Exploring Novel Antimalarial Compounds Targeting Plasmodium falciparum Enoyl-ACP Reductase: Computational and Experimental Insights.

Malaria, caused by Plasmodium protozoa with Plasmodium falciparum as the most virulent species, continues to pose significant health challenges. Despite the availability of effective antimalarial drugs, the emergence of resistance has heightened the urgency for developing novel therapeutic compounds. In this study, we investigated the enoyl-ACP reductase enzyme of P. falciparum (PfENR) as a promising target for antimalarial drug discovery. Through a comprehensive analysis, we conducted a comparative evaluation of two lead compounds, LD1 (CID: 44405336, lead compounds 1) and LD2 (CID: 72703246, lead compounds 2), obtained from the PubChem/NCBI ligand database, to serve as reference molecules in the identification of potential derivatives using virtual screening assays. Among the newly identified candidates, Ligand 1 (LG1) and Ligand 2 (LG2) exhibited intriguing characteristics and underwent further investigation through docking and molecular dynamics simulations. Ligand 1 (LG1) demonstrated interactions similar to LD1, including hydrogen bonding with Asp218, while Ligand 2 (LG2) displayed superior binding energy comparable to LD1 and LD2, despite lacking hydrogen bonding interactions observed in the control compounds triclosan and its derivative 7-(4-chloro-2-hydroxyphenoxy)-4-methyl-2H-chromen-2-one (CHJ). Following computational validation using the MM/GBSA method to estimate binding free energy, commercially acquired LG1 and LG2 ligands were subjected to in vitro testing. Inhibition assays were performed to evaluate their potential as PfENR inhibitors alongside triclosan as a control compound. LG1 exhibited no inhibitory effects, while LG2 demonstrated inhibitory effects like triclosan. In conclusion, this study contributes valuable insights into developing novel antimalarial drugs by identifying LG2 as a potential ligand and employing a comprehensive approach integrating computational and experimental methodologies.

Aptamer-Based Recognition of Breast Tumor Cells: A New Era for Breast Cancer Diagnosis.

Breast cancer is one of the leading causes of death among women worldwide and can be classified into four major distinct molecular subtypes based on the expression of specific receptors. Despite significant advances, the lack of biomarkers for detailed diagnosis and prognosis remains a major challenge in the field of oncology. This study aimed to identify short single-stranded oligonucleotides known as aptamers to improve breast cancer diagnosis. The Cell-SELEX technique was used to select aptamers specific to the MDA-MB-231 tumor cell line. After selection, five aptamers demonstrated specific recognition for tumor breast cell lines and no binding to non-tumor breast cells. Validation of aptamer specificity revealed recognition of primary and metastatic tumors of all subtypes. In particular, AptaB4 and AptaB5 showed greater recognition of primary tumors and metastatic tissue, respectively. Finally, a computational biology approach was used to identify potential aptamer targets, which indicated that CSKP could interact with AptaB4. These results suggest that aptamers are promising in breast cancer diagnosis and treatment due to their specificity and selectivity.

PACAP key interactions with PAC1, VPAC1, and VPAC2 identified by molecular dynamics simulations.

The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) belongs to the glucagon/secretin family. PACAP interacts with the pituitary adenylate cyclase-activating polypeptide receptor type 1 (PAC1) and vasoactive intestinal peptide receptors 1 and 2 (VPAC1 and VPAC2), exhibiting functions in the immune, endocrine, and nervous systems. This peptide is upregulated in numerous instances of brain injury, acting as a neuroprotective agent. It can also suppress HIV-1 and SARS-CoV-2 viral replication in vitro. This work aimed to identify, in each peptide-receptor system, the most relevant residues for complex stability and interaction energy communication via Molecular Dynamics (MD), Free Energy calculations, and Protein-energy networks, thus revealing in detail the underlying mechanisms of activation of these receptors. Hydrogen bond formation, interaction energies, and computational alanine scanning between PACAP and its receptors showed that His1, Asp3, Arg12, Arg14, and Lys15 are crucial to the peptide's stability. Furthermore, several PACAP interactions with structurally conserved positions deemed necessary in GPCR B1 activation, including Arg2.60, Lys2.67, and Glu7.42, were significant for the peptide's stability within the receptors. According to the protein-energy network, the connection between Asp3 of PACAP and the receptors' conserved Arg2.60 represents a critical energy communication hub in all complexes. Additionally, the ECDs of the receptors were also found to function as energy communication hubs for PACAP. Although the overall binding mode of PACAP in the three receptors was found to be highly conserved, Arg12 and Tyr13 of PACAP were more prominent in complex with PAC1, while Ser2 of PACAP was with VPAC2. The detailed analyses performed in this work pave the way for using PACAP and its receptors as therapeutic targets.Communicated by Ramaswamy H. Sarma.

