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.

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Relazione gestante-feto, modalità del parto e sviluppo fisico del bambino

Extensive literature outlined that the quality of the mother-foetus relationship is considered the main feature with regard to the quality of postnatal mother-infant interaction and also to the child’s psychical development. Nowadays the relationship between the pregnant woman and her foetus is viewed as the central factor of the somatic dialogue between the functioning of the maternal and the foetal organisms. This dialogue is responsible for the physic development of the child, as well as of its psychosomatic structure. Therefore the research area has necessarily had to extend to the analysis of psychological processes concerning: the pregnancy, the couple that is bound by parenthood, the influence of intergenerational dynamics. In fact, the formation of maternal identity, as well as that of the relationship between the woman and the foetus, refers to the pregnant woman’s relationship with her parents, especially with her mother. The same pregnancy, considered as a psychosomatic event, is directly influenced by relational, affective and social factors, particularly by the quality of the interiorized parental relations and the quality of the current relationships (such as that with her partner and with her family of origin). Some studies have begun to investigate the relationship between the pregnant woman and the foetus in term of “prenatal attachment” and its relationship with socio-demographic, psychological e psychopathological aspects (such as pre and post partum depression), but the research area is still largely unexplored. The present longitudinal research aimed to investigate the quality of the pregnant womanfoetus relationship by the prenatal attachment index, the quality of the interiorized relationship with woman’s parents, the level of alexithymic features and maternity social support, in relation with the modulation of the physiology of delivery and of postpartum, as well as of the physical development of the child. A consecutive sample of 62 Italian primipara women without any kind of pathologies, participated in the longitudinal study. In the first phase of this study (third trimester of the pregnancy), it has investigated the psychological processes connected to the affective investment of the pregnant women towards the unborn baby (by Prenatal Attachment Inventory), the mothers’ interiorized relationship with their own parents (by Parental Bonding Instrument), the social and affective support from their partner and their family of origin are able to supply (by Maternity Social Support Scale), and the level of alexithymia (by 20-Toronto Alexithymia Scale). In the second phase of this study, some data concerning the childbirth course carried out from a “deliverygram” (such as labour, induction durations and modalities of delivery) and data relative to the newborns state of well-being (such as Apgar and pH indexes). Finally, in the third phase of the study women have been telephoned a month after the childbirth. The semistructured interview investigated the following areas: the memory concerning the delivery, the return to home, the first interactions between the mother and the newborn, the breastfeeding, the biological rhythms achieved from newborns. From the data analysis a sample with a good level of prenatal attachment and of support social and a good capability to mental functioning emerged. An interesting result is that the most of the women have a great percentage of “affectionless control style” with both parents, but data is not sufficient to interpret this result. Moreover, considering the data relative to the delivery, medical and welfare procedures, that have been necessary, are coherent with the Italian mean, while the percentage of the caesarean section (12.9%) is inferior to the national percentage (30%). The 29% of vaginal partum has got epidural analgesia, which explains the high number (37%) of obstetrician operations (such as Kristeller). The data relative to the newborn (22 male, 40 female) indicates a good state of well-being because Apgar and pH indexes are superior to 7 at first and fifth minutes. Concerning the prenatal phase, correlation analysis showed that: the prenatal attachment scores positively correlated with the expected social support and negatively correlated with the “externally oriented thinking” dimension of alexithymia; the maternity social support negatively correlated with total alexithymia score, particularly with the “externally oriented thinking” dimension, and negatively correlated with maternal control of parental bonding. Concerning the delivery data, there are many correlations (after all obvious) among themselves. The most important are that the labour duration negatively correlated with the newborn’s index state of well-being. Finally, concerning the data from the postpartum phase the women’ assessments relative to the partum negatively correlated with the duration of the delivery and positively correlated with the assessment relative to the return to home and the interaction with the newborn. Moreover the length of permanence in the hospital negatively correlated with women’s assessments relative to the return to home that, in turn, positively correlated with the quality of breastfeeding, the interaction between the mother and the newborn and the biological regulation of the child. Finally, the women’ assessments relative to breastfeeding positively correlated with the mother-child interactions and the biological rhythms of children. From the correlation analysis between the variables of the prenatal phase and the data relative to the delivery, emerged that the prenatal attachment scores positively correlated with the dilatation stage scores and with the newborn’s Apgar index at first minute, the paternal care dimension of parental bonding positively correlated with the lengths of the various periods of childbirth like so the paternal control dimension with placental stage. Moreover, emerged that the expected social support positively correlated with the lengths of the various periods of childbirth and that the global alexithymia scores, particularly “difficulty to describe emotions” dimension, negatively correlated with total childbirth scores. From the correlation analysis between the variables of the prenatal phase and variable of the postpartum phase emerged that the total alexithymia scores positively correlated with the time elapsed from the childbirth to the breastfeeding of the child, the difficulty to describe emotions dimension of the alexithymia negatively correlated with the quality of the breastfeeding, the “externally oriented thinking” dimension of the alexithymia negatively correlated with mother-child interactions, and finally the paternal control dimension of the parental bonding negatively correlated with the time elapsed from the child to the breastfeeding of the child. Finally, from the analysis of the correlation between the data of the partum and the women’s assessments of the postpartum phase, emerged the negative correlation between the woman’s assessment relative to the delivery and the quantitative of obstetrician operations and the lengths of the various periods of childbirth, the positive correlation between the women’s assessment about the length of delivery periods and the real lengths of the same ones, the positive relation between woman’s assessment relative to the delivery and the Apgar index of children. In conclusion, there is a remarkable relation between the quality of the relationship the woman establishes with the foetus that influences the course of the pregnancy and the delivery that, in turn, influences the postpartum outcome, particularly relative to the mother-children relationship. Such data should be confirmed by heterogeneous populations in order to identify vulnerable women and to project focused intervention.

