Rational Design of Selective Adenine-Based Scaffolds for Inactivation of Bacterial Histidine Kinases

Abstract

Bacterial histidine kinases (HKs) are quintessential regulatory enzymes found ubiquitously in bacteria. Apart from their regulatory roles, they are also involved in the production of virulence factors and conferring resistance to various antibiotics in pathogenic microbes. We have previously reported compounds that inhibit multiple HKs by targeting the conserved catalytic and ATP-binding (CA) domain. Herein, we conduct a detailed structure–activity relationship assessment of adenine-based inhibitors using biochemical and docking methods. These studies have resulted in several observations. First, interaction of an inhibitor’s amine group with the conserved active-site Asp is essential for activity and likely dictates its orientation in the binding pocket. Second, a N-NH-N triad in the inhibitor scaffold is highly preferred for binding to conserved Gly:Asp:Asn residues. Lastly, hydrophobic electron-withdrawing groups at several positions in the adenine core enhance potency. The selectivity of these inhibitors was tested against heat shock protein 90 (HSP90), which possesses a similar ATP-binding fold. We found that groups that target the ATP-lid portion of the catalytic domain, such as a six-membered ring, confer selectivity for HKs.

Disarming the virulence arsenal of Pseudomonas aeruginosa by blocking two-component system signaling

“…1b ). 11 Consistent with this, we found that the positional isomer in which the –NH 2 and –CH 3 groups are switched shows minimal activity (comparison of Rilu-3 and 7 , IC 50 = 1.4 mM). The more potent lead from the HTS, Rilu-2 , contains two benzothiazole rings, likely promoting additional polar interactions within the active site.…”

Screening serine/threonine and tyrosine kinase inhibitors for histidine kinase inhibition

“…5). 18,21 Asp 411 and Gly 415 participate in hydrogen bonding interactions to the nitrogen atoms in the bicyclic core in the same manner to that observed in the adenine core. In addition, the pyridine nitrogen is predicted to participate in a hydrogen bond with Asn 380, mimicking the same interaction we had previously reported, though this may be water-mediated given the distance (3.3 Å).…”

“…9 Initial attempts in the 1990s to identify bioactive molecules that targeted HKs were thwarted by problematic compounds that inhibited through aggregation of the protein. 16 Although research has been progressing to identify molecules that inhibit HKs, 17–21 none have progressed to a clinical stage.…”

“…Through docking studies, we postulated the necessity of a nitrogen for hydrogen bonding in the HK active site through a conserved aspartate residue. 21 Compound 32 shares some structural similarities with this base, but it is composed of pyrazine fused to a pyrrole as opposed to a pyrimidine and an imidazole. We could also glean information from the examination of related compounds from the library that were not leads from the HTS (Fig.…”

Strategies to attenuate the competence regulon in Streptococcus pneumoniae

“…With the peptide approach, altering the peptide scaffold to construct pharmacologically enhanced peptidomimetic scaffolds could offer a viable pathway to make these lead compounds more druggable. Alternatively, diverging completely from the peptidic scaffolds into small molecule-based scaffolds that still interact with the target histidine kinase receptor, as was successfully implemented in several other systems, [90][91][92][93] may prove to be the way to convert these anti-virulence compounds into drug leads.…”