Optimization Based Tumor Classification from Microarray Gene Expression Data

An important use of data obtained from microarray measurements is the classification of tumor types with respect to genes that are either up or down regulated in specific cancer types. A number of algorithms have been proposed to obtain such classifications. These algorithms usually require parameter optimization to obtain accurate results depending on the type of data. Additionally, it is highly critical to find an optimal set of markers among those up or down regulated genes that can be clinically utilized to build assays for the diagnosis or to follow progression of specific cancer types. In this paper, we employ a mixed integer programming based classification algorithm named hyper-box enclosure method (HBE) for the classification of some cancer types with a minimal set of predictor genes. This optimization based method which is a user friendly and efficient classifier may allow the clinicians to diagnose and follow progression of certain cancer types.We apply HBE algorithm to some well known data sets such as leukemia, prostate cancer, diffuse large B-cell lymphoma (DLBCL), small round blue cell tumors (SRBCT) to find some predictor genes that can be utilized for diagnosis and prognosis in a robust manner with a high accuracy. Our approach does not require any modification or parameter optimization for each data set. Additionally, information gain attribute evaluator, relief attribute evaluator and correlation-based feature selection methods are employed for the gene selection. The results are compared with those from other studies and biological roles of selected genes in corresponding cancer type are described.The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers

Classification of HCV NS5B Polymerase Inhibitors Using Support Vector Machine

Using a support vector machine (SVM), three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV) NS5B polymerase NNIs (non-nucleoside analogue inhibitors) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors, 2D and 3D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Three models were developed with the combination of different types of descriptors. Model 2 based on 16 global and 2D autocorrelation descriptors gave the highest prediction accuracy of 88.24% and MCC (Matthews correlation coefficient) of 0.789 on test set. Model 1 based on 13 global descriptors showed the highest prediction accuracy of 86.25% and MCC of 0.732 on external test set (including 80 compounds). Some molecular properties such as molecular shape descriptors (InertiaZ, InertiaX and Span), number of rotatable bonds (NRotBond), water solubility (LogS), and hydrogen bonding related descriptors performed important roles in the interactions between the ligand and NS5B polymerase

Machine Learning for Kinase Drug Discovery

Cancer is one of the major public health issues, causing several million losses every year. Although anti-cancer drugs have been developed and are globally administered, mild to severe side effects are known to occur during treatment. Computer-aided drug discovery has become a cornerstone for unveiling treatments of existing as well as emerging diseases. Computational methods aim to not only speed up the drug design process, but to also reduce time-consuming, costly experiments, as well as in vivo animal testing. In this context, over the last decade especially, deep learning began to play a prominent role in the prediction of molecular activity, property and toxicity. However, there are still major challenges when applying deep learning models in drug discovery. Those challenges include data scarcity for physicochemical tasks, the difficulty of interpreting the prediction made by deep neural networks, and the necessity of open-source and robust workflows to ensure reproducibility and reusability. In this thesis, after reviewing the state-of-the-art in deep learning applied to virtual screening, we address the previously mentioned challenges as follows: Regarding data scarcity in the context of deep learning applied to small molecules, we developed data augmentation techniques based on the SMILES encoding. This linear string notation enumerates the atoms present in a compound by following a path along the molecule graph. Multiplicity of SMILES for a single compound can be reached by traversing the graph using different paths. We applied the developed augmentation techniques to three different deep learning models, including convolutional and recurrent neural networks, and to four property and activity data sets. The results show that augmentation improves the model accuracy independently of the deep learning model, as well as of the data set size. Moreover, we computed the uncertainty of a model by using augmentation at inference time. In this regard, we have shown that the more confident the model is in its prediction, the smaller is the error, implying that a given prediction can be trusted and is close to the target value. The software and associated documentation allows making predictions for novel compounds and have been made freely available. Trusting predictions blindly from algorithms may have serious consequences in areas of healthcare. In this context, better understanding how a neural network classifies a compound based on its input features is highly beneficial by helping to de-risk and optimize compounds. In this research project, we decomposed the inner layers of a deep neural network to identify the toxic substructures, the toxicophores, of a compound that led to the toxicity classification. Using molecular fingerprints —vectors that indicate the presence or absence of a particular atomic environment —we were able to map a toxicity score to each of these substructures. Moreover, we developed a method to visualize in 2D the toxicophores within a compound, the so- called cytotoxicity maps, which could be of great use to medicinal chemists in identifying ways to modify molecules to eliminate toxicity. Not only does the deep learning model reach state-of-the-art results, but the identified toxicophores confirm known toxic substructures, as well as expand new potential candidates. In order to speed up the drug discovery process, the accessibility to robust and modular workflows is extremely advantageous. In this context, the fully open-source TeachOpenCADD project was developed. Significant tasks in both cheminformatics and bioinformatics are implemented in a pedagogical fashion, allowing the material to be used for teaching as well as the starting point for novel research. In this framework, a special pipeline is dedicated to kinases, a family of proteins which are known to be involved in diseases such as cancer. The aim is to gain insights into off-targets, i.e. proteins that are unintentionally affected by a compound, and that can cause adverse effects in treatments. Four measures of kinase similarity are implemented, taking into account sequence, and structural information, as well as protein-ligand interaction, and ligand profiling data. The workflow provides clustering of a set of kinases, which can be further analyzed to understand off-target effects of inhibitors. Results show that analyzing kinases using several perspectives is crucial for the insight into off-target prediction, and gaining a global perspective of the kinome. These novel methods can be exploited in the discovery of new drugs, and more specifically diseases involved in the dysregulation of kinases, such as cancer

