Multi-and many-objective optimization: present and future in de novo drug design.

de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field.

Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants.

The COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. At present, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein, and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations to identify possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br .

SISS-Geo: Leveraging Citizen Science to Monitor Wildlife Health Risks in Brazil.

The well-being of human and wildlife health involves many challenges, such as monitoring the movement of pathogens; expanding health surveillance; collecting data and extracting information to identify and predict risks; integrating specialists from different areas to handle data, species and distinct social and environmental contexts; and the commitment to bringing relevant information to society. In Brazil, there is still the difficulty of building a system that is not impaired by its large territorial extension and its poorly integrated sectoral policies. The Brazilian Wildlife Health Information System, SISS-Geo (SISS-Geo is the abbreviation of "Sistema de Informação em Saúde Silvestre Georreferenciado" (which translates to "Georeferenced Wildlife Health Information System") and can be accessed at http://www.biodiversidade.ciss.fiocruz.br or http://sissgeo.lncc.br (in Portuguese)), is a platform for collaborative monitoring that intends to overcome the challenges in wildlife health. It aims at the integration and participation of various segments of society, encompassing the registration of animals occurrences by citizen scientists; the reliable diagnosis of pathogens from the laboratory and expert networks; and computational and mathematical challenges in analytical and predictive systems, model interpretation, data integration and visualization, and geographic information systems. It has been successfully applied to support decision-making on recent wildlife health events, such as a Yellow Fever epizootic.

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments.

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process.

Multiobjective grammar-based genetic programming applied to the study of asthma and allergy epidemiology.

BACKGROUND: Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tools such as genetic programming could be important for the understanding the causal mechanisms explaining those conditions. Here, we applied a multiobjective grammar-based genetic programming (MGGP) to a dataset composed by 1047 subjects. The dataset contains information on the environmental, psychosocial, socioeconomics, nutritional and infectious factors collected from participating children. The objective of this work is to generate models that explain the occurrence of asthma, and two markers of allergy: presence of IgE antibody against common allergens, and skin prick test positivity for common allergens (SPT). RESULTS: The average of the accuracies of the models for asthma higher in MGGP than C4.5. IgE were higher in MGGP than in both, logistic regression and C4.5. MGGP had levels of accuracy similar to RF, but unlike RF, MGGP was able to generate models that were easy to interpret. CONCLUSIONS: MGGP has shown that infections, psychosocial, nutritional, hygiene, and socioeconomic factors may be related in such an intricate way, that could be hardly detected using traditional regression based epidemiological techniques. The algorithm MGGP was implemented in c ++ and is available on repository: http://bitbucket.org/ciml-ufjf/ciml-lib .

NICeSim: an open-source simulator based on machine learning techniques to support medical research on prenatal and perinatal care decision making.

OBJECTIVE: This paper describes NICeSim, an open-source simulator that uses machine learning (ML) techniques to aid health professionals to better understand the treatment and prognosis of premature newborns. METHODS: The application was developed and tested using data collected in a Brazilian hospital. The available data were used to feed an ML pipeline that was designed to create a simulator capable of predicting the outcome (death probability) for newborns admitted to neonatal intensive care units. However, unlike previous scoring systems, our computational tool is not intended to be used at the patients bedside, although it is possible. Our primary goal is to deliver a computational system to aid medical research in understanding the correlation of key variables with the studied outcome so that new standards can be established for future clinical decisions. In the implemented simulation environment, the values of key attributes can be changed using a user-friendly interface, where the impact of each change on the outcome is immediately reported, allowing a quantitative analysis, in addition to a qualitative investigation, and delivering a totally interactive computational tool that facilitates hypothesis construction and testing. RESULTS: Our statistical experiments showed that the resulting model for death prediction could achieve an accuracy of 86.7% and an area under the receiver operating characteristic curve of 0.84 for the positive class. Using this model, three physicians and a neonatal nutritionist performed simulations with key variables correlated with chance of death. The results indicated important tendencies for the effect of each variable and the combination of variables on prognosis. We could also observe values of gestational age and birth weight for which a low Apgar score and the occurrence of respiratory distress syndrome (RDS) could be less or more severe. For instance, we have noticed that for a newborn with 2000 g or more the occurrence of RDS is far less problematic than for neonates weighing less. CONCLUSIONS: The significant accuracy demonstrated by our predictive model shows that NICeSim might be used for hypothesis testing to minimize in vivo experiments. We observed that the model delivers predictions that are in very good agreement with the literature, demonstrating that NICeSim might be an important tool for supporting decision making in medical practice. Other very important characteristics of NICeSim are its flexibility and dynamism. NICeSim is flexible because it allows the inclusion and deletion of variables according to the requirements of a particular study. It is also dynamic because it trains a just-in-time model. Therefore, the system is improved as data from new patients become available. Finally, NICeSim can be extended in a cooperative manner because it is an open-source system.

