The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions

Accepted for publication in a future issue of Future Medicinal Chemistry.The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.Peer reviewe

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification

Motivation: Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process. Results: Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancerrelevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results. Availability and implementation: ClinOmicsTrailbc can be freely accessed at https://clinomicstrail. bioinf.uni-sb.de

Pharmacological Study of Phenolic Components in Parkinson's Disease

In this study, cell experiments were conducted to investigate the effects of extracts on cell viability and apoptosis of Parkinson model in vitro, as well as the expression of cysteine protease-3 (Caspase-3) and B lymphocytoma-2-associated X protein (BAX). The results showed that extract of phenols could improve the loss of cell viability and apoptosis induced by MPP+, and inhibit the enhanced expression of Bax and Caspase-3 by MPP+. The potential targets and signaling pathways of phenols in the treatment of Parkinson's disease were predicted by network pharmacology

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

Novel translational approaches to the search for precision therapies for acute respiratory distress syndrome.

In the 50 years since acute respiratory distress syndrome (ARDS) was first described, substantial progress has been made in identifying the risk factors for and the pathogenic contributors to the syndrome and in characterising the protein expression patterns in plasma and bronchoalveolar lavage fluid from patients with ARDS. Despite this effort, however, pharmacological options for ARDS remain scarce. Frequently cited reasons for this absence of specific drug therapies include the heterogeneity of patients with ARDS, the potential for a differential response to drugs, and the possibility that the wrong targets have been studied. Advances in applied biomolecular technology and bioinformatics have enabled breakthroughs for other complex traits, such as cardiovascular disease or asthma, particularly when a precision medicine paradigm, wherein a biomarker or gene expression pattern indicates a patient's likelihood of responding to a treatment, has been pursued. In this Review, we consider the biological and analytical techniques that could facilitate a precision medicine approach for ARDS

Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance.

BACKGROUND: Understanding mechanisms underlying specific chemotherapeutic responses in subtypes of cancer may improve identification of treatment strategies most likely to benefit particular patients. For example, triple-negative breast cancer (TNBC) patients have variable response to the chemotherapeutic agent cisplatin. Understanding the basis of treatment response in cancer subtypes will lead to more informed decisions about selection of treatment strategies. METHODS: In this study we used an integrative functional genomics approach to investigate the molecular mechanisms underlying known cisplatin-response differences among subtypes of TNBC. To identify changes in gene expression that could explain mechanisms of resistance, we examined 102 evolutionarily conserved cisplatin-associated genes, evaluating their differential expression in the cisplatin-sensitive, basal-like 1 (BL1) and basal-like 2 (BL2) subtypes, and the two cisplatin-resistant, luminal androgen receptor (LAR) and mesenchymal (M) subtypes of TNBC. RESULTS: We found 20 genes that were differentially expressed in at least one subtype. Fifteen of the 20 genes are associated with cell death and are distributed among all TNBC subtypes. The less cisplatin-responsive LAR and M TNBC subtypes show different regulation of 13 genes compared to the more sensitive BL1 and BL2 subtypes. These 13 genes identify a variety of cisplatin-resistance mechanisms including increased transport and detoxification of cisplatin, and mis-regulation of the epithelial to mesenchymal transition. CONCLUSIONS: We identified gene signatures in resistant TNBC subtypes indicative of mechanisms of cisplatin. Our results indicate that response to cisplatin in TNBC has a complex foundation based on impact of treatment on distinct cellular pathways. We find that examination of expression data in the context of heterogeneous data such as drug-gene interactions leads to a better understanding of mechanisms at work in cancer therapy response