Discovery of Novel Glycogen Synthase Kinase-3beta Inhibitors: Molecular Modeling, Virtual Screening, and Biological Evaluation

Glycogen synthase kinase-3 (GSK-3) is a multifunctional serine/threonine protein kinase which is engaged in a variety of signaling pathways, regulating a wide range of cellular processes. Due to its distinct regulation mechanism and unique substrate specificity in the molecular pathogenesis of human diseases, GSK-3 is one of the most attractive therapeutic targets for the unmet treatment of pathologies, including type-II diabetes, cancers, inflammation, and neurodegenerative disease. Recent advances in drug discovery targeting GSK-3 involved extensive computational modeling techniques. Both ligand/structure-based approaches have been well explored to design ATP-competitive inhibitors. Molecular modeling plus dynamics simulations can provide insight into the protein-substrate and protein-protein interactions at substrate binding pocket and C-lobe hydrophobic groove, which will benefit the discovery of non-ATP-competitive inhibitors. To identify structurally novel and diverse compounds that effectively inhibit GSK-3â, we performed virtual screening by implementing a mixed ligand/structure-based approach, which included pharmacophore modeling, diversity analysis, and ensemble docking. The sensitivities of different docking protocols to the induced-fit effects at the ATP-competitive binding pocket of GSK-3â have been explored. An enrichment study was employed to verify the robustness of ensemble docking compared to individual docking in terms of retrieving active compounds from a decoy dataset. A total of 24 structurally diverse compounds obtained from the virtual screening experiment underwent biological validation. The bioassay results shothat 15 out of the 24 hit compounds are indeed GSK-3â inhibitors, and among them, one compound exhibiting sub-micromolar inhibitory activity is a reasonable starting point for further optimization. To further identify structurally novel GSK-3â inhibitors, we performed virtual screening by implementing another mixed ligand-based/structure-based approach, which included quantitative structure-activity relationship (QSAR) analysis and docking prediction. To integrate and analyze complex data sets from multiple experimental sources, we drafted and validated hierarchical QSAR, which adopts a multi-level structure to take data heterogeneity into account. A collection of 728 GSK-3 inhibitors with diverse structural scaffolds were obtained from published papers of 7 research groups based on different experimental protocols. Support vector machines and random forests were implemented with wrapper-based feature selection algorithms in order to construct predictive learning models. The best models for each single group of compounds were then selected, based on both internal and external validation, and used to build the final hierarchical QSAR model. The predictive performance of the hierarchical QSAR model can be demonstrated by an overall R2 of 0.752 for the 141 compounds in the test set. The compounds obtained from the virtual screening experiment underwent biological validation. The bioassay results confirmed that 2 hit compounds are indeed GSK-3â inhibitors exhibiting sub-micromolar inhibitory activity, and therefore validated hierarchical QSAR as an effective approach to be used in virtual screening experiments. We have successfully implemented a variant of supervised learning algorithm, named multiple-instance learning, in order to predict bioactive conformers of a given molecule which are responsible for the observed biological activity. The implementation requires instance-based embedding, and joint feature selection and classification. The goal of the present project is to implement multiple-instance learning in drug activity prediction, and subsequently to identify the bioactive conformers for each molecule. The proposed approach was proven not to suffer from overfitting and to be highly competitive with classical predictive models, so it is very powerful for drug activity prediction. The approach was also validated as a useful method for pursuit of bioactive conformers

Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics

This book is a collection of original research articles in the field of computer-aided drug design. It reports the use of current and validated computational approaches applied to drug discovery as well as the development of new computational tools to identify new and more potent drugs

Modelos bioinformáticos y estudio de receptores de proteínas mediante el uso de redes complejas para el desarrollo y diseño de fármacos eficaces en patologías del sistema nervioso central

La búsqueda y desarrollo de fármacos eficaces para el tratamiento de enfermedades neurodegenerativas ha generado grandes expectativas, debido a la relevancia que tienen sobre la economía de los sistemas sanitarios y la tremenda carga y desgaste que sufren familia y cuidadores. Por ello, la industria farmacéutica se ha volcado sobre estas patologías en las últimas tres décadas, pero las dificultades de realizar ensayos sobre el SN provoca que los gastos y tiempos de investigación se disparen, limitando de forma considerable la rentabilidad de los procesos tradicionales en el desarrollo de nuevos medicamentos. Es en este apartado donde realiza sus aportaciones el diseño de fármacos, dedicando una parte del mismo al desarrollo de modelos matemáticos que permitan predecir propiedades de interés para una gran variedad de sistemas químicos incluyendo moléculas de bajo peso molecular, polímeros, biopolímeros, sistemas heterogéneos, formulaciones farmacéuticas, conglomerados de moléculas e iones, materiales, nano-estructuras y otros. En dicho sentido, los estudios QSAR (Quantitative Structure-Activity-Relationships) son usados cada vez mas como herramientas para el descubrimiento molecular. Estos modelos QSAR pueden ser diseñados para que predigan la probabilidad de que un fármaco sea efectivo contra una enfermedad degenerativa determinada ya sea la enfermedad de Parkinson, Alzheimer o cualquier otra, actuando sobre una diana molecular específica. En esta memoria presentamos de manera conjunta la revisión de modelos previos y trabajos específicos novedosos, en los que se han introducido nuevos índices numéricos utilizados para describir tanto la estructura molecular de fármacos como la estructura macromolecular de sus dianas o receptores (proteínas y/o ADN/ARN). Con estos ITs hemos sido capaces de desarrollar nuevos modelos multiQSAR de gran interés por su doble función en la predicción de fármacos y sus dianas moleculares. Estos trabajos permitirán la introducción de nuevos conceptos teóricos y la evolución hacia modelos con posibles aplicaciones en la búsqueda de nuevos fármacos neuroprotectores útiles en el tratamiento de las enfermedades de Parkinson y Alzheimer y/o nuevas dianas moleculares para estos fármacos. Este tipo de investigación abarca un área general-básica en la que interactúan la Bioinformática y la Quimioinformática

