The Biological and Computational Chemistry group focus its activity on pursuing new insights in to our understanding of health related biological processes. With a wide experience on asymmetric organic synthesis the group is interested in the design and synthesis of small molecules for therapeutic application or their use in the elucidation of biological functions. By combining a series of multidisciplinary tools and techniques including in-house developed synthetic methodologies, computer-based molecular modelling (QM calculations, docking and Molecular Dynamics) and advanced spectroscopic techniques (i.e. STD-NMR), the main activity of the group concerns identification of small molecules as key modulators and/or inhibitors of target enzymes associated to specific biological functions. This approach provides target validation as well as starting points for further drug discovery.

Currently, the group is dedicating major efforts in the computational study of diverse mechanisms of enzymatic reactions using QM/MM methods. We are also interested in organic reaction mechanisms, with special dedication to organocatalytic and metal-catalyzed reactions.

Currently we are working on several enzymatic mechanisms using QM/MM techniques and various organic reactions mechanism using classical QM but also less used MD simulatons with explicit solvents

Figure. Left: A transition structure of a glycosylation reaction. iddle Left: An organic reacion embedded in a box of THF molecules and a transition structure. Middle Right: A NCI analysis of non-covalent ineractions in a transition structure.Right. QM/MD of a bifurcation reaction.

we report the development 19 of a GalNAc-T2 inhibitor with higher potency compared to those 20 of the T1 and T3 isoforms. The most promising candidate features bivalent GalNAc and thiophene moieties on a peptide chain, 21 enabling binding to both the lectin and catalytic domains of the enzyme. The binding mode was confirmed by competitive saturation 22 transfer difference NMR experiments and validated through molecular dynamics simulations. The inhibitor demonstrated an IC50 of 23 21.4 μM for GalNAc-T2, with 8- and 32-fold higher selectivity over the T3 and T1 isoforms, respectively, representing a significant 24 step forward in the synthesis of specific GalNAc-T inhibitors tailored to the unique structural features of the targeted isoform.

N-Acetylgalactosamine (GalNAc)-type O-glycosylation is an essential posttranslational modification (PTM) that plays fundamental roles in biology. Malfunction of this PTM is exemplified by the presence of truncated O-glycans in cancer.

Mechanistically, this approach exploits two concomitant photochemical processes that sequentially ring-expand the nitroarene into an azepine and then fold it into a rigid bicycle pyrroline by means of singlet nitrene-mediated nitrogen insertion and excited-state-4π electrocyclization.

2-Alkenyl-substituted cyclopropylacetaldehydes undergo enantioselective vinylcyclopropane-cyclopentene (VCP-CP) rearrangement using a Jorgensen-Hayashi-type catalyst. The reaction proceeds through enamine/iminium activation and comprises the in situ generation of a donor-acceptor cyclopropane intermediate that undergoes ring-opening/cyclization. Computational studies together with the experimental data support a type-II DYKAT process operating.

HsPoFUT2 follows a classical SN2 reaction mechanism in which water molecules contribute to a great extent in facilitating the release of the leaving pyrophosphate unit, causing the H transfer from the acceptor nucleophile (Thr/Ser) to the catalytic base, which is the last event in the reaction. This demonstrates the importance of water molecules not only in recognition of the ligands but also in catalysis.

Full mechanistic model, based on computations, demonstrates that the acyl migration proceeds through an anionic stepwise mechanism with linear dependence on the [OH- ] and the pKa of the hydroxyl group toward which the acyl group is migrating.

Stable complexes of piperidine ligands bearing alkyl chains were reached after 10 ns of simulation and continued to be stable for 250 ns 462 (all MD simulations were replicated four times). The complexes showed the ligand in the binding site establishing different interactions with key residues Asp128, Trp180, Asn235, Glu236, Tyr314, and Glu341 and with the correct orientation of the piperidine ring. The ligands showed a complete stability of chair conformations and tend to arrange the aliphatic chains toward the external part, exposed to the solvent, in order to keep interactions of the hydroxyl groups of the piperidine ring.

A copper-catalyzed asymmetric intramolecular reductive cyclization for the synthesis of dibenzo[b,d]azepines is described. Use of 2'-vinyl-biaryl-2-imines as substrates and in situ formed [CuI/(Ph-BPE)] as the catalyst enables the synthesis of 7-membered bridged biarylamines containing both central and axial stereogenic elements in high yields (up to 98%) and with excellent diastereo- and enantioselectivities (>20:1 dr, up to 99% ee).

