MedChemLab -Medicinal Chemistry Lab

Macroarea: Medicinal Chemistry

ERC Sectors: PE5_18 Medicinal Chemistry

Web-site: https://labmedchem.unipv.it/

Lab Managers: Simona Collina (Full Professor), Daniela Rossi (Associate Professor), Pasquale Linciano (Assistant Professor), Giacomo Rossino (Assistant Professor)

Junior Staff: Roberta Listro (PhD student), Martina Garbagnoli (PhD student), Elisabetta Tuminelli (Research Fellow)

The research group’s activities are focused on the identification and characterization of new molecules to modulate targets and biological processes involved in neurodegeneration and tumors, with the aim of developing new therapeutic approaches. The inter-disciplinary approach is the driving force of the research activity, which entails the design, synthesis and analysis of new focused compound libraries, as well as the preparation and characterization of chiral compounds. The group also experiments the implementation of green strategies for the synthesis and purification of the compounds that are the subjects of the research topics. The application of Green Chemistry’s principles to the synthesis of compounds of pharmaceutical interest is crucial and concerns various aspects, such as the development of new, effective and eco-friendly synthetic methods, aimed to the reduction of waste, the optimization of resources exploitation and risk containment.Over the years, the group has prepared more than 1000 molecules (both natural and synthetic compounds) with drug-like properties. The biological investigations are carried out with several national and international collaborations. The main research topics (target classes and diseases) are highlighted hereafter.

1. New neuroprotective agents: agonists of the sigma1 receptor (S1R). S1R is involved in several physio-pathological functions of the central nervous system (CNS), including neuroplasticity and neuroprotection, and plays a key role in neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis (ALS), Multiple sclerosis (MS), Alzheimer Disease and neuropathies. S1R modulators with agonist profile can be considered both as pharmacological tools to investigate the molecular mechanisms underlying neurodegenerative diseases, and as promising neuroprotective agents to counteract them. On the other hand, S1R antagonists are being studied as potential analgesics for the treatment of neuropathic pain. Our team developed a wide series of S1R ligands. Among them, (R)-RC33 (a selective S1R agonist, metabolically stable) is currently under optimization for ALS treatment. Concurrently, we have developed and patented a small library of selective S1R antagonists, from which compound PV-752 emerged for its high efficacy in two animal models of neuropathic pain. The group has also identified, for the first time, some S1R agonists able to modulate the activity of aquaporins (AQPs), which are membrane channels involved in water permeability and scavenging of reactive oxygen species.

2. New anticancer agents.
The research is aimed at the identification of novel anticancer agents, which mechanism of action involves the modulation, selective or simultaneous, of sigma receptors, of proteasome and/or of fibroblast growth factor receptors (FGFR). Each of these proteins is involved in different processes related to cell survival and proliferation, and they are therefore considered promising therapeutic targets in the fight against cancer. In particular, it is known that compounds with S1R antagonist and S2R agonist profile have anti-proliferative and pro-apoptotic effects in different experimental models. Compound RC-106, result of our group’s research, is able to modulate both receptor subtypes is endowed with anticancer activity toward a wide panel of cancer cell lines. A new series of analogues (which is the subject of an international patent) has recently been designed and synthetized. These compounds exhibited promising activity against aggressive tumors, such as multiple myeloma and glioblastoma, and they act through multiple mechanisms of action, including the inhibition of proteasome (a multi-catalytic machinery involved in the degradation of proteins which upregulation is correlated to the etiology of various tumors). Our group has also identified a secondary metabolite from a plant extract endowed with moderate inhibitory activity toward proteasome (see research line 5). A series of novel derivatives has been prepared through a rational design approach, and the SAR profile is currently being drawn. Contextually, we have identified ligands selective for the extracellular domains of FGFR, which could represent an additional weapon against neoplasms, since the FGF/FGFR pathway plays a key role in tumor progression and in drug resistance. The ultimate goal of the research is the development of new molecules endowed with bifunctional activity, good selectivity toward cancer cells and efficacy on multi-drug resistant (MDR) cells.

