VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation.

Throughout evolution, pathogenic viruses have developed different strategies to evade the response of the adaptive immune system. To carry out successful replication, some pathogenic viruses encode different proteins that manipulate the molecular mechanisms of host cells. Currently, there are different bioinformatics tools for virus research; however, none of them focus on predicting viral proteins that evade the adaptive system. In this work, we have developed a novel tool based on machine and deep learning for predicting this type of viral protein named VirusHound-I. This tool is based on a model developed with the multilayer perceptron algorithm using the dipeptide composition molecular descriptor. In this study, we have also demonstrated the robustness of our strategy for data augmentation of the positive dataset based on generative antagonistic networks. During the 10-fold cross-validation step in the training dataset, the predictive model showed 0.947 accuracy, 0.994 precision, 0.943 F1 score, 0.995 specificity, 0.896 sensitivity, 0.894 kappa, 0.898 Matthew's correlation coefficient and 0.989 AUC. On the other hand, during the testing step, the model showed 0.964 accuracy, 1.0 precision, 0.967 F1 score, 1.0 specificity, 0.936 sensitivity, 0.929 kappa, 0.931 Matthew's correlation coefficient and 1.0 AUC. Taking this model into account, we have developed a tool called VirusHound-I that makes it possible to predict viral proteins that evade the host's adaptive immune system. We believe that VirusHound-I can be very useful in accelerating studies on the molecular mechanisms of evasion of pathogenic viruses, as well as in the discovery of therapeutic targets.

Enzyme Engineering Strategies for the Bioenhancement of L-Asparaginase Used as a Biopharmaceutical.

Over the past few years, there has been a surge in the industrial production of recombinant enzymes from microorganisms due to their catalytic characteristics being highly efficient, selective, and biocompatible. L-asparaginase (L-ASNase) is an enzyme belonging to the class of amidohydrolases that catalyzes the hydrolysis of L-asparagine into L-aspartic acid and ammonia. It has been widely investigated as a biologic agent for its antineoplastic properties in treating acute lymphoblastic leukemia. The demand for L-ASNase is mainly met by the production of recombinant type II L-ASNase from Escherichia coli and Erwinia chrysanthemi. However, the presence of immunogenic proteins in L-ASNase sourced from prokaryotes has been known to result in adverse reactions in patients undergoing treatment. As a result, efforts are being made to explore strategies that can help mitigate the immunogenicity of the drug. This review gives an overview of recent biotechnological breakthroughs in enzyme engineering techniques and technologies used to improve anti-leukemic L-ASNase, taking into account the pharmacological importance of L-ASNase.

Current state of molecular and metabolic strategies for the improvement of L-asparaginase expression in heterologous systems.

Heterologous expression of L-asparaginase (L-ASNase) has become an important area of research due to its clinical and food industry applications. This review provides a comprehensive overview of the molecular and metabolic strategies that can be used to optimize the expression of L-ASNase in heterologous systems. This article describes various approaches that have been employed to increase enzyme production, including the use of molecular tools, strain engineering, and in silico optimization. The review article highlights the critical role that rational design plays in achieving successful heterologous expression and underscores the challenges of large-scale production of L-ASNase, such as inadequate protein folding and the metabolic burden on host cells. Improved gene expression is shown to be achievable through the optimization of codon usage, synthetic promoters, transcription and translation regulation, and host strain improvement, among others. Additionally, this review provides a deep understanding of the enzymatic properties of L-ASNase and how this knowledge has been employed to enhance its properties and production. Finally, future trends in L-ASNase production, including the integration of CRISPR and machine learning tools are discussed. This work serves as a valuable resource for researchers looking to design effective heterologous expression systems for L-ASNase production as well as for enzymes production in general.

Helicobacter pyloril-asparaginase: a study of immunogenicity from an in silico approach.

Helicobacter pylori has become the causal agent of multiple forms of gastric disease worldwide, including gastric cancer. The enzyme l-asparaginase (ASNase) has been studied as a virulence factor. In this work, we performed an in silico investigation to characterize the immunological profile of H. pylori ASNase (HpASNase) to ascertain the possible implication of HpASNase immunogenicity in the H. pylori virulence mechanism. We applied a workflow based on bioinformatics tools, which, by calculating the relative frequency of immunogenic T-cell and B-cell epitopes, allowed us to predict the immunogenicity and allergenicity of HpASNase in silico. We also visualized the epitopes by mapping them into the native structure of the enzyme. We report for the first time the T-cell and B-cell epitope composition that contributes to the immunogenicity of this HpASNase, as well as the regions that could generate a hypersensitivity response in humans. ASNase from H. pylori resulted in highly immunogenic and allergenic. The high immunogenicity of HpASNase could imply the pathogenic mechanisms of H. pylori. This knowledge could be important for the development of new drugs against H. pylori infections. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03359-0.

