Development of Novel Antitubercular Drugs

14 Aug
Published by Miguel Mitchell
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This is a call for creating a tuberculosis research community.

Background

Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), infects approximately two billion people. The World Health Organization estimates that about two million people die each year from TB due to the lack of and inability to afford proper health care.1 Overcrowding and ill-nourishment of poor people living in large cities leads to a high incidence of the disease due to the ease at which the infection can be transferred.2 This contributes to the accelerated speed at which TB spreads in underdeveloped countries. There is also an alarming increase in cases of TB caused by multidrug-resistant strains of Mycobacterium tuberculosis (Mtb), due in part to inadequate drug therapy as a result of incorrectly selected medications or suboptimal drug dosing.3 Thus, there is a need for new drugs targeting enzymes essential to mycobacterial survival.

Research Focus 

My lab is focusing on the inhibition of type II NADH-menaquinone dehydrogenase (ndh-2). By inhibiting ndh-2, the electron transport chain in Mtb becomes blocked and shuts down. Ndh-2 is the only NADH dehydrogenase enzyme expressed in Mtb and is thus vital to its survival.4 Ndh-2 is also found in a number of other bacteria such as Staphylococcus aureus and Enterococcus faecalis but is not expressed in humans.5 Humans rely only on type I NADH dehydrogenase (ndh-1) and thus minimal toxicity in humans is predicted with ndh-2 inhibitors.

Current State of Affairs

My lab has discovered two quaternized promazine derivatives (QPDs), 1 and 2, that both have an MIC (minimum inhbitory concentration) of 3.13 μg/mL vs. Mycobacterium tuberculosis H37Rv and SI values (IC50 vs. human Vero cells/MIC) of 7.6 and 4.1, respectively. 

 compounds 1 and 2

Changing the para substituent to H, CH3O, or NO2 (or replacing benzyl by allyl) raises the MIC.  The pharmacophore definitely needs something aromatic on the quaternized N (84% inhibition for benzyl at 6.25 μg/mL; only 47% inhibition for allyl at 6.25 μg/mL). Our goal:  MIC ≤ 3.13 μg/mL against both current drug regimen-sensitive and multidrug-resistant Mtb and SI ≥ 30.

Although my lab can do good synthetic work, we are solely a post-doc free, undergraduate chemistry department and need assistance in several areas:

  • Antitubercular testing.  So far we have depended on TAACF (Tuberculosis Antimicrobial Acquisition and Coordinating Facility) to get free MIC and SI data.  TAACF is a great resource, but it takes over a year to get data!!  We want to develop better TB cures in a reasonable (<10 yr) timeline. We'd like to work with a group or groups dedicated to testing our compounds and willing to post the MIC and SI data on this site to speed up critical evaluation of potential leads. 
  • Proposing potential ndh-2 inhibiting antitubercular compounds.
  • Letting us know what doesn't work (too toxic, high MIC).
  • Helping with inexpensive synthetic routes to targets.  TB is predominately a disease of the poor and we must be able to scale up the chemistry at low cost.
  • Helping with greener synthetic routes to targets.  It would be great to have efficient atom-economy and minimum hazardous waste production.
  • Synthesizing new QPDs or analogs.  The goal is to stop TB, so go for it!  Just let us know what's happening on this site so that we (and others) don't reinvent the wheel.

This is my first time freely discussing yet to be published medicinal chem research.  It is both daunting and invigorating.  I hope that there are some allies in this effort to stop TB.

