We wish to thank Johnson &amp; Johnson, the TB Alliance, Astra Zeneca, Rib-X and Trius Therapeutics for providing bedaquiline, PA-824 (pretomanid), AZD5847, radezolid and tedizolid, respectively. Brendan Prideaux, Matthew Zimmerman, Stephen Juzwin, Emma Rey-Jurado, Nancy Ruel, Leyan Li and Danielle Weiner provided support with MALDI analysis, bioanalytical methods, preparation of the caseum surrogate, chemical synthesis, and isolation of rabbit caseum. This work was conducted with funding from the Bill and Melinda Gates Foundation, award # OPP1044966 and OPP1024050 to V. Dartois, NIH Shared Instrumentation Grant S10OD018072, as well as joint funding from the Bill and Melinda Gates Foundation and Wellcome Trust for A Centre of Excellence for Lead Optimization for Diseases of the Developing World to P. Wyatt.

All animal studies were carried out in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health with approval from the Institutional Animal Care and Use Committee of the NIAID (NIH), Bethesda, MD. All studies involving M. tuberculosis were performed in a laboratory with biosafety containment level 3 (BSL-3).
1. Rabbit Infection Model and Caseum Collection
<ol>
	<li>Infect New Zealand white rabbits with M. tuberculosis using a nose-only aerosol exposure system as previously described.12,13 Allow the infection to progress for 12-16 weeks. Sedate the rabbits with 35 mg/kg ketamine and 5 mg/kg xylazine intramuscularly, euthanize the rabbits with 0.22 mL/kg pentobarbital sodium and phenytoin sodium intravenously and proceed with the necropsies.</li>
	<li>Using tweezers and a scalpel, remove lungs from the chest cavity. From each lung lobe, dissect out individual cavities and large necrotic granulomas using a scalpel. Carefully scrape off caseum from the cavity and granuloma walls. Weigh, record and store samples in 2 mL screw-capped tubes at -20 &#176;C until ready for use.</li>
	<li>Gamma-irradiate the infectious caseum samples at 3 MegaRad on dry ice to render them uninfectious and safe for use in a BSL-2 lab.</li>
</ol>
2. In Vitro Generation of Caseum Surrogate from THP-1 Cells
<ol>
	<li>Grow THP-1 monocytes in RPMI 1640 medium (2 mM L-glutamine and 10% fetal bovine serum) in T175 cell culture flasks (80 mL/flask). Incubate the flasks in a 5% CO2 atmosphere at 37 &#176;C for 3-4 days.</li>
	<li>Centrifuge the culture from a T175 flask in two 50 mL conical tubes at 150 x g for 5 min. Discard the supernatant and suspend the pellet in 10 mL of RPMI 1640 media.</li>
	<li>Pipette 5 &#181;L of this culture into a 1.5 mL tube containing 45 &#181;L of trypan blue. Mix thoroughly by pipetting. Transfer 10 &#181;L to a hemocytometer and count the number of viable THP-1 monocytes (unstained) using a light microscope (10X magnification). Calculate the number of viable cells per mL of the culture. Dilute it with RPMI media to the final density of 1.25 x 106 cells/mL.</li>
	<li>Load 40 mL of the culture on a large cell culture plate (50 x 106 cells/plate). Add 40 &#181;L of 100 &#181;M PMA (phorbol 12-myristate13-acetate prepared in ethanol) and allow cells to adhere overnight in the incubator. 
	NOTE: Final concentration of PMA is 100 nM.</li>
	<li>Dilute pure oleic acid (OA) (0.89 g/mL) in ethanol to the concentration of 0.1 M (i.e. 31.7 &#181;L OA in 968.3 &#181;L ethanol). Dilute this solution in fresh pre-warmed RMPI media to a concentration of 10 mM. Dilute this OA suspension to 0.4 mM (final working concentration) in RPMI medium pre-warmed to 37 &#176;C.</li>
	<li>Remove the existing media and non-adhered cells from the cell culture plates and gently add 40 mL of 0.4 mM OA to the THP-1 macrophages (THP-M). Incubate at 37 &#176;C in the incubator overnight.</li>
	<li>Use a light microscope at 40x magnification to visually confirm the presence of numerous lipid body inclusions in each THP-M. Remove all RPMI medium from the cell culture plates and gently wash the adherent cells twice with phosphate buffered saline (PBS) using a 50 mL serological pipette. 
