High-throughput screening of SARS-CoV-2 main and papain-like protease inhibitors

The global COVID-19 coronavirus pandemic has infected over 109 million people, leading to over 2 million deaths up to date and still lacking of effective drugs for patient treatment. Here, we screened about 1.8 million small molecules against the main protease (Mpro) and papain like protease (PLpro), two major proteases in severe acute respiratory syndrome-coronavirus 2 genome, and identified 1851Mpro inhibitors and 205 PLpro inhibitors with low nmol/l activity of the best hits. Among these inhibitors, eight small molecules showed dual inhibition effects on both Mpro and PLpro, exhibiting potential as better candidates for COVID-19 treatment. The best inhibitors of each protease were tested in antiviral assay, with over 40% of Mpro inhibitors and over 20% of PLpro inhibitors showing high potency in viral inhibition with low cytotoxicity. The X-ray crystal structure of SARS-CoV-2 Mpro in complex with its potent inhibitor 4a was determined at 1.8 Å resolution. Together with docking assays, our results provide a comprehensive resource for future research on anti-SARS-CoV-2 drug development.

Coagulation modifiers targeting SARS-CoV-2 main protease Mpro for COVID-19 treatment: an in silico approach

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection depends on viral polyprotein processing, catalysed by the main proteinase (Mpro). The solution of the SARS-CoV-2 Mpro structure allowed the investigation of potential inhibitors. This work aims to provide first evidences of the applicability of commercially approved drugs to treat coronavirus disease-19 (COVID-19). We screened 4,334 compounds to found potential inhibitors of SARS-CoV-2 replication using an in silico approach. Our results evidenced the potential use of coagulation modifiers in COVID-19 treatment due to the structural similarity of SARS-CoV-2 Mpro and human coagulation factors thrombin and Factor Xa. Further in vitro and in vivo analysis are needed to corroborate these results.

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)

Efeito de inibidores da atividade proteolítica na resistência de união de pino de fibra de vidro à dentina radicular após 12 meses / Effect of proteolytic activity inhibitors on bond strength of glass-fiber post to radicular dentin up to 12 months

O estabelecimento de uma camada híbrida adequada no canal radicular representa um dos principais desafios clínicos devido à dificuldade de acesso. Dessa forma, o uso de inibidores proteolíticos poderia tornar-se um recurso favorável. O objetivo deste estudo foi avaliar o efeito de inibidores proteolíticos na união de pino de fibra de vidro fixado com cimento adesivo, considerando os terços radiculares e tempos distintos, por meio da resistência de união (RU). Cento e quarenta e quatro raízes bovinas foram selecionadas e divididas em 6 grupos de tratamento, e redivididas em 3 subgrupos de acordo com os tempos de avaliação de 24 horas, 6 e 12 meses (n=8). Após o tratamento endodôntico e desobturação padronizados, as raízes foram cimentadas com pinos de fibra de vidro cônicos (Exacto/Angelus). As raízes foram tratadas com sistema adesivo convencional de três passos, Adper Scotchbond Multipurpose/ 3M ESPE (SBMP) e cimento dual RelyX ARC/ 3M ESPE. Após prévia divisão, foram alocadas em grupos CN (Controle Negativo- sem pré tratamento associado), CP (Controle Positivo- com agentes ativador e catalisador), EDTA (ácido etilenodiamino tetra-acético a 17%), CHX (digluconato de clorexidina a 2%), E-5 (E- 64 a 5 µM) e E-10 (E-64 a 10 µM). Após 24 horas, as raízes foram seccionadas perpendicularmente ao longo eixo e identificadas quanto à região, obtendo-se fatias de 1 mm de espessura (cervical, médio e apical), que foram armazenadas em saliva artificial para serem testadas. Todas as fatias foram submetidas ao teste de extrusão (push-out) na máquina de teste universal (Instron) com célula de carga de 50 N a 0,5 mm/min. Os dados foram analisados pelo teste de ANOVA a três critérios e comparações múltiplas com Tukey, ambos com p<0,05. Após 24 horas, não se observou diferenças entre os tratamentos. Após 6 meses, a CHX demonstrou melhor desempenho, cujo efeito não se prorrogou até os 12 meses. O uso de inibidores proteolíticos não foram capazes de preservar a resistência de união dos pinos intrarradiculares até o tempo de 12 meses.(AU)

