Hit-to-Lead Development of Phenotypic and Mechanism-based Screen Hits
Project Completed
Please click to see the final report.

Introduction and Background of the Project


In the fight against TB the number of drugs available is quite limited and many of them are 40 to 50 years old.  They need to be administered to the patients for at least 6 months in the best case and much longer in the case of drug-resistant TB.  New drugs are needed to shorten the treatment duration and to combat drug-resistant strains.  In order to identify prototypes of potential new TB drugs (hits) Takeda Pharmaceutical Company (Takeda) and TB Alliance jointly carried out screening campaigns.  We ultimately identified two series of compounds, one from phenotypic screening a large number of compounds with Takeda library for their ability to kill Mycobacterium tuberculosis (Mtb, the pathogen causing TB), and another from mechanism-based screening for their ability to inhibit a particular enzyme in Mtb from Takeda internal portfolio.  In this Hit-to-Lead project we intend to improve their potency and properties to make them suitable for treatment.


Project objective

The objectives of this project are to improve the potency of the hits to kill Mtb but at the same time to make them safe to be used in humans.  We also want to prove that the eventual drugs derived from these prototypes can be dosed orally and in reasonable doses to be widely accepted among TB patients worldwide.


Project design

To achieve these objectives, we will synthesize several dozens of analogues in each series to evaluate them in the assays related to the objectives above.  We will test selected analogues in mice to evaluate their activity in animal models.  The design, synthesis, and testing are an iterative process until we identify a compound best satisfying the objectives above.

How can your partnership (project) address global health challenges?

More than 1.5 million people die from TB every year worldwide, and in order to decrease the suffering and the economic loss due to TB, we need novel drugs with increased efficacy, safety, and affordability.  Furthermore, to combat the emerging drug resistant strains we need drug with a new mechanism of action so that there is no preexisting resistance.  The two series in this project appear to have new mechanisms of action.

What sort of innovation are you bringing in your project?

In the series of the hits based on their ability to kill Mtb we are bringing in a new chemical series potentially possessing a novel mechanism to kill the pathogen.  We will determine the mechanism of killing Mtb and this knowledge can be used to search for additional chemical series having the same target but of different chemical structures.  In the series of the hits based on their ability to inhibit a specific enzyme in Mtb, this is the first attempt to find drugs inhibiting this specific enzyme in Mtb.  The structure of this enzyme in various bacteria are known and this information will enable us to utilize structure-based computational approaches in designing new analogues.

Role and Responsibility of Each Partner

The Takeda scientists will design new analogues to synthesize and apply their expertise in drug research and development to successfully navigate many stages of drug development.  The TB Alliance scientists will utilize their network of academic investigators and contract research organizations to synthesize and evaluate the analogues.  The design of the new analogues and their testing will be done in full consultation between the Takeda and TB Alliance groups.

Final Report

1. Project objective

This project was a continuation of H2015-201 and it involved two separate series, A) a phenotypic screening hit series and B) inhibitors of a known enzyme in Mycobacterium tuberculosis (Mtb) involved in protein biosynthesis.  The main objective is to develop either A or B series to identify a lead by demonstrating its efficacy in mouse.     


2. Project design

We planned to prepare analogues in series A to identify an analogue of sufficient stability to be used in a mouse TB infection.  We then would follow it up in a mechanistic study to determine its mechanism of action.  In series B we planned to prepare analogues to test in a target enzyme assay and in a cell-based assay using Mtb.  We planned to make use of the structural information of the enzyme to design new analogues.  Analogues would then be tested in an enzyme assay and in a whole cell assay.  Then selected analogues would be tested in a mouse TB infection model.


3. Results, lessons learned

Analogues in series A were potent in cell-based assays but they were metabolically unstable.  Our effort to identify analogues of increased stability and of retained anti-Mtb activity failed and after one year, we devoted our effort to series B, a project targeting a known Mtb enzyme.  Based on the known structure of the target enzyme, a potent series of compounds was identified.  It took us some time to demonstrate their activity in a whole cell assay.  To our knowledge this was the first series of analogues active against this target Mtb enzyme.  We ran out of time to develop analogues for in vivo proof of concept.  It could have been helpful if we had a method to determine how much of an analogue was getting into Mtb and retained in Mtb.