Structure-based drug discovery against M. tuberculosis MptpB: a novel strategy

Lead Research Organisation: University of Manchester
Department Name: Life Sciences

Abstract

Tuberculosis is one of the oldest and most persistent bacterial infectious diseases that affect humans. Despite significant advances to control the spread of tuberculosis with the introduction of vaccines and antibiotics, one third of the human population is still infected. The recent resurgence of the disease, together with the development of drug resistance, is threatening to expand into a future epidemic. New therapeutic approaches are then urgently needed to fight the pathogens. A main bottleneck in the development of drugs is that generally resources and expertise are concentrated in the private sector. In addition companies are highly reluctant to allocate serious investments in poor people s diseases that would certainly compromise their return benefits. We have characterised the activity profile of a protein known to be a virulence factor for tuberculosis causing bacteria and we propose to develop a new drug candidate against this target to treat tuberculosis. We have already identified compounds, which are potent inhibitors of this protein. To take our ambitions further, we must now develop some of the leads we have identified and be able to test them with in vivo mouse models. This will only be possible in a non-profit academic environment at this stage. To do that, we will analyse the molecular interactions of the inhibitors and substrates with the target protein by X-ray crystallography and computer simulations. The information obtained from the structural analysis will be used to design and synthesise new compounds with more specific and selective properties. These new compounds will then be tested for activity against the protein and in cell assays and mouse models to select the best drug candidate for future clinical trials.

Technical Summary

Tuberculosis, one the oldest human infectious disease known, still poses a serious threat to all nations. Tuberculosis incidence and mortality continues to grow worldwide triggered by new viral infections like HIV. The long and complex current treatments discourage compliance from patients and have resulted in multi-drug resistant strains further promoting persistence of the disease. Clearly, new approaches and therapeutical treatments are urgently needed to tackle the increasing spread of the infection, by reducing drug resistance, time of treatment and to be compatible with anti-retroviral therapies. For this, new targets need to be identified and inhibitory compounds explored as suitable drugs anti-tuberculosis. We propose to do that using a novel target, the MptpB phosphatase, a virulence factor from M. tuberculosis. We have recently discovered a new phosphoinositide phosphatase activity for this protein, which is an important factor for the survival of mycobacteria in infected macrophages. Following our biochemical characterisation and the identification of essential catalytic residues, we tested the effect of specific phosphatase inhibitors against MptpB. We found potent inhibitors of this enzyme, which are active in mycobacteria-infected macrophages. MptpB is a unique gene in mycobacterium with no human orthologue, suggesting that it is a potential good candidate for selective drug targeting against tuberculosis. We believe that inhibition of MptpB would potentially trigger the innate immune response in infected patients accelerating the treatment and reducing drug resistance.
Our aim is to develop a drug candidate by optimising the lead compounds we identified. For this, we need to understand the mechanism of inhibition of the compounds and define the molecular determinants for ligand binding to MptpB. We propose a structure-based drug discovery programme that will involve X-ray crystallographic analysis of MptpB in complex with substrates and inhibitors, computer docking simulations, compound synthesis of new specific inhibitors, and integrated with toxicity and activity essays in in vitro cell cultures and in mouse models. The expected outcome of this multidisciplinary programme of work will be new anti-tuberculosis drug candidate for further clinical studies.
 
Description Concept in Confidence
Amount £87,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 12/2014 
End 07/2015
 
Description MCBN-pump priming
Amount £10,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2013 
End 01/2014
 
Description OOSA-MRC
Amount £97,237 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2010 
End 12/2011
 
Description Proof of principle award
Amount £24,800 (GBP)
Organisation University of Manchester 
Department Innovation Group (UMI3)
Sector Private
Country United Kingdom
Start 04/2012 
End 12/2012
 
Description Sparking Impact Award
Amount £11,900 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2014 
End 12/2014
 
Description MRCT-LO 
Organisation MRC-Technology
Country United Kingdom 
Sector Private 
PI Contribution We are testing compounds developed by MRCT in cell toxicity assays and in macrophage infection assays with BCG and Mtb to evaluate efficacy of the compounds
Collaborator Contribution MRCt are responsible for computational chemistry and design and synthesis of new compounds, as well as evaluation of activity on the target
Impact still are early stage bu we have already 10 new compounds to evaluate
Start Year 2016
 