The adequate establishment of hybrid layer in the root canal on bonding process is still a clinical challenge due to its hard access. Thus, the use of proteolytic inhibitors could become a favorable tool. The aim of this study was to evaluate the effect of proteolytic inhibitors in the bonding of a glass- fiber post fixed with a luting cement, regarding the root thirds and different times through the bond strength. One hundred and forty four bovine roots were selected and divided into 6 treatment groups, and subdivided according to the time of evaluation of 24 hours, 6 and 12 months (n=8). After endodontic treatment and standardized removal procedure, the roots were cemented with tapered glass fiber posts (Exacto/ Angelus). The roots were treated with three-step etch-and-rinse adhesive system Adper Scotchbond Multipurpose/ 3M ESPE (SBMP) and dual cement RelyX ARC/ 3M ESPE. After previous division, CN (negative- control without pre associated treatment), CP (Control positive- with activator and catalyst agents) EDTA (17% ethylenediaminetetraacetic acid) CHX (2% chlorhexidine digluconate) E-5 (5µM E-64) and E-10 (10µM E-64). After 24h, the roots were sectioned perpendicular to the long axis and identified according to third in 1mm thick slices (cervical, middle and apical), which were stored in artificial saliva to be tested. All slices were subjected to extrusion tests (push-out) in the universal test machine (Instron) at 50 N load cell at 0.5 mm/min. Data were analyzed with three-way ANOVA and multiple comparisons with Tukey test, both with p <0.05. After 24 hours, no differences were observed between treatments. After 6 months, CHX showed better performance, which did not last up 12 months. The proteolytic inhibitors performed differently in the bonding process over time; only CHX promoted inhibition at 6 months. The use of proteolytic inhibitors were not able to maintain the bond strength of intraradicular posts up time of 12 months.(AU)

Purification of a protease inhibitor from Dolichos biflorus using immobilized metal affinity chromatography.

Plant protease inhibitors (PIs) are generally small proteins which play key roles in regulation of endogenous proteases and may exhibit antifeedant, antifungal, antitumor and cytokine inducing activities. Dolichos biflorus (horse gram) is an unexploited legume, which is rich in nutrients and also has therapeutic importance. It contains a double-headed PI, which is an anti-nutritional factor. As there is no report available on its simultaneous removal and purification in single step, in this study, a double-headed PI active against both trypsin and chymotrypsin was purified from Dolichos biflorus to ~14-fold with ~84% recovery using an immobilized metal affinity chromatography (IMAC) medium consisting of Zn-alginate beads. The method was single-step, fast, simple, reliable and economical. The purified inhibitor showed a single band on SDS-PAGE corresponding to molecular mass of 16 kDa and was stable over a pH range of 2.0-12.0 and up to a temperature of 100°C for 20 min. The optimum temperature for trypsin and chymotrypsin inhibitor was observed to be 50°C and 37°C, respectively and pH optimum was pH 7.0 and 8.0, respectively. Thus, IMAC using Zn-alginate beads was useful in simultaneous purification and removal of an anti-nutritional factor from horse gram flour in single step. This procedure may also be employed for purification of other plant PIs in one step.

Selección de cepas nativas con actividad quitino-proteolítica de bacillus sp aisladas de suelos tropicales / Selecting native Bacillus sp strains having chitinolytic and proteolytic activity which have been isolated from tropical soils

El objetivo de este trabajo fue la selección de cepas nativas del género Bacillus con actividad quitinolíticay proteolítica, en suelo tropical en la costa de Oaxaca, México. Se aislaron 150 cepas, de las cuales 22fueron seleccionadas por presentar actividad quitinolítica y proteolítica. Dicha actividad se evaluó porla formación de halo de hidrólisis alrededor de la colonia en medios de cultivo suplementados con quitinacoloidal al 5% y leche descremada al 1% respectivamente. Las cepas LUM B001, B003, B013, B015y B065 presentaron mayor actividad quitinolítica y proteolítica, por lo que tienen el potencial para serevaluadas en control biológico de hongos fitopatógenos. Se encontró al género Bacillus distribuido ensuelos cultivados y no cultivados, no se encontraron diferencias estadísticas según el cultivo establecido(P<0,05), sin embargo se encontraron diferencias significativas (P<0,05) entre las zonas estudiadas, correspondiendolas menores recuperaciones de cepas a los terrenos del municipio de Tututepec, Oaxaca.

