rpoBeta Inhibitors

Rifampicin (RMP) is one of the most common and efficient natural antibiotics for the treatment of tuberculosis. It binds DNA-dependent RNA polymerase and blocks the exit of the RNA. Drug resistance is a very serious problem since it emerges in 19.3% percent of the population after 12 month of treatment with pure rifampicin or its combinations. Treatment course typically lasts from 6 to 18 month.

The aim of this project is to create a small drug molecule that binds and inhibits RNA polymerase in a similar to rifampicin manner for which drug resistance can not emerge.

Molecular details of mechanism of work of rifampicin are:

   1. Enzyme has to catalyze local melting of the DNA and complementary assembly of mRNA, that’s why at the replication fork both products have to be precisely positioned.

   2. Rifampicin binds nearby the replication fork and occludes part of the RNA exit channel.

   3. In order for mutation to cause resistance it has to block binding of rifampicin while leaving the replication fork unaffected.

Figure 1: Tuberculosis resistance mutations occur at places where drug regions protrude beyond substrate envelope

Crystal structures of bacterial rpoB in complex with RNA hybrid and rifampicin (PDB: 4GZY,1I6V) are overlapped. Three common in the population rifampicin resistant mutants are shown as VdW. Only a small part of rifampicin protrudes beyond the volume of the pocket that has to be occupied by RNA. This region is a hotspot for emergence of resistance, for example, S531Y causes steric clash with the RMP, but not with the RNA.

Our idea is based on “substrate-envelope” hypothesis that originated in Celia Schiffer's group and later developed by Tidor’s lab at MIT. We design our inhibitors to be completely hidden inside the volume RNA occupies. In this case resistance to small molecule is much harder to evolve. This is because mutations that clash with the binding site of a small molecule also have to occlude the substrate-binding site.

This approach has been implemented before to design effectors of quickly evolving proteins for some cancers and HIV.

People: Maksym Korablyov, Huanqin Dai, Gil Alterovitz

References:

1) Campbell EA, Korzheva N, Mustaev A, et al. Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell. 2001;104(6):901-12.

2) Weixlbaumer A, Leon K, Landick R, Darst SA. Structural basis of transcriptional pausing in bacteria. Cell. 2013;152(3):431-41.

3) King NM, Prabu-jeyabalan M, Nalivaika EA, Schiffer CA. Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chem Biol. 2004;11(10):1333-8.

4) Nalam MN, Ali A, Altman MD, et al. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010;84(10):5368-78.

5) Parai MK, Huggins DJ, Cao H, et al. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem. 2012;55(14):6328-41.

6) Animation