Method of screening antibacterial compounds as inhibitor of Mfd
Embodiments of the present disclosure relate to methods of screening and optionally designing compounds as inhibitors of Mfd (Mutation Frequency Decline), such compounds being useful for the treatment of bacterial infections. Embodiments of the methods include culturing pathogenic bacteria expressing functional Mfd with various concentrations of 1 mM or less, incubating the cultures with and without nitric oxide stress conditions, evaluating bacterial survival in each of the cultures, and calculating the concentration of the molecule required to decrease by 50% the survival rate of the bacteria (IC50) by comparing the cfu of the untreated cultures and cultures following nitric oxide stress.
1. An in vitro method of screening an antibacterial molecule that inhibits mutation frequency decline (Mfd peptide) activity comprising the steps of:
(a) preparing several pairs of cultures of a pathogenic bacteria expressing a functional Mfd in culture media containing different concentrations of said molecule to be tested; wherein said concentrations of molecule to be tested are less than or equal to 1 mM;
(b) incubating one of each pair of cultures in nitric oxide stress conditions obtained by addition of NO donors in said culture media, leaving the other culture of each pair untreated;
(c) evaluating the bacterial survival in each of the cultures;
(d) calculating the concentration of the molecule to be tested required to decrease by 50% the survival rate of the bacteria (IC50) by comparing the cfu of the culture with the molecule to be tested in two conditions: untreated and following nitric oxide stress;
(d2) selecting the molecule showing an IC50 less or equal to 200 μM;
(e) incubating the Mfd peptide with the molecule identified as a Mfd inhibitor;
(f) determining whether or not the ATPase activity of Mfd is reduced relative to the activity of a Mfd that has not been contacted with said molecule.
2. The in vitro method of screening an antibacterial molecule according to claim 1 , wherein said pathogenic bacteria is a Gram-positive or a Gram-negative human pathogenic bacteria.
3. The in vitro method of screening an antibacterial molecule according to claim 1 , wherein said nitric oxide stress is artificially produced in vitro by addition of NO donors at concentration between 0.1 and 2 mM.
4. The in vitro method of screening an antibacterial molecule according to claim 1 , wherein the evaluation of the bacterial survival of step (c) is performed by plating on agar plates the harvested bacteria obtained after incubation of step (b), by flow cytometry, or by using a live and dead kit.
5. The in vitro method of screening an antibacterial molecule that inhibits the Mfd activity according to claim 1 , comprising additional steps prior to said step (a) consisting of in silico screening for potential Mfd inhibitors including:
(a1) generating using a homology modelling program to generate a three-dimensional model of the ATP-binding domain of Mfd using three-dimensional atomic coordinates of the ATP-binding domain of Mfd;
(a2) screening a library of physically-available small molecules for compounds predicted to occupy the ATP-binding site by a docking computational method, a pharmacophore search computational method, a de novo design method, or an active site comparison method; and
(a3) selecting virtual hits for experimental validation according to a docking score, a pharmacophore fitness value, a predicted binding free energy, or an active site similarity score.
6. The in vitro method of screening an antibacterial molecule according to claim 2 , wherein the human pathogenic bacteria is selected from Bacillus cereus group members, Shigella, Salmonella, Clostridium, Staphylococcus, Klebsiella, E. coli, Neisseria, Yersinia, Listeria, Streptococcus, Mycobacterium, Clamydia and Helicobacter species.