Mannich reaction derivatives of novobiocin with modulated physiochemical properties and their antibacterial activities

Abstract

Synthetic derivatives of the natural product antibiotic novobiocin were synthesized in order to improve their physiochemical properties. A Mannich reaction was used to introduce new side chains at a solvent-exposed position of the molecule, and a diverse panel of functional groups was evaluated at this position. Novobiocin and the new derivatives were tested for their binding to gyrase B and their antibacterial activities against Staphylococcus aureus, Mycobacterium tuberculosis, Francisella tularensis and Escherichia coli. While the new derivatives still bound the gyrase B protein potently (0.07-1.8 μM, IC(50)), they had significantly less antibacterial activity. Two compounds were identified with increased antibacterial activity against M. tuberculosis, with a minimum inhibitory concentration of 2.5 μg/ml.

Figure 1

The structure of novobiocin is comprised of three primary chemical groups: a noviose group, an aminocoumarin group and a hydroxybenzoate group. Previous SAR data and the crystal structure of novobiocin bound to a 43-kD fragment of gyrase B (1KIJ) indicates that the position ortho to the phenol on the hydroxybenzoate group (white arrow) is well positioned for appending an additional solvent-exposed side chain.

Figure 1

The structure of novobiocin is comprised of three primary chemical groups: a noviose group, an aminocoumarin group and a hydroxybenzoate group. Previous SAR data and the crystal structure of novobiocin bound to a 43-kD fragment of gyrase B (1KIJ) indicates that the position ortho to the phenol on the hydroxybenzoate group (white arrow) is well positioned for appending an additional solvent-exposed side chain.

Scheme 1

Reagents and conditions: (a) Amine (1.1 eq), paraformaldehyde (1.1 eq), CH₃COOH (2.0 eq), THF, 120 °C (2 hrs); (b) Acid chlorides and anhydrides (1.2 eq), pyridine, rt (1–4 hrs); (c) acids (1.2 eq), HBTU (1.2 eq), DIPEA (3.0 eq), MeCN, rt (1–4 hrs).