Next Generation of Ovarian Cancer Detection Using Aptamers.

Ovarian cancer is among the seven most common types of cancer in women, being the most fatal gynecological tumor, due to the difficulty of detection in early stages. Aptamers are important tools to improve tumor diagnosis through the recognition of specific molecules produced by tumors. Here, aptamers and their potential targets in ovarian cancer cells were analyzed by in silico approaches. Specific aptamers were selected by the Cell-SELEX method using Caov-3 and OvCar-3 cells. The five most frequent aptamers obtained from the last round of selection were computationally modeled. The potential targets for those aptamers in cells were proposed by analyzing proteomic data available for the Caov-3 and OvCar-3 cell lines. Overexpressed proteins for each cell were characterized as to their three-dimensional model, cell location, and electrostatic potential. As a result, four specific aptamers for ovarian tumors were selected: AptaC2, AptaC4, AptaO1, and AptaO2. Potential targets were identified for each aptamer through Molecular Docking, and the best complexes were AptaC2-FXYD3, AptaC4-ALPP, AptaO1-TSPAN15, and AptaO2-TSPAN15. In addition, AptaC2 and AptaO1 could detect different stages and subtypes of ovarian cancer tissue samples. The application of this technology makes it possible to propose new molecular biomarkers for the differential diagnosis of epithelial ovarian cancer.

Relações entre psicologia e pobreza: propostas de atuação decolonial / Relationships between psychology and poverty: decolonial action proposals / Relación entre psicología y pobreza: propuestas de acción descoloniales

O desenvolvimento das desigualdades sociais, raciais e de gênero no Brasil tem suas origens no processo de colonização. Igualmente, a origem eurocêntrica, cientificista e colonial atravessa a Psicologia a partir da colonialidade. Utilizando fundamentos da Psicologia da Libertação e dos estudos decoloniais, tem-se como objetivo analisar a atuação com as comunidades em situação de pobreza como estratégia de decolonização da Psicologia brasileira. Resgatar a memória histórica, potencializar as ações de resistências coletivas interseccionais e enfrentar as desigualdades coloniais são estratégias apontadas para transformar de forma decolonial esse modo de fazer da Psicologia. O profissional deve questionar seus marcadores de privilégio e de opressão baseados em raça, classe, gênero e território. A atuação precisa utilizar metodologias participativas, potencializando as estratégias de resistências históricas das populações negras e indígenas e escolhendo as comunidades em situação de pobreza como campo de ação. (AU)

The development of social, racial and gender inequalities in Brazil has its origins in the colonization process. Likewise, the Eurocentric, scientistic and colonial origin crosses Psychology from coloniality. Using the foundations of Liberation Psychology and decolonial studies, the aim is to analyze the work with communities in poverty as a strategy to decolonize Brazilian Psychology. Rescuing the historical memory, potentiating the actions of collective resistance and facing colonial inequalities are strategies pointed out to transform in a decolonial way this way of doing Psychology. The professional must question his markers of privilege and oppression based on race,class, gender, and territory. The action needs to use participative methodologies, empowering the historical interseccional resistance strategies of the black and indigenous populations and choosing communities in poverty as a field of action. (AU)

El desarrollo de las desigualdades sociales, raciales y de género en Brasil tiene su origen en el proceso de colonización. Asimismo, los orígenes eurocéntricos, cientificistas y coloniales recorren la Psicología desde la colonialidad. Utilizando los fundamentos de la Psicología de la Liberación y de los estudios decoloniales, se pretende analizar el trabajo con comunidades en situación de pobreza como estrategiapara descolonizar la Psicología brasileña. Rescatar la memoria histórica, potenciar las acciones de resistencia colectiva interseccional y enfrentar las desigualdades coloniales son estrategias señaladas para transformar de manera decolonial esta forma dehacer Psicología. Los profesionales deben cuestionar sus marcadores de privilegio y opresión basados en la raza, la clase, el género y el territorio. La acción debe utilizar metodologías participativas, reforzando las estrategias históricas de resistenciade las poblaciones negras e indígenas y eligiendo a las comunidades en situación de pobreza como campo de acción. (AU)

