Main Research Areas: Chimica Organica
PI: Mauro Freccero, Filippo Doria, Valentina Pirota
ERC Sectors: PE5_17 Organic chemistry, PE5_18 Medicinal chemistry, PE5_11 Biological chemistry and chemical biology
Account social:
- Twitter: @G4labP
- Instagram: @G4Lab_Pavia
1. Synthesis of Functional ligands for Nucleic Acid Secondary Structures.
G-Quadruplex (G4) is a four-stranded nucleic acid (NA) secondary structure held together by hydrogen bonding between four guanines. The existence of G4 in genomes, transcriptome, and telomeres implies significant biological functions regulating replication, transcription, translation, and telomere maintenance. The natural G4 folding/unfolding equilibria can be tuned by small molecules acting as nucleic acid ligands (G4L). We design and synthesise selective G4Ls, via modern organic chemistry, recognizing G4 by their topology and structures. The ligands are engineered to carry additional functional groups that change the properties of the ligand upon binding, undergoing catalytically-relevant ligand-target reactivity (alkylation, cross-linking and cleavage) which may be induced also by an external stimulus (induced by light or oxidative stress). The characterization of the ligand properties and reactivity, including G4/ligand interactions is completed by several techniques including circular dichroism (CD), mass spectrometry (MS) and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting and G4-fluorescent intercalator displacement assay (G4-FID).
2. Development of Selective Fluorescent Probe for Nucleic Acids.
The detection of G4 and other NA secondary structures is a key research area in NA diagnostics. Several experimental techniques are capable of characterizing G4 in vitro, but they are difficult to be applied in vivo. To explore G4 transient formations and functions in cells, fluorescent probes are required. We are developing innovative small molecules and conjugates lighting up upon binding, selectively recognizing DNA and RNA G4 and other secondary structures, according their topology structure and sequence. Target selectivity and cell entry are boosted by peptide nucleic acid (PNA) and peptide synthesis and conjugation.
3. Target Guided Synthesis for Nucleic Acid Secondary Structures
Target guided synthesis (TGS) approach is a powerful method to discover novel and selective ligands/drugs assembling structural moieties by click chemistry, guided by a binding pocket. NA secondary structures, such as LTRIII G4, will be used as a template to synthesize the best binders starting from a series of small molecule fragments, functionalized with complementary reacting groups. To date only few examples have been reported where G4 nucleic acids are used as targets, using click catalyzed cycloadditions reactions. We are developing a novel photochemical TGS approach (photo-click-reaction) achievable without metal catalysis, taking advantage of the photochemical generation of reactive moieties pre-organized on the templating G4.
4. Novel photo-generated reactive species for photoaffinity labelling.
Understanding how small molecules interact with proteins and NA at a molecular level is a central challenge of modern chemical biology and drug development and chemistry can provide investigative tools. This can be chemically achieved incorporating photoreactive moieties into small probes, engineered to trap small molecule-protein interactions (SMPIs). This strategy, is termed photoaffinity labelling (PAL). We are designing PAL strategies for NA and NA-binding proteins using photogenerated reactive intermediates such as quinone methides, carbocations, phenoxyl radicals, nitrenes and carbenes, which have to be generated from stable precursors (Mannich bases, aryl azides and diazirines) conjugated to NA-ligands.
5. Synthesis of selective Splicing Inhibitors for anticancer therapy.
The spliceososome (SPL) is a large array of complexes made by small nuclear RNAs and proteins and it is a complex machinery of eukaryotic cells. When splicing factors (protein removing strings of mRNA) undergo somatic mutations the binding/recognition of NC sequences may be defective, inducing the selection of a cryptic (erroneous) SS and resulting into aberrantly spliced transcripts. This aberrant splicing induced by slicing factors’ mutations has been discerned as a key pathway in cancer onset. Small-molecules targeting specific components of SPL offer the intriguing perspectives for devising drug-candidates for cancers due to splicing de-regulation. To achieve this aim, we are focusing our effort on two different approaches. Total synthesis of new herboxidiene derivatives able to selectively bind our target acting as splicing modulators. Synthesis of stable and cyclic peptides, as computational analysis suggested that the allosteric binding pocket can be recognized by specific peptides as well.
6. Biocatalytic "green transition" of industrial processes for the production of Cephalosporin and Carbapenem antibiotics.
Biocatalysis has been recognized as fundamental for the achievement of new sustainable industrial processes in the synthesis of cephalosporin and carbapenem antibiotics. The operative plan envisages the identification of synthetic processes at high cost and high environmental impact as well as the research and the optimization of an enzymatic alternative. The new synthetic processes under investigation have been designed in aqueous solution to replace toxic solvents, and at room temperature, leading to a strong energy saving and a significant reduction of carbon dioxide emissions.
Prof. Sara N. Richter, Dip. di Istologia, Microbiologia e Biotecnologie Mediche (IMBM) , Padua, (Italy).
Prof. Daniela Montesarchio, Dipartimento di Scienze Chimiche, Università di Napoli Federico Secondo, Napoli, (Italy).
Dr. Daniela Verga, Institut Curie, Paris, (France).
Dr. Juan Carlos Morales, Consejo Superior de Investigaciones Científicas (CSIC), Instituto di Parasitologia y Biomedicina, 18016 Armilla, Granada, (Spain).
Prof. Oscar Kuipers, Faculty of Science and Engineering, University of Groningen (Holland).
Dr. Alessandra Magistrato, CNR-IOM Trieste SISSA (Italy).
Dr. Ilse Manet, Istituto per la Sintesi Organica e la Fotoreattività, CNR , Bologna, (Italy).
Dr. Annamaria Biroccio, Istituto Regina Elena, Roma, (Italy).