Recent advances in the design of antimicrobial peptide conjugates.

Antimicrobial peptides (AMPs) are ubiquitous host defense peptides characterized by their antibiotic activity and lower propensity for developing resistance compared to classic antibiotics. While several AMPs have shown activity against antibiotic-sensitive and even multi-drug resistant strains, some bottlenecks to further development and clinical applications are still present, for instance, low antimicrobial activity, instability under physiological conditions, systemic toxicity and the potential for compromising the innate host defense immunity. Conjugation to molecules such as proteins, synthetic polymers, small molecules and nanoparticles are strategies under investigation to boost the therapeutic efficacy of AMPs. This review focuses on the design and application of AMPs' conjugates. In silico tools for creating new AMPs and AMPs' conjugates and their clinical development are also discussed. Furthermore, key future considerations regarding the major achievements and challenges of AMPs' conjugates in the antimicrobial resistance context are presented as a take-home message.

A bioinformatics analysis of the CatSper channel in the class Actinopterygii.

The regulation of sperm motility is controlled by several variables, including mainly ion concentrations. In fish, Ca2+ concentrations play an important role in the regulation of sperm motility, and several reports highlight the importance of certain Ca2+ channels in the regulation of this cell function. CatSper is a calcium channel scarcely studied in fish. In the species Salmo salar, it has been shown that it is key in the regulation of sperm motility. Taking into account the relevance of this channel in sperm activation in fish, in this study we evaluated the presence and probable functionality of this channel in the class Actinopterygii. For this purpose, a rational bioinformatic analysis was carried out, which had been previously validated using in vitro techniques by our group. The bioinformatic analysis of the present work revealed that the functionality of CatSper of the species of the class Actinopterygii could be exclusive to freshwater and anadromous fish species. The results of this study showed that only some anadromous and freshwater fish species contain 11 subunits of the CatSper channel, which are enough to trigger sperm motility. Consequently, this study provides new data for a better understanding of the sperm activation mechanism in fish.

Glycyrrhiza Genus: Enlightening Phytochemical Components for Pharmacological and Health-Promoting Abilities.

The Glycyrrhiza genus, generally well-known as licorice, is broadly used for food and medicinal purposes around the globe. The genus encompasses a rich pool of bioactive molecules including triterpene saponins (e.g., glycyrrhizin) and flavonoids (e.g., liquiritigenin, liquiritin). This genus is being increasingly exploited for its biological effects such as antioxidant, antibacterial, antifungal, anti-inflammatory, antiproliferative, and cytotoxic activities. The species Glycyrrhiza glabra L. and the compound glycyrrhizin (glycyrrhizic acid) have been studied immensely for their effect on humans. The efficacy of the compound has been reported to be significantly higher on viral hepatitis and immune deficiency syndrome. This review provides up-to-date data on the most widely investigated Glycyrrhiza species for food and medicinal purposes, with special emphasis on secondary metabolites' composition and bioactive effects.

The voltage-gated T-type Ca2+ channel is key to the sperm motility of Atlantic salmon (Salmo salar).

Ca2+ is a key element in the sperm activation process of Salmo salar. However, the molecular mechanisms by which this ion enters the sperm cell have been poorly studied. In this study, we examined, for the first time, the role of the voltage-gated T-type Ca2+ channel in the activation of sperm motility of Salmo salar. Using an in vitro inhibition assay, a significant decrease in total and progressive motility (P < 0.0001) was observed in Salmo salar sperm when they were treated with NNC-55-0396, a highly selective blocker. The in silico analysis showed that this blocker is docked with a strong affinity for the pore of the voltage-gated T-type calcium channel suggesting the blocking of Ca2+ ions. The results show that the T-type voltage-gated Ca2+ channel is key to sperm motility in Salmo salar.

PPLK+C: A Bioinformatics Tool for Predicting Peptide Ligands of Potassium Channels Based on Primary Structure Information.

