained for the receptor-docked alignment with a CoMFA standard model (q (2) = 0.696 and r (2) = 0.980) and with CoMSIA combined electrostatic, and hydrophobic fields (q (2) = 0.711 and r (2) = 0.992). Both models were validated by a test set of nine compounds and gave satisfactory predictive r (2) (pred) values of 0.76 and 0.74, respectively. CoMFA and CoMSIA contour maps were used to identify critical regions where any change in the steric, electrostatic, and hydrophobic fields may affect the inhibitory activity, and to highlight the key structural features required for biological activity. Moreover, the results obtained from 3D-QSAR analyses were superimposed on the Plasmodium Falciparum cysteine proteases active site and the main interactions were studied. The present work provides extremely useful guidelines for future structural modifications of this class of compounds towards the development of superior antimalarials.