Tuberculosis (TB) bacteria infect a third of the world's population and the disease kills 1.8 million people  annually.

Scientists have determined the three-dimensional structure of the target of the first-line anti-tuberculosis drug rifampin. They have also discovered a new class of potential anti-tuberculosis drugs that kill rifampin-resistant and multi-drug-resistant tuberculosis bacteria.

Rifampin, a compound that kills TB bacteria, has been the cornerstone of anti-TB therapy since its discovery in 1961. However, rifampin-resistant TB has spread widely, posing an urgent public health crisis.

Rifampin resistant TB arises when TB bacteria acquire mutations that alter the binding site for rifampin on the enzyme it inhibits in TB bacteria, Mtb RNA polymerase (Mtb RNAP). The alterations of the rifampin binding site prevent rifampin from binding to and inhibiting Mtb RNAP, preventing rifampin from killing TB bacteria.

Intensive efforts also have been underway to develop new, non rifampin-related Mtb RNAP inhibitors that function through binding sites on Mtb RNAP that do not overlap the rifampin binding site and that thus can kill rifampin-resistant TB bacteria. However, until now, these efforts have been hampered by the absence of structural information for Mtb RNAP, making rational, structure-based drug discovery for Mtb RNAP impossible.

In a paper published in Molecular Cell  scientists report the three-dimensional structures of Mtb RNAP and Mtb RNAP bound to rifampin. The structures were determined by use of X-ray crystallography and are at a resolution sufficient to define the positions, conformations and interactions of individual amino acid residues of Mtb RNAP. The results reveal the interactions between Mtb RNAP and rifampin, reveal the mechanism by which rifampin inhibits Mtb RNAP, and enable rational, structure-based design of improved rifampin derivatives for inhibition of Mtb RNAP.

In addition, the scientists report the discovery and properties of new, non‑rifampin‑related compounds--Na-aroyl-N-aryl-phenylalaninamides (AAPs)--that potently and selectively inhibit Mtb RNAP and potently and selectively kill TB bacteria.

They also report the structures of Mtb RNAP bound to an AAP and Mtb RNAP bound to both an AAP and rifampin. The results show that AAPs inhibit Mtb RNAP through a binding site that does not overlap the rifampin binding site and thus can inhibit rifampin-resistant Mtb RNAP and kill rifampin-resistant TB bacteria. The results further show that AAPs function additively if co-administered with rifampin and show that AAPs suppress the emergence of resistance if co-administered with rifampin. Taken together, the results show that AAPs are exceptionally promising new lead compounds for anti-TB drug development.

"AAPs represent an entirely new class of Mtb RNAP inhibitors and are, without question, the most promising Mtb RNAP inhibitors for anti-TB drug development since rifampin," senior author said. "We are very actively pursing AAPs. We have synthesized and evaluated more than 600 novel AAPs and have identified AAPs with high potencies and favorable intravenous and oral pharmacokinetics."
 
http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30168-5