(In)tolerância como política: os discursos de direita e de esquerda no facebook / (In)tolerance as policy: the rightist and leftist discourses on facebook / (In)tolerancia como política: los discursos de la derecha y la izquierda en facebook

Este estudo tem como objetivo analisar traços da mentalidade potencialmente autoritária a partir do discurso de usuários do Facebook vinculados a páginas de cunho político autodeclarado de direita e de esquerda no Brasil. A Netnografia é utilizada como aporte metodológico para imersão on-line nas páginas "Eu era Direita e não sabia" e "Jovens de Esquerda", selecionadas por meio do Facebook Audience Insights, ferramenta disponibilizada pelo Facebook. Delas, foram extraídas oito postagens com maior engajamento (número de comentários, curtidas e compartilhamentos), identificadas pelo Netvizz. Foram coletados 3.489 comentários, os quais foram organizados em um corpus textual submetido ao software IRAMUTEQ e analisados sob a perspectiva da análise crítica imanente da teoria crítica. Como resultado, apresenta-se a forma como o pensamento autoritário se manifesta na racionalização da sociedade contemporânea e nas práticas discursivas em redes sociais on-line, enraizada no âmbito sociopolítico brasileiro, ameaçando o processo democrático e a construção de uma sociedade plural e liberta.(AU)

This study aims to analyze traits of the potentially authoritarian mentality from the speech of Facebook users linked to political pages self-declared as rightist and leftist in Brazil. Netnography is used as a methodological contribution for online immersion in the pages "Eu era Direita e não sabia" and "Jovens de Esquerda" selected via Facebook Audience Insights, a tool provided by Facebook. From these, eight posts with greater engagement (number of comments, likes and shares), identified by Netvizz, were extracted. We collected 3,489 comments, which were organized in a textual corpus submitted to IRAMUTEQ software and analyzed from the perspective of immanent critical analysis of Critical Theory. As a result, we present the way in which authoritarian thinking manifests itself in the rationalization of contemporary society and in discursive practices in online social networks, rooted in the Brazilian socio-political sphere, threatening the democratic process and the construction of a plural and free society.(AU)

Este estudio tiene como objetivo analizar las huellas de la mentalidad potencialmente autoritaria a partir de los discursos de usuarios en Facebook vinculados a páginas políticas autodeclaradas de derecha y de izquierda en Brasil. La netnografía se utiliza como marco metodológico para la inmersión en línea en las páginas "Eu era Direita e não sabia" y "Jovens de Esquerda", seleccionadas por Facebook Audience Insights, herramienta proporcionada por Facebook. Se extrajeron las ocho publicaciones con mayor compromiso (número de comentarios, gustos y compartidas), identificadas por Netvizz. Se recogieron 3.489 comentarios, los cuales fueron organizados en un corpus textual sometido al software IRAMUTEQ y analizado bajo la perspectiva del análisis crítico inmanente de la teoría crítica. Los resultados presentan la forma en que el pensamiento autoritario se manifiesta en la racionalización de la sociedad contemporánea y en prácticas discursivas en redes sociales en línea, arraigada en el ámbito sociopolítico brasileño, que amenazan el proceso democrático y la construcción de una sociedad plural y liberada.(AU)

Transfobia, linchamento virtual e o pensamento antidemocrático no twitter / Transfobia, linchamiento virtual y pensamiento antidemocrático en twitter / Transphobia, virtual lynching and antidemocratic thinking on twitter

Resumo Analisamos um episódio no Twitter de linchamento virtual de um homem trans pela sua participação em campanha publicitária do Dia dos Pais em 2020. Os comentários foram analisados a partir do primado do objeto, fundamentado na Teoria Crítica, nos Estudos sobre a Personalidade Autoritária e em A Dialética do Esclarecimento. Das 461 postagens selecionadas, derivamos 7 categorias: 1. Conservador religioso; 2. Elementos projetivos; 3. Elementos de destrutividade; 4. Preocupação com o sexo; 5. Humor e ironia; 6. Base político-econômica; 7. Defesa da empresa e/ou de Thammy. Pretendemos contribuir científica e criticamente com a compreensão sobre o que fundamenta as relações contemporâneas, em especial no ambiente virtual.

