PhD in Chemistry. School of Chemistry, Cardiff University, Wales, United Kingdom Thesis title: Design and development of novel organocatalytic artificial enzymes.
Master degree in Pharmaceutical Chemistry (Chimica e Tecnologia Farmaceutiche). Dipartimento di scienze della vita, University of Modena and Reggio Emilia (UNIMORE), Italy. Thesis title: Synthesis of phosphonamidate (ProTides) and phosphonodiamidate prodrugs of novel acyclic nucleoside phosphonates as potential antibacterial, anthelmintic and antiviral compounds.
Boronate-Based Inhibitors of Penicillin-Binding Proteins: An Underestimated Avenue for Antibiotic Discovery? Valentina Villamil, Luca Svolacchia Brusoni, Fabio Prati, Emilia Caselli, Nicolò Santi Pharmaceuticals, 2025 Penicillin-binding proteins (PBPs) are essential enzymes involved in bacterial cell wall biosynthesis and represent the primary targets of β-lactam antibiotics. However, the efficacy of these agents is threatened by β-lactamase production and PBP alterations, prompting the search for alternative strategies. In this context, boronic acids, long established as potent inhibitors of serine β-lactamases (SBLs), have been proposed as scaffolds for PBP inhibition based on the shared structural and mechanistic features of these enzyme families. This perspective provides a literature-based survey with structural analysis to evaluate emerging evidence on the potential role of boronic acids as PBP-targeting agents, with a particular focus on peptidomimetic boronic acids, repurposed β-lactamase inhibitors, and novel scaffold architectures. While early work showed limited activity against low-molecular-mass PBPs, more recent compounds, particularly certain bicyclic boronates, have demonstrated potent binding and, in some cases, antibacterial activity. Structural analyses reveal diverse binding modes and underscore the role of conformational dynamics in modulating affinity. Despite these advances, significant challenges remain, including target selectivity, membrane permeability, and species-specific differences. Nevertheless, the direct inhibition of PBPs by boronic acids, while still in early development, may offer a viable complement or alternative to β-lactam therapy, warranting further exploration through structure-guided design and comprehensive biological evaluation. Here, we analyze the potential of boronic acid inhibitors (BAIs) to target PBP enzymes, considering their promise as non-β-lactam antimicrobial agents with possible clinical relevance.
Discovery of Boronic Acids-Based β-Lactamase Inhibitors Through In Situ Click Chemistry Nicolò Santi, Alessandra Piccirilli, Federico Corsini, Magdalena A. Taracila, Mariagrazia Perilli, Robert A. Bonomo, Francesco Fini, Fabio Prati, Emilia Caselli International Journal of Molecular Sciences, 2025 In this study, we evaluated in situ click chemistry as a platform for discovering boronic acid-based β-lactamase inhibitors (BLIs). Unlike conventional drug discovery approaches requiring multi-step synthesis, protection strategies, and extensive screening, the in situ method can allow for the generation and identification of potent β-lactamase inhibitors in a rapid, economic, and efficient way. Using KPC-2 (class A carbapenemase) and AmpC (class C cephalosporinase) as templates, we demonstrated their ability to catalyse azide-alkyne cycloaddition, facilitating the formation of triazole-based β-lactamase inhibitors. Initial screening of various β-lactamases and boronic warheads identified compound 3 (3-azidomethylphenyl boronic acid) as the most effective scaffold for kinetic target-guided synthesis (KTGS). KTGS experiments with AmpC and KPC-2 yielded triazole inhibitors with Ki values as low as 140 nM (compound 10a, AmpC) and 730 nM (compound 5, KPC-2). Competitive inhibition studies confirmed triazole formation within the active site, while an LC–MS analysis verified that the reversible covalent interaction of boronic acids did not affect detection of the in situ-synthesised product. While KTGS successfully identified potent inhibitors, limitations in amplification coefficients and spatial constraints highlight the need for optimised warhead designs. This study validates KTGS as a promising strategy for BLI discovery and provides insights for further refinement in fighting β-lactamase-mediated antibiotic resistance.