This work was aimed at selecting native strains from the Bacillus genus having chitinolytic and proteolytic activityfrom soil from the tropical coast of Oaxaca, Mexico. 150 strains were isolated, 22 of which were selectedas they presented chitinolytic and proteolytic activity. Such activity was assessed by the formation of a hydrolysishalo around the colony in culture media supplemented with 5% colloidal chitin and 1% skimmed milk.The LUM B001, B003, B013, B015 and B065-chitin strains presented higher quitinolytic and proteolytic activity,thereby having the potential for being evaluated in the biological control of phytopathogenic fungi. TheBacillus genus was found in cultivated and uncultivated soils; no statistical differences were found accordingto established crop (p <0.05); however, significant differences (p <0.05) were found between the areas beingstudied regarding the smaller amount of strains collected from land in the municipality of Tututepec, Oaxaca.

Proteínas que intervienen en la homeostasis bucal / Proteins that intervene in bucal homoestasis

Se presentan algunos aspectos generales de un grupo de proteínas que recientemente han sido descritas y cuya función es determinante para el mantenimiento de la homeostasis de la cavidad bucal. Estas proteínas son las histatinas, antibióticos naturales; las cistatinas, que inhiben la acción de las proteasas bacterianas en la enfermedad periodontal; y la estaterina, que regula la precipitación del dosfato de calcio en la saliva. Las histatinas, cistatinas y estaterina han sido aisladas, caracterizadas y secuenciadas. Se piensa que en un futuro no muy lejano estas moléculas podrán ser utilizadas para dar una mejor calidad de vida a pacientes con infecciones bucales causadas por hongos o con otras enfermedades relacionadas

Chemical modification and complex formation studies with jack bean proteinase inhibitor.

Pretreatment of the purified jack bean inhibitor with enterokinase activated human pancreatic preparation for 1 hr decreased its inhibitory capacity against crystalline bovine alpha-chymotrypsin by 30% but did not affect its trypsin inhibitory activity. Preincubation of the inhibitor with bovine chymotrypsin for 60 min resulted in partial loss of the inhibitory potency. Complex formation studies by gel chromatography on Sephadex G-100 indicated that the trypsin-inhibitor and chymotrypsin-inhibitor complexes dissociated to release inactivated inhibitor and active proteinases. Gel chromatography of the inhibitor in presence of 1.5 M ammonium sulphate indicated that the inhibitor showed a tendency to aggregate without loss of biological activity. However, in 4.2 M salt medium after 3 hr, antichymotryptic activity was lost completely without any effect on antitryptic activity. Treatment with methylamine, a nucleophile, caused a greater loss of antichymotryptic activity. Trinitrobenzene sulphonate and ethylacetamidate, the amino group modifiers, affected only the antichymotryptic activity. Treatment with ninhydrin, a specific arginine modifier, at pH 9.0 abolished the antitryptic activity whereas only 50% of the antichymotryptic activity was lost. Diethylpyrocarbonate, a histidine reagent, also decreased only the antitryptic activity. Modification of tryptophan and cysteine residues of the inhibitor had no effect on its inhibitory potency. Treatment with mercaptoethanol and sodium borohydride caused nearly 50% loss of antitryptic and antichymotryptic activities. Chloramine-T, a reagent that modifies methionine residues, inactivated the inhibitor.

Nature of the tryptic/chymotryptic inhibitor from horsegram (Dolichos biflorus).

A protease inhibitor specific to trypsin and chymotrypsin was purified from horsegram (Dolichos biflorus) with the inhibition index 0.24 micrograms/micrograms for trypsin and 0.36 micrograms/micrograms for chymotrypsin. In SDS-PAGE, the inhibitor protein was seen as a single band with apparent molecular mass Mr = 15,500. However, on fast protein liquid chromatography (FPLC) or non-denaturating PAGE, the inhibitor resolved into four components revealing the existence of isoinhibitors. Data on amino acid analysis indicate that the isoinhibitors are closely related. The major amino acids in the inhibitor are half cystine (18.9 mole %), aspartic acid (12.7 mole %) and serine (14.3 mole %). The inhibitor was partially stable to 0.1% sodium dodecyl sulphate, 8M urea or 6M guanidine hydrochloride. The inhibitory activity was lost on reduction or carboxamidomethylation or acetylation. Modification of the arginine groups or CNBr cleavage of the protein did not result in significant loss of either tryptic or chymotryptic inhibitory activities. The isoinhibitors separated by FPLC reacted with polyclonal antibody raised in rabbits and had pI values ranging from 4.8-5.1. The horsegram inhibitor thus resembles other Bowman-Birk protease inhibitors.