Biology subjects

Amaral, M. S.

Publications and source records attributed to Amaral, M. S..

7 recordsLinked to original sources

bioRxiv2025

Pre-clinical studies of Schistosoma mansoni vaccines: a scoping review

BackgroundSchistosomiasis is caused by infection with worms of the genus Schistosoma including S. mansoni. Over 200 million people are infected, sterile immunity does not naturally develop, and no vaccine is available. A vaccine could be a critical tool to achieve control and elimination. Numerous candidates have been tested in pre-clinical models, but there is not yet an approved vaccine. Methodology/Principal FindingsWe conducted a scoping review using a keyword search on Web of Science and a MeSH term search on PubMed. Articles were screened and included if they tested a defined vaccine candidate in a pre-clinical protection assay against S. mansoni between 1994-2024. Vaccine formulation, study design, and efficacy parameters from all articles were extracted. This data was summarised graphically, with the influence of different parameters appraised. A total of 141 candidate antigens were tested in 108 articles over the last 30 years, with most antigens tested only once and three (Sm-CatB, Sm-p80, and Sm-14) tested over 20 times. The median protective efficacy against worms was 35%. 10 antigens achieved over 60% efficacy, and only two (Sm-p80 and Sm-CatB) over 90%. Large variations in efficacy were observed with all repeatedly tested antigens, likely attributable to differing formulations and study designs. The effect of these varying parameters on the resultant efficacy was evaluated. ConclusionsA few vaccine candidates have achieved promising efficacy in pre-clinical studies. Most vaccines tested however have efficacy that falls short of that required for an impactful schistosomiasis vaccine. The diversity in study designs makes comparing vaccine targets a challenge. Use of consistent and optimized vaccine formulation (including adjuvant and platform) and study design parameters is critical to expedite the development of a schistosome vaccine. Author SummarySchistosomiasis, a major neglected tropical disease, is caused by infection with parasitic worms of the Schistosoma species, including Schistosoma mansoni. Individuals can be repeatedly re-infected, and there is no available vaccine. An initial stage of vaccine development is testing in a pre-clinical animal model. Here we have summarised tests of Schistosoma mansoni vaccines in the last three decades. 100+ vaccine candidates have been tested, with only 10 of these achieving efficacy of over 60%, and only 2 at over 90%. When the same vaccine candidate (antigen) is tested in a different formulation, or using different study design the efficacy varies greatly. We have summarised the formulations and study designs used, and highlighted how certain parameters affect efficacy. Finally, we have assembled a series of recommendations to researchers on how to perform vaccine tests in the future.

immunology↗

bioRxiv2023

The human developing cerebral cortex is characterized by an increased de novo expression of lncRNAs in excitatory neurons

BackgroundOutstanding human cognitive abilities are computed in the cerebral cortex, a mammalian-specific brain region and the place of massive biological innovation. Long noncoding RNAs (lncRNAs) have emerged as gene regulatory elements with higher evolutionary turnover than mRNAs. The many lncRNAs identified in neural tissues make them candidates for molecular sources of cerebral cortex evolution and disease. Here, we characterized the genomic and cellular shifts that occurred during the evolution of the lncRNA repertoire expressed in the developing cerebral cortex of humans and explored their role in the evolution of this brain region. ResultsUsing systems biology approaches and comparative transcriptomics, we comprehensively annotated the cortical transcriptomes of humans, macaques, mice, and chickens and classified human cortical lncRNAs into evolutionary groups as a function of their predicted minimal ages. LncRNA evolutionary groups showed differences in expression levels, splicing efficiencies, transposable element contents, genomic distributions, and transcription factor binding to their promoters. Furthermore, older lncRNAs showed preferential expression in germinative zones, outer radial glial cells, and cortical inhibitory neurons. In comparison, younger lncRNAs showed preferential expression in cortical excitatory neurons, belonged to human-specific gene coexpression modules, and were dysregulated in autism spectrum disorder. ConclusionsThese results suggest a shift in the roles of cortical lncRNAs over evolution, highlighting the antique lncRNAs as a source of molecular evolution of conserved developmental programs; conversely, the de novo expression of primate and human-specific lncRNAs are sources of molecular evolution and dysfunction of cortical excitatory neurons.

evolutionary biology↗

bioRxiv2021

Design of D-amino acids SARS-CoV-2 Main protease inhibitors using the cationic peptide from rattlesnake venom as a scaffold