Prof. Antonella Forlino, Dipartimento di Medicina Molecolare, Università degli studi di Pavia (Italy).
Prof. Yanez Plavec. Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, (Slovenia).
Prof Antonio Antoccia, Dip. Di Scienze, Università “Roma Tre”, Roma, (Italy)
Prof. Giorgio Colombo, Dipartimento di Chimica, Università degli studi di Pavia (Italy).
Dr. Aldo Tava. Polo delle Microalghe, CREA , Lodi (Italy).
Prof. Giulia Grancini. Dipartimento di Chimica, Università degli studi di Pavia (Italy).
Prof. Jean Louis Mergny. Ecole Polytechnique, Paris (France).
Prof. Stefano Alcaro. Dipartimento di Scienze della Salute, Università Magna Grecia di Catanzaro (Italy).
Prof. Giovanni Capranico, Molecular biology Department of Pharmacy & BioTechnology, University of Bologna (Italy).
ACS Dobfar, Tribbiano (Italia)
Chemservice srl, Milano (Italia)
3VSigma, Bergamo (Italia)
- 2020-2025 Project:”Targeting splicing abnormalities in cancer: Developing new splicing modulators for tissue-agnostic therapy”. (Founded by AIRC). Filippo Doria, Head of the Organic Chemistry unit.
- 2021-2023 Project: “Novel bone specific pharmacological treatment for osteogenesis imperfecta” (Founded by NIH:1R21HD106607-01). Filippo Doria, Head of the Organic Chemistry unit.
Novel Therapeutic Horizons: SNCA Targeting in Parkinson’s Disease
A.M. Caramiello, *V. Pirota
Biomolecules 2024, 14(8), 949; doi: 10.3390/biom14080949
Structural Unfolding of G-Quadruplexes: From Small Molecules to Antisense Strategies;
G. Fracchioni, S. Vailati, M. Grazioli, *V. Pirota;
Molecules, 2024, 29, 3488, doi: 10.3390/molecules29153488
Effective lowering of α-synuclein expression by targeting G-quadruplex structures within the SNCA gene
*Pirota, V.; Rey, F.; Esposito, L.; Fantini, V.; Pandini, C.; Gerlando, R.D.; Doria, F.; Mella, M.; Pansarasa, O.; Gandellini, P.; Freccero, M.; *Carelli, S.; Cereda, C.
Int. J. Biol. Macromol., 2024, 134417. https://doi.org/10.1016/j.ijbiomac.2024.134417
Structure–Activity Study on Substituted, Core-Extended, and Dyad Naphthalene Diimide G-Quadruplex Ligands Leading to Potent Antitrypanosomal Agents
Benassi, A., Peñalver, P., Pérez-Soto, M., Pirota, V., Freccero, M., *Morales, J.C., *Doria, F.
J. Med. Chem. 2024, 67, 13, 10643–10654, doi:10.1021/acs.jmedchem.4c00135
Naphthalene Diimide-Tetraazacycloalkane Conjugates Are G-Quadruplex-Based HIV-1 Inhibitors with a Dual Mode of Action;
Nadai, M., Doria, F., Frasson, I., Perrone R., Pirota V.,Bergamaschi G., *Freccero, M., *Richter, S.N.
ACS Infectious Diseases, 2024, 10(2), 489–499, doi:10.1021/acsinfecdis.3c00453
cRGD-Functionalized Silk Fibroin Nanoparticles: A Strategy for Cancer Treatment with a Potent Unselective Naphthalene Diimide Derivative;
V. Pirota, Bisbano G., *Serra M., Torre M. L., Doria F., *Bari E., *Paolillo M.
Cancers, 2023, 15(6), 1725, doi: 10.3390/cancers15061725
G-quadruplex DNA as a target in pathogenic bacteria: efficacy of an extended naphthalene diimide ligand and its mode of action;
R. Cebrián, E. Belmonte-Reche, V. Pirota, A. De Jong, J. C. Morales, M. Freccero, *F. Doria, *O. P. Kuipers;
JMedChem, 2022, 65, 6, 4752–4766. doi: 10.1021/acs.jmedchem.1c01905
Multimeric G-quadruplexes: A review on their biological roles and targeting.
frasson I, Pirota V, *Richter SN, *Doria F.
Int J Biol Macromol. 2022 doi: 10.1016/j.ijbiomac.2022.01.197.
G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action.
Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, *Doria F, *Kuipers OP.
J Med Chem. 2022 doi: 10.1021/acs.jmedchem.1c01905.
Thiosugar naphthalene diimide conjugates: G-quadruplex ligands with antiparasitic and anticancer activity.
Belmonte-Reche E, Benassi A, Peñalver P, Cucchiarini A, Guédin A, Mergny JL, Rosu F, Gabelica V, Freccero M, *Doria F, *Morales JC.
Eur J Med Chem. 2022 doi: 10.1016/j.ejmech.2022.114183.
The Quest for the Right Trade-Off for an Efficient Photoclick Monitoring Reaction.
Benassi A., Pirota V., *Doria F., *Freccero M.,
ChemPhotoChem 2022, 6, e202100204.
Selective targeting of mutually exclusive DNA G-quadruplexes: HIV-1 LTR as paradigmatic model.
Tassinari M, Zuffo M, Nadai M, Pirota V, Sevilla Montalvo AC, Doria F, *Freccero M, *Richter SN.
Nucleic Acids Res. 2020 doi: 10.1093/nar/gkaa186.
A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids.
Nadai M, Doria F, Scalabrin M, Pirota V, Grande V, Bergamaschi G, Amendola V, Winnerdy FR, Phan AT, *Richter SN, *Freccero M.
J Am Chem Soc. 2018 doi: 10.1021/jacs.8b05337.