Resumen Analizamos un episodio del linchamiento virtual por su participación en una campaña publicitaria del Día del Padre en 2020. Los comentarios fueron analizados a partir de primacía del objeto, con base en la Teoría Crítica, en los Estudios sobre la Personalidad Autoritaria y en La Dialéctica de la Ilustración. De las 461 publicaciones seleccionadas, derivamos 7 categorías: 1. Conservador religioso; 2. Elementos proyectivos; 3. Elementos de destructividad; 4. Preocupación por el sexo; 5. Humor e ironía; 6. Base político-económica; 7. Defensa de la empresa y/o Thammy. Pretendemos contribuir científicamente y críticamente a la comprensión lo que subyace las relaciones contemporáneas, especialmente en el torno virtual.

Abstract We analyzed an episode on Twitter of the virtual lynching of a trans man for his participation in a Father's Day advertising campaign in 2020. The comments were analyzed based on the primacy of the object, underpinned on Critical Theory, in Studies on the Authoritarian Personality and on The Dialectics of Enlightenment. From the 461 posts, we derived 7 categories: 1 Religious Conservative; 2. Projective elements; 3. Elements of destructiveness; 4. Preoccupation sex; 5. Humor and irony; 6. Political-economic base; 7. Defense of the company and/ or Thammy. We intend to contribute scientifically and critically to the understanding of what underlies contemporary relationships, especially in virtual environment.

RASopathy Cohort of Patients Enrolled in a Brazilian Reference Center for Rare Diseases: A Novel Familial LZTR1 Variant and Recurrent Mutations.

Purpose: Noonan syndrome and related disorders are genetic conditions affecting 1:1000-2000 individuals. Variants causing hyperactivation of the RAS/MAPK pathway lead to phenotypic overlap between syndromes, in addition to an increased risk of pediatric tumors. DNA sequencing methods have been optimized to provide a molecular diagnosis for clinical and genetic heterogeneity conditions. This work aimed to investigate the genetic basis in RASopathy patients through Next Generation Sequencing in a Reference Center for Rare Diseases (IFF/Fiocruz) and implement the precision medicine at a public health institute in Brazil. Patients and Methods: This study comprises 26 cases with clinical suspicion of RASopathies. Sanger sequencing was used to screen variants in exons usually affected in the PTPN11 and HRAS genes for cases with clinical features of Noonan and Costello syndrome, respectively. Posteriorly, negative and new cases with clinical suspicion of RASopathy were analyzed by clinical or whole-exome sequencing. Results: Molecular analysis revealed recurrent variants and a novel LZTR1 missense variant: 24 unrelated individuals with pathogenic variants [PTPN11(11), NF1(2), SOS1(2), SHOC2(2), HRAS(1), BRAF(1), LZTR (1), RAF1(1), KRAS(1), RIT1(1), a patient with co-occurrence of PTPN11 and NF1 mutations (1)]; familial cases carrying a known pathogenic variant in PTPN11 (mother-two children), and a previously undescribed paternally inherited variant in LZTR1. The comparative modeling analysis of the novel LZTR1 variant p.Pro225Leu showed local and global changes in the secondary and tertiary structures, showing a decrease of about 1% in the ß-sheet content. Furthermore, evolutionary conservation indicated that Pro225 is in a highly conserved region, as observed for known dominant pathogenic variants in this protein. Conclusion: Bringing precision medicine through NGS towards congenital syndromes promotes a better understanding of complex clinical and/or undiagnosed cases. The National Policy for Rare Diseases in Brazil emphasizes the importance of incorporating and optimizing diagnostic methodologies in the Unified Brazilian Health System (SUS). Therefore, this work is an important step for the NGS inclusion in diagnostic genetic routine in the public health system.

Differences in Charge Distribution in Leishmania tarentolae Leishmanolysin Result in a Reduced Enzymatic Activity.