1. Maher, D. & Raviglionem, M. C. (1999) in Tuberculosis and Nontuberculous
Mycobacterial Infections, ed. Schlossberg, D. (Saunders, Philadelphia), 4th Ed., pp.104-115.
2. Lowell, A. M. (1999) in Tuberculosis and Nontuberculous Mycobacterial Infections, ed. Schlossberg, D. (Saunders, Philidelphia), 4th Ed., pp. 3-15.
3. Bearing, S. E.; Peloquin, C.A.; Patel, K.B. (1999) in Tuberculosis and Nontuberculous Mycobacterial Infections, ed. Schlossberg, D. (Saunders,
Philadelphia), 4th Ed., pp. 83-91.
4. Weinstein, E.A.; Yano, T.; Li, L.S.; Avarbock, D.; Avarbock, A.; Helm, D.; McColm, A.A.; Duncan, K.; Lonsdale, J.T.; Rubin, H. PNAS 2005, 102, 4548-4553.
5. Melo, A. M. P.; Bandeiras, T. M.; Teixeira, M. Microbiol. Mol. Biol. Rev. 2004, 68, 603-616. 

Comments

gtaylor's picture

Miguel,

I'd love to open a research community for TB. The need is huge!

Are you willing and an appropriate person to be the online community leader/champion/connector? I need a passionate (you seem to have that going for you :-) scientist connected to other researchers in the field to lead each research community. For example for the TB community I need somebody who will try and pull in others and help connect TB researchers to each other and their projects as appropriate. It looks like you're an undergrad. If that's correct, perhaps you play the part of an interim community leader to get it started while we (and you) look for another person. My assumption of course being that as an undergrad you probably haven't yet developed a lot of connections. The great news I think projects like this will help in this area.

I should also note there are also a few minor deliverables I need from a community leader. Things like:

  • Profile information about you so I can add it in the appropriate places on the site e.g. a status note announcing the community and our about page
  • TB specific text for a communty welcome page e.g. the part just above "Join Us and Login" on our welcome page for malaria. I can create the page if you want. I just need the supplemental information.
  • Information for TB specific  research tools page e.g. the research tools page for malaria. (I can help with the formatting of the web page if you just want to send a word document as you get comfortable with our tools.)
  • And lastly if you know of any RSS feeds that are TB specific, that would be great too. If you don't that's ok. I'm finding good diseases specific feeds from connotea and citeulike.

Or would you rather just run the above project and we find another TB community leader? And I really shouldn't say "just". That's a huge contribution in and of itself and I'd like to thank you for taking the leap!

Cheers! 

Ginger 

P.S.

I fixed the formatting issue with your post. I promise, no edits were done. Hope you don't mind. I'm not quite sure, but it looks like you may have hit the enter/return key to create a new line.  You don't need to do that with our site posts. Just type. The only time you need to hit the enter key is for a new paragraph. Then again, perhaps it was a cut/paste thing??

Ginger,

Thanks for fixing the formatting! Yes, I would be happy to be the online community leader.  I'm actually an Associate Professor of Chemistry at Salisbury University in Salisbury, Maryland, USA.  I have 3 undergrads working on TB drug development in my lab each semester and summer and we just submitted our first publication in this area.  My previous med chem pubs have been on synthesis and testing of antibacterial agents against other targets (S. aureus, MRSA, VRE) and the development of targeted anticancer prodrugs for prostate cancer treatment/imaging. You can use this information about me for the about page.  Please let me know if you need more.

If you would create the Welcome Page for TB, that would be great. For TB-relevant content, here's the citation-free background from the original blog entry: Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), infects approximately two billion people. The World Health Organization estimates that about two million people die each year from TB due to the lack of and inability to afford proper health care. Overcrowding and ill-nourishment of poor people living in large cities leads to ahigh incidence of the disease due to the ease at which the infection can be transferred. This contributes to the accelerated speed at which TB spreads in underdeveloped countries. There is also an alarming increase in cases of TB caused by multidrug-resistant strains of Mycobacterium tuberculosis (Mtb), due in part to inadequate drug therapy as a result of incorrectly selected medications or suboptimal drug dosing. Thus, there is a need for new drugs targeting enzymes essential to mycobacterial survival.

For research tools, here are the following links: 1) Global Alliance for TB Drug Development 2) Free TB Research Materials (incl. live Mtb and Mtb proteins/cell lysates) 3) TAACF (the public database of compounds tested against Mtb is particularly useful starting point for antitubercular drug design).  I'm also willing to upload any relevant journal articles that are already public access material.  I don't have RSS feeds.