3. Small molecules able to interfere with ELAV proteins.
ELAV proteins belong to the class of RNA-binding proteins (RBPs) which malfunction is associated to different pathologies, including neurodegeneration and cancer. Our team, exploiting a medicinal chemistry approach, studied in-depth the concept of druggability of complexes between mRNA and HuR, a protein of the ELAV family. Through docking studies, we examined the possible interactions of compounds already identified as inhibitors of HuR–RNA, thus hypothesizing the binding pocket, which served as starting point for the design of specific ligands. Combining interaction studies based on NMR techniques and in silico investigations, different chemotypes have been studied, and the main structural requirements for the HuR-ligand interaction have been identified. Based on the obtained results, new chemical entities have been designed and synthesized, which are now under evaluation.

4. Bacterial Quorum Sensing (QS) inhibitors as tools to counteract antimicrobials resistance.
An innovative strategy to counteract antimicrobial resistance (AMR) is to interfere with the biofilm formation and with QS signaling, the cell-to-cell mechanism that bacteria use to communicate, coordinate and act as a population. The bacterial kinase LsrK plays a key role in the QS process. Our team studies the druggability of LsrK, evaluating its potential as a new pharmacological target to develop novel drugs, to be used alone or in combination with current antimicrobials. To identify new potential and developable LsrK inhibitors, we combined virtual screening of an in-house library of plant secondary metabolites with a focused synthesis of small molecules. Selected compounds were tested against LsrK, and the analogue search conducted based on the positive hits led to the identification of low-micromolar LsrK inhibitors. The research, which is currently in its early phase, may lead to the identification of new antibacterial compounds with innovative modes of action.

5. Nature-aided drug discovery.
This research topic is transverse to the others. Indeed, natural products play a major role in the discovery of valuable bioactive molecules. The extraction, characterization and biological evaluation of secondary metabolites can lead to the discovery of compounds endowed with high therapeutic potential. Our group has investigated both local and non-local plant extracts with a bio-guided fractionation approach. Particularly, natural matrices were extracted via conventional (maceration) and innovative (microwave and ultrasound assisted extraction) methods. Over the years, we have identified molecules with neuroprotective, anti-inflammatory and anticancer activities, as well as compounds able to interfere with ELAV-RNA complex (research topic 3) and inhibitors of LsrK (research topic 4).