Leishmania tarentolae is a non-pathogenic trypanosomatid isolated from lizards widely used for heterologous protein expression and extensively studied to understand the pathogenic mechanisms of leishmaniasis. The repertoire of leishmanolysin genes was reported to be expanded in L. tarentolae genome, but no proteolytic activity was detected. Here, we analyzed L. tarentolae leishmanolysin proteins from the genome to the structural levels and evaluated the enzymatic activity of the wild-type and overexpressing mutants of leishmanolysin. A total of 61 leishmanolysin sequences were retrieved from the L. tarentolae genome. Five of them were selected for phylogenetic analysis, and for three of them, we built 3D models based on the crystallographic structure of L. major ortholog. Molecular dynamics simulations of these models disclosed a less negative electrostatic potential compared to the template. Subsequently, L. major LmjF.10.0460 and L. tarentolae LtaP10.0650 leishmanolysins were cloned in a pLEXSY expression system into L. tarentolae. Proteins from the wild-type and the overexpressing parasites were submitted to enzymatic analysis. Our results revealed that L. tarentolae leishmanolysins harbor a weak enzymatic activity about three times less abundant than L. major leishmanolysin. Our findings strongly suggest that the less negative electrostatic potential of L. tarentolae leishmanolysin can be the reason for the reduced proteolytic activity detected in this parasite.

Bacterial 2'-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study.

The spread of antibiotic-resistant bacteria represents a substantial health threat. Current antibiotics act on a few metabolic pathways, facilitating resistance. Consequently, novel regulatory inhibition mechanisms are necessary. Riboswitches represent promising targets for antibacterial drugs. Purine riboswitches are interesting, since they play essential roles in the genetic regulation of bacterial metabolism. Among these, class I (2'-dG-I) and class II (2'-dG-II) are two different 2'-deoxyguanosine (2'-dG) riboswitches involved in the control of deoxyguanosine metabolism. However, high affinity for nucleosides involves local or distal modifications around the ligand-binding pocket, depending on the class. Therefore, it is crucial to understand these riboswitches' recognition mechanisms as antibiotic targets. In this work, we used a combination of computational biophysics approaches to investigate the structure, dynamics, and energy landscape of both 2'-dG classes bound to the nucleoside ligands, 2'-deoxyguanosine, and riboguanosine. Our results suggest that the stability and increased interactions in the three-way junction of 2'-dG riboswitches were associated with a higher nucleoside ligand affinity. Also, structural changes in the 2'-dG-II aptamers enable enhanced intramolecular communication. Overall, the 2'-dG-II riboswitch might be a promising drug design target due to its ability to recognize both cognate and noncognate ligands.

In silico investigation of riboswitches in fungi: structural and dynamical insights into TPP riboswitches in Aspergillus oryzae.

Riboswitches are RNA sensors affecting post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch plays a crucial role in regulating genes involved in synthesizing or transporting thiamine and phosphorylated derivatives in bacteria, archaea, plants, and fungi. Although TPP riboswitch is reasonably well known in bacteria, there is a gap in the knowledge of the fungal TPP riboswitches structure and dynamics, involving mainly sequence variation and TPP interaction with the aptamers. On the other hand, the increase of fungal infections and antifungal resistance raises the need for new antifungal therapies. In this work, we used computational approaches to build three-dimensional models for the three TPP riboswitches identified in Aspergillus oryzae, in which we studied their structure, dynamics, and binding free energy change (ΔGbind) with TPP. Interaction patterns between the TPP and the surrounding nucleotides were conserved among the three models, evidencing high structural conservation. Furthermore, we show that the TPP riboswitch from the A. oryzae NMT1 gene behaves similarly to the E. coli thiA gene concerning the ΔGbind. In contrast, mutations in the fungal TPP riboswitches from THI4 and the nucleoside transporter genes led to structural differences, affecting the binding-site volume, hydrogen bond occupancy, and ΔGbind. Besides, the number of water molecules surrounding TPP influenced the ΔGbind considerably. Notably, our ΔGbind estimation agreed with previous experimental data, reinforcing the relationship between sequence conservation and TPP interaction.

