Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors

[Abstract] The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order kth (Wk). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the Wk(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated Wk(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation)

Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates

In a multi-target complex network, the links (Lij) represent the interactions between the drug (di) and the target (tj), characterized by different experimental measures (Ki, Km, IC50, etc.) obtained in pharmacological assays under diverse boundary conditions (cj). In this work, we handle Shannon entropy measures for developing a model encompassing a multi-target network of neuroprotective/neurotoxic compounds reported in the CHEMBL database. The model predicts correctly >8300 experimental outcomes with Accuracy, Specificity, and Sensitivity above 80%–90% on training and external validation series. Indeed, the model can calculate different outcomes for >30 experimental measures in >400 different experimental protocolsin relation with >150 molecular and cellular OPEN ACCESS Int. J. Mol. Sci. 2014, 15 17036 targets on 11 different organisms (including human). Hereafter, we reported by the first time the synthesis, characterization, and experimental assays of a new series of chiral 1,2-rasagiline carbamate derivatives not reported in previous works. The experimental tests included: (1) assay in absence of neurotoxic agents; (2) in the presence of glutamate; and (3) in the presence of H2O2. Lastly, we used the new Assessing Links with Moving Averages (ALMA)-entropy model to predict possible outcomes for the new compounds in a high number of pharmacological tests not carried out experimentallyThe authors thank the Xunta de Galicia for financial support of this work under project 07CSA008203PRS

MI-NODES multiscale models of metabolic reactions, brain connectome, ecological, epidemic, world trade, and legal-social networks

[Abstract] Complex systems and networks appear in almost all areas of reality. We find then from proteins residue networks to Protein Interaction Networks (PINs). Chemical reactions form Metabolic Reactions Networks (MRNs) in living beings or Atmospheric reaction networks in planets and moons. Network of neurons appear in the worm C. elegans, in Human brain connectome, or in Artificial Neural Networks (ANNs). Infection spreading networks exist for contagious outbreaks networks in humans and in malware epidemiology for infection with viral software in internet or wireless networks. Social-legal networks with different rules evolved from swarm intelligence, to hunter-gathered societies, or citation networks of U.S. Supreme Court. In all these cases, we can see the same question. Can we predict the links based on structural information? We propose to solve the problem using Quantitative Structure-Property Relationship (QSPR) techniques commonly used in chemo-informatics. In so doing, we need software able to transform all types of networks/graphs like drug structure, drug-target interactions, protein structure, protein interactions, metabolic reactions, brain connectome, or social networks into numerical parameters. Consequently, we need to process in alignment-free mode multitarget, multiscale, and multiplexing, information. Later, we have to seek the QSPR model with Machine Learning techniques. MI-NODES is this type of software. Here we review the evolution of the software from chemoinformatics to bioinformatics and systems biology. This is an effort to develop a universal tool to study structure-property relationships in complex systems

MIANN models in medicinal, physical and organic chemistry

[Abstract] Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.Ministerio de Ciencia e Innovación; CTQ2009-07733Universidad del Pais Vasco; UFI11/22Universidad del Pais Vasco; GIU 094

Herramientas informáticas y de inteligencia artificial para el meta-análisis en la frontera entre la bioinformática y las ciencias jurídicas