A highly enantio- and diastereoselective thioureacatalyzed dearomatization of isoquinolines employing N-tert-butyl hydrazones as neutral α-azo carbanion and masked acyl anion equivalents has been developed. Experimental and computational data supports the generation of highly ordered complexes wherein the chloride behaves as a template for the catalyst, the hydrazone reagent and the isoquinolinium cation, providing an excellent stereocontrol in the formation of two contiguous stereogenic centers. Ensuing selective and high-yielding transformations provide appealing dihydroisoquinoline derivatives.

Glycosylations promoted by triflate-generating reagents are widespread synthetic methods for the construction
of glycosidic scaffolds and glycoconjugates of biological and chemical interest. These processes are thought to proceed with the participation of a plethora of activated high energy intermediates such as the α- and β-glycosyl triflates, or even increasingly unstable glycosyl oxocarbenium-like species, among which only α-glycosyl triflates have been well characterized under representative reaction conditions. Interestingly, the remaining less accessible intermediates, yet to be experimentally described, seem to be particularly relevant in α-selective processes, involving weak acceptors. A detailed analysis of several paradigmatic and illustrative examples of such reactions, employing a combination of chemical, NMR, kinetic and theoretical approaches, culminating in the unprecedented detection and quantification of the true β-glycosyl triflate intermediates within activated donor mixtures conclusively show that, even for highly dissociative reactions involving β-close ion pair
(β-CIP) species, the formation of the α-glycoside is necessarily preceded by a bimolecular α → β triflate interconversion, which under certain circumstances becomes the rate-limiting step. Overall, our results rule out the prevalence of the Curtin−Hammett fastexchange assumption for most glycosylations and highlight the distinct reactivity properties of α- and β-glycosyl triflates against neutral and anionic acceptors.

The phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential peripheral membrane glycosyltransferase that initiates the biosynthetic pathway of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. PimA undergoes functionally important conformational changes, including (i) α-helix-to-β-strand and β-strand-to-α-helix transitions and (ii) an “open-toclosed” motion between the two Rossmann-fold domains, a conformational change that is necessary to generate a catalytically competent active site. The nucleotide moiety of GDPMan, and not the sugar ring, facilitates the “open-to-closed” motion, with the β-phosphate group providing the high-affinity binding to PimA. Altogether, the experimental data contribute to a better understanding of the structural determinants involved in the “opento-closed” motion not only observed in PimA but also visualized and/or predicted in other glycosyltransfeases.

The enantioselective synthesis of tropanols has been accomplished through chiral phosphoric acid catalyzed pseudotransannular ring opening of 1-aminocyclohept-4-enederived epoxides. The reaction proceeds together with the desymmetrization of the starting material and leads to the direct formation of the 8-azabicyclo[3.2.1]octane scaffold with excellent stereoselectivity. The synthetic applicability of the reaction was demonstrated by the enantioselective synthesis of the two natural products ()-a-tropanol and (+)-ferruginine.

The mechanism of (4+3) cycloaddition reactions of nitrones with 1,2-diaza-1,3-dienes has been studied by using density functional theory (DFT) methods. The cycloaddition reaction takes place through an asynchronous concerted transition state that reflects a two-stage process in which the formation of the first bond occurs close to the transition state, while the second bond forms well after the transition state.

The addition of 2-bromobenzylmagnesium bromide to chiral N-tert-butanesulfinyl imines provided sulfinamide derivatives that were transformed into dibenzoazaspiro compounds after a palladiumcatalyzed
intramolecular N-arylation. DFT calculations have been performed to rationalize the stereochemical course of the reaction. NCI topological calculations have also been used to evidence crucial noncovalent interactions.The azaspiro compounds reduced the viability of chronic myeloid leukemia cells in the micromolar
range.

A series of glycomimetics of UDP-GlcNAc in which the β-phosphate has been replaced by either an alkyl chain or a triazolyl ring and the sugar moiety has been replaced by a pyrrolidine ring counterbalance with the presence of hydrophobic groups the lack of beta-phosphate. Two of the glycomimetics prepared reach inhibition in the micromolar scale.

Fungal beta-1,3-glucan glucanosyltransferases are glucan-remodeling enzymes that play important roles in cell wall integrity, and are essential for the viability of pathogenic fungi/yeasts. A structure-guided design using a highly conserved transglycosylase from Sacharomyces cerevisiae led to carbohydrate derivatives with high affinity for Aspergillus fumigatus Gel4. Topological anayses seerved to identify main interactions.

A fruitful collaboration led to discover that small molecules are capable of inhibiting glycosyltransferases in sch a efficient way like complex bisubstrates. This study study provides a base of structure and kinetics for further optimization to develop more potent and specific selective inhibitor of ppGalNAc-T to explore site-specific O-GalNAc glycosylation and a new perspective for exploring the molecular mechanism of luteolin.