Psicoterapia on-line e economia do compartilhamento: um estudo de caso do aplicativo FalaFreud / Online psychotherapy and sharing economy: a case study of the FalaFreud application / Psychothérapie en ligne et économie de partage: une étude de cas de l'application FalaFreud / Psicoterapia en línea y economía compartida: un caso de estudio de la aplicación FalaFreud

Resumo Este artigo resulta de estudos empíricos e teóricos sobre a captação da psicologia pelo digital e a lógica de mercado que atravessa a psicoterapia on-line. Nosso objeto de estudo é a plataforma FalaFreud, analisada a partir do aporte teórico-metodológico da Teoria Crítica da Sociedade. Na primeira fase, realizamos uma imersão netnográfica no aplicativo, seu site oficial, blog, e páginas em redes sociais. Na segunda, coletamos avaliações do aplicativo na Play Store de uma e cinco estrelas, e realizamos análises estatísticas e lexicográficas através do software Iramuteq. Os resultados apontaram quatro questões principais: a tecnologia como entrave à terapia, o usuário como entrave ao lucro, a terapia distante do aplicativo e, por fim, a felicidade como obrigação. Sugerimos a diferenciação entre terapia on-line e psicoterapia mediada por computadores, e apontamos a necessidade de discussão dessas questões no contexto da formação em psicologia em conjunto com a compreensão da sociedade mercadológica atual.

Abstract This paper stems from empirical and theoretical research on psychology as captured by the digital environment and the market logic that permeates online psychotherapy. To do so, it analyzes the FalaFreud platform based on Critical Theory. First, a netnographic immersion was carried out in the application, its official website, company blog, and social networks. Then, one- and five-stars reviews were collected from the app on Play Store, and examined by statistical and lexicographic analyzes using the Iramuteq software. The findings pointed to four main issues: technology as a barrier to therapy; the user as a barrier to profit; therapy outside the application; and happiness as an obligation. The text suggests differentiating between online therapy and computer-mediated psychotherapy, and points out the need to discuss these issues within psychology education considering the current consumer society.

Résumé Cet article est issu de recherches empiriques et théoriques sur la psychologie telle qu'elle est saisie par le numérique et la logique du marché qui imprègne la psychothérapie en ligne. Pour ce faire, il analyse la plateforme de thérapie brésilienne FalaFreud à partir de la théorie critique. Tout d'abord, une immersion netnographique a été réalisée dans l'application, son site officiel, son blog et ses réseaux sociaux. Ensuite, des critiques d'une et cinq étoiles ont été collecté sur Play Store, et examinées par des analyses statistiques et lexicographique à l'aide du logiciel Iramuteq. Les résultats ont mis en évidence quatre enjeux principaux : la technologie comme obstacle à la thérapie ; l'usager comme obstacle au profit ; la thérapie en dehors de l'application ; et le bonheur comme obligation. Le texte suggère de faire la distinction entre la thérapie en ligne et la psychothérapie médiatisée par l'ordinateur, et souligne la nécessité de discuter de ces problématiques dans le cadre de la Licence ès Psychologie en tenant compte de la société de consommation actuelle.

Resumen Este artículo es el resultado de estudios empíricos y teóricos sobre el uso de los medios digitales en las prácticas de psicologia y la lógica del mercado que pasa por la psicoterapia en línea. Nuestro objeto es la plataforma FalaFreud, y el aporte teórico-metodológico, la Teoría Crítica de la Sociedad. En la primera fase, realizamos una inmersión netnográfica en la aplicación, su página oficial, blog y páginas en redes sociales. En la segunda fase, recopilamos calificaciones de una y cinco estrellas de la aplicación en Play Store y realizamos análisis estadísticos y lexicográficos utilizando el software Iramuteq. Los resultados señalaron cuatro cuestiones principales: la tecnología como obstáculo para la terapia, el usuario como obstáculo para el lucro, la terapia alejada de la aplicación y, finalmente, la felicidad como obligación. Sugerimos la diferenciación entre la terapia en línea y la psicoterapia mediada por computadora, y señalamos la necesidad de discutir estos temas en el contexto de la formación en psicología, en conjunto con la comprensión de la sociedad de mercado actual.

Revisiting Jatropha curcas Monomeric Esterase: A Dienelactone Hydrolase Compatible with the Electrostatic Catapult Model.