[Resumen] Los modelos computacionales, conocidos por su acrónimo en idioma Inglés como QSPR (Quantitative Structure-Property Relationships) pueden usarse para predecir propiedades de sistemas complejos. Estas predicciones representan una aplicación importante de las Tecnologías de la Información y la Comunicación (TICs). La mayor relevancia es debido a la reducción de costes de medición experimental en términos de tiempo, recursos humanos, recursos materiales, y/o el uso de animales de laboratorio en ciencias biomoleculares, técnicas, sociales y/o jurídicas. Las Redes Neuronales Artificiales (ANNs) son una de las herramientas informáticas más poderosas para buscar modelos QSPR. Para ello, las ANNs pueden usar como variables de entrada (input) parámetros numéricos que cuantifiquen información sobre la estructura del sistema. Los parámetros conocidos como Índices Topológicos (TIs) se encuentran entre los más versátiles. Los TIs se calculan en Teoría de Grafos a partir de la representación de cualquier sistema como una red de nodos interconectados; desde moléculas a redes biológicas, tecnológicas, y sociales. Esta tesis tiene como primer objetivo realizar una revisión y/o introducir nuevos TIs y software de cálculo de TIs útiles como inputs de ANNs para el desarrollo de modelos QSPR de redes bio-moleculares, biológicas, tecnológico-económicas y socio-jurídicas. En ellas, por una parte, los nodos representan biomoléculas, organismos, poblaciones, leyes tributarias o concausas de delitos. Por otra parte, en la interacción TICs-Ciencias Biomoleculares- Derecho se hace necesario un marco de seguridad jurídica que permita el adecuado desarrollo de las TICs y sus aplicaciones en Ciencias Biomoleculares. Por eso, el segundo objetivo de esta tesis es revisar el marco jurídico-legal de protección de los modelos QSAR/QSPR de sistemas moleculares. El presente trabajo de investigación pretende demostrar la utilidad de estos modelos para predecir características y propiedades de estos sistemas complejos.[Resumo] Os modelos de ordenador coñecidos pola súas iniciais en inglés QSPR (Quantitative Structure-Property Relationships) poden prever as propiedades de sistemas complexos e reducir os custos experimentais en termos de tempo, recursos humanos, materiais e/ou o uso de animais de laboratorio nas ciencias biomoleculares, técnicas, e sociais. As Redes Neurais Artificiais (ANNs) son unha das ferramentas máis poderosas para buscar modelos QSPR. Para iso, as ANNs poden facer uso, coma variables de entrada (input), dos parámetros numéricos da estrutura do sistema chamados Índices Topolóxicos (TIs). Os TI calcúlanse na teoría dos grafos a partir da representación do sistema coma unha rede de nós conectados, incluíndo tanto moléculas coma redes sociais e tecnolóxicas. Esta tese ten como obxectivo principal revisar e/ou desenvolver novos TIs, programas de cálculo de TIs, e/ou modelos QSPR facendo uso de ANNs para predicir redes bio-moleculares, biolóxicas, económicas, e sociais ou xurídicas onde os nós representan moléculas biolóxicas, organismos, poboacións, ou as leis fiscais ou as concausas dun delito. Ademais, a interacción das TIC con as ciencias biolóxicas e xurídicas necesita dun marco de seguridade xurídica que permita o bo desenvolvemento das TIC e as súas aplicacións en Ciencias Biomoleculares. Polo tanto, o segundo obxectivo desta tese é analizar o marco xurídico e legal de protección dos modelos QSPR. O presente traballo de investigación pretende demostrar a utilidade destes modelos para predicir características e propiedades destes sistemas complexos.[Abstract] QSPR (Quantitative Structure-Property Relationships) computer models can predict properties of complex systems reducing experimental costs in terms of time, human resources, material resources, and/or the use of laboratory animals in bio-molecular, technical, and/or social sciences. Artificial Neural Networks (ANNs) are one of the most powerful tools to search QSPR models. For this, the ANNs may use as input variables numerical parameters of the system structure called Topological Indices (TIs). The TIs are calculated in Graph Theory from a representation of any system as a network of interconnected nodes, including molecules or social and technological networks. The first aim of this thesis is to review and/or develop new TIs, TIs calculation software, and QSPR models using ANNs to predict bio-molecular, biological, commercial, social, and legal networks where nodes represent bio-molecules, organisms, populations, products, tax laws, or criminal causes. Moreover, the interaction of ICTs with Biomolecular and law Sciences needs a legal security framework that allows the proper development of ICTs and their applications in Biomolecular Sciences. Therefore, the second objective of this thesis is to review the legal framework and legal protection of QSPR techniques. The present work of investigation tries to demonstrate the usefulness of these models to predict characteristics and properties of these complex systems

Modelos multi-escala de inteligencia artificial para diseño quimio-informático y fármaco-epidemiológico de terapias anti-VIH en Condados de Estados Unidos