Potassium channels play a key role in regulating the flow of ions through the plasma membrane, orchestrating many cellular processes including cell volume regulation, hormone secretion and electrical impulse formation. Ligand peptides of potassium channels are molecules used in basic and applied research and are now considered promising alternatives in the treatment of many diseases, such as cardiovascular diseases and cancer. Currently, there are various bioinformatics tools focused on the prediction of peptides with different activities. However, none of the current tools can predict ligand peptides of potassium channels. In this work, we developed a tool called PPLK+C; this is the first tool that can predict peptide ligands of potassium channels. We also evaluated several amino acid molecular features and four machine-learning algorithms for the prediction of potassium channel ligand peptides: random forest, nearest neighbors, support vector machine and artificial neural network. All the biological data used in this study for training and validating models were obtained from peptides with experimentally verified activity. PPLK+C is a bioinformatics software written in the Python programming language, which showed a high predictive capacity with a model generated with the random forest algorithm: 0.77 sensitivity, 0.94 specificity, 0.91 accuracy and 0.70 Matthews correlation coefficient. PPLK+C is a novel tool with a friendly interface that can be used for the discovery of novel ligand peptides of potassium channels with high reliability, using only primary structure information.

Role of voltage-gated L-type calcium channel in the spermatozoa motility of Atlantic salmon (Salmo salar).

Ca2+ cations play a key role in the initiation of spermatozoa motility in Atlantic salmon (Salmo salar). In this study we assess the importance of the voltage-gated L-type calcium channels in the spermatozoa motility of Atlantic salmon by combined in vitro and in silico approaches. The results of this study showed that as in other fish species, voltage-gated L-type calcium channels are significant in the spermatozoa motility of Salmo salar. The in vitro assays showed that total and progressive motilities decrease significantly (****p < .001) when Salmo salar spermatozoa are treated with verapamil, which has its binding site in the pore of the voltage-gated L-type calcium channel according to the in silico analysis.

A structural in silico analysis of the immunogenicity of l-asparaginase from Escherichia coli and Erwinia carotovora.

Acute lymphoblastic leukemia (ALL) is a type of cancer with a high incidence in children. The enzyme l-asparaginase (ASNase) constitutes a key element in the treatment of this disease. Four formulations of ASNase from a bacterial source are currently available. However, these formulations are characterized by their high immunogenicity, resulting in the inactivation of the drug, as well as in the occurrence of hypersensitivity reactions in a large number of patients. In this work, we performed an immunoinformatic analysis in order to clarify structural aspects of the immunogenicity of the asparaginase from Escherichia coli and Erwinia carotovora. For this purpose, we performed the prediction of immunogenic and allergenic epitopes in the structure of asparaginases by using the relative frequency of immunogenic peptides for the eight alleles most frequently distributed worldwide. This study showed that there are no significant differences in the level of immunogenicity between the two enzymes, while asparaginase from E. coli presented a higher relative frequency of allergenic epitopes. These results are consistent with previously published reports. However, from a structural point of view, to the best of our knowledge, this is the first report describing the structural determinants that contribute to the hypersensitivity response to this treatment.

AntiVPP 1.0: A portable tool for prediction of antiviral peptides.

Viruses are worldwide pathogens with a high impact on the human population. Despite the constant efforts to fight viral infections, there is a need to discover and design new drug candidates. Antiviral peptides are molecules with confirmed activity and constitute excellent alternatives for the treatment of viral infections. In the present study, we developed AntiVPP 1.0, an accurate bioinformatic tool that uses the Random Forest algorithm for antiviral peptide predictions. The model of AntiVPP 1.0 for antiviral peptide predictions uses several features of 1088 peptides for training and validation. During the validation of the model we achieved the TPR = 0.87, SPC = 0.97, ACC = 0.93 and MCC = 0.87 performance measures, which were indicative of a robust model. AntiVPP 1.0 is a fast, accurate and intuitive software focused on the assessment of antiviral peptides candidates. AntiVPP 1.0 is available at https://github.com/bio-coding/AntiVPP.

From Synthesis to Characterization of Site-Selective PEGylated Proteins.

Covalent attachment of therapeutic proteins to polyethylene glycol (PEG) is widely used for the improvement of its pharmacokinetic and pharmacological properties, as well as the reduction in reactogenicity and related side effects. This technique named PEGylation has been successfully employed in several approved drugs to treat various diseases, even cancer. Some methods have been developed to obtain PEGylated proteins, both in multiple protein sites or in a selected amino acid residue. This review focuses mainly on traditional and novel examples of chemical and enzymatic methods for site-selective PEGylation, emphasizing in N-terminal PEGylation, that make it possible to obtain products with a high degree of homogeneity and preserve bioactivity. In addition, the main assay methods that can be applied for the characterization of PEGylated molecules in complex biological samples are also summarized in this paper.