The C30 Endopeptidase (3C-like protease; 3CLpro) is essential for the life cycle of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) since it plays a pivotal role in viral replication and transcription and is hence a promising drug target. Molecules isolated from animals, insects, plants or microorganisms can serve as a scaffold for the design of novel biopharmaceutical products. Crotamine, a small cationic peptide from the venom of the rattlesnake Crotalus durissus terrificus has been the focus of many studies since it exhibits activities such as analgesic, in vitro antibacterial and hemolytic activities. The crotamine derivative L-peptides (L-CDP) that inhibit the 3CL protease in the low {micro}M range were examined since they are susceptible to proteolytic degradation; we explored the utility of their D-enantiomers form. Comparative uptake inhibition analysis showed D-CDP as a promising prototype for a D-peptide-based drug. We also found that the D-peptides can impair SARS-CoV-2 replication in vivo, probably targeting the viral protease 3CLpro.

biochemistry↗

bioRxiv2020

In silico investigation of Aedes aegypti male-determining factor (NIX): RNA recognition motif-3, structural model and selective nucleic acid binding mode.

Mosquito borne viruses and their corresponding human infections have a fast growing impact on worldwide public health systems; in particular, Aedes aegypti and Aedes albopictus are transmitting these viruses. Only female mosquitoes bite and spread diseases. Male development in A. aegypti is initiated by male determining factors. These factors are potential candidates for the implementation of vector control strategies. Where at an early stage in gender development female mosquitoes are converted into harmless males. Among these factors, a novel gene, NIX, has been identified that shares moderate identity with transformer-2, one of the key sex-determination genes in Drosophila melanogaster. Hall et al. 2015 described two RNA recognition motifs (RRMs) in the NIX sequence, but a UniProt database search showed that A. aegypti NIX contains three RNA RRM. A homology model of NIX_RRM-3 was generated to investigate the interaction with RNA using molecular dynamics simulations. The sequence AGACGU was the most interesting result. During the binding process A1, G2 and G5 adopt an unusual syn conformation. The results let assume that the C-terminus of NIX_RRM-3 is involved in the recognition process of the target RNA motif (e.g. AG) and controls the interaction between target RNA and A. aegypti NIX.

bioinformatics↗

bioRxiv2020

The repurposed drugs suramin and quinacrine inhibit cooperatively in vitro SARS-CoV-2 3CLpro

Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) up to now WHO reported more than 50 million confirmed cases and more than one million losses, globally. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide resulting in a pandemic of unprecedented magnitude. To date, no clinically safe drug or vaccine is available and the development of molecules to combat SARS-CoV-2 infections is imminent. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is the repurposing of clinically developed drugs, e.g., anti-parasitic drugs. The results described in this study demonstrate the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules present a competitive and non-competitive mode of inhibition, respectively, with IC50 and KD values in low M range. Using docking and molecular dynamics simulations we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin in combination with quinacrine showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. The identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease. Drug repositioning offers hope to the SARS-CoV-2 control.

biochemistry↗

bioRxiv2019

Differential gene expression elicited by ZIKV infection in trophoblasts from congenital Zika syndrome discordant twins