A genetic algorithm for the ligand-protein docking problem

We analyzed the performance of a real coded "steady-state" genetic algorithm (SSGA) using a grid-based methodology in docking five HIV-1 protease-ligand complexes having known three-dimensional structures. All ligands tested are highly flexible, having more than 10 conformational degrees of freedom. The SSGA was tested for the rigid and flexible ligand docking cases. The implemented genetic algorithm was able to dock successfully rigid and flexible ligand molecules, but with a decreasing performance when the number of ligand conformational degrees of freedom increased. The docked lowest-energy structures have root mean square deviation (RMSD) with respect to the corresponding experimental crystallographic structure ranging from 0.037 Å to 0.090 Å in the rigid docking, and 0.420 Å to 1.943 Å in the flexible docking. We found that not only the number of ligand conformational degrees of freedom is an important aspect to the algorithm performance, but also that the more internal dihedral angles are critical. Furthermore, our results showed that the initial population distribution can be relevant for the algorithm performance.

Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm

An approach to the hydrophobic-polar (HP) protein folding model was developed using a genetic algorithm (GA) to find the optimal structures on a 3D cubic lattice. A modification was introduced to the scoring system of the original model to improve the model's capacity to generate more natural-like structures. The modification was based on the assumption that it may be preferable for a hydrophobic monomer to have a polar neighbor than to be in direct contact with the polar solvent. The compactness and the segregation criteria were used to compare structures created by the original HP model and by the modified one. An islands' algorithm, a new selection scheme and multiple-points crossover were used to improve the performance of the algorithm. Ten sequences, seven with length 27 and three with length 64 were analyzed. Our results suggest that the modified model has a greater tendency to form globular structures. This might be preferable, since the original HP model does not take into account the positioning of long polar segments. The algorithm was implemented in the form of a program with a graphical user interface that might have a didactical potential in the study of GA and on the understanding of hydrophobic core formation.

A importância do diagnóstico da cisticercose bovina / The importance of bovine cysticercosis diagnostic

A cisticercose bovina é uma enfermidade cosmopolita, que afeta principalmente as regiöes cuja populaçäo apresenta baixas condiçöes sócio-econômicas. No Brasil, a prevalência dessa zoonose, é obtida através de dados fornecidos pelos serviços de inspeçäo, em matadouros. Várias pesquisas indicam a baixa sensibilidade da inspeçäo "post-mortem", associando-se a isso a incapacidade dos métodos parasitológicos de demonstrarem a presença desse parasita nos bovinos; torna-se necessário o desenvolvimento de métodos de diagnóstico mais eficazes e seguros que possam ser realizados no animal antes do abate.

Ethyl methanesulfonate-induce mutations in Phaseoulus vulgaris L.

Os alcalóides furoquinoleínico esquimianina e benzofenantridínico celeritrina, extraídos de uma espécie da família Rutaceae foram testados quanto ao aspecto tóxico-genético através do cromoteste-SOS. Nos testes realizados na ausência de metabolizaçäo, ambos alcalóides näo mostraram atividade genotóxica, sendo que a esquimianina apresentou um efeito citotóxico nas concentraçöes mais elevadas. Na presença de mistura de ativaçäo metabólica, a esquimianina mostrou-se genotóxica sendo que este efeito foi mais acentuado quando se empregou fraçäo microssomal induzida com Aroclor 1254 em relaçäo aquela induzida com 3-metilcolantreno