	NOTE: Lipid bodies appear as small, clear, spherical structures in the cytoplasm of the THP-M.</li>
	<li>Add 40 mL of 5 mM ethylenediaminetetraacetic acid (EDTA) in PBS to each plate. Incubate for 15 min at 37 &#176;C.</li>
	<li>Detach the foamy macrophages (FM) by repeatedly pipetting up and down over the surface of the whole plate using a 10-mL serological pipette. Transfer the cell suspension to a 50-mL conical tube and spin down at 150 x g for 5 min.</li>
	<li>Resuspend the cell pellet in 10 mL of PBS (third PBS wash) and transfer to a pre-weighed 15-mL conical tubes. Spin down again at 150 x g for 5 min. Carefully aspirate the supernatant using a serological pipette and discard.</li>
	<li>Subject the FM pellets to 3 freeze-thaw cycles to lyse the cells and incubate them at 75 &#176;C for 20-30 min to denature proteins in the matrix. Store the pellets at -20 &#176;C until ready for use.</li>
</ol>
3. Rapid Equilibration Dialysis (RED) Assay
<ol>
	<li>Prepare 10 mM stock solutions of all test compounds in dimethyl sulfoxide (DMSO). Dilute to 500 &#181;M working solutions in DMSO prior to each assay.</li>
	<li>Weigh the tube containing the caseum surrogate pellet. Subtract the weight of the empty tube to derive the weight of the pellet alone. Add 2-3 metal beads per tube and, using a tissue homogenizer at 1,200 strokes/min for 1 min, disrupt caseum or the surrogate matrix in PBS (1:9 w/v) to achieve 10x diluted suspension of each matrix.</li>
	<li>Spike 6.5 &#181;L of the 500 &#181;M solution of the test compound into 643.5 &#181;L of the homogenate to achieve the final concentration of 5 &#181;M (&#8804;1% DMSO) and vortex.</li>
	<li>Place the RED inserts into the base plate. Add 200 &#181;L of the drug-spiked matrix into the donor chamber (red ring) of each RED insert and 350 &#181;L of PBS into each receiver chamber. Prepare 3 inserts for each test compound (triplicate samples). Seal plate with an adhesive plate seal and incubate at 37 &#176;C on the thermomixer at 200 rpm (1 x g) for 4 h.</li>
	<li>After the incubation, gently mix the contents of the donor and receiver chambers by pipetting up and down 2-3 times. Pipette out 20 &#181;L aliquots of homogenate from the donor chambers and add to 20 &#181;L of clean PBS in a 1.5 mL tube (1:1). Similarly, pipette out 20 &#181;L aliquots of PBS samples from the receiver chambers and add to 20 &#181;L of clean homogenate (matrix matching).8 
	NOTE: Matrix-matching eliminates the need for 2 separate calibration curves (in homogenate and PBS) to be made for quantitative analysis. Contents of the donor chamber may sediment over time. Gently mix the contents by pipetting prior to removing aliquots.</li>
</ol>
4. LC-MS Quantification and Data Analysis
<ol>
	<li>Add 160 &#181;L of 1:1 methanol:acetonitrile containing 500 ng/mL diclofenac or 10 ng/mL verapamil (internal standard) to each tube and vortex to precipitate proteins. Centrifuge at 10,000 x g for 5 min to sediment the precipitate and transfer supernatants into 96-well deep-well plates for liquid chromatography-mass spectrometry (LCMS) analysis.7</li>
	<li>Build calibration curves from 1-1,000 nM for each test compound while keeping the same matrix composition as the samples above. Quantify the concentration of test compound in samples from the donor and receiver chambers using an LC-MS method.</li>
	<li>Calculate the unbound fraction (fu) of the drug in diluted matrix using equation 1. Calculate the fu in undiluted matrix using equation 2 (D = dilution factor of 10).14 
	<img alt="Equation 1" src="/files/ftp_upload/55559/55559eq1.jpg" /> 
	<img alt="Equation 2" src="/files/ftp_upload/55559/55559eq2.jpg" /></li>
	<li>Check the recovery (mass balance) of each compound using equation 3 to identify compounds with stability/metabolism/non-specific binding issues. 