• 1. Research topic: neuroprotective S1R modulators.
  • Rossino, G.; Rui, M.; Linciano, P.; Rossi, D.; Boiocchi, M.; Peviani, M.; Poggio, E.; Curti, D.; Schepmann, D.; Wünsch, B.; González-Avendaño, M.; Vergara-Jaque, A.; Caballero, J.; Collina, S. Bitopic Sigma 1 Receptor Modulators to Shed Light on Molecular Mechanisms Underpinning Ligand Binding and Receptor Oligomerization. J. Med. Chem. 2021. https://doi.org/10.1021/acs.jmedchem.1c00886. o
  • Pellavio, G.; Rossino, G.; Gastaldi, G.; Rossi, D.; Linciano, P.; Collina, S.; Laforenza, U. Sigma-1 Receptor Agonists Acting on Aquaporin-Mediated H2O2 Permeability: New Tools for Counteracting Oxidative Stress. Int. J. Mol. Sci. 2021, 22 (18), 9790. https://doi.org/10.3390/ijms22189790.
• 2. Research topic: novel anticancer agents.
  • Listro, R.; Stotani, S.; Rossino, G.; Rui, M.; Malacrida, A.; Cavaletti, G.; Cortesi, M.; Arienti, C.; Tesei, A.; Rossi, D.; Giacomo, M. D.; Miloso, M.; Collina, S. Exploring the RC-106 Chemical Space: Design and Synthesis of Novel (E)-1-(3-Arylbut-2-En-1-Yl)-4-(Substituted) Piperazine Derivatives as Potential Anticancer Agents. Front. Chem. 2020, 8. https://doi.org/10.3389/fchem.2020.00495.
  • Tesei, A.; Cortesi, M.; Pignatta, S.; Arienti, C.; Dondio, G. M.; Bigogno, C.; Malacrida, A.; Miloso, M.; Meregalli, C.; Chiorazzi, A.; Carozzi, V.; Cavaletti, G.; Rui, M.; Marra, A.; Rossi, D.; Collina, S. Anti-Tumor Efficacy Assessment of the Sigma Receptor Pan Modulator RC-106. A Promising Therapeutic Tool for Pancreatic Cancer. Front. Pharmacol. 2019, 10. https://doi.org/10.3389/fphar.2019.00490.
• 3. Research topic: small molecules interfering with RBPs.
  • Della Volpe, S.; Linciano, P.; Listro, R.; Tumminelli, E.; Amadio, M.; Bonomo, I.; Elgaher, W. A. M.; Adam, S.; Hirsch, A. K. H.; Boeckler, F. M.; Vasile, F.; Rossi, D.; Collina, S. Identification of N,N-Arylalkyl- icolinamide Derivatives Targeting the RNA-Binding Protein HuR, by Combining Biophysical Fragment-Screening and Molecular Hybridization. Bioorganic Chem. 2021, 116, 105305. https://doi.org/10.1016/j.bioorg.2021.105305.
  • Ambrosio, F. A.; Coricello, A.; Costa, G.; Lupia, A.; Micaelli, M.; Marchesi, N.; Sala, F.; Pascale, A.; Rossi, D.; Vasile, F.; Alcaro, S.; Collina, S. Identification of Compounds Targeting HuD. Another Brick in the Wall of Neurodegenerative Disease Treatment. J. Med. Chem. 2021, 64 (14), 9989–10000. https://doi.org/10.1021/acs.jmedchem.1c00191.
• 4. Research topic: Fighting Antimicrobials Resistance by interfering with bacterial Quorum Sensing.
  • Linciano, P., Cavalloro, V., Martino, E., Kirchmair, J., Listro, R., Rossi, D., Collina, S. Tackling Antimicrobial Resistance with Small Molecules Targeting LsrK: Challenges and Opportunities. J.Med.Chem., 63, 15243-15257, 2020. https://dx.doi.org/10.1021/acs.jmedchem.0c01282.
  • Stotani, S.; Gatta, V.; Madarametla, P.; Padmanaban, M.; Karawajczyk, A.; Giordaletto, F.; Tammela, P.; Laitinen, T.; Poso, A.; Tzalis, D., Collina, S. DPD-inspired discovery of novel LsrK kinase inhibitors: an opportunity to fight antimicrobial resistance. J. Med. Chem., 62, 5, 2720-2737, 2019. https://doi.org/10.1021/acs.jmedchem.9b00025.
• 5. Research topic: nature-aided drug discovery.
  • Malacrida, A.; Cavalloro, V.; Martino, E.; Costa, G.; Ambrosio, F.A.; Alcaro, S.; Rigolio, R.; Cassetti, A.; Miloso, M.; Collina, S. Anti-Multiple Myeloma Potential of Secondary Metabolites from Hibiscus sabdariffa — Part 2. Molecules 2021, 26, 6596. https://doi.org/10.3390/molecules26216596.
  • Cavalloro, V.; Marrubini, G.; Stabile, R.; Rossi, D.; Linciano, P.; Gheza, G.; Assini, S.; Martino, E.; Collina, S. Microwave-Assisted Extraction and HPLC-UV-CD Determination of (S)-Usnic Acid in Cladonia Foliacea. Molecules 2021, 26 (2), 455. https://doi.org/10.3390/molecules26020455.

National collaborations 

• New neuroprotective agents: agonists of the sigma1 receptor (S1R). Collaborations: D. Curti (Biology and Biotechnology Department “L. Spallanzani” – University of Pavia), G. Cavaletti, A. Scuteri (Experimental neurology Unit – Milano-Bicocca University), S. Rossi (Drug Science Department, Biopharmaceutics and Formulation Development Laboratory – University of Pavia), U. Laforenza (Department of Molecular Medicine, Section of Human Physiology – University of Pavia).

