a.a. 2023/2024

Prebiotics are well known health-promoting bioactive compounds in foods. Main prebiotics are non-digestible oligosaccharides (NDOs). Oligosaccharides can be naturally present in foods, generated during human digestion as well as enzymatically synthesized [1]. The large request of prebiotic ingredients for food, feeds, food supplements, and “cosmeceutical” purposes confirms a significant positive trend in characterization and production of new “functional” ingredients with prebiotic properties. The extraction, isolation, and characterization of bioactive and functional compounds from by-products and wastes recovered from agri-food chains is a challenging and strategic aim in modern food science. According with the “circular economy” concept, often strictly related to the development of bio-based “green” solutions, many by-products is an interesting source of new bioactive ingredients, addressed to functional foods and food supplements market, beside the pharmaceutical one. Pigments, antioxidants, fibers, within a potential unique role in nutrition and food technology, can be extracted, isolated and – following scale up - used. Unfortunately, some performing technical processes sometimes faces with some regulatory-related limits, leading to novel ingredients and novel foods (Regulation EU 2015/2283). Within the extreme large portfolio of bioactive compounds useful as food ingredients with peculiar characteristics, NDOs from animal and plant sources represent an interesting case study in circular economy. Human and bovine milk oligosaccharides (HMOs, BMOs) are well characterized, representing a peculiar strategic tool to improve nutritional quality of milk formula or food for children [2]. Moreover, many plant-derived oligosaccharides can be easily isolated from wastes and by-products (e.g., perisperm/hulls from roasted seeds; grape seed; wastes from vegetables processing) [3-6], as well as produced using enzyme processing. The precision fermentation will allow in the next future the availability of new interesting bioactive ingredients, particularly regarding the fiber-rich material valorization. Moreover, the peculiar capacity of NDOs to be fermented by probiotic bacteria strains as well as from human colonic microbiota, leads to the production of short chain fatty acids (SFAs), strictly correlated with a healthy status in human. These secondary molecules can trigger anti-inflammatory, immunoregulatory, anti-obesity, anti-cancer, anti-diabetes, cardiovascular- and hepato-protective, as well as neuroprotective activities. The in vitro simulated human digestion (INFOGEST and SHIME protocols) can be effectively used to assess and estimate the real prebiotic activity of NDOs, considering the effect of the digestion enzymatic processing. This seminar, starting with the definition of the NDO class and the elucidation of their chemical composition, will explore the interplays between the circular economy challenges, the green chemistry, and the bio-based approaches, especially focusing on the production and isolation of prebiotic ingredients for food and food supplements, debating about the main technical, nutritional and safety-related gaps, finally evaluating the expectations and the challenge of the next future.

This course aims to provide a comprehensive overview of the design, formulation, preparation, control and regulatory aspects of Advanced Therapy Medicinal Products (ATMPs). In the first part, the regulatory framework and scientific basis of ATMPs will be presented, while the second part of the course will be focused on the formulation and technological aspects as well as the industrial production according to the Good Manufacturing Practice (GMP).

Public speaking is a skill that can benefit anyone, whether it is for a professional, academic, or personal purpose. However, many people struggle with anxiety, lack of confidence, or poor communication techniques when they have to speak in front of an audience. This brief course will start from analysing how to overcome these challenges and improve the ability to deliver effective and engaging presentations. This public speaking course will cover the following topics:

 • The basics of public speaking, such as understanding the target audience, planning and organizing the content.

• The techniques of public speaking, such as using appropriate language, voice, gestures, eye contact, and visual aids, and adapting to different situations and feedback.

• The practice of public speaking, such as preparing and rehearsing the speech, managing nervousness and stress, and handling questions and objections.

 During the course, attendees are asked to prepare a brief speech and deliver it to their peers so that together they will analyse strong and weak aspects of their performance.
Public speaking is a skill that anyone can learn, manage and improve and is beneficial not only for professional preparation but it helps increase self-confidence. In other words, students might find it helpful even for more personal aspects in their daily life.

