Clifton Barry III, Ph.D.

Key LCID Collaborators

Steve Holland
Ken Olivier

Key TBRS Collaborators

NCGC: NIH Chemical Genomics Center
OXU: Ben Davis’ laboratory at Oxford University
PITT: Joanne Flynn’s laboratory at the University of Pittsburgh
MRL: Merck Research Laboratories, Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033).
SUN: Gerhard Walzl’s laboratory at Stellenbosch University
GSK: GlaxoSmithKline, Tres Cantos, Spain
DDU: Drug discovery unit, University of Dundee
NCI: Barry O’Keefe’s Natural Products Branch of NCI
OCICB: NIAID’s Office of Cyber Infrastructure and Computational Biology
SBRI: David Sherman's laboratory at the Seattle Biomedical Research Institute
TASK: Andreas Diacon’s clinical team at TASK Applied Science in Stellenbosch
UMDNJA: David Alland’s laboratory at the University of Medicine and Dentistry of New Jersey

Tools/Resources

• BSL-3 High-throughput screening laboratory, Helena I. M. Boshoff, Staff Scientist
• TB Imaging Program (TBIP), Laura Via, Staff Scientist

Project Listing

TBRS works on myriad projects, ranging from drugs currently in clinical trials through cell and molecular biology and down to basic chemistry.

• Predict TB Clinical Trial
• PET/CT Imaging: NexGen EBA
• Chemical Genetics
• Mechanism of Action Studies
• TB Drug Accelerator

Predict TB Clinical Trial (SUN, TASK)

Shortening the duration of treatment for patients with drug sensitive tuberculosis from 6 to 4 months has been attempted many times in clinical trials but thus far all have failed. These failures reveal our incomplete understanding of factors driving the need for such extensive treatments. Consistently, trials have demonstrated that 80-85% of patients are successfully cured after 4 months of therapy, including the extensive set of studies from the British Medical Research Council (BMRC) in the 1970s and 1980, the Tuberculosis Research Unit (TBRU) treatment shortening study in non-cavitary patients who achieve early culture conversion, and the more recent treatment shortening trials using fluoroquinolones like REMoxTB. The current standard of care is to over-treat all patients for a total of 6-months to avoid relapse in a small subset of patients at higher risk for incompletely understood reasons.

For decades, clinical investigators have attempted to establish culture conversion as a predictor of treatment success. Despite the appealing logic, the real correlation of culture conversion as a surrogate endpoint has been consistently disappointing. In the REMoxTB trial, in particular, the intensive microbiological data collected revealed unambiguously that clearance of bacteria from the sputum did not sufficiently correlate with relapse risk to be a useful surrogate for durable cure. An important subset of patients, despite clearing their sputum of TB quickly and complying with all of their medications, still remained at high risk of relapsing with active disease after stopping treatment. Likewise, there are patients who clear their sputum of bacteria slowly that nonetheless go on to achieve durable cure. Intuitively this makes sense: only those bacteria at the surface of a cavity are directly open to the airways to seed the sputum. Yet this is not the full story as there are also heterogeneous lesions within each individual patient which respond differently to treatment with chemotherapy.

This protocol builds upon the historical trials and several successful small studies that suggest that directly monitoring lung pathology using (18F)- FDG PET/CT correlates better with treatment outcome than culture status. We will prospectively identify patients at low risk based on their baseline radiographic extent of disease, and further refine this risk score by evaluating the rate of resolution of the lung pathology (CT) and inflammation (PET) at one month as well as checking an end-of treatment GeneXpert test for the sustained presence of bacteria. Patients classified as low risk will be randomized to receive a shortened 4- month or a full 6-month course of therapy. If successful, this trial will both offer a badly needed alternative to culture status as a trial-level surrogate marker for outcome as well as provide critical information for preclinical and early clinical efforts to identify new agents and combinations with the potential to shorten therapy.

Hypothesis: A combination of radiographic characteristics at baseline, the rate of change of these features at one month, and markers of residual bacterial load at the end of treatment will identify patients with tuberculosis who are cured with 4 months (16 weeks) of standard treatment.

