The Optimisation and Derivative Design of Lead Compounds to Inhibit Staphylococcus aureus Surface Proteins Using Computational Tools

Atopic dermatitis (AD), also known as eczema, is a genetically transmitted chronic skin disorder that is associated with other conditions such as asthma and allergic rhinitis. It affects people at all stages of life and can seriously impair quality of life due to repeated itching and scratching resulting in crusted lesions and sleep loss. Staphylococcus aureus colonisation on the skin of patients with AD exacerbates the symptoms. Current treatments for S. aureus colonised AD skin are antibiotics, however resistance in S. aureus has been reported. Clumping factor B (ClfB), a S. aureus surface protein, is an important virulence factor for AD skin colonisation and ligands for ClfB are exposed on AD skin. Allantodapsone is a lead compound that inhibits ClfB and clumping factor A (ClfA), however, there are toxicity concerns regarding the compounds structure. Therefore, derivatives of allantodapsone and other derivatives were investigated in silico and in vitro.Analysis of all of the ClfB and ClfA crystal structures was carried out and docking studies performed for the previously identified compounds allantodapsone, MB03, MMV006962 and MMV019241. Furthermore, docking of proposed allantodapsone and MB03 derivatives was also performed. A fragment based approach to MB03 derivative design was also used. Synthesised allantodapsone derivatives were tested in vitro for their inhibitory activity on ClfB mediated S. aureus adhesion to the loricrin loop region L2V. Three allantodapsone-ClfB binding modes were identified, as well as binding modes for ClfA. Binding modes for MB03, MMV006962 and MMV019241 with ClfB and ClfA were also identified. Based on molecular docking analysis and fragment based design, two derivatives of allantodapsone (thioether and ether) and five derivatives of MB03 were proposed as likely to improve binding. A range of similar compounds to allantodapsone were tested. One of the eleven synthesised compounds (FBCI) displayed ClfB inhibition in vitro. Models of Fibronectin Binding Protein B (FnBPB) in apo and bound forms were generated and validated. Subsequent molecular docking predicted inhibitors of ClfA and ClfB to also bind FnBPA and FnBPB. This suggests that these compounds may act as pan-inhibitors similar to some of the peptide ligands that bind to the receptors.</div

Allantodapsone is a Pan-Inhibitor of Staphylococcus aureus Adhesion to Fibrinogen, Loricrin, and Cytokeratin 10

Staphylococcus aureus infections have become a major challenge in health care due to increasing antibiotic resistance. We aimed to design small molecule inhibitors of S. aureus surface proteins to be developed as colonization inhibitors. We identified allantodapsone in an initial screen searching for inhibitors of clumping factors A and B (ClfA and ClfB). We used microbial adhesion assays to investigate the effect of allantodapsone on extracellular matrix protein interactions. Allantodapsone inhibited S. aureus Newman adhesion to fibrinogen with an IC(50) of 21.3 μM (95% CI 4.5-102 μM), minimum adhesion inhibitory concentration (MAIC) of 100 μM (40.2 μg/mL). Additionally, allantodapsone inhibited adhesion of Lactococcus lactis strains exogenously expressing the clumping factors to fibrinogen (L. lactis ClfA, IC(50) of 3.8 μM [95% CI 1.0–14.3 μM], MAIC 10 μM, 4.0 μg/mL; and L. lactis ClfB, IC(50) of 11.0 μM [95% CI 0.9–13.6 μM], MAIC 33 μM, 13.3 μg/mL), indicating specific inhibition. Furthermore, the dapsone and alloxan fragments of allantodapsone did not have any inhibitory effect. Adhesion of S. aureus Newman to L2v loricrin is dependent on the expression of ClfB. Allantodapsone caused a dose dependent inhibition of S. aureus adhesion to the L2v loricrin fragment, with full inhibition at 40 μM (OD(600) 0.11 ± 0.01). Furthermore, recombinant ClfB protein binding to L2v loricrin was inhibited by allantodapsone (P < 0.0001). Allantodapsone also demonstrated dose dependent inhibition of S. aureus Newman adhesion to cytokeratin 10 (CK10). Allantodapsone is the first small molecule inhibitor of the S. aureus clumping factors with potential for development as a colonization inhibitor. IMPORTANCE S. aureus colonization of the nares and the skin provide a reservoir of bacteria that can be transferred to wounds that can ultimately result in systemic infections. Antibiotic resistance can make these infections difficult to treat with significant associated morbidity and mortality. We have identified and characterized a first-in-class small molecule inhibitor of the S. aureus clumping factors A and B, which has the potential to be developed further as a colonization inhibitor