Exploring Molecular Diversity: There is Plenty of Room at Markush's

L'estratègia de les etapes inicials del descobriment de fàrmacs està normalment basada en un procés anomenat hit-to-lead que implica un extens estudi entorn de la síntesi de derivats d'una molècula original que prèviament hagi mostrat certa activitat biològica davant d'una diana concreta. Per tant, aquest procés comporta la síntesi de molts anàlegs que descriurien una subquimioteca, que generalment evidencia que aquests estudis estan molt focalitzats al voltant de l'espai químic del compost original. Així i tot, quan aquesta molècula és finalment patentada, es descriu un espai químic molt més vast per mitjà d'estructures Markush donant per suposat que alguns dels seus derivats puguin presentar també activitat biològica. Tot i això, la presència d'aquestes estructures no implica la síntesi comprovada de tota la biblioteca molecular sinó només una petita mostra de la mateixa. La nostra hipòtesi és que hi ha una gran part de l’espai químic d’aquestes biblioteques que està sense explorar i pot amagar possibles candidats que poden fins i tot superar l’activitat del hit original. A través d'aquest projecte, es proposa una alternativa que sosté que una selecció racional de poques molècules – basat en l'agrupament segons semblança molecular – pot representar de manera més significativa l'espai químic establert, oferint la possibilitat d'explorar regions desconegudes que podrien amagar més potencial biològic. Després de revisar els darrers fàrmacs aprovats per la FDA en el període del 2008 al 2020 i la base de dades de molècules bioactives de ChEMBL, s'ha dut a terme una exploració de l'ampli espai químic resultant de molècules petites amb propietats similars a les dels medicaments per definir nous espais accessibles que podrien ocultar activitat. Els resultats obtinguts de set casos d'estudis reals han demostrat que tant la selecció racional com l’aleatòria representen més significativament les biblioteques combinatòries declarades a les patents, que les molècules descrites fins ara. S'han realitzat dos estudis pràctics que implementen aquesta metodologia suggerida per descriure millor l'espai químic del fàrmac antipalúdic Tafenoquina i del Dacomitinib, un inhibidor de tirosina cinases de segona generació per al tractament del càncer de pulmó de cèl·lules no petites. L’exploració de l’espai químic d’aquestes dues famílies ha portat a la síntesi racional de set anàlegs antipalúdics i vuit inhibidors de cinases que han mostrat interessants activitats inhibidores. Aquests resultats demostren que l'aplicació de la quimioinformàtica per a la selecció de biblioteques pot millorar la capacitat d'inspeccionar millor els conjunts de dades químiques per identificar nous compostos precandidats i representar grans biblioteques per a posteriors campanyes de reposicionament.La estrategia de las etapas iniciales del descubrimiento de fármacos está normalmente basada en un proceso denominado hit-to-lead que implica un extenso estudio entorno a la síntesis de derivados de una molécula original que previamente haya expresado cierta actividad biológica frente a una diana concreta. Por ende, este proceso conlleva la síntesis de muchos análogos que describirían una sublibrería química, la cual generalmente evidencia que estos estudios están muy focalizados alrededor del espacio químico del compuesto original. Aún y así, cuando esta molécula es finalmente patentada, se describe un espacio químico mucho más vasto por medio de estructuras Markush teorizando que algunos de sus derivados puedan presentar también actividad biológica. Sin embargo, la presencia de estas estructuras no implica la síntesis comprobada de toda la biblioteca molecular sino solo una pequeña muestra de la misma. Nuestra hipótesis es que hay una gran parte del espacio químico de estas bibliotecas que está sin explorar y puede ocultar posibles candidatos que pueden hasta superar la actividad del hit original. A través de este proyecto, se propone una alternativa que sostiene que una selección racional de pocas moléculas – fundada en el agrupamiento según su similitud química – puede representar de manera más significativa el espacio químico establecido, ofreciendo la posibilidad de explorar regiones desconocidas que podrían ocultar más potencial biológico. Después de revisar los últimos fármacos aprobados por la FDA en el período de 2008 a 2020 y la base de datos de moléculas bioactivas de ChEMBL, se ha llevado a cabo una exploración del amplio espacio químico resultante de moléculas pequeñas con propiedades similares a las de los medicamentos para definir nuevos espacios accesible que podrían ocultar actividad. Los resultados obtenidos de siete casos de estudios reales han demostrado que tanto la selección racional como la aleatoria representan más significativamente las bibliotecas combinatorias declaradas en las patentes que las moléculas descritas hasta la fecha. Se han desarrollado dos estudios prácticos que implementan esta metodología sugerida para describir mejor el espacio químico del fármaco antipalúdico Tafenoquina y Dacomitinib, un inhibidor de la tirosina quinasa de segunda generación para el tratamiento del cáncer de pulmón de células no pequeñas. La exploración del espacio químico de estas dos familias ha llevado a la síntesis racional de siete análogos antipalúdicos y ocho inhibidores de quinasas que han mostrado interesantes actividades inhibidoras. Estos resultados demuestran que la aplicación de la quimioinformática para la selección de bibliotecas puede mejorar la capacidad de inspeccionar mejor los conjuntos de datos químicos para identificar nuevos potenciales hits y representar grandes bibliotecas para fines de reposicionamiento.The early Drug Discovery strategy is commonly based on a hit-to-lead process which involves large research on the synthesis of derivatives of an original molecule that had previously shown biological activity against a specific biological target. Therefore, this process implies the synthesis of many analogs leading to the description of a chemical sub-library which generally leads to a highly focused study on the chemical space nearby the hit compound. However, when this drug is finally patented, a wider chemical space derived from a Markush structure is described, theorizing that some analogs within may present biological activity. Nevertheless, this claim involving the Markush structure does not imply the proven synthesis of all the chemical library but just a small population of it. We hypothesize that there is a great part of the chemical space of these libraries that is unexplored and can hide potential lead candidates which may even surpass the activity of the original hit. Through this project, an alternative is proposed claiming that a rational selection of a short sample of small molecules – founded on similarity-based clustering – can represent more significatively the stated chemical space offering the possibility to explore the unknown space that could hide more potential biological activity. After a review on the latest approved drugs by the FDA in the period from 2008 to 2020 and the ChEMBL database of bioactive molecules, an exploration of the resulting wide chemical space of small molecules with drug-like properties has been assessed in order to define accessible spots that might hide biological activity. The obtained results from seven real cases of study have proven that random and rationally selected molecules represent more significantly the combinatorial libraries stated in the patents rather than the reported molecules until date. Furthermore, two practical studies implementing our suggested methodology have been developed to better describe the chemical space of the antimalarial drug Tafenoquine and Dacomitinib, a second-generation tyrosine kinase inhibitor for non-small-cell lung cancer treatment. The assessment driven by a better chemical space exploration of these two families have led to the rational synthesis of seven antimalarial analogs and eight kinase inhibitors which have shown interesting inhibitory activities. Our results evince that the application of cheminformatics for library selection may improve the ability to better inspect chemical datasets in order to identify new potential hits and represent large libraries for further reprofiling purposes

