Protein Functional Families to characterise drug-target interactions.

The quest for “magic bullets” has been the driving force in drug discovery during the last two decades. However, the increasing rate of drug failure over this period has occurred concurrently with the assumption that a drug is a selective ligand for a single target. It now seems likely that polypharmacology is the rule rather than the exception [1]. Our previous research shows that protein domains are a good proxy for drug targets, and that drug polypharmacology emerges as a consequence of the multi-domain composition of proteins [2]. In this study, we investigate further the idea that the domain is the druggable entity within a protein target. We have identified a specific class of domains (CATH Functional Families) as the best currently available for identifying drug-target interactions. We show how this opens a new direction in target identification with potential application in drug repurposing.1. Hopkins, AL. (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol; 4: 682 2. Moya-García AA & Ranea JAG (2013) Insights into polypharmacology from drug-domain associations. Bioinformatics 29: 1934–1937)Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Universidad de Granad

UNDERSTANDING CONDITIONAL MODES OF ACTIONS IN CHEMICAL-INDUCED TOXICITY USING RULE MODELS

It is estimated that 115 million animals are used in experimental testing each year. Hence, shifting efforts toward alternative methods for toxicity assessment is essential. However, slow regulatory acceptance of new approaches is governed by knowledge gaps in toxicity modes of action. In this thesis, I describe these challenges and the use of in vitro screening as an alternative of animal testing. I also discuss common data-based methods to derive hypotheses about toxicity modes of actions, and the associated limitations in capturing multiple biological perturbations. I applied novel data-based workflows, using rule models, to prioritize in vitro assays predictive of toxicity as well as to detect significant polypharmacology profiles. I explain how constraints were applied to rule-based models to inform meaningful mechanistic interpretation for two toxicity endpoints: rat hepatotoxicity and acute toxicity. I compared assays selected, by rules, for predicting hepatotoxicity with endpoints used in in vitro models from commercial sources. An overlap was observed including cytochrome activity, mitochondrial toxicity and immunological responses. However, nuclear receptor activity, identified in rules, is not currently covered in commercial setups. I also demonstrate that endocrine disruption endpoints extrapolate better into in vivo toxicity when a set of specific conditions are met, such as physicochemical properties associated with good bioavailability. Next, I examined synergistic interactions between conditions in rules describing acute toxicity. I gained novel insights into how specific stressors potentiate the perturbation by known key events, such as acetylcholinesterase inhibition and neuro-signalling disruption. I show that examining polypharmacology profiles is particularly important at low bioactive potencies. Further, the overall predictive performance of rules describing acute toxicity was tested against a benchmark Random Forest model in a conformal prediction framework. Irrespective to the data type used in the training, the models were prone to bias over compounds promiscuity, by which high promiscuous compounds were more likely to be predicted as toxic. Overall, the studies conducted in this thesis provide novel insights into molecular mechanisms of toxicity, namely hepatotoxicity and acute toxicity, and with regards to chemical properties and polypharmacology. This knowledge can be used to improve the utility and design of alternative methods for toxicity, and hence, accelerate the regulatory acceptance.Islamic Development Bank Cambridge Trust Fun

Integrative Systems Approaches Towards Brain Pharmacology and Polypharmacology

Polypharmacology is considered as the future of drug discovery and emerges as the next paradigm of drug discovery. The traditional drug design is primarily based on a “one target-one drug” paradigm. In polypharmacology, drug molecules always interact with multiple targets, and therefore it imposes new challenges in developing and designing new and effective drugs that are less toxic by eliminating the unexpected drug-target interactions. Although still in its infancy, the use of polypharmacology ideas appears to already have a remarkable impact on modern drug development. The current thesis is a detailed study on various pharmacology approaches at systems level to understand polypharmacology in complex brain and neurodegnerative disorders. The research work in this thesis focuses on the design and construction of a dedicated knowledge base for human brain pharmacology. This pharmacology knowledge base, referred to as the Human Brain Pharmacome (HBP) is a unique and comprehensive resource that aggregates data and knowledge around current drug treatments that are available for major brain and neurodegenerative disorders. The HBP knowledge base provides data at a single place for building models and supporting hypotheses. The HBP also incorporates new data obtained from similarity computations over drugs and proteins structures, which was analyzed from various aspects including network pharmacology and application of in-silico computational methods for the discovery of novel multi-target drug candidates. Computational tools and machine learning models were developed to characterize protein targets for their polypharmacological profiles and to distinguish indications specific or target specific drugs from other drugs. Systems pharmacology approaches towards drug property predictions provided a highly enriched compound library that was virtually screened against an array of network pharmacology based derived protein targets by combined docking and molecular dynamics simulation workflows. The developed approaches in this work resulted in the identification of novel multi-target drug candidates that are backed up by existing experimental knowledge, and propose repositioning of existing drugs, that are undergoing further experimental validations