	NOTE: Recovery typically falls between 70% and 130%.15 
	<img alt="Equation 3" src="/files/ftp_upload/55559/55559eq3.jpg" /></li>
</ol>

<ol><li>Sacchettini, J. C., Rubin, E. J., Freundlich, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Drugs+versus+bugs%3A+in+pursuit+of+the+persistent+predator+Mycobacterium+tuberculosis%5BTitle%5D)+AND+%22Nat+Rev+Microbiol%22%5BJournal%5D)">Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis.</a> Nat Rev Microbiol. 6 (1), 41-52 (2008).</li>
<li>Zhang, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Persistent+and+dormant+tubercle+bacilli+and+latent+tuberculosis%5BTitle%5D)+AND+%22Front+Biosci%22%5BJournal%5D)">Persistent and dormant tubercle bacilli and latent tuberculosis.</a> Front Biosci. 1 (9), 1136-1156 (2004).</li>
<li>Aber, V. R., Nunn, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Short+term+chemotherapy+of+tuberculosis.+Factors+affecting+relapse+following+short+term+chemotherapy%5BTitle%5D)+AND+%22Bull+Int+Union+Tuberc%22%5BJournal%5D)">Short term chemotherapy of tuberculosis. Factors affecting relapse following short term chemotherapy.</a> Bull Int Union Tuberc. 53 (4), 276-280 (1978).</li>
<li>Chang, K. C., Leung, C. C., Yew, W. W., Ho, S. C., Tam, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+nested+case-control+study+on+treatment-related+risk+factors+for+early+relapse+of+tuberculosis%5BTitle%5D)+AND+%22Am+J+Respir+Crit+Care+Med%22%5BJournal%5D)">A nested case-control study on treatment-related risk factors for early relapse of tuberculosis.</a> Am J Respir Crit Care Med. 170 (10), 1124-1130 (2004).</li>
<li>Dartois, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+path+of+anti-tuberculosis+drugs%3A+from+blood+to+lesions+to+mycobacterial+cells%5BTitle%5D)+AND+%22Nature+Rev+Microbiol%22%5BJournal%5D)">The path of anti-tuberculosis drugs: from blood to lesions to mycobacterial cells.</a> Nature Rev Microbiol. 12 (3), 159-167 (2014).</li>
<li>Prideaux, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+association+between+sterilizing+activity+and+drug+distribution+into+tuberculosis+lesions%5BTitle%5D)+AND+%22Nat+Med%22%5BJournal%5D)">The association between sterilizing activity and drug distribution into tuberculosis lesions.</a> Nat Med. 21 (10), 1223-1227 (2015).</li>
<li>Sarathy, J. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Prediction+of+Drug+Penetration+in+Tuberculosis+Lesions%5BTitle%5D)+AND+%22ACS+Infect+Dis%22%5BJournal%5D)">Prediction of Drug Penetration in Tuberculosis Lesions.</a> ACS Infect Dis. 2 (8), 552-563 (2016).</li>
<li>Waters, N. J., Jones, R., Williams, G., Sohal, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Validation+of+a+rapid+equilibrium+dialysis+approach+for+the+measurement+of+plasma+protein+binding%5BTitle%5D)+AND+%22J+Pharm+Sci%22%5BJournal%5D)">Validation of a rapid equilibrium dialysis approach for the measurement of plasma protein binding.</a> J Pharm Sci. 97 (10), 4586-4595 (2008).</li>
<li>Singh, J. K., Solanki, A., Maniyar, R. C., Banerjee, D., Shirsath, V. S. <a target="_blank" href="http://jpharmsci.org/article/S0022-3549(16)32735-6/pdf">Rapid Equilibrium Dialysis (RED): an In-vitro High-Throughput Screening Technique for Plasma Protein Binding using Human and Rat Plasma.</a> J Bioequiv Availab. 14, 1-4 (2012).</li>
<li>Liu, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Unbound+drug+concentration+in+brain+homogenate+and+cerebral+spinal+fluid+at+steady+state+as+a+surrogate+for+unbound+concentration+in+brain+interstitial+fluid%5BTitle%5D)+AND+%22Drug+Metab+Dispos%22%5BJournal%5D)">Unbound drug concentration in brain homogenate and cerebral spinal fluid at steady state as a surrogate for unbound concentration in brain interstitial fluid.</a> Drug Metab Dispos. 37 (4), 787-793 (2009).</li>
<li>Able, S. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Receptor+localization%2C+native+tissue+binding+and+ex+vivo+occupancy+for+centrally+penetrant+P2X7+antagonists+in+the+rat%5BTitle%5D)+AND+%22Br+J+Pharmacol%22%5BJournal%5D)">Receptor localization, native tissue binding and ex vivo occupancy for centrally penetrant P2X7 antagonists in the rat.</a> Br J Pharmacol. 162 (2), 405-414 (2011).</li>
<li>Subbian, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Chronic+pulmonary+cavitary+tuberculosis+in+rabbits%3A+a+failed+host+immune+response%5BTitle%5D)+AND+%22Open+Biol%22%5BJournal%5D)">Chronic pulmonary cavitary tuberculosis in rabbits: a failed host immune response.</a> Open Biol. 1 (4), 1-14 (2011).</li>
<li>Via, L. E., et al. <a target="_blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423064/">Tuberculous Granulomas are Hypoxic in Guinea pigs, Rabbits, and Non-Human Primates.</a> Infect Immun. 76 (6), 2333-2340 (2008).</li>