[Resumen]Los métodos que relacionan la estructura química con la actividad biológica se conocen como “relaciones cuantitativas estructura-actividad” (en adelante QSAR). Es fundamental entender y cuantificar la relación entre la estructura y la actividad biológica de los potenciales fármacos para realizar su estudio eficiente. Este tipo de estudio consiste en correlacionar, por medio de descriptores moleculares, distintas propiedades químicas o fisicoquímicas de las moléculas en cuestión con valores de actividad biológica. Actualmente, el desarrollo de medicamentos más seguros y efectivos en el tratamiento de enfermedades como el SIDA es un objetivo que requiere del esfuerzo de un elevado número de especialistas en diferentes campos de la Ciencia, y donde el azar ha tenido un gran protagonismo. Sin embargo, parece razonable pensar que nunca se obtendrán medicamentos eficaces y seguros con sólo acudir al azar. Para ser más eficientes en el desarrollo de nuevos fármacos, la investigación en el tratamiento de las enfermedades requiere poseer mecanismos predictivos de algunas actividades. Los modelos basados en “redes de neuronas artificiales” (en adelante RRNNAA) son un ejemplo de modelos teóricos de predicción, ampliamente utilizados en muchas áreas de la Ciencia, como medicina, química, bioquímica…, así como también en el desarrollo de medicamentos. En esto último, son muy útiles para la predicción de propiedades de los potenciales fármacos. Las RRNNAA se aproximan a la forma de operar que usa el cerebro humano, con habilidad para abordar con éxito los datos, las informaciones y los conocimientos naturales, o del mundo real, que están afectados por lo que se conoce como la “maldición de la cuádruple I”, por ser datos: inciertos, inconsistentes, incompletos e imprecisos. Esta particularidad hace que sean difíciles de gestionar adecuadamente por las técnicas computacionales convencionales, haciendo precisa la utilización de técnicas de Inteligencia Artificial, como son las ya citadas RRNNAA. La mayor ventaja de estos modelos inteligentes de predicción es que permiten evitar costes innecesarios producidos por desarrollos de nuevos compuestos con potencialidad terapéutica que resultarán estériles.Por lo tanto, el objetivo principal de la tesis aquí presentada es el desarrollo, con técnicas de inteligencia artificial, de una metodología “quimioinformática multi-escala” que permita relacionar cuantitativamente datos químicos y pre-clínicos con datos epidemiológicos, para llevar a cabo predicciones “fármaco-epidemiológicas”, teniendo en cuenta la imposibilidad práctica y legal de obtener datos experimentales, en la fase IV del proceso de desarrollo de nuevos compuestos[Resumo]Os métodos que relacionan a estrutura química coa actividade biolóxica son chamados “relacións cuantitativas estrutura – actividade” (en adiante QSAR). É esencial para entender e cuantificar a relación entre a estrutura e a actividade biolóxica dos potenciais fármacos para realizar o seu estudio eficiente. Este tipo de estudo consiste en correlacionar, a través de descritores moleculares, distintas propiedades químicas ou fisicoquímicas de las moleculas en cuestión, con valores de actividade biolóxica. Actualmente, o desenvolvemento de medicamentos máis seguros e efectivos no tratamento de enfermidades como o SIDA é un obxectivo que require do esforzo de un gran número de especialistas en diferentes campos da ciencia, e onde o azar tivo un gran protagonismo. Nembergantes, parece razoable pensar que nunca se obterían medicamentos eficaces e seguros con só acudir ao azar. Para ser máis eficaces no desenvolvemento de novos farmacos, a investigación para o tratamento de enfermidades require mecanismos preditivos de algunhas actividades. Os modelos baseados en redes neurais artificiais (en adiante RRNNAA) son un exemplo de modelos teóricos de predición amplamente utilizado en moitas áreas da ciencia, como medicina, química, bioquímica..., así como tamén no desenvolvemento de medicamentos. Nesto último, son moi útiles para a predición de propiedades dos potenciais medicamentos. As RRNNAA achegánse ao xeito de funcionar do cerebro humano, coa capacidade para abordar con éxito los datos, las informaciones y los conocimientos naturales, o del mundo real, que están afectados polo que se coñece como a “maldición da cuadrúple I”, por ser dados: incertos, inconsistentes, incompletos e imprecisos. Esta particularidade fai que sexan díficiles de xestionar axeitadamente coas técnicas computacionais convencionais, facendo preciso o uso de técnicas de Intelixencia Artificial, como son as xa citadas RRNNAA. A maior vantaxe destes modelos preditivos intelixentes é que permiten evitar custos innecesarios producidos polos desenvolvementos de novos compostos con potencial terapéutico que resultaran esteriles. Polo tanto o obxectivo principal da tese aquí presentada é o desenvolvemento, con tecnicas de intelixencia artificial dunha metodoloxía “quimioinformática multi-escala” que permita relacionar cuantitativamente datos químicos e pre-clínicos con datos epidemiolóxicos, para levar a cabo predicións fármaco-epidemiolóxicas, tendo en conta a imposibilidade práctica e legal de obter datos experimentais na fase IV do proceso de desenvolvemento de novos compostos.[Abstract]The methods relating chemical structure to biological activity are called “Quantitative Structure Activity Relationships” (QSAR). It is essential to understand and quantify the relationships between the structure and biological activity of potential drugs to develop an efficient study on them. This kind of study consists of the correlation of the molecular descriptors based on several chemical or physicochemical properties with biological activity. Currently, the development of safer and more effective drugs in the treatment of diseases such as AIDS is a goal that requires a joint effort of a large number of specialists from different fields of science, and where chance also has a major role. However, it seems reasonable that no effective and safe drugs will be obtained based on chance only. To be more efficient in developing new drugs, the research for the treatment of diseases requires predictive mechanisms of some biological activities. The models based on "Artificial Neural Networks" (ANNs) are an example of theoretical prediction models, widely used in many areas of science such as Medicine, Chemistry, Biochemistry, etc. as well as in Drug Development. In the latter, they are very useful for predicting properties of potential drugs. ANNs approach the modus operandi used by the human brain, being able to successfully manage data, information and natural knowledge, or from the real world, which are affected by the so-called "curse of the fourfold I", dealing with information which is uncertain, inconsistent, incomplete and inaccurate. This feature makes it difficult to properly manage by conventional computational techniques, making the use of Artificial Intelligence (AI) techniques necessary, such as the above-mentioned ANNs. The most important advantage of these intelligent prediction models is the fact that they avoid unnecessary production costs associated with the development of new compounds with therapeutic potential which proved to be inactive. Therefore, the main objective of the thesis is the development of a chemoinformatics multi-scale methodology using artificial intelligence techniques to quantitatively relate chemical and pre-clinical data with epidemiological data, with the aim of performing "drug - epidemiological" predictions, taking into account the practical and legal impossibility of obtaining experimental data in Phase IV of the development process of new compounds

Molecular Science for Drug Development and Biomedicine

With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of “Molecular Science for Drug Development and Biomedicine”, in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine