Ateneo - UPO

The course deals with drugs as chemical objects: how molecular structure determines properties, target recognition and metabolic fate, and which structural modifications a medicinal chemist can introduce to improve a compound's profile. The module includes 40 hours of lectures and 24 hours of molecular modeling laboratory in a computer room, in which students apply the concepts to a real series of compounds, from searching public databases to the structural interpretation of activity data.

Recommended textbooks (one to be chosen as the main reference):
- Chimica farmaceutica (second edition), A. Gasco, F. Gualtieri, C. Melchiorre, 2020. ISBN 978-8808420268
- Principi di chimica farmaceutica (seventh edition), W. O. Foye, T. L. Lemke, S. W. Zito, V. F. Roche et al., 2021. ISBN 978-8829931538
- An Introduction to Medicinal Chemistry (seventh edition), G. Patrick, 2023. ISBN 978-0198866664
- Chimica Farmaceutica (first edition), G. Costantino, G. Sbardella, 2024. ISBN 978-8836231522

Teaching material provided by the lecturer and available on the D.I.R. platform (http://www.dir.uniupo.it): lecture slides, exercise sheets with commented solutions, step-by-step guides and working files for the laboratory sessions, primary literature articles related to the case studies.

Guidance for exam preparation: for the written test, the chosen textbook and the lecture slides are appropriate; for the laboratory report and its discussion, the operating guides, the working files and the articles indicated for the assigned case are essential.

The course contributes to the educational objectives of the Degree in Biotechnology, chemical-pharmaceutical curriculum, by providing the medicinal chemistry competences needed to understand the drug research and development process and to contribute to it within a multidisciplinary team.

Breakdown of credits by type of teaching activity (7 ECTS, 175 total hours):
- lecture-based teaching (DE): 32 hours of classroom lectures;
- interactive teaching (DI): 32 hours, of which 8 of guided exercises and classroom discussion and 24 of laboratory in a computer room, with individual and small-group work;
- self-study: 111 hours, including individual study, consultation of the materials on D.I.R. and preparation of the laboratory report.

Specific objectives. At the end of the course students are able to:
1. trace the behaviour of a pharmaceutically relevant molecule (ionization state, lipophilicity, target recognition, metabolic stability) back to its structural features;
2. propose and justify structural modifications aimed at a stated goal — increasing potency, selectivity, metabolic stability or solubility — using the repertoire of bioisosterism and drug design strategies;
3. build and interpret a structure-activity series starting from data retrieved in public databases, assessing their quality and comparability;
4. independently use the basic computational tools of medicinal chemistry (chemical and structural databases, descriptor calculation and ADMET prediction, conformational analysis, analysis of a ligand-protein complex, guided docking) and discuss their limitations;
5. document and discuss, in the form of a short technical report, an analysis carried out on a real case, so that others can reproduce it.

No formal prerequisites are required. In order to follow the course profitably, students should have the following knowledge, acquired in the courses of the first two years of the Degree programme:
- organic chemistry: recognition and reactivity of the main functional groups; stereochemistry (absolute configuration, chirality, conformational isomerism); acidity and basicity of organic compounds; elementary reaction mechanisms (nucleophilic substitution, addition, hydrolysis, oxidation and reduction);
- general chemistry: acid-base equilibria, pH and pKa, intermolecular interactions, basic thermodynamics (free energy, enthalpy, entropy);
- biochemistry and molecular biology: structure of amino acids, proteins and nucleic acids; general principles of enzyme catalysis; organization of the cell membrane.

No previous computing skills are required beyond ordinary use of a personal computer: the programs used in the laboratory are introduced starting from elementary operations.

The course consists of 40 hours of lectures and 24 hours of laboratory in a computer room, with one workstation per student.

Lectures are given in four-hour blocks, made of two two-hour modules separated by a break. The first module introduces the conceptual framework with the support of slides, made available on D.I.R. before the lecture; the second applies it to real molecules through guided exercises carried out in class and discussed collectively, so as to practise structural analysis and the formulation of modification hypotheses. This alternation is the means by which the learning outcomes concerning the ability to apply knowledge and making judgements are pursued.

The laboratory follows a single case study, which each student develops individually starting from an assigned series of compounds: every session produces a partial output that feeds into the final report. Sessions are run with a short initial demonstration followed by assisted independent work, and close with a comparison of the results obtained by the different groups. The laboratory is the means by which the learning outcomes concerning the use of computational tools, making judgements and communication skills are pursued.

The D.I.R. platform (http://www.dir.uniupo.it) hosts the slides, the operating guides and working files of the laboratory, the exercise sheets with commented solutions and a discussion forum moderated by the lecturer.

Students who are unable to attend find on D.I.R. all the necessary material, including instructions to reproduce the laboratory sessions independently on a personal workstation, and may arrange with the lecturer dedicated office-hour meetings to check the progress of their report.

For further information please refer to the course page on D.I.R. at http://www.dir.uniupo.it

This module is part of the integrated course MS1851 - Drug design. Assessment is single and collegial; please refer to the record of the integrated course for the overall arrangements.

Laboratory activities are carried out on the computer-room workstations using software that is freely accessible also from a personal computer, so that every activity can be repeated outside class hours.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities
Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the lecturer in charge of the course to define the examination modalities, concerning academic aspects.

The module belongs to the integrated course MS1851: the final mark is single and is awarded collegially by the examination board in the same session, jointly considering the assessment elements of all modules, without averaging separately awarded marks. For the part pertaining to this module, assessment consists of two tests, both compulsory and neither selective with respect to the other.

Test 1 - computer-based test (45 minutes, 30 multiple-choice questions with four alternatives). It assesses knowledge of the contents and the ability to apply them to molecules not discussed in class: recognition of functional groups, acidic, basic and stereogenic centres, prediction of the ionization state, identification of metabolic soft spots and plausible intermolecular interactions, choice of a justified bioisosteric modification. Each correct answer is worth 1 point; wrong and unanswered questions are worth 0 points and carry no penalty.

Test 2 - laboratory report and discussion. Individual report of 3-5 pages on the assigned case, submitted the day of the examination date, followed by a discussion of about 10 minutes. It assesses the ability to apply computational tools, making judgements in assessing data quality and method limitations, and communication skills.

Correspondence between level achieved and mark bands:
- 18-20: correctly recognizes the structural features of a molecule and carries out the laboratory procedures following the instructions; presents in an essential but correct way.
- 21-23: connects structure and properties with appropriate language; interprets the results obtained, recognizing their main limitations.
- 24-26: proposes justified structural modifications consistent with a stated goal; critically assesses the quality of the collected data.
- 27-29: independently integrates concepts from different sections of the programme and discusses the limitations of the computational methods used with original arguments.
- 30 and 30 cum laude: independently tackles a problem not discussed in class, formulates an original design hypothesis and argues its weak points, presenting in a rigorous and concise way.

The minimum pass level requires both tests to be passed.

PART A - LECTURES (40 hours)

Section 1 - The drug as a chemical object (4 hours). Identity and method of medicinal chemistry; the hit-lead-candidate path and the chemist's role within it. Chemical anatomy of a drug molecule: scaffold, decoration, linker; recognition of functional groups; acidic and basic centres; stereogenic centres.

Section 2 - Physicochemical properties and drug-likeness (4 hours). pKa and ionization state at physiological pH; lipophilicity (logP, logD) and partition coefficient; solubility as a molecular property; topological polar surface area, hydrogen bond donors and acceptors, sp3 fraction, rotatable bonds. Empirical drug-likeness rules (Lipinski, Veber) and their limits; property-based design; ligand efficiency and lipophilic efficiency.

Section 3 - Molecular recognition (4 hours). Hydrogen bond, halogen bond, ionic and ion-dipole interactions, cation-pi and pi-pi interactions, van der Waals forces, hydrophobic effect; role of water and desolvation cost. Enthalpic and entropic contributions to the binding free energy; preorganization and conformational cost. Stereochemistry of recognition: three-point contact model, eutomer and distomer, eudismic ratio, chiral switch.

Section 4 - The target from a chemical standpoint (4 hours). Types of binding site: orthosteric, allosteric, protein-protein interfaces, covalent sites, cryptic pockets. Chemistry of the site: available residues, metals, structured waters; druggability. Design consequences: competitive, reversible covalent and irreversible inhibitors (warhead chemistry), transition-state analogues, chelators; chemical basis of selectivity among homologous targets.

Section 5 - Structure-activity relationships and modification strategies (4 hours). Building and reading a series; matched molecular pairs; activity cliffs; comparability of potency data. Identification and use of the pharmacophore. Classical and non-classical isosterism and bioisosterism. Repertoire of structural modifications: extension, homologation, vinylogy, benzology, ring expansion and contraction, ring variation and fusion, simplification, rigidification, conformational blockers, twin drugs and hybrids.

Section 6 - Metabolic fate as chemical reactivity (4 hours). Phase I and phase II transformations read as functional group chemistry; identification of metabolic soft spots from the structure. Chemical strategies to modulate them: fluorination, deuterium isotope effect, rigidification, removal or masking of labile groups. Reactive metabolites and structural alerts; assay-interfering compounds. Prodrugs and mutual prodrugs as linker and reactivation chemistry.

Section 7 - Finding a starting point (4 hours). Chemical space and compound libraries; high-throughput screening and its chemical artefacts; DNA-encoded libraries. Fragment-based approach: ligand efficiency, growing, linking, merging. Other starting points: endogenous ligand, me-too, SOSA approach, repurposing, natural product as a starting scaffold.

Section 8 - From hit to candidate (4 hours). Multiparameter optimization and the trade-off between potency, selectivity, properties and synthetic accessibility. Designing analogues with the synthetic route in mind. Outline of the patentability of a series and its consequences on design.

Section 9 - Integrated case studies (4 hours). Reconstruction of three real stories chosen to revisit different parts of the programme: a classical structure-based case, a selectivity case, an unconventional case. Critical reading of the primary literature.

Section 10 - Beyond the small molecule (4 hours). Chemistry of new therapeutic modalities: peptides and peptidomimetics (N-methylation, stapling, macrocyclization, unnatural amino acids); antibody-drug conjugates (linker chemistry, conjugation sites, payload); degraders and molecular glues; therapeutic oligonucleotides (backbone and sugar modifications, conjugation).

PART B - MOLECULAR MODELING LABORATORY (24 hours, computer room)
The six sessions follow a single case study, from the assigned series of compounds to its structural interpretation.

L1 - The chemical structure as data (4 hours). Drawing and editing structures; SMILES, SMARTS, InChI; file formats and information loss in conversions; generation of three-dimensional coordinates; stereochemistry, tautomers and protonation states.

L2 - Databases and building a series (4 hours). Searching PubChem, ChEMBL, DrugBank, BindingDB; substructure and similarity searching, fingerprints and Tanimoto coefficient; extraction and curation of a structure-activity series: units, assay comparability, duplicates, outliers.

L3 - Properties and drug-likeness in silico (4 hours). Descriptor calculation and profiling of the series; ADMET prediction with freely accessible tools; ligand and lipophilic efficiency computed on the series; applicability domain and limits of predictors.

L4 - The three-dimensional ligand (4 hours). Force-field minimization and conformational analysis; bioactive conformer and conformational penalty; alignment and superposition of analogues; building and using a three-dimensional pharmacophore.

L5 - The target structure and its interactions (4 hours). Protein Data Bank: searching, anatomy of the file, model quality (resolution, B-factor, occupancies, unmodelled regions); structure preparation; analysis of the interactions in a crystallographic complex and comparison with the structure-activity series.

L6 - Guided docking and closing the project (4 hours). Redocking of the crystallographic ligand and assessment by RMSD; docking of the series; comparison between score and experimental activity and critical discussion of the limitations; writing of the report.

INTEGRATION OF THE GENDER DIMENSION
About two hours in total, within Sections 2, 6 and 9, are devoted to the chemical determinants of sex differences in drug response: effect of body composition on the distribution of lipophilic compounds, differences in the expression of metabolizing enzymes and their consequences for the design of analogues, risk of QT interval prolongation and hERG channel affinity, teratogenicity and the role of stereochemistry. The under-representation of female subjects and female animal models in preclinical and clinical studies is also discussed, together with its consequences on the quality of activity and safety data available in the databases used in the laboratory. In Section 9 one case study is devoted to Gertrude Elion's contribution to the birth of rational drug design.

Knowledge and understanding. Students know: the physicochemical properties that determine the behaviour of a drug molecule and the descriptors that quantify them; the nature and geometry of ligand-target interactions; the chemistry of binding sites and the corresponding inhibition strategies; the repertoire of bioisosterism and structural modifications; metabolic transformations read as functional group reactivity; the criteria for choosing a starting point and the logic of multiparameter optimization; the operating principles of the computational tools used in the laboratory.

Applying knowledge and understanding. Students are able to: predict ionization state, lipophilicity and metabolic soft spots from a structure not discussed in class; propose justified structural modifications with respect to a stated goal; extract and curate a structure-activity series from public databases; compute and interpret descriptors and ADMET predictions; analyse a ligand-protein complex and its interactions; run a guided docking calculation and assess its outcome.

Making judgements. Students are able to assess the quality and comparability of activity data retrieved from databases, the quality of an experimental structure and the reliability of a computational prediction, recognizing when a result is not usable; they are able to identify the limits of their own conclusions.

Communication skills. Students are able to write a short technical report, using appropriate terminology also in English, and to discuss its content and limitations orally; they are able to represent a structure and its interactions in a readable way.

Learning skills. Students are able to read a medicinal chemistry paper identifying its design logic, and to learn independently how to use a computational tool starting from the available documentation.

Minimum pass level: recognizing the structural features of a molecule and the main interactions with the target, carrying out the laboratory procedures following the instructions provided, presenting the results in an essential but correct way. Advanced level: independently setting up the analysis of a case not covered in class, proposing and arguing a structural modification hypothesis, critically discussing its limitations and connecting contents from different sections of the programme.