Examination of Molecular Recognition in Protein-Ligand Interactions

This dissertation is a compilation of two main projects that were investigated during my thesis research. The first project was a prospective study which identified and characterized drug-like inhibitors of a prototype of bacterial two-component signal transduction response regulator using computational and experimental methods. The second project was the development and validation of a scoring function, PHOENIX, derived using high-resolution structures and calorimetry measurements to predict binding affinities of protein-ligand interactions. Collectively, my thesis research aimed to better understand the underlying driving forces and principles which govern molecular recognition and molecular design. A prospective study coupled computational predictions with experimental validation resulted in the discovery of first-in-class inhibitors targeting a signal transduction module important for bacterial virulence. Development and validation of the PHOENIX scoring function for binding affinity prediction derived using high-resolution structures and calorimetry measurements should guide future molecular recognition studies and endeavors in computer-aided molecular design. To request for an electronic copy of this dissertation, please email the author: yattang at gmail dot com)

Computer modelling approaches for improving analysis of 1 anti-malarial clinical trials

Clinical trials of treatments for Plasmodium falciparum are an integral aspect of a continually evolving evidence base that informs public health policy with the aim of reducing malaria morbidity, mortality, preventing the emergence of parasite resistance to drugs and, eventually, permitting elimination of the disease. Despite their importance, obtaining useful information from in vivo trials can be hindered through methodological gaps that make it difficult to obtain or analyse results (through an inability to quantify important parameters in vivo), cost, required patient numbers or ethical considerations. This thesis uses a computer modelling approach to address two key research problems relating to in vivo trials: Firstly, it quantifies the accuracy failure rate estimates obtained during trials for routine monitoring of artemisinin-based combination therapy (ACT) efficacy in cases of uncomplicated malaria, noting that currently available methods for genotyping patient blood samples are imperfect, and that patients can be infected by new parasite clones (termed reinfection) during the follow-up period which may share (by chance) genetic data with clones present at the time of treatment. Consequently, it is possible for drug failure to be misclassified as a reinfection or vice versa, inducing error in drug failure rate estimates. The true drug failure rate cannot be known in vivo so the accuracy of each method is not known. The results presented here show that currently used methods (length-polymorphic markers and microsatellite markers) are under-estimating true drug failure rate and preventing the detection of failing drugs (~10% failure rate). Accuracy of failure rate estimates was greatly improved by using alternative statistical algorithms or through use of novel Amplicon Sequencing techniques for genotyping blood samples. Secondly, clinical trials of severe malaria generally use reduction in circulating parasite numbers as a clinical endpoint but sequestered - not circulating - parasites are responsible for pathology in severe malaria. A mathematical model was developed to quantify the pathology of severe malaria in an in silico patient population based on sequestered parasite numbers. Results from this model then indicated that a simplified treatment regimen was generally non-inferior to the World Health Organization (WHO) recommended regimen, though specific sub-groups of patients may be at increased risk. Model results also indicated that the emergence of resistance to artesunate in parasite early ring-stages would have severe consequences for patient prognosis in cases of severe malaria