<li>Kalvass, J. C., Maurer, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Influence+of+nonspecific+brain+and+plasma+binding+on+CNS+exposure%3A+implications+for+rational+drug+discovery%5BTitle%5D)+AND+%22Biopharm+Drug+Dispos%22%5BJournal%5D)">Influence of nonspecific brain and plasma binding on CNS exposure: implications for rational drug discovery.</a> Biopharm Drug Dispos. 23 (8), 327-338 (2002).</li>
<li>Di, L., Umland, J. P., Trapa, P. E., Maurer, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Impact+of+recovery+on+fraction+unbound+using+equilibrium+dialysis%5BTitle%5D)+AND+%22J+Pharm+Sci%22%5BJournal%5D)">Impact of recovery on fraction unbound using equilibrium dialysis.</a> J Pharm Sci. 101 (3), 1327-1335 (2012).</li>
<li>Lenaerts, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Location+of+persisting+mycobacteria+in+a+Guinea+pig+model+of+tuberculosis+revealed+by+r207910%5BTitle%5D)+AND+%22Antimicrob+Agents+Chemother%22%5BJournal%5D)">Location of persisting mycobacteria in a Guinea pig model of tuberculosis revealed by r207910.</a> Antimicrob Agents Chemother. 51 (9), 3338-3345 (2007).</li>
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There are no competing financial interests.

Pulmonary necrotic lesions and cavities in tuberculosis-infected patients contain subpopulations of bacteria that are recalcitrant to drug treatment. The caseous cores of these structures are particularly responsible for harboring these persisters in an extracellular environment.16 Favorable distribution of anti-bacterial agents into these remote locations is believed to be an important determinant of tuberculosis drug efficacy. Prior to the validation of this protocol, there were no available <em...

The treatment of pulmonary tuberculosis disease requires effective distribution of drugs into different types of lesions. Necrotic lesions and cavities contain caseous centers that harbor subpopulations of drug-tolerant or &#39;persistent&#39; bacteria.1,2 The cavitary disease is associated with inferior cure rates and poor prognosis.3,4 Previous studies have shown, using quantitative and imaging techniques, that the ability to penetrate caseum varies significantly from one drug class to another.5,6 These methods, however, require the use of animal infection models that are slow and tedious. An in vitro assay that measures drug binding to ex vivo caseum was designed. This binding was found to inversely correlate with drug penetration in caseous granulomas and, hence, is used as a predictive tool.7
Equilibrium dialysis is regarded as the gold standard approach to plasma protein binding studies. The rapid equilibrium dialysis (RED) device provides a quick, easy-to-use and reliable system for performing such assays.8 The device is made up of two components: single-use, disposable inserts consisting of 2 chambers separated by a vertical cylinder of semi-permeable membrane; and reusable base plates that can hold up to 48 inserts at a time. The dialysis membrane has an 8 kDa molecular weight cut-off (MWCO) that is ideal for drug-macromolecule binding studies. The high surface area-to-volume ratio of the membrane compartment allows rapid dialysis and equilibration. Both the inserts and the base plate have been validated for minimal non-specific binding. The combination of the RED device with bioanalytical techniques provides accurate estimations of the unbound fractions of drugs in plasma.8,9
Although originally designed to measure plasma protein binding, the RED device has been used in several tissue binding studies using homogenates.10,11 In this protocol, we measure drug binding to caseum, the necrotic debris excised from the necrotic lesions and cavities of tuberculosis-infected rabbits. The acellular and non-vascular nature of caseous material makes it easy to homogenize into a homogenous suspension that is compatible with the assay.
Given that caseum is tedious to produce and hard to come by, the protocol has also been validated for use with a surrogate matrix that is prepared from foamy macrophages. THP-1 monocyte-derived macrophages are induced with oleic acid to accumulate multiple lipid bodies that give them their &#39;foamy&#39; appearance. These lipid-loaded cells are harvested and processed to produce a matrix that we use as a surrogate to caseum. This study has shown that drug binding to this surrogate matrix correlates well with binding to caseum, effectively mimicking the in vivo process that hinders drug penetration in the caseous core of granulomas and cavities.

