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MRC DiMeN Doctoral Training Partnership: Development and understanding modes of action of novel inhibitors of RNA polymerase effective against multi-drug-resistant Mycobacterium tuberculosis

MRC DiMeN Doctoral Training Partnership

, Dr Michael John Hall Wednesday, January 27, 2021 Competition Funded PhD Project (Students Worldwide)
Newcastle United Kingdom Biochemistry Biophysics Biotechnology Genetics Microbiology Molecular Biology Organic Chemistry Pharmaceutical Chemistry Pharmacy Structural Biology

About the Project

Around the world approximately 10 million people fall ill with Tuberculosis (TB) each year. This disease is caused by Mycobacterium tuberculosis, which is responsible for around 1.7 million deaths per year, and is the leading cause of infectious disease, ranking above HIV/Aids. One of the main antibiotics for TB is the antibiotic Rifampicin, which inhibits bacterial RNA polymerase (RNAP). However, rapid selection for mutations in the Rifampicin-binding pocket of RNAP results in frequent occurrence of drug-resistant strains of the disease. In 2016, there were 600,000 new cases of TB which showed resistance to Rifampicin, making treatment difficult and leading to many more deaths from this disease. 

The proposed project is based on our recent discovery of natural relatives of Rifampicin that are effective against Rifampicin-resistant M. tuberculosis (Mol Cell 2018, and unpublished). Like, Rifampicin, the newly discovered molecules also bind in the Rifampicin-binding pocket of RNAP. However, their unique chemistry allows them to both ignore the mutations that lead to Rifampicin resistance, and to alter their mode of action, resulting in greater potency. The finding provides a much needed lead for development of new class of anti-TB drugs.


The primary aim of the proposed project is to investigate in detail the mode of action of these newly discovered relatives of Rifampicin, and to understand how they maintain their activity against Rifampicin-resistant RNAPs and bacteria. As a secondary aim we intent to use our understanding to design and prepare semisynthetic versions of these compounds, with both optimised efficacy and improved pharmacokinetics.

The results will provide a rationale for the further development of drugs against Rifampicin-resistant TB. Besides translational importance, inhibitors of RNAP are powerful molecular tools for understanding the functions of this key complex enzyme that performs first step of gene expression in all living organisms, and malfunctions of which were linked to serious human diseases.

Experimental Approach.

In tight collaboration with local bio-tech company Demuris Ltd (, we will produce and isolate (including fermentation, HPLC, LC-MS) the newly discovered antibiotics. To investigate the modes of action of these RNAP inhibitors we will apply possibly the widest arsenal of molecular biology techniques (including cloning, protein purification from various bacteria, transcription in vitro with different RNAPs, etc.). These will be complemented by microbiology, genetics and structural biology methods. Semisynthetic modifications of the natural compounds will be carried out using organic chemistry (verified by NMR and crystallography).

Prof Zenkin

Dr Hall

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:

Further information on the programme and how to apply can be found on our website: 

Funding Notes

Funded by the MRC for 3.5yrs, including a minimum of 3 months working within the industry partner.

Funding will cover UK tuition fees and an enhanced stipend (around £17,785) only. We aim to support the most outstanding applicants from outside the UK. We are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme. Please read additional guidance here: View Website
Studentships commence: 1st October 2021.
Good luck!


1. Stevenson-Jones F., Woodgate J., Castro-Roa D, Zenkin N*. (2020) Ribosome reactivates transcription by physically pushing RNA polymerase out of transcription arrest. Proc Natl Acad Sci U S A. pii: 201919985. doi: 10.1073/pnas.1919985117
2. Mosaei H., Molodtsov, V., Kepplinger B., Harbottle J., Moon C., Jeeves R., Ceccaroni L., Shin, Y., Morton-Laing S., Marrs M., Wills C., Clegg W., Yuzenkova Y., Perry J., Bacon J., Errington J., Allenby N., Hall M., Murakami K., Zenkin N*.(2018) Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis. Molecular Cell 72(2):263 doi: 10.1016/j.molcel.2018.08.028
3. Yuzenkova, Y., Roghanian, M., Bochkareva, A., Zenkin, N*. (2013) Tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex. Nucleic Acids Res 41:9257-65

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