Zika virus (ZIKV) causes congenital Zika syndrome (CZS), which is characterized by fetal demise, microcephaly and other abnormalities. ZIKV in the pregnant woman circulation must cross the placental barrier that includes fetal endothelial cells and trophoblasts, in order to reach the fetus. CZS occurs in [~]1-40% of cases of pregnant women infected by ZIKV, suggesting that mothers infection by ZIKV during pregnancy is not deterministic for CZS phenotype in the fetus. Therefore, other susceptibility factors might be involved, including the host genetic background. We have previously shown that in three pairs of dizygotic twins discordant for CZS, neural progenitor cells (NPCs) from the CZS-affected twins presented differential in vitro ZIKV susceptibility compared with NPCs from the non-affected. Here, we analyzed human-induced-pluripotent-stem-cell-derived (hiPSC-derived) trophoblasts from these twins and compared by RNA-Seq the trophoblasts from CZS-affected and non-affected twins. Following in vitro exposure to a Brazilian ZIKV strain (ZIKVBR), trophoblasts from CZS-affected twins were significantly more susceptible to ZIKVBR infection when compared with trophoblasts from the non-affected. Transcriptome profiling revealed no differences in gene expression levels of ZIKV candidate attachment factors, IFN receptors and IFN in the trophoblasts, either before or after ZIKVBR infection. Most importantly, ZIKVBR infection caused, only in the trophoblasts from CZS-affected twins, the downregulation of genes related to extracellular matrix organization and to leukocyte activation, which are important for trophoblast adhesion and immune response activation. In addition, only trophoblasts from non-affected twins secreted significantly increased amounts of chemokines RANTES/CCL5 and IP10 after infection with ZIKVBR. Overall, our results showed that trophoblasts from non-affected twins have the ability to more efficiently activate genes that are known to play important roles in cell adhesion and in triggering the immune response to ZIKV infection in the placenta, and this may contribute to predict protection from ZIKV dissemination into fetuses tissues. Author summaryThe Zika virus (ZIKV) infection in adults is usually characterized by mild flu-like symptoms, with most cases remaining asymptomatic. However, in the last years, widespread ZIKV infection was shown for the first time to be associated with congenital Zika syndrome (CZS) and death of neonates. CZS is a very debilitating condition that includes microcephaly and mental retardation, leading to a strong social and health impact. This dramatic condition calls for a careful evaluation of the molecular mechanisms involved in ZIKV infection in the maternal-fetal interface. It is estimated that CZS occurs in [~]1-40% of cases of pregnant women infected by ZIKV, which suggests that different susceptibility factors might be involved, including the host genetic background. By analyzing trophoblast cells that recapitulate the placenta from three pairs of dizygotic twins discordant for CZS, we were able to show that trophoblasts from CZS-affected twins were significantly more susceptible to ZIKV infection when compared with trophoblasts from the non-affected twins. We also provide a detailed picture of genes differentially expressed by trophoblasts from the discordant twins after infection with ZIKV. These genes can be further investigated as possible therapeutic targets to avoid viral dissemination into developing fetus tissues.

microbiology↗

bioRxiv2019

Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni

Treatment and control of schistosomiasis still rely on only one effective drug, praziquantel (PZQ), and due to mass treatment, the increasing risk of selecting for schistosome strains that are resistant to PZQ has alerted investigators to the urgent need to develop novel therapeutic strategies. The histone-modifying enzymes (HMEs) represent promising targets for the development of epigenetic drugs against Schistosoma mansoni. In the present study, we targeted the S. mansoni lysine-specific demethylase 1 (SmLSD1), a transcriptional corepressor, using a novel and selective synthetic inhibitor, MC3935. We synthesized a novel and potent LSD1 inhibitor, MC3935, which was used to treat schistosomula or adult worms in vitro. By using cell viability assays and optical and electron microscopy, we showed that treatment with MC3935 affected parasite motility, egg-laying, tegument, and cellular organelle structures, culminating in the death of schistosomula and adult worms. In silico molecular modeling and docking analysis suggested that MC3935 binds to the catalytic pocket of SmLSD1. Western blot analysis revealed that MC3935 inhibited SmLSD1 demethylation activity of H3K4me1/2. Knockdown of SmLSD1 by RNAi recapitulated MC3935 phenotypes in adult worms. RNA-seq analysis of MC3935-treated parasites revealed significant differences in gene expression related to critical biological processes. Collectively, our findings show that SmLSD1 is a promising drug target for the treatment of schistosomiasis and strongly support the further development and in vivo testing of selective schistosome LSD1 inhibitors. Author SummarySchistosomiasis mansoni is a chronic and debilitating tropical disease caused by the helminth Schistosoma mansoni. The control and treatment of the disease rely almost exclusively on praziquantel (PZQ). Thus, there is an urgent need to search for promising protein targets to develop new drugs. Drugs that inhibit enzymes that modify the chromatin structure have been developed for a number of diseases. We and others have shown that S. mansoni epigenetic enzymes are also potential therapeutic targets. Here we evaluated the potential of the S. mansoni histone demethylase LSD1 (SmLSD1) as a drug target. We reported the synthesis of a novel and potent LSD1 inhibitor, MC3935, and show that it selectively inhibited the enzymatic activity of SmLSD1. Treatment of juvenile or adult worms with MC3935 caused severe damage to the tegument of the parasites and compromised egg production. Importantly, MC3935 proved to be highly toxic to S. mansoni, culminating in the death of juvenile or adult worms within 96 h. Transcriptomic analysis of MC3935-treated parasites revealed changes in the gene expression of hundreds of genes involved in key biological processes. Importantly, SmLSD1 contains unique sequences within its polypeptide chain that could be explored to develop a S. mansoni selective drug.

molecular biology↗