14 day PET/CT changes in a subject treated with quadruple drug standard of care treatment consisting of rifampicin, isoniazid, ethambutol and pyrazinamide. The top row depicts lesions immediately prior to beginning treatment and the bottom shows the aligned 14-day scan response.

Credit: NIAID

Positron emission tomography (PET) scans illuminate areas of inflammation using radiolabeled tracers. Computed tomography (CT) takes high-resolution X-ray images of the body, allowing reconstruction of the 3-D structure of the scanned region. By simultaneously performing PET/CT scans, we can monitor Mtb infections in subjects over time to correlate lung structure and functional Mtb activity and measure the impact of new and existing chemotherapies.

PET/CT is an important endpoint in our on-going clinical trials, and we have used this as a surrogate endpoint for trials of new drugs for TB. We have developed quantitative segmentation and classification tools together with OCICB. We have developed the ability to monitor PET/CT changes in animal models of TB and are developing Mtb-specific PET probes to improve this technology.

Chemical Genetics—NCGC, NCI

(Left to right) Clif Barry, Helena Boshoff, Jessica Medrano (front), Jenna Andrews (back), Neha Malhotra, Alice Bell and Nelson Reyes collect samples from a bog in Maine in 2018.

Credit: NIAID

One of the primary problems in new drug discovery for TB is the selection of appropriate targets that will have a therapeutic impact and kill the bacteria. This project seeks to screen for activity against whole cells of Mtb and then use these as starting points for target identification. By performing a variety of screens against Mtb under in vivo-relevant conditions (such as hypoxia, growth on lipid sources, and starvation), we have started assembling a “toolbox” of compounds that specifically inhibit growth of the pathogen under these conditions. One unique source of compounds is the “grey-layer” decomposition zone deep within sphagnum bogs (peat moss). This environment is highly acidic and microaerophilic, similar to that within human lungs where Mtb is thought to reside. Natural selection has endowed other microorganisms living in these nutrient-bare sphagnum areas with the ability to compete with endogenous slow-growing mycobacteria for these scarce nutrients by secreting secondary metabolites. Using microarray analysis and whole genome re-sequencing to identify the targets of these compounds, we can then identify potentially druggable leads.

TRS is also working with the Natural Products Branch of the NCI to screen and evaluate their new collection of over 1 million natural products contained in the NCI Program for Natural Product Discovery (NPNPD) Prefractionated Library.

TB Drug Accelerator

TRS works closely with the TB Drug Accelerator program of the Bill and Melinda Gates Foundation (https://globalhealthprogress.org/collaboration/tb-drug-accelerator-program/). We have a newly upgraded high-throughput screening facility within a Biosafety Level 3 containment suite that is routinely used to screen large compound libraries from collaborators (DDU, MRL). In addition, we conduct mechanism of action studies and formal hit assessment activities including a medicinal chemistry program to develop novel TB drugs.

We are also using a high throughput screening (HTS) robot to help quickly screen for potential drug targets that are revealed as necessary for Mtb survival under a range of growth conditions. These conditions, such as hypoxia, starvation, etc., mimic conditions that Mtb might encounter during the course of disease in a human host. We have adopted a quantitative HTS approach that screens all compounds as a titration series in order to get dose-response curves. The targets inhibited by these compound hits are subsequently identified by a variety of methods, including microarray analysis to compare profiles to our existing database of drug-induced transcriptional profiles, whole genome sequencing of resistant mutants, and macromolecular incorporation assays. Thus, the multitude of hits that are identified by HTS will enable the rapid discovery of multiple inhibitor-susceptible pathways that contain steps that are bottlenecks in the metabolism essential for survival under these conditions.

As part of this program, TRS recently concluded a partnership lead optimization program with MRL to develop a TB-specific oxazolidinone similar to linezolid without the known safety risks associated with mitochondrial toxicity. This program resulted in a candidate molecule that is about to begin clinical testing.