• New anticancer agents. Collaborations: A. Tesei (Laboratorio di Radiobiologia e Farmacologia Preclinica – IRCCS, Meldola, FC), M. Paolillo (Drug Sciences Department, Section of Pharmacology – University of Pavia) D. Curti (Biology and Biotechnology Department “L. Spallanzani” – University of Pavia)

• Small molecules able to interfere with ELAV proteins. Collaborations: F. Vasile (Chemistry Department – University of Milan), A. Pascale, M. Amadio (Drug Sciences Department, Section of Pharmacology – University of Pavia), G. Costa, S. Alcaro (Department of Health Sciences – University “Magna Græcia” of Catanzaro), A. Provenzani, C. Zucal (Department of Cellular, Computational and Integrative Biology CIBIO – Università di Trento).

• Bacterial Quorum Sensing (QS) inhibitors as tools to counteract antimicrobials resistance. Collaborators: G. Pietrocola (Department of Molecular Medicine – University of Pavia).

• Nature-aided drug discovery. Collaborations: E. Martino (Earth and Enviromental Sciences Department – University of Pavia), M. Miloso (Experimental Neurology Unit – Milano-Bicocca University), M. Paolillo (Drug Sciences Department, Section of Pharmacology – University of Pavia)

International collaborations

• New neuroprotective agents: agonists of the sigma1 receptor (S1R). Collaborations: B. Wünsch (Institute of Pharmaceutical and Medicinal Chemistry – University of Münster, Germany), J. Caballero (Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Cile).

• Small molecules able to interfere with ELAV proteins. Collaborations: A.K.H. Hirsch (Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany), M. Sattler (Institute of Structural Biology – Helmholtz Zentrum München).

• Nature-aided drug discovery. Collaborations: M. Sousa (Center for Neurosciences and Cell Biology – University of Coimbra, Portugal) and M. Machado (Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Vairão, Portugal), T. Langer (Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry – Faculty of Life Sciences, University of Vienna).

Project commissioned by CNR (Consiglio Nazionale delle Ricerche), Translational Pharmacology Institute, Rome, and conducted in collaboration with the pharmaceutical technology research group, coordinated by prof. Silvia Rossi, and with the company Silk Biomaterial

The team has a long experience in the medicinal chemistry field (synthesis, structural characterization, and structure-activity relationship studies of potentially bioactive molecules) as well as in the identification and isolation of natural compounds and secondary metabolites from plant extracts. The high inter-disciplinary approach is aimed to the identification and optimization of new molecules able to interact with new targets, focusing on therapeutic applications. The team has also a solid experience in the preparation and characterization of enantiopure compounds. The research group has access to a fully equipped laboratory with all the facilities and instrumentation to perform organic synthesis on bench scale and for scale-up synthesis (tens-gram scale), as well as for the extraction of secondary metabolites from natural sources, under the most modern standards of production and rapid purification systems. It possesses two microwave reactors – one dedicated to organic synthesis (CEM Discovery) and one for microwave-assisted extraction (CEM MARSX) – and a FT-IR spectrometer. The laboratory is also equipped with two analytical/semi-preparative HPLCs coupled with Photo Diode Array (PDA) and circular dichroism detectors, several stationary phases (both chiral and achiral) and a polarimeter equipped with Na and Hg lamps. The laboratory is also equipped with hardware and software dedicated to molecular modelling studies. The research group also benefits from the scientific and technical expertise and services provided by the CGS Infrastructure (Centro Grandi Strumenti) which offers up-to-date high-tech instruments for the structural determination and analysis of the synthesized new chemical entities.

SIMONA COLLINA - simona.collina@unipv.it

DANIELA ROSSI - daniela.rossi@unipv.it

PASQUALE LINCIANO - pasquale.linciano@unipv.it

GIACOMO ROSSINO - giacomo.rossino@unipv.it