Best regards,

Miguel 

 

gtaylor's picture

This is great! Barring the unforseen I'll have the community up this week.

As for uploading articles, all you have to do is tag articles in either Connotea or CiteULike with "Tuberculosis" and we will automatically subscribe to those headlines in the TB community. This encourages you to bookmark interesting articles on TB for all scientists to see.

Cheers and welcome aboard! 

gtaylor's picture

Take a look. It's there. Please either email me or create a post if you find mistakes - whether typos, cut/paste or factual.

Cheers! 

Hi Mitchell,

Congrats on your paper coming out.

I was wondering if perhaps a homology model of ndh-2 would be of interest to you? I was looking around a bit and can't find one. I think it might be possible to construct one.

Also, it seems like a doable project for this medium.

..

hmm, well to answer my own question. There is a homology model at A.Sali's ModBase, P95160.

I wonder if you have tried to fit your compounds into the model? Perhaps you will find a binding mode that is consistent with you SAR data?

 

-Bart

Hi Bart!

Yes, trying to fit our compounds into an ndh-2 homology model would be great. Having never used ModBase, I would be happy for any assistance.

Miguel

marcius's picture

Hi Miguel and Bart,

My name is Marc A. Marti-Renom, I am one of the people involved from the beginning with The Tropical Disease Initiative (TDI, http://tropicaldisease.org). I was also the founder of the Malaria Community here, which is now MUCH BETTER represented by Saj.

I happen also to be one of the developers of MODELLER and can try to give you some feedback about the model you are talking about. In principle, the model was built in a fully automatic manner with ModPipe (Sali's pipeline for automatic modeling). This means that no human intervention was made during the modeling exercise. The model you are considering is based on a sequence identity of ~20% to the selected template. At this level of identity we know that the model will have substantial errors even though the model quality score is 0.95 (quite good). The quality score is telling you that the model has the correct fold but is not telling you if the model has errors in particular regions (most notably loops or side-chain placing). Since you would like to do Docking of small compounds with the model, I would suggest that somebody has a close look at the model and the alignments before hand. This is a model that I would not readily use for docking. There may be the need of using other templates or multiple templates, as well as change the alignment, in order to produce a more reliable model.

If you need more details on how to do this you can read some of the more general reviews about MODELLER that the Sali Lab has produced over the years: http://salilab.org/publications/ in particular, publications # 181, which is the most current.

Hope that helps,
Marc A. Marti-Renom

Actually, I think the model is a pretty good starting point.

I superimposed the structures of 1XHC(22%identity) and 1LVL(23% identity) with 2CVJ (21% identity) and P95160 (model made based on 2CVJ structure by ModBase). Overall, the superpositions looks good. Luckily, the enzyme class has a fairly well studied fold. I haven't delved too much into amino acid orientations, but the overall fold looks good.

I agree that the model may not be that suitable for docking studies. However, I think that it is an easier task to try and rationalize a set of SAR data based on a theoretical model, than it would be to actually dock ab initio an isolatedcompound.

Also, I think it's a fair bet to overlaypromazine with the flavin component of FAD. There is a bit of similarity between promazine and riboflavin.

I'm not to familiar with MODELLER, I'd like to see models of AAK46173 based on 1XHC and 1LVL, and then compare them to P95160.

cheers,

Bart

There is apparently protein available from MCSG
 

Source Organism
Mycobacterium tuberculosis H37Rv
Target Name
ndh gene product [Mycobacterium tuberculosis H37Rv]
Target Category
biomedical,disease,individual organism,PSI Biology partnership
Target Rationale
We identified an inhibitor active on whole cells that appears to target this protein.
Status
soluble
Site
MCSG
Site ID
APC105972
Partnership
MTBI
Lab List
ANL
URL
http://kiemlicz.med.virginia.edu/...
Last Update
2012-04-14
Project List
PSI-3
Database References
MCSG: APC105972, GenBank: 15608991