Jatropha curcas contains seeds with a high oil content, suitable for biodiesel production. After oil extraction, the remaining mass can be a rich source of enzymes. However, data from the literature describing physicochemical characteristics for a monomeric esterase from the J. curcas seed did not fit the electrostatic catapult model for esterases/lipases. We decided to reevaluate this J. curcas esterase and extend its characterization to check this apparent discrepancy and gain insights into the enzyme's potential as a biocatalyst. After anion exchange chromatography and two-dimensional gel electrophoresis, we identified the enzyme as belonging to the dienelactone hydrolase family, characterized by a cysteine as the nucleophile in the catalytic triad. The enzyme displayed a basic optimum hydrolysis pH of 9.0 and an acidic pI range, in contrast to literature data, making it well in line with the electrostatic catapult model. Furthermore, the enzyme showed low hydrolysis activity in an organic solvent-containing medium (isopropanol, acetonitrile, and ethanol), which reverted when recovering in an aqueous reaction mixture. This enzyme can be a valuable tool for hydrolysis reactions of short-chain esters, useful for pharmaceutical intermediates synthesis, due to both its high hydrolytic rate in basic pH and its stability in an organic solvent.

Shared Binding Mode of Perrottetinene and Tetrahydrocannabinol Diastereomers inside the CB1 Receptor May Incentivize Novel Medicinal Drug Design: Findings from an in Silico Assay.

In recent years, therapeutic compounds derived from phytocannabinoids have brought renewed attention to the benefits they offer to ameliorate chronic disease symptoms. Among cannabinoids, tetrahydrocannabinol (THC) is a well-known component of the Cannabis plant, whose active principles have been studied through the years. Another psychoactive phytocannabinoid, derived from liverworts Radula, perrottetinene (PET), has created interest, especially as a pharmaceutical product and for its legal recreational use. Unfortunately, so far, the interaction mode of these compounds at the type 1 cannabinoid receptors (CB1R) binding site remains unknown, and no experimental three-dimensional structure in complex with THC or PET is available in the Protein Data Bank. Today, many computational methodologies can assist in this crusade and help unveil how these molecules bind, based on the already known pose of a structurally similar compound. In this work, we aim to elucidate the binding mode of THC and PET molecules in both cis and trans conformers, using a combination of several computational methodologies, including molecular docking, molecular dynamics, free energy calculations, and protein-energy network studies. We found that THC and PET interact similarly with the CB1R, in a different conformation depending on the considered diastereomer. We have observed that cis ligands adopted a half-chair conformation of the cycle ring containing the dimethyl group, assuming an axial or equatorial conformation producing a different induced fitting of the surrounding residues compared with trans ligands, with higher interaction energy than the trans conformer. For PET, we have seen that Trp-279 and Trp-356 have a marked influence on the binding. After binding, Trp-279 accommodates its side chain to better interact with the PET's terminal phenyl group, disturbing CB1R residues communication. The interaction with Trp-356 might impair the activation of CB1R and can influence the binding of PET as a partial agonist. Understanding the PET association with CB1R from a molecular perspective can offer a glimpse of preventing potential toxicological or recreational effects since it is an attractive lead for drug development with fewer side effects than trans-THC.

The rare lncRNA GOLLD is widespread and structurally conserved among Mycobacterium tRNA arrays.

Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from Lactobacillales and Actinomycetales orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of Mycobacterium and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. Mycobacterium GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) Mycobacterium exclusive; (ii) Mycobacterium and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3' half conserved structure, including utter E-loops pseudoknots substructures, also shared by non-Mycobacterium GOLLD while the 5' half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in Mycobacterium within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.

Identification of Novel and Recurrent RMRP Variants in a Series of Brazilian Patients with Cartilage-Hair Hypoplasia: McKusick Syndrome.

Cartilage-hair hypoplasia syndrome (CHH) is an autosomal recessive disorder caused by pathogenic variants of the RMRP gene and characterized by metaphyseal bone dysplasia associated with hypotrichosis, immunodeficiency, and predisposition to malignancy. However, the genotype-phenotype correlation in CHH is not well understood. Here, we report a single country cohort of 23 Brazilian patients with clinical and radiological features consistent with CHH. We found 23 different pathogenic variants in the RMRP gene - 12 novel and 11 previously described in the literature. Interestingly, the most frequent Finnish pathogenic variant related to CHH (g.71A>G) was not found in our cohort. In contrast, more than 50% of the patients carried the rare g.196C>T variant suggesting a possible founder effect in the Brazilian population. In silico analysis showed that pathogenic variants occurred either in the regions conserved in mammalian species or within essential domains for the ribonucleoprotein complex. Pathogenicity prediction studies can improve the understanding of how these variants affect RNA.