Biomaterials used in orthopedic applications: advantages and disadvantages. - Tissue engineering may offer new treatment alternatives: scaffolds and cells. - Regenerative medicine: want to replace and repair lost or damaged tissues by stimulating the natural regeneration process. The gap between the damaged fragments has to be filled with functional materials that act as a substrate and as a physical three-dimensional microenvironment for inducing the migration and organization of cells from the native tissue. - Differentiation and maturation signals that positively promote osteogenesis or chondrogenesi.

Bioorganic chemistry deals with the understanding of biochemical processes and their application for the development of novel organic chemistry tools. Throughout the course, you will gain a basic understanding of bioorganic chemistry: starting from its key concepts, the course will develop through the analogies between organic reactions and biochemical transformations (Biomimetic Chemistry), the catalytic mechanisms of several classes of enzymes, and how some of the effects we observe in enzyme mechanisms can be applied to organic synthesis as well. Prerequisites Basic knowledge: acid-base theories; principles of chemical kinetics and fundamentals of thermodynamics. Knowledge of organic chemistry: structure, properties, and activities of the main functional groups of organic chemistry; fundamentals of stereochemistry.

!!! ATTENZIONE !!! Sebbene il docente di questo corso sia un chimico organico, questo sicuramente NON È il classico corso di CHIMICA! Non è necessario essere un chimico per apprezzare le tematiche proposte in questo corso. Non importa quale sia la tua preparazione, gli argomenti trattati sono di tipo divulgativo e adatti a tutti, indipendentemente dal background CHIM, BIO o altro. Esplorando leggende, racconti e piccole gemme storiche che si intersecano e si mescolano con la chimica vedremo come singole molecole, prevalentemente di origine vegetale, abbiano avuto un ruolo importante nell’influenzare (e talvolta stravolgere completamente) il corso della storia dell’umanità. Data la natura degli argomenti trattati, il corso sarà tenuto esclusivamente in lingua italiana.

In the field of pharmacological research, scientists employ various experimental methods to understand

complex biological processes. Two fundamental approaches of this exploration involve the development of In vivo and In vitro studies. These terms represent two distinct experimental complementary contexts with unique advantages, applications, and limitations. In vitro models represent the first approaches used in the drug discovery process to characterize the activity, efficacy, toxicity, and biocompatibility of new drug candidates giving information further exploitable in in vivo studies. Moreover, in vitro models represent simplified but versatile models of in vivo tissue/organs that help researcher to obtain many results that can also be spend to better plan their in vivo research.

Once a drug candidate demonstrates effectiveness in in vitro experiments, in vivo models can be employed to advance drug development studies. These preclinical studies typically involve the use of animals to evaluate safety, efficacy and delivery of a drug candidate. On the other hand, in vivo models provide some drawbacks like difference in biokinetics parameters or extrapolation of results to human.

The aim of this course is to illustrate to PhD students how to critically choose between in vitro and in vivostudies, to understand their usefulness and to explore their mutual complementarity. During classes, examples of in vitro and in vivo models used nowadays for the development of drug candidates will be addressed.

A critical piece in drug discovery and development is conducting DMPK (Drug Metabolism and Pharmacokinetics) studies, often referred to as ADME-T (Absorption, Distribution, Metabolism, Elimination, Toxicity). ADME studies are designed to investigate how a chemical (e.g. a drug candidate) is processed by a living organism and how ADME properties could affect its activity. For a drug candidate, "optimizing" ADME properties before clinical investigation is of utmost importance to ensure it is as effective and safe as possible; it is estimated that close to 50% of drug candidates fail because of unacceptable efficacy due to an unfavourable ADME profile. This course aims to provide PhD students engaged in the early drug discovery process awareness about the importance of preclinical ADME investigation, the strategies and the methodologies that assist to achieve efficiency in the hit-to-lead process.

In the last few years, an expanding range of chemical modalities have emerged to modulate cellular pathways and address biological targets previously considered undruggable. Compared to more traditional approaches, these chemical modalities modulate target expression rather than target function, and include RNA therapeutics, protein degraders (e.g., PROteolysis TArgeting Chimeras - PROTACs and molecular glues - MGs), peptide macrocycles, antibody drug conjugates (ADCs), and gene therapy. Most of these technologies have come of age, demonstrating clinical success and opening opportunities for biopharmaceutical innovation. This course aims at providing an overview of new chemical modalities in drug discovery, with a special focus on proximity-based modalities (e.g., MGs, PROTACs, trivalent or trifunctional molecules), as well as covalent drugs, therapeutic peptides and ADCs. Particular attention will be given to explaining how these new modalities are rationally designed and developed, to discussing their advantages and challenges in drug discovery practices over conventional small molecules, as well as to highlighting their current applications and future directions.

Nociceptors are peripheral sensory neurones which respond to painful (noxious) stimuli thanks the expression of nociceptive ion channels. Nociceptors express a unique repertoire of voltage-gated channels, as well as cation channels of the transient receptor potential (TRP), acid-sensing ion channel (ASIC), and purinergic P2X families. The course will focus on the specific properties of nociceptive channels and their role in a number of pain modalities, including inflammatory pain, neuropathic pain, visceral pain, and pain associated to certain pathological conditions, including cancer or migraine.

This course will provide an overview of the fundamental concepts of protein science and drug discovery. The course will cover the basics of protein structure, function, and interactions, as well as the principles of drug discovery and development, including the use of computational methods.

NMR spectroscopy is routinely used to evaluate identity and purity of chemical substances. Most users produce NMR reports based solely on the recording and interpretation of simple 1H and 13C spectra, leaving out information that could be easily recovered with a more in-depth interpretation or with simple additional 1D or 2D NMR experiments. A brief introduction to simple 1D and 2D experiments will be provided, along with instructions for interpreting and reporting NMR data (0.5 CFU). A case study with the complete assignment of the 1H and 13C resonances for a steroid will be presented and discussed (0.5 CFU). 

This short course is targeted at those who wish to learn the basics and challenges of drug screening on information rich cell based models. Cell-based assays, because of their advantages in terms of predictability, multiplexing, miniaturization and automation seem the most appealing tool for the high demands and high quality standards of the early stages of the drug-discovery process. Nevertheless, scientists working on assay development for cellular screening still face a variety of challenges. Aspects of assay design ranging from cell type choice, readout selection, standardization, miniaturization, data analysis, will be covered. Moreover, advantages of targeted versus phenotypic assays in drug screening will be discussed.

Discovery of Green Fluorescent Protein (GFP) has revolutionized Biomedical Sciences, making it possible optical visualization and imaging of organs, cells, sub-cellular structures and proteins in living animals and plants. Generation of full color palette of fluorescent proteins (PFs) and biotechnological engineering of fluorescent probes, based on FRET (fluorescence resonance energy transfer) and cpGFP (circularly permuted GFP), enabled monitoring of dynamic changes of intracellular concentrations of ions and second messengers. Split-GFP probes allowed dynamic visualization of interaction between proteins and organelles. All this made the fluorescent proteins an integral part of the discovery process from basic research to biotechnological tools and products. This course will provide a basic knowledge on structure and usage of GFP and its analogues/derivatives. Examples will include multicolor transgenic animals, structure and usage of probes for investigation of cellular signaling processes, protein-protein interaction and drug screening.

Design of Experiments consists of a panel of chemometric procedures and algorithms aimed at planning the experimental work in a rational way, which means projecting the experiments in order to acquire the highest amount of high-quality and relevant information while performing the lowest number of experiments, thus reducing the experimental effort. In this scenario, the aim of the course is to introduce
the Design of Experiments to beginners, providing a simple description of the mathematical principles
behind these tools but mainly focusing on practical aspects, real-case application and results interpretation thanks to a large variety of practical examples and real datasets. Together with the theoretical description of the most common designs, a few practical exercises will be proposed and carried out together with the students by means of the open-source software CAT, freely downloadable, to provide the students with all the basic knowledge to autonomously apply Design of Experiments in their future career. Finally, brief hints to more advanced techniques aimed at investigating more complex or specific problems will be presented to provide the students a wider panorama of the countless opportunities offered by Design of Experiments.

Proteins crosstalk as well as protein-ligand interactions play essential roles in many biological processes including signaling pathways, transcriptional regulation and numerous other metabolic reactions. In order to understand the role of such protein interactions in biological processes it is important to investigate the interaction dynamics describing the stoichiometry of the complexes, the binding free energy and their binding cooperativity as inter-molecular communication. These biochemical parameters are complementary to structural biology studies. In particular, the enthalpic and entropic components of the binding free energy directly refer to the mechanistic aspects of the binding and have been widely exploited in drug discovery research pipeline. The aim of this course is the description of practical and theoretical aspects of biophysical methods used for measuring the stoichiometry and affinity of many protein interactions. In particular, the course will focus on the application potential of the following techniques in the field of biochemistry structural biology: i) small-angle X-ray scattering; ii) isothermal titration calorimetry (ITC); iii) differential scanning fluorescence (DSF); iv) surface plasmon resonance (SPR) and v) microscale thermophoresis (MST).

The course traces the historical roots of light-based therapies, dating back to ancient Egypt, and navigates through the evolution of photodynamic therapy (PDT) and photothermal therapy (PTT) to their recent applications. Exploring the historical precedents that recognized light as therapeutic potential sets the stage for understanding modern techniques harnessing light for medical treatments. The discussion focuses into the principles underlying PDT and PTT, elucidating how light activates photosensitizing agents to selectively target and destroy diseased cells. This journey spans from early experiments to current advancements, showcasing the precision and versatility these therapies offer in treating cancers, infections, and other medical conditions. Furthermore, the course explores the latest trends and innovations in PDT and PTT, highlighting emerging technologies, novel photosensitizers, and advancements in light delivery systems. The focus lies on elucidating the ongoing research and clinical applications shaping the future landscape of light-based therapies.

The course aims to provide a comprehensive exploration of fluorescence, spanning from its fundamental principles to cutting-edge applications. Beginning with an overview of the basic concepts, attendees will gain a solid foundation in the underlying principles of fluorescence. The discussion will then progress to examine the various factors influencing fluorescence and how they can be manipulated for optimal outcomes. The second part of the course will deal with the diverse applications of fluorescence, with a

particular focus on its pivotal role in bioimaging, medical diagnostics, molecular biology, chemical analysis, and material science. Examples of fluorescent probes and their applications in these fields will be elucidated, emphasizing the impact of fluorescence on advancing our understanding of biological systems. By bridging the foundational principles with the latest advancements, this course aims to

provide a comprehensive understanding of fluorescence, empowering students to apply this versatile phenomenon across a spectrum of scientific disciplines and technological domains.

The natural compounds are an endless source of ideas for the discovery of new drugs to treat diseases, and the total synthesis of complex natural products still represents a big challenge for the organic chemist. While many strategies applied to the synthesis of complex natural products are based on the construction of individual rings or fragments of the natural products followed by a unification step, or by the iterative annulation of one ring onto a preexisting ring, an efficient alternative strategy could be represented by the transannular cyclization reactions. Transannular reactions are defined as "those reactions which lead to the formation of covalent bond between atoms on opposite sides of the ring compound". They usually occur in macrocyclic compounds that, to minimize transannular strain (Prelog strain), are constricted in rigid conformations that force some functional groups to be close to each other. This intimacy between functional groups confers entropic advantages "to enable transformations that are otherwise difficult in intermolecular and intramolecular settings", making transannular reactions a highly efficient tool for the construction of complex polycyclic architectures. Transannular reactions are classified according to the reaction type involved in the cyclization process [Diels-Alder (TADA), ene reaction, [2+2] and other cycloadditions, Michael addition, aldol condensation, Mannich and miscellaneous reaction]. The transannular cyclisation process is the result of a series of cascade reactions that allow us to obtain a complex polycyclic architecture from an easily accessible macrocyclic compound, representing a shortcut in the synthesis of complex natural products. The entire process can be highly influenced by several factors such as the conformation of the macrocycle and the activation strategy. This course will outline the main features and the applications of transannular ring closure reactions and examples will be given to validate this approach as a versatile, efficient and flexible strategy to access new polycyclic structures on the way to the synthesis of important natural products.

Preclinical models that faithfully recapitulate the genomic and histopathological features of cancer are critical for the development of new treatments. The most used models are two-dimensional cell lines established from primary tumors or fluids. While these have provided some important insights into cancer biology, these cell models have significant limitations. To address some of these limitations, spheroids, tumor-derived organoids and microfluidic chips have more recently been used to investigate the role of the three-dimensional environment. Efforts have also been made to develop animal models, including genetically modified mice and patient-derived xenografts. We will highlight strengths and weaknesses of the available in vitro and in vivo models.

For PhD students, the prospect of writing their very own scientific research paper may be both exciting and hard. The goal of this course is to provide effective tools to improve writing skills and manuscript writing process.

Organic chemistry and pharmacognosy have long been an almost unique discipline, with natural products acting as a major driver of advancement for both areas. With the advent of molecular assays, the development of spectroscopy, and the growing sophistication of current synthetic organic chemistry, a comprehensive technical expertise in both fields has become impossible and natural products research has become sectarian and articulated in several sub-disciplines. In this scenario, the role of organic chemistry has undergone a change, moving from a tool of structure elucidation to a mean to manipulate natural products structures and explore their associated biological space. In this context, organic chemistry is metamorphosing into medicinal chemistry, but the transition is essentially molecular in nature, and has been well managed, with organic chemistry retaining a critical role in the development of a scalable synthesis for natural products difficult and/or expensive to obtain by isolation. On the other hand, there is growing evidence that, rather than magic bullets, natural products are magic shotguns, targeting a host of molecular end-points that are often part of homeostatic feed-back loops difficult to perturb with focused monomolecular agents. In this context, mixtures of products like extracts might play an important role, but working with mixtures rather than monomolecular agents is a challenging task that is only now coming of age. 

The interdisciplinary course will provide an overview of the immunomodulatory activity of microbiome and its impact on the pathogenesis of human diseases, cancer in particular. Approaches to modulate gut microbiota composition to enhance response to cancer therapy will be also discussed. Particular attention will be given to the study of the dominant members of the skin and gut microbial ecosystem, their spatial distribution among physical niches and their crucial functions in human health.

The course aims to enrich the theoretical knowledge of statistics and probability with suitable data analysis skills; the course focuses also on data visualization and is based on the free and open source software R.

Formulation step represents a key point in the development of finished pharmaceutical and cosmetic products. The aim of this course is to provide a theoretical and practical overview of formulation approaches and strategies to obtain a successful product.

Cancers promote immunological stresses that induce alterations of the myelopoietic output, defined as emergency myelopoiesis, which lead to the generation of different myeloid populations endowed with tumor-promoting activities. New evidence indicates that acquisition of this tumor-promoting phenotype by myeloid cells is the result of a multistep process, encompassing initial events originating into the bone marrow and later steps operating in the tumor microenvironment. The careful characterization of these sequential mechanisms is likely to offer new potential therapeutic opportunities. The course will describe relevant mechanisms of myeloid cells reprogramming that instate immune dysfunctions and limit  effective responses to anticancer therapy and discuss the influence that metabolic events, as well as chemotherapy, elicit on such events. 

The course aims to present the recent developments in targeting design and strategies for biological and biotechnological drug delivery employing nanoparticulate systems. smart nanocarriers composed of organic (polymeric micelles and vesicles, liposomes, dendrimers, and hydrogels) and inorganic (quantum dots, gold, and mesoporous silica nanoparticles) materials will be described.

Il corso si propone di raccontare la vita e le più importanti scoperte scientifiche di alcuni giganti della chimica dei tempi passati, con particolare enfasi sulle nuove reazioni da loro individuate. In questo ciclo verranno ricordati i seguenti chimici: Ronald Breslow, Francesco Selmi, Cesare Bertagnini, Melvin Calvin. Il corso sarà tenuto in italiano ed in presenza.

The aim of this course is to present and show the potentiality of the archetypical click reactions (CuAAC, Bertozzi copper free click chemistry, Staudinger ligation, SuFex reaction) in different areas of research such as drug discovery, bioconjugation, in vivo imaging. In the first part, the molecular mechanisms of these reactions will be presented and discussed, while in the second part of the course will be presented real applications of these techniques.