A multilayer network approach for guiding drug repositioning in neglected diseases

Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature.Fil: Berenstein, Ariel José. Fundación Instituto Leloir; Argentina. Universidad de Buenos Aires. Facultad de Ingeniería. Departamento de Física; ArgentinaFil: Magariños, María Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Chernomoretz, Ariel. Fundación Instituto Leloir; Argentina. Universidad de Buenos Aires. Facultad de Ingeniería. Departamento de Física; ArgentinaFil: Fernandez Aguero, Maria Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentin

Acceleration and Verification of Virtual High-throughput Multiconformer Docking

The work in this dissertation explores the use of massive computational power available through modern supercomputers as a virtual laboratory to aid drug discovery. As of November 2013, Tianhe-2, the fastest supercomputer in the world, has a theoretical performance peak of 54,902 TFlop/s or nearly 55 thousand trillion calculations per second. The Titan supercomputer located at Oak Ridge National Laboratory has 560,640 computing cores that can work in parallel to solve scientific problems. In order to harness this computational power to assist in drug discovery, tools are developed to aid in the preparation and analysis of high-throughput virtual docking screens, a tool to predict how and how well small molecules bind to disease associated proteins and potentially serve as a novel drug candidate. Methods and software for performing large screens are developed that run on high-performance computer systems. The future potential and benefits of using these tools to study polypharmacology and revolutionizing the pharmaceutical industry are also discussed

Computational Approaches for Predicting Drug Targets

This thesis reports the development of several computational approaches to predict human disease proteins and to assess their value as drug targets, using in-house domain functional families (CATH FunFams). CATH-FunFams comprise evolutionary related protein domains with high structural and functional similarity. External resources were used to identify proteins associated with disease and their genetic variations. These were then mapped to the CATH-FunFams together with information on drugs bound to any relatives within the FunFam. A number of novel approaches were then used to predict the proteins likely to be driving disease and to assess whether drugs could be repurposed within the FunFams for targeting these putative driver proteins. The first work chapter of this thesis reports the mapping of drugs to CATHFunFams to identify druggable FunFams based on statistical overrepresentation of drug targets within the FunFam. 81 druggable CATH-FunFams were identified and the dispersion of their relatives on a human protein interaction network was analysed to assess their propensity to be associated with side effects. In the second work chapter, putative drug targets for bladder cancer were identified using a novel computational protocol that expands a set of known bladder cancer genes with genes highly expressed in bladder cancer and highly associated with known bladder cancer genes in a human protein interaction network. 35 new bladder cancer targets were identified in druggable FunFams, for some of which FDA approved drugs could be repurposed from other protein domains in the FunFam. In the final work chapter, protein kinases and kinase inhibitors were analysed. These are an important class of human drug targets. A novel classification protocol was applied to give a comprehensive classification of the kinases which was benchmarked and compared with other widely used kinase classifications. Druginformation from ChEMBL was mapped to the Kinase-FunFams and analyses of protein network characteristics of the kinase relatives in each FunFam used to identify those families likely to be associated with side effects

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with similar to 400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for de novo drug polypharmacology predictions. Dose-response and perturbational profiles for 32 kinase inhibitors are provided to 21 teams who are blind to the identity of the compounds. The teams are asked to predict high-affinity binding targets of each compound among similar to 1,300 targets cataloged in DrugBank. The best performing methods leverage gene expression profile similarity analysis as well as deep-learning methodologies trained on individual datasets. This study lays the foundation for future integrative analyses of pharmacogenomic data, reconciliation of polypharmacology effects in different tumor contexts, and insights into network-based assessments of drug mechanisms of action.Peer reviewe