New dengue virus inhibitors targeting NS3-NS5 interaction identified by in silico screening Giulio Nannetti, Beatrice Mercorelli, Alessandro Bazzacco, Nicolò Santi, Marta Celegato, Salvatore Ferla, Mattia Sturlese, Niklaas J. Buurma, Andrea Brancale, Arianna Loregian Frontiers in Microbiology, 2025 Dengue virus (DENV) poses a major public health concern as it is responsible for approximately 100 million human infections annually. Since no antiviral drugs are currently available to treat DENV infection, the development of effective therapeutic strategies is urgently needed. For anti-DENV drug discovery, the interaction between DENV NS3 and NS5 proteins represents an attractive target, as it is essential for viral replication and is highly conserved across all DENV serotypes. In this study, we report two distinct virtual screenings of commercially available drug-like compounds, which were performed to identify inhibitors of the NS3-NS5 interaction. Both screening approaches led to the identification of hit compounds that were able to reduce NS3-NS5 binding in vitro in a dose-dependent manner, as measured by an ELISA-based assay. Moreover, the hits inhibited the replication of DENV-2 at low micromolar and non-cytotoxic concentrations. Among these, hit 3 exhibited the highest selectivity index and showed antiviral activity against all four DENV serotypes. Biophysical studies indicated that hit 3 exerts its antiviral activity by directly binding to NS5. Hit 3 was then selected for structure-activity relationship studies, leading to the identification of structural analogues that retained anti-DENV activity through the disruption of NS3-NS5 interaction. Overall, this study reports the identification of a series of novel chemical scaffolds endowed with pan-dengue antiviral activity, representing a promising foundation for the development of new anti-DENV agents.
Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter-Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum Rachel A. Powers, Cynthia M. June, Micah C. Fernando, Erin R. Fish, Olivia L. Maurer, Rachelle M. Baumann, Trevor J. Beardsley, Magdalena A. Taracila, Susan D. Rudin, Kristine M. Hujer, Andrea M. Hujer, Nicolò Santi, Valentina Villamil, Maria Luisa Introvigne, Fabio Prati, Emilia Caselli, Robert A. Bonomo, Bradley J. Wallar Journal of Medicinal Chemistry, 2023 High Resolution Image Download MS PowerPoint Slide Class C Acinetobacter -derived cephalosporinases (ADCs) represent an important target for inhibition in the multidrug-resistant pathogen Acinetobacter baumannii . Many ADC variants have emerged, and characterization of their structural and functional differences is essential. Equally as important is the development of compounds that inhibit all prevalent ADCs despite these differences. The boronic acid transition state inhibitor, MB076, a novel heterocyclic triazole with improved plasma stability, was synthesized and inhibits seven different ADC β-lactamase variants with K i values <1 μM. MB076 acted synergistically in combination with multiple cephalosporins to restore susceptibility. ADC variants containing an alanine duplication in the Ω-loop, specifically ADC-33, exhibited increased activity for larger cephalosporins, such as ceftazidime, cefiderocol, and ceftolozane. X-ray crystal structures of ADC variants in this study provide a structural context for substrate profile differences and show that the inhibitor adopts a similar conformation in all ADC variants, despite small changes near their active sites.
The role of streptavidin and its variants in catalysis by biotinylated secondary amines Alexander R. Nödling, Nicolò Santi, Raquel Castillo, Magdalena Lipka-Lloyd, Yi Jin, Louis C. Morrill, Katarzyna Świderek, Vicent Moliner, Louis Y. P. Luk Organic and Biomolecular Chemistry, 2021 Here, we combine the use of host screening, protein crystallography and QM/MM molecular dynamics simulations to investigate how protein enviroment affects iminium catalysis by biotinylated secondary amines in a model 1,4 conjugate addition reaction.