Quali-quantitative study of the phenolic and polyphenolic compounds and their antioxidant capacity in vegetal matrix processed with different technologies

Food technologies today mean reducing agricultural food waste, improvement of food security, enhancement of food sensory properties, enlargement of food market and food economies. Food technologists must be high-skilled technicians with good scientific knowledge of food hygiene, food chemistry, industrial technologies and food engineering, sensory evaluation experience and analytical chemistry. Their role is to apply the modern vision of science in the field of human nutrition, rising up knowledge in food science. The present PhD project starts with the aim of studying and improving frozen fruits quality. Freezing process in very powerful in preserve initial raw material characteristics, but pre-treatment before the freezing process are necessary to improve quality, in particular to improve texture and enzymatic activity of frozen foods. Osmotic Dehydration (OD) and Vacuum Impregnation (VI), are useful techniques to modify fruits and vegetables composition and prepare them to freezing process. These techniques permit to introduce cryo-protective agent into the food matrices, without significant changes of the original structure, but cause a slight leaching of important intrinsic compounds. Phenolic and polyphenolic compounds for example in apples and nectarines treated with hypertonic solutions are slightly decreased, but the effect of concentration due to water removal driven out from the osmotic gradient, cause a final content of phenolic compounds similar to that of the raw material. In many experiment, a very important change in fruit composition regard the aroma profile. This occur in strawberries osmo-dehydrated under vacuum condition or under atmospheric pressure condition. The increment of some volatiles, probably due to fermentative metabolism induced by the osmotic stress of hypertonic treatment, induce a sensory profile modification of frozen fruits, that in some way result in a better acceptability of consumer, that prefer treated frozen fruits to untreated frozen fruits. Among different processes used, a very interesting result was obtained with the application of a osmotic pre-treatment driven out at refrigerated temperature for long time. The final quality of frozen strawberries was very high and a peculiar increment of phenolic profile was detected. This interesting phenomenon was probably due to induction of phenolic biological synthesis (for example as reaction to osmotic stress), or to hydrolysis of polymeric phenolic compounds. Aside this investigation in the cryo-stabilization and dehydrofreezing of fruits, deeper investigation in VI techniques were carried out, as studies of changes in vacuum impregnated prickly pear texture, and in use of VI and ultrasound (US) in aroma enrichment of fruit pieces. Moreover, to develop sensory evaluation tools and analytical chemistry determination (of volatiles and phenolic compounds), some researches were bring off and published in these fields. Specifically dealing with off-flavour development during storage of boiled potato, and capillary zonal electrophoresis (CZE) and high performance liquid chromatography (HPLC) determination of phenolic compounds.