Associating adverse drug effects with protein targets by integrating adverse event, in vitro bioactivity, and pharmacokinetic data

Adverse drug effects are unintended and undesirable effects of medicines, causing attrition of molecules in drug development and harm to patients. To anticipate potential adverse effects early, drug candidates are commonly screened for pharmacological activity against a panel of protein targets. However, there is a lack of large-scale, quantitative information on the links between routinely screened proteins and the reporting of adverse events (AEs). This work describes a systematic analysis of associations between AEs observed in humans and bioactivities of drugs while taking into account drug plasma concentrations. In the first chapter, post-marketing drug-AE associations are derived from the United States Food and Drug Administration Adverse Event Reporting System using disproportionality methods, while applying Propensity Score Matching to reduce confounding factors. The resulting drug-AE associations are compared to those from the Side Effect Resource, which are primarily derived from clinical trials. The analysis reveals that the datasets generally share less than 10% of reported AEs for the same drug and have different distributions of AEs across System Organ Classes (SOCs). Using the drugs from the two AE datasets described in the first chapter, the second chapter integrates corresponding bioactivities, i.e. measured potencies and affinities from the ChEMBL database and ligand-based target predictions obtained with the tool PIDGIN, with drug plasma concentrations compiled from literature, such as Cmax. Compared to a constant bioactivity cut-off of 1 uM, using the ratio of the unbound drug plasma concentration over the drug potency, i.e. Cmax/XC50, results in different binary activity calls for protein targets. Whether deriving activity calls in this way results in the selection of targets with greater relevance to human AEs is investigated in the third chapter, which computes relationships between targets and AEs using different measures of statistical association. Using the Cmax/XC50 ratio results in higher Likelihood Ratios and Positive Predictive Values (PPVs) for target-AE associations that were previously reported in the context of secondary pharmacology screening, at the cost of a lower recall, possibly due to the smaller size of the dataset with available plasma concentrations. Furthermore, a large-scale quantitative assessment of bioactivities as indicators of AEs reveals a trade-off between the PPV and how many AE-associated drugs can potentially be detected from in vitro screening, although using combinations of targets can improve the detection rate in ~40% of cases at limited cost to the PPV. The work highlights AEs most strongly related to bioactivities and their SOC distribution. Overall, this thesis contributes to knowledge of the relationships between in vitro bioactivities and empirical evidence of AEs in humans. The results can inform the selection of proteins for secondary pharmacology screening and the development of computational models to predict AEs.Lhasa Limite

CRC Platform: A Colorectal Cancer Domain-specific Chemogenomics Knowledgebase for Polypharmacology and Target Identification Research

Colorectal cancer (CRC) is the third most common cancer, causing more than 600,000 deaths worldwide annually. Due to the involvement of complicated signaling pathways, epigenetic changes and genetic/genomic alterations, it is still challenging to develop effective treatments to reverse CRC progression. In order to facilitate developing new drugs for CRC treatment and revealing the mechanisms of CRC drug action at molecular level, we have constructed a computational CRC Platform (http://www.cbligand.org/CRC/), a domain-specific chemogenomics knowledgebase. The CRC platform consists of four database modules, e.g. 762 CRC related genes and proteins, 411 known CRC drugs and chemicals, 168383 CRC related bioassays, and 269 CRC pathways, as well as searching tools for multi-function retrieval. It is also featured with powerful cloud computation technologies and computational tools to expedite target identification, polypharmacology and drug synergy analysis for CRC research. We have also demonstrated the application of the CRC platform in the case studies: (1) computational exploration of FDA-approved CRC drugs for polypharmacology and drug synergy analysis; (2) in silico target identification of small chemical molecules from natural products with anti-CRC bioactivity; and (3) target identification and experimental validation for our in-house compounds. CRC platform will not only enrich our knowledge of CRC target identification, polypharmacology analysis, and biomarkers investigation, but also enhance the CRC chemogenomics data sharing and information exchange globally, and assist new drug design discovery and development for CRC treatment