Potential fluorescent ligands for Zn-containing bacterial enzymes: in silico evaluation, synthesis and optical properties

Zinc-containing enzymes play essential roles in bacteria. From the other hand, fluorescent properties of a compound provide a way for it selective and sensitive detection. Here we report about fluorescent derivative with zinc-binding groups, namely, 7-nitrobenzofurazan-4-yl (NBD) 2-picolylamine (NPic2, AKOS008922865), ciprofloxacin 2-picolyl carboxamide (CPFPic2, a homologue of AKOS005560555) and N-NBD-ortho-phenylenediamine (NDBOPD, SCHEMBL19269457). Using the docking-based virtual screening approach and Autodock Vina, MGL Tools and helper program FYTdock we have found that NDBOPD can be bound close to Zn2+ of bacterial metallolactamases (PDB id 2P50) showing docking score from -8.9 to -9.0. Analogously, NPic2 was shown to be able to be bound close to Zn2+ of N-acetyl-D-Glucosamine-6-Phosphate deacetylase of Escherichia coli (2P50), Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase (3ELF), Staphylococcus aureus 3-dehydroquinate synthase (1XAH) and 10 more enzymes with docking score from -7.0 to -8.9, whereas CPFPic2 demonstrated such binding for Bacillus subtilis M32 carboxypeptidase (3HQ2), E. coli Oligoribonuclease (2IGI) and 10 more. Also, the energies of the ground S0 and excited S1 states, the energy levels of the HOMO and LUMO and chemical reactivity descriptors were calculated for NBD-derivatives using the density functional theory at B3LYP/6-31+ g(d,p) level. The compounds were synthesized using SnAr NBD-ylation with NBD-Cl and conjugation using N-hydroxysuccinimide/carbodiimide. Solvatochromic effects together with albumin binding tryptophan fluorescence quenching data were received. Our results support further in vitro antibacterial test opening a way to new “weapon” against pathogenic bacteria.
The work was supported by grants GPSR № 20210560, BRFFI X21-131 as well as Wargaming Stipend grant for V.Z.