Algorithmic Mapping and Characterization of the Drug-Induced Phenotypic-Response Space of Parasites Causing Schistosomiasis

Abstract

Neglected tropical diseases, especially those caused by helminths, constitute some of the most common infections of the world's poorest people. Amongst these, schistosomiasis (bilharzia or 'snail fever'), caused by blood flukes of the genus Schistosoma, ranks second only to malaria in terms of human impact: two hundred million people are infected and close to 800 million are at risk of infection. Drug screening against helminths poses unique challenges: the parasite cannot be cloned and is difficult to target using gene knockouts or RNAi. Consequently, both lead identification and validation involve phenotypic screening, where parasites are exposed to compounds whose effects are determined through the analysis of the ensuing phenotypic responses. The efficacy of leads thus identified derives from one or more or even unknown molecular mechanisms of action. The two most immediate and significant challenges that confront the state-of-the-art in this area are: the development of automated and quantitative phenotypic screening techniques and the mapping and quantitative characterization of the totality of phenotypic responses of the parasite. In this paper, we investigate and propose solutions for the latter problem in terms of the following: (1) mathematical formulation and algorithms that allow rigorous representation of the phenotypic response space of the parasite, (2) application of graph-theoretic and network analysis techniques for quantitative modeling and characterization of the phenotypic space, and (3) application of the aforementioned methodology to analyze the phenotypic space of S. mansoni - one of the etiological agents of schistosomiasis, induced by compounds that target its polo-like kinase 1 (PLK 1) gene - a recently validated drug target. In our approach, first, bio-image analysis algorithms are used to quantify the phenotypic responses of different drugs. Next, these responses are linearly mapped into a low- dimensional space using Principle Component Analysis (PCA). The phenotype space is modeled using neighborhood graphs which are used to represent the similarity amongst the phenotypes. These graphs are characterized and explored using network analysis algorithms. We present a number of results related to both the nature of the phenotypic space of the S. mansoni parasite as well as algorithmic issues encountered in constructing and analyzing the phenotypic-response space. In particular, the phenotype distribution of the parasite was found to have a distinct shape and topology. We have also quantitatively characterized the phenotypic space by varying critical model parameters. Finally, these maps of the phenotype space allows visualization and reasoning about complex relationships between putative drugs and their system-wide effects and can serve as a highly efficient paradigm for assimilating and unifying information from phenotypic screens both during lead identification and lead optimization.

Structure‐Based Design, Synthesis, and Biological Evaluation of Triazole‐Based smHDAC8 Inhibitors

“…This despite an apparently favorable lipophilicity index. A variety of schistosome viability assays are currently used in the field [e. g. Panic et al ., Singh et al …”

“…that do not always concur. However, since we have compared compounds that a priori have the same biological target, it is unlikely that they will have different effects on the parasite and that a different viability assay, for example based on morphological characteristics, would give different results. Nevertheless, in view of the potency of the triazole‐based smHDAC8 inhibitors on the enzyme, their further development, aimed at improving their bioavailability, is justified.…”

Quantifying the mechanics of locomotion of the schistosome pathogen with respect to changes in its physical environment

“…This new capacity could complement recent advances in the multi-parametric characterization of schistosome phenotypic space in response to drug insult (8,(61)(62)(63). Future efforts shall focus on establishing proof-of-concept of these parameters for drug discovery with particular attention to their 20 sensitivity and specificity, and address the scalability of the proposed methodologies to higher throughput.…”

Quantifying the mechanics of locomotion of the schistosome pathogen with respect to changes in its physical environment

“…As the mechanism of action of many anthelmintic drugs involves dysregulation of neuromuscular homeostasis [21] or, in the specific case of the schistosome parasite, disruption of the organization of the tegument including its component tubercles [57,58,60], the ability to measure these parameters under no-flow, flow and/or confinement conditions offers an unprecedented degree of sophistication. This new capacity could complement recent advances in the multi-parametric characterization of schistosome phenotypic space in response to drug insult [8,[61][62][63]. Future efforts shall focus on establishing proof-of-concept of these parameters for drug discovery with particular attention paid to their sensitivity and specificity, and address the scalability of the proposed methodologies to higher throughput.…”