Structural insights into NS5B protein of novel equine hepaciviruses and pegiviruses complexed with polymerase inhibitors.

Infections produced by hepaciviruses have been associated with liver disease in horses. Currently, at least three viruses belonging to the Flaviviridae family are capable of producing a chronic infection in equines: non-primate hepacivirus (NPHV), Theiler's disease-associated virus (TDAV), and equine pegivirus (EPgV). The RNA-dependent RNA polymerases of viruses (RdRp) (NS5 protein), from the flavivirus family, use de novo RNA synthesis to initiate synthesis. The two antiviral drugs currently used to treat hepatitis C (HCV), sofosbuvir and dasabuvir, act on the viral NS5B polymerase as nucleoside and non-nucleoside inhibitors, respectively. Both drugs have shown significant clinical inhibition of viral response. In this work, we aimed to model the NS5B polymerase of the equine hepacivirus (EHCV) subtypes 1 and 2, TDAV and EPgV, to assess whether current direct-acting antiviral drugs against HCV interact with these proteins. Crystal structures of HCV-NS5B were used as templates for modeling target sequences in both conformations (open and closed). Also, molecular docking of sofosbuvir and dasabuvir were performed to predict their possible binding modes at the modeled NS5B polymerase binding sites. We observed that the NS5B models of the EHCV and EPgV shared well-conserved 3D structures to HCV-NS5B and other RdRps, suggesting functional conservation. Interactions of EHCV subtypes 1, 2 and TDAV polymerases with sofosbuvir showed a similar molecular interaction pattern compared to HCV-NS5B, while interactions with dasabuvir were less conserved. In silico studies of molecular interactions between these modeled structures and sofosbuvir suggest that this compound could be efficient in combating equine pathogens, thus contributing to animal welfare.

Mycobacterium tuberculosis and M. bovis BCG Moreau Fumarate Reductase Operons Produce Different Polypeptides That May Be Related to Non-canonical Functions.

Tuberculosis is a world widespread disease, caused by Mycobacterium tuberculosis (M.tb). Although considered an obligate aerobe, this organism can resist life-limiting conditions such as microaerophily mainly due to its set of enzymes responsible for energy production and coenzyme restoration under these conditions. One of these enzymes is fumarate reductase, an heterotetrameric complex composed of a catalytic (FrdA), an iron-sulfur cluster (FrdB) and two transmembrane (FrdC and FrdD) subunits involved in anaerobic respiration and important for the maintenance of membrane potential. In this work, aiming to further characterize this enzyme function in mycobacteria, we analyzed the expression of FrdB-containing proteins in M.tb and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) Moreau, the Brazilian vaccine strain against tuberculosis. We identified three isoforms in both mycobacteria, two of them corresponding to the predicted encoded polypeptides of M.tb (27 kDa) and BCG Moreau (40 kDa) frd sequences, as due to an insertion on the latter's operon a fused FrdBC protein is expected. The third 52 kDa band can be explained by a transcriptional slippage event, typically occurring when mutation arises in a repetitive region within a coding sequence, thought to reduce its impact allowing the production of both native and variant forms. Comparative modeling of the M.tb and BCG Moreau predicted protein complexes allowed the detection of subtle overall differences, showing a high degree of structure and maybe functional resemblance among them. Axenic growth and macrophage infection assays show that the frd locus is important for proper bacterial development in both scenarios, and that both M.tb's and BCG Moreau's alleles can partially revert the hampered phenotype of the knockout strain. Altogether, our results show that the frdABCD operon of Mycobacteria may have evolved to possess other yet non-described functions, such as those necessary during aerobic logarithmic growth and early stage steps of infection.

Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior.

The Trypanosoma cruzi ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas' disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11+‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102+), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102+, and exclusive suboptimal paths for His11+‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further in silico drug discovery studies. Communicated by Ramaswamy H. Sarma.

Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease.

Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.