A Law and Economics Analysis of Lobbying Regulation Towards an optimal structure through the Cost Indicator Index

This research primarily represents a contribution to the lobbying regulation research arena. It introduces an index which for the first time attempts to measure the direct compliance costs of lobbying regulation. The Cost Indicator Index (CII) offers a brand new platform for qualitative and quantitative assessment of adopted lobbying laws and proposals of those laws, both in the comparative and the sui generis dimension. The CII is not just the only new tool introduced in the last decade, but it is the only tool available for comparative assessments of the costs of lobbying regulations. Beside the qualitative contribution, the research introduces an additional theoretical framework for complementary qualitative analysis of the lobbying laws. The Ninefold theory allows a more structured assessment and classification of lobbying regulations, both by indication of benefits and costs. Lastly, this research introduces the Cost-Benefit Labels (CBL). These labels might improve an ex-ante lobbying regulation impact assessment procedure, primarily in the sui generis perspective. In its final part, the research focuses on four South East European countries (Slovenia, Serbia, Montenegro and Macedonia), and for the first time brings them into the discussion and calculates their CPI and CII scores. The special focus of the application was on Serbia, whose proposal on the Law on Lobbying has been extensively analysed in qualitative and quantitative terms, taking into consideration specific political and economic circumstances of the country. Although the obtained results are of an indicative nature, the CII will probably find its place within the academic and policymaking arena, and will hopefully contribute to a better understanding of lobbying regulations worldwide.

Semi-synthetic bile acids as novel drug candidate in liver diseases: physico-chemical characterization and HPLC-ES-MS/MS methods for their quali-quantitative analysis in different experimental animal models

The physico-chemical characterization, structure-pharmacokinetic and metabolism studies of new semi synthetic analogues of natural bile acids (BAs) drug candidates have been performed. Recent studies discovered a role of BAs as agonists of FXR and TGR5 receptor, thus opening new therapeutic target for the treatment of liver diseases or metabolic disorders. Up to twenty new semisynthetic analogues have been synthesized and studied in order to find promising novel drugs candidates. In order to define the BAs structure-activity relationship, their main physico-chemical properties (solubility, detergency, lipophilicity and affinity with serum albumin) have been measured with validated analytical methodologies. Their metabolism and biodistribution has been studied in “bile fistula rat”, model where each BA is acutely administered through duodenal and femoral infusion and bile collected at different time interval allowing to define the relationship between structure and intestinal absorption and hepatic uptake ,metabolism and systemic spill-over. One of the studied analogues, 6α-ethyl-3α7α-dihydroxy-5β-cholanic acid, analogue of CDCA (INT 747, Obeticholic Acid (OCA)), recently under approval for the treatment of cholestatic liver diseases, requires additional studies to ensure its safety and lack of toxicity when administered to patients with a strong liver impairment. For this purpose, CCl4 inhalation to rat causing hepatic decompensation (cirrhosis) animal model has been developed and used to define the difference of OCA biodistribution in respect to control animals trying to define whether peripheral tissues might be also exposed as a result of toxic plasma levels of OCA, evaluating also the endogenous BAs biodistribution. An accurate and sensitive HPLC-ES-MS/MS method is developed to identify and quantify all BAs in biological matrices (bile, plasma, urine, liver, kidney, intestinal content and tissue) for which a sample pretreatment have been optimized.