Description Med-Chem 
Organisation University of Manchester
Department School of Chemistry Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution We have started a collaboration with Prof J. Thomas in the chemistry deparment to develop our initial inhibitors against the TB target in the project. Additional funds were requested to the MRC to fund a chemist to do the synthesis of the various compounds we designed.
Impact To date the group of Prof Thomas has provided synthetic compounds for the infection studies and animals tests.
Start Year 2010
 
Description PHRI 
Organisation Rutgers University
Department Public Health Research Institute PHRI
Country United States 
Sector Academic/University 
PI Contribution We have provided the compound for the tests and the protocols for the infections as performed in Manchester.
Collaborator Contribution They have tested our compounds in resistant strains of TB using human macrophage infection models. Currently they are testing them in mouse models of TB
Impact We have preliminary data on the effect of the compounds in resistant strains of TB. We are now working towards obtaining data on the mouse models of TB
Start Year 2009
 
Description TBD-UK 
Organisation University of St Andrews
Department TBD-UK, Tuberculosis drug discovery consortium
Country United Kingdom 
Sector Academic/University 
PI Contribution To date I have been invited to the annual meeting n Glasgow 22-23th November, to present our research
Collaborator Contribution I have been invited to participate in the consortium which is primary focused on developing join initiatives for future funding application and exchange of expertise in drug discovery for TB
Impact This is still early days to measure an output but the impact of the TBD-UK consortium in the Tb research in UK is extremely significant and the aim is to prepare funding applications between different groups in the consortium
Start Year 2010
 
Description TBRC 
Organisation University of Illinois
Department Tuberculosis Reserach Centre
Country United States 
Sector Academic/University 
PI Contribution We have initially included Prof Franzblau as a collaborator for the Medicinal Chemistry efforts and animal tests. This collbaoration was discontinued due to the lack of parsonnel available at the TB Reserach Centre in Chicago to undertake the work. Since then we have initiated other collaborations to cover this work, boht on the chemistry fornt and the animal work.
Collaborator Contribution They produced some synthetic compounds for our assays
Impact The TBRC initially provide some small amount of the compounds we needed for the macrophage infections. After that they could not longer support the chemical synthesis required according to the collaboration.
Start Year 2008
 
Title NOvel MptpB inhibitors 
Description New compounds that inhibit our tuberculosis target MptpB were desgin based on the structure and virtual screening. Synthesis of a family of compounds based on the design were synthesised and tested biochemically. The new compounds show 10 times more activity that the parent compound and have IC50 of 0.4 to 0.7 microM. A patent file is under process 
IP Reference Insufficient Information 
Protection Patent application published
Year Protection Granted
Licensed No
Impact It is early yet to define this until animal efficacy is proven
 
Description BBC 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact A BBC documentary was recorded on TB for the "Insight out" series and I was invited to contribute with an interview regarding our research

This reached the general public and provided an update on the new efforts in drug discovery on TB
Year(s) Of Engagement Activity 2008
 
Description BBC radio world service (Newsday) interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interview for the BBC world service Newsday (prime time) interview as a result of our publication (Vickers et al., 2018)
Year(s) Of Engagement Activity 2018
 
Description HPA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact 50-60 Health professionals attended the Health Protection Agency meeting in Leeds to discuss urgent needs in treatment of TB and future targets

The professionals were very interested in our work, however no significant outcomes resulted form this activity.
Year(s) Of Engagement Activity 2009
 
Description MEN 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Media (as a channel to the public)
Results and Impact A Press release from our Faculty was published in Manchester Evening news summarising our research project recently funded by MRC

This initiated a series of contacts with both professionals and scientists (eg. RSM invitation) in the field. Even members of the public and patients contacted me
Year(s) Of Engagement Activity 2008
 
Description RSM 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited talk at the Royal Society of Medicine as part of the meeting on new drugs against TB.
Audience was about 150 health professionals which showed high interest in our research.

As a result as was later invited to attend a meeting of the Health Protection Agency in Leeds to talk to nurses and doctors on our discoveries
Year(s) Of Engagement Activity 2009