Identifying and validating the presence of guanine-quadruplexes (G4) within the blood fluke parasite schistosoma mansoni Holly M. Craven, Riccardo Bonsignore, Vasilis Lenis, Nicolo Santi, Daniel Berrar, Martin Swain, Helen Whiteland, Angela Casini, Karl F. Hoffmann Plos Neglected Tropical Diseases, 2021 Schistosomiasis is a neglected tropical disease that currently affects over 250 million individuals worldwide. In the absence of an immunoprophylactic vaccine and the recognition that mono-chemotherapeutic control of schistosomiasis by praziquantel has limitations, new strategies for managing disease burden are urgently needed. A better understanding of schistosome biology could identify previously undocumented areas suitable for the development of novel interventions. Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within theSchistosoma mansonigenome. We find that G4 are present in both intragenic and intergenic regions of the seven autosomes as well as the sex-defining allosome pair. Amongst intragenic regions, G4 are particularly enriched in 3´ UTR regions. Gene Ontology (GO) term analysis evidenced significant G4 enrichment in thewntsignalling pathway (p<0.05) and PQS oligonucleotides synthetically derived fromwnt-related genes resolve into parallel and anti-parallel G4 motifs as elucidated by circular dichroism (CD) spectroscopy. Finally, utilising a single chain anti-G4 antibody called BG4, we confirm thein situpresence of G4 within both adult female and male worm nuclei. These results collectively suggest that G4-targeted compounds could be tested as novel anthelmintic agents and highlights the possibility that G4-stabilizing molecules could be progressed as candidates for the treatment of schistosomiasis.
Streptavidin-hosted organocatalytic aldol addition Nicolò Santi, Louis C. Morrill, Louis Y. P. Luk Molecules, 2020 In this report, the streptavidin-biotin technology was applied to enable organocatalytic aldol addition. By attaching pyrrolidine to the valeric motif of biotin and introducing it to streptavidin (Sav), a protein-based organocatalytic system was created, and the aldol addition of acetone with p-nitrobenzaldehyde was tested. The conversion of substrate to product can be as high as 93%. Although the observed enantioselectivity was only moderate (33:67 er), further protein engineering efforts can be included to improve the selectivity. These results have proven the concept that Sav can be used to host stereoselective aldol addition.
Enabling protein-hosted organocatalytic transformations Alexander R. Nödling, Nicolò Santi, Thomas L. Williams, Yu-Hsuan Tsai, Louis Y. P. Luk Rsc Advances, 2020 This review describes the recent approaches on integrating organocatalysis in protein systems.
New dengue virus inhibitors targeting NS3-NS5 interaction identified by in silico screening G Nannetti, B Mercorelli, A Bazzacco, N Santi, M Celegato, S Ferla, ... Frontiers in Microbiology 16, 1663404 , 2025 2025 Citations: 2
Boronate-Based Inhibitors of Penicillin-Binding Proteins: An Underestimated Avenue for Antibiotic Discovery? V Villamil, LS Brusoni, F Prati, E Caselli, N Santi Pharmaceuticals 18 (9), 1325 , 2025 2025 Citations: 3
Discovery of Boronic Acids-Based β-Lactamase Inhibitors Through In Situ Click Chemistry N Santi, A Piccirilli, F Corsini, MA Taracila, M Perilli, RA Bonomo, F Fini, ... International Journal of Molecular Sciences 26 (9), 4182 , 2025 2025 Citations: 4
Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants … RA Powers, CM June, MC Fernando, ER Fish, OL Maurer, RM Baumann, ... Journal of Medicinal Chemistry 66 (13), 8510-8525 , 2023 2023 Citations: 14
Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni HM Craven, R Bonsignore, V Lenis, N Santi, D Berrar, M Swain, ... PLoS Neglected Tropical Diseases 15 (2), e0008770 , 2021 2021 Citations: 8