Optimization of molecular and crystalline forms of drugs, agrochemicals, pesticides in relation to activity, bioavailability, patentability and to the fabrication of polymorphs, solvates, co-crystals with green chemistry methods

This doctorate was funded by the Regione Emilia Romagna, within a Spinner PhD project coordinated by the University of Parma, and involving the universities of Bologna, Ferrara and Modena. The aim of the project was: - Production of polymorphs, solvates, hydrates and co-crystals of active pharmaceutical ingredients (APIs) and agrochemicals with green chemistry methods; - Optimization of molecular and crystalline forms of APIs and pesticides in relation to activity, bioavailability and patentability. In the last decades, a growing interest in the solid-state properties of drugs in addition to their solution chemistry has blossomed. The achievement of the desired and/or the more stable polymorph during the production process can be a challenge for the industry. The study of crystalline forms could be a valuable step to produce new polymorphs and/or co-crystals with better physical-chemical properties such as solubility, permeability, thermal stability, habit, bulk density, compressibility, friability, hygroscopicity and dissolution rate in order to have potential industrial applications. Selected APIs (active pharmaceutical ingredients) were studied and their relationship between crystal structure and properties investigated, both in the solid state and in solution. Polymorph screening and synthesis of solvates and molecular/ionic co-crystals were performed according to green chemistry principles. Part of this project was developed in collaboration with chemical/pharmaceutical companies such as BASF (Germany) and UCB (Belgium). We focused on on the optimization of conditions and parameters of crystallization processes (additives, concentration, temperature), and on the synthesis and characterization of ionic co-crystals. Moreover, during a four-months research period in the laboratories of Professor Nair Rodriguez-Hormedo (University of Michigan), the stability in aqueous solution at the equilibrium of ionic co-crystals (ICCs) of the API piracetam was investigated, to understand the relationship between their solid-state and solution properties, in view of future design of new crystalline drugs with predefined solid and solution properties.

Modelling UV response of biomolecules: from electronic structure to ab-initio dynamics.

The interaction of organic chromophores with light initiates ultrafast processes in the timescale of femtoseconds. An atomistic understanding of the mechanism driving such photoinduced reactions opens up the door to exploit them for our benefit. This thesis studies the interactions of ultraviolet light with the DNA/RNA molecules and the amino-acid tryptophan. Using some of the most accurate electronic structure methods and sophisticated environmental modelling, the works documented herein enable quantitative comparisons with cutting-edge experimental data. The relaxation pathways undertaken by the excited molecule are revealed through static and dynamical investigations of the excited-state potential energy surface. The profound role played by the dynamic response of the environment to guide the excitation in these timescales is addressed thoroughly.

Comprehensive characterization of snowfall in terms of microphysical features, quantitative precipitation estimation and scavenging properties by in situ and remote sensing observations at an Antarctic coastal site

Snow plays a crucial role in the Earth's hydrological cycle and energy budget, making its monitoring necessary. In this context, ground-based radars and in situ instruments are essential thanks to their spatial coverage, resolution, and temporal sampling. Deep understanding and reliable measurements of snow properties are crucial over Antarctica to assess potential future changes of the surface mass balance (SMB) and define the contribution of the Antarctic ice sheet on sea-level rise. However, despite its key role, Antarctic precipitation is poorly investigated due to the continent's inaccessibility and extreme environment. In this framework, this Thesis aims to contribute to filling this gap by in-depth characterization of Antarctic precipitation at the Mario Zucchelli station from different points of view: microphysical features, quantitative precipitation estimation (QPE), vertical structure of precipitation, and scavenging properties. For this purpose, a K-band vertically pointing radar collocated with a laser disdrometer and an optical particle counter (OPC) were used. The radar probed the lowest atmospheric layers with high vertical resolution, allowing the first trusted measurement at only 105 m height. Disdrometer and OPC provided information on the particle size distribution and aerosol concentrations. An innovative snow classification methodology was designed by comparing the radar reflectivity (Ze) and disdrometer-derived reflectivity by means of DDA simulations. Results of classification were exploited in QPE through appropriate Ze-snow rate relationships. The accuracy of the resulting QPE was benchmarked against a collocated weighing gauge. Vertical radar profiles were also investigated to highlight hydrometeors' sublimation and growth processes. Finally, OPC and disdrometer data allowed providing the first-ever estimates of scavenging properties of Antarctic snowfall. Results presented in this Thesis give rise to advances in knowledge of the characteristics of snowfall in Antarctica, contributing to a better assessment of the SMB of the Antarctic ice sheet, the major player in the global sea-level rise.