<table><tbody><tr><td>New Zealand White Rabbits</td><td>Covance</td><td>-</td><td></td></tr><tr><td>HN878 Mycobacterium tuberculosis</td><td>BEI Resources</td><td>NR-13647&amp;nbsp;</td><td></td></tr><tr><td>Ketathesia (Ketamine) 100 mg/mL C3N</td><td>Henry Schein Animal Health</td><td>56344</td><td></td></tr><tr><td>Anased (Xylazine) 100 mg/mL</td><td>Henry Schein Animal Health</td><td>33198</td><td></td></tr><tr><td>Euthasol (pentobarbital sodium and phenytoin sodium) Solution&amp;nbsp;</td><td>Virbac</td><td>710101</td><td></td></tr><tr><td>THP-1 monocytic cell line</td><td>ATCC</td><td>ATCC TIB-202</td><td></td></tr><tr><td>175 cm&amp;sup2; TC-Treated Flask (T175)</td><td>Fisher Scientific</td><td>T-3400-175</td><td></td></tr><tr><td>RPMI 1640 media w/o glutamine</td><td>Fisher Scientific</td><td>MT-15-040-CV</td><td></td></tr><tr><td>Hyclone Fetal Bovine Serum, Gamma irradiated&amp;nbsp;</td><td>Fisher Scientific</td><td>SH3091003IR</td><td></td></tr><tr><td>Hyclone L-glutamine, 200 mM</td><td>Fisher Scientific</td><td>SH3003401</td><td></td></tr><tr><td>Cellstar TC dish, 145 mm x 20 mm, vented</td><td>Fisher Scientific</td><td>T-2881-1</td><td></td></tr><tr><td>Phorbol 12-myristate 13-acetate (PMA)</td><td>Fisher Scientific</td><td>BP685-1</td><td></td></tr><tr><td>Ethylenediaminetetraacetic acid</td><td>Sigma</td><td>E6758</td><td></td></tr><tr><td>Oleic acid&amp;nbsp;</td><td>Fisher Scientific</td><td>ICN15178101</td><td></td></tr><tr><td>Pierce RED Device Reusable Base Plate</td><td>Fisher Scientific</td><td>PI-89811</td><td></td></tr><tr><td>Pierce RED Device Inserts, 50/box&amp;nbsp;</td><td>Fisher Scientific</td><td>PI-89809</td><td></td></tr><tr><td>Pierce RED insert removal tool&amp;nbsp;</td><td>Fisher Scientific</td><td>89812</td><td></td></tr><tr><td>Adhesive plate seal</td><td>Fisher Scientific</td><td>08-408-240</td><td></td></tr><tr><td>PBS, pH 7.4, 10x 500 mL (Gibco)&amp;nbsp;</td><td>Life Technologies&amp;nbsp;</td><td>10010-049</td><td></td></tr><tr><td>DMSO</td><td>Sigma</td><td>472301</td><td></td></tr><tr><td>Acetonitrile</td><td>Sigma</td><td>34998</td><td></td></tr><tr><td>Methanol</td><td>Sigma</td><td>34860</td><td></td></tr><tr><td>Verapamil hydrochloride</td><td>Sigma</td><td>V4629</td><td></td></tr><tr><td>Diclofenac sodium salt</td><td>Sigma</td><td>93484</td><td></td></tr><tr><td>Trypan Blue Solution, 0.4%</td><td>Fisher Scientific</td><td>15-250-061</td><td></td></tr><tr><td>Ethanol, 200 proof</td><td>Fisher Scientific</td><td>04-355-451</td><td></td></tr><tr><td>2010 Geno/Grinder</td><td>SPEX SamplePrep</td><td>2010</td><td></td></tr><tr><td>Bead Mill Homogenizer Accessory, Metal Bulk Beads</td><td>Fisher Scientific</td><td>15-340-158</td><td></td></tr><tr><td>484R Cobalt 60 Irradiator</td><td>JL Shepard</td><td>7810-484-1</td><td></td></tr><tr><td>INCYTO&amp;nbsp;C-Chip Disposable Hemacytometers</td><td>Fisher Scientific</td><td>22-600-100</td><td></td></tr><tr><td>Upright Light Microscope</td><td>Leica</td><td>DM1000</td><td></td></tr><tr><td>Binary Liquid Chromatography system</td><td>Agilent</td><td>1260</td><td>Multi-compenent</td></tr><tr><td>Mass spectrometer</td><td>AB Sciex</td><td>4000</td><td></td></tr></tbody></table>

an in vitro caseum binding assay that predicts drug penetration in tuberculosis lesions

The eradication of tuberculosis disease