The role of streptavidin and its variants in catalysis by biotinylated secondary amines AR Nödling, N Santi, R Castillo, M Lipka-Lloyd, Y Jin, LC Morrill, ... Organic & biomolecular chemistry 19 (47), 10424-10431 , 2021 2021 Citations: 4
Transfer hydrogenations catalyzed by streptavidin-hosted secondary amine organocatalysts N Santi, LC Morrill, K Świderek, V Moliner, LYP Luk Chemical Communications 57 (15), 1919-1922 , 2021 2021 Citations: 17
Comparative biological evaluation and G-quadruplex interaction studies of two new families of organometallic gold (I) complexes featuring N-heterocyclic carbene and alkynyl ligands SM Meier-Menches, B Aikman, D Döllerer, WT Klooster, SJ Coles, N Santi, ... Journal of Inorganic Biochemistry 202, 110844 , 2020 2020 Citations: 54
Reactions of biologically inspired hydride sources with B (C6F5) 3 LC Wilkins, N Santi, LYP Luk, RL Melen Philosophical Transactions of the Royal Society A: Mathematical, Physical … , 2017 2017 Citations: 11
Design and Synthesis of Phosphonamidates (ProTides) and Phosphonodiamidates prodrugs of novel Acyclic Nucleoside Phosphonates as potential antibacterial, anthelmintic and … N SANTI Università degli Studi di Modena e Reggio Emilia , 2016 2016
MOST CITED SCHOLAR PUBLICATIONS
Comparative biological evaluation and G-quadruplex interaction studies of two new families of organometallic gold (I) complexes featuring N-heterocyclic carbene and alkynyl ligands SM Meier-Menches, B Aikman, D Döllerer, WT Klooster, SJ Coles, N Santi, ... Journal of Inorganic Biochemistry 202, 110844 , 2020 2020 Citations: 54
Transfer hydrogenations catalyzed by streptavidin-hosted secondary amine organocatalysts N Santi, LC Morrill, K Świderek, V Moliner, LYP Luk Chemical Communications 57 (15), 1919-1922 , 2021 2021 Citations: 17
Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants … RA Powers, CM June, MC Fernando, ER Fish, OL Maurer, RM Baumann, ... Journal of Medicinal Chemistry 66 (13), 8510-8525 , 2023 2023 Citations: 14
Reactions of biologically inspired hydride sources with B (C6F5) 3 LC Wilkins, N Santi, LYP Luk, RL Melen Philosophical Transactions of the Royal Society A: Mathematical, Physical … , 2017 2017 Citations: 11
Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni HM Craven, R Bonsignore, V Lenis, N Santi, D Berrar, M Swain, ... PLoS Neglected Tropical Diseases 15 (2), e0008770 , 2021 2021 Citations: 8
Discovery of Boronic Acids-Based β-Lactamase Inhibitors Through In Situ Click Chemistry N Santi, A Piccirilli, F Corsini, MA Taracila, M Perilli, RA Bonomo, F Fini, ... International Journal of Molecular Sciences 26 (9), 4182 , 2025 2025 Citations: 4
The role of streptavidin and its variants in catalysis by biotinylated secondary amines AR Nödling, N Santi, R Castillo, M Lipka-Lloyd, Y Jin, LC Morrill, ... Organic & biomolecular chemistry 19 (47), 10424-10431 , 2021 2021 Citations: 4
Boronate-Based Inhibitors of Penicillin-Binding Proteins: An Underestimated Avenue for Antibiotic Discovery? V Villamil, LS Brusoni, F Prati, E Caselli, N Santi Pharmaceuticals 18 (9), 1325 , 2025 2025 Citations: 3
New dengue virus inhibitors targeting NS3-NS5 interaction identified by in silico screening G Nannetti, B Mercorelli, A Bazzacco, N Santi, M Celegato, S Ferla, ... Frontiers in Microbiology 16, 1663404 , 2025 2025 Citations: 2
Design and development of novel organocatalytic artificial enzymes N Santi Cardiff University , 2020 2020
Design and Synthesis of Phosphonamidates (ProTides) and Phosphonodiamidates prodrugs of novel Acyclic Nucleoside Phosphonates as potential antibacterial, anthelmintic and … N SANTI Università degli Studi di Modena e Reggio Emilia , 2016 2016
