Anticancer drug discovery using artificial intelligence: an application in pharmacological activity prediction

Hematological cancers are a heterogeneous family of diseases that can be divided into leukemias, lymphomas, and myelomas, often called “liquid tumors”. Since they cannot be surgically removable, chemotherapy represents the mainstay of their treatment. However, it still faces several challenges like drug resistance and low response rate, and the need for new anticancer agents is compelling. The drug discovery process is long-term, costly, and prone to high failure rates. With the rapid expansion of biological and chemical "big data", some computational techniques such as machine learning tools have been increasingly employed to speed up and economize the whole process. Machine learning algorithms can create complex models with the aim to determine the biological activity of compounds against several targets, based on their chemical properties. These models are defined as multi-target Quantitative Structure-Activity Relationship (mt-QSAR) and can be used to virtually screen small and large chemical libraries for the identification of new molecules with anticancer activity. The aim of my Ph.D. project was to employ machine learning techniques to build an mt-QSAR classification model for the prediction of cytotoxic drugs simultaneously active against 43 hematological cancer cell lines. For this purpose, first, I constructed a large and diversified dataset of molecules extracted from the ChEMBL database. Then, I compared the performance of different ML classification algorithms, until Random Forest was identified as the one returning the best predictions. Finally, I used different approaches to maximize the performance of the model, which achieved an accuracy of 88% by correctly classifying 93% of inactive molecules and 72% of active molecules in a validation set. This model was further applied to the virtual screening of a small dataset of molecules tested in our laboratory, where it showed 100% accuracy in correctly classifying all molecules. This result is confirmed by our previous in vitro experiments.

Development of multicomponent models for the prediction of lubricant oil-fuel dilution in internal combustion engines

The current environmental crisis is forcing the automotive industry to face tough challenges for the Internal Combustion Engines development in order to reduce the emissions of pollutants and Greenhouse gases. In this context, in the last decades, the main technological solutions adopted by the manufacturers have been the direct injection and the engine downsizing, which led to the rising of new concerns related to the fuel-cylinder walls physical interaction. The fuel spray possibly impacts the cylinder liner wall, which is wetted by the lubricant oil thus causing the derating of the lubricant properties, increasing the oil consumption, and contaminating the lubricant oil in the crankcase. Also, concerning hydrogen fuelled internal combustion engines, it is likely that the high near-wall temperature, which is typical of the hydrogen flame, results in the evaporation of a portion of the lubricant oil, increasing its consumption. With regards on the innovative combustion systems and their control strategies, optical accessible engines are fundamental tools for experimental investigations on such combustion systems. Though, due to the optical measurement line, optical engines suffer from a high level of blow-by, which must be accounted for. In light of the above, this thesis work aims to develop numerical methodologies with the aim to build useful tools for supporting the design of modern engines. In particular, a one-dimensional modelling of the lubricant oil-fuel dilution and oil evaporation has been performed and coupled with an optimization algorithm to achieve a lubricant oil surrogate. Then, a quasi-dimensional blow-by model has been developed and validated against experimental data. Such model, has been coupled with CFD 3D simulations and directly implemented in CFD 3D. Finally, CFD 3D simulations coupled with the VOF method have been performed in order to validate a methodology for studying the impact of a liquid droplet on a solid surface.

Cancers of unknown primary site (CUPs) as a model of metastatic process.

Cancers of unknown primary site (CUPs) are a rare group of metastatic tumours, with a frequency of 3-5%, with an overall survival of 6-10 month. The identification of tumour primary site is usually reached by a combination of diagnostic investigations and immunohistochemical testing of the tumour tissue. In CUP patients, these investigations are inconclusive. Since international guidelines for treatment are based on primary site indication, CUP treatment requires a blind approach. As a consequence, CUPs are usually empiric treated with poorly effective. In this study, we applied a set of microRNAs using EvaGreen-based Droplet Digital PCR in a retrospective and prospective collection of formalin-fixed paraffin-embedded tissue samples. We assessed miRNA expression of 155 samples including primary tumours (N=94), metastases of known origin (N=10) and metastases of unknown origin (N=50). Then, we applied the shrunken centroids predictive algorithm to obtain the CUP’s site(s)-of-origin. The molecular test was successfully applied to all CUP samples and provided a site-of-origin identification for all samples, potentially within a one-week time frame from sample inclusion. In the second part of the study we derived two CUP cell lines, and corresponding patient-derived xenografts (PDXs). CUP cell lines and PDXs underwent histological, molecular, and genomic characterization confirming the features of the original tumour. Tissues-of-origin prediction was obtained from the tumour microRNA expression profile and confirmed by single cell RNA sequencing. Genomic testing analysis identified FGFR2 amplification in both models. Drug-screening assays were performed to test the activity of FGFR2-targeting drug and the combination treatment with the MEK inhibitor trametinib, which proved to be synergic and exceptionally active, both in vitro and in vivo. In conclusion, our study demonstrated that miRNA expression profiling could be employed as diagnostic test. Then we successfully derived two CUP models from patients, used for therapy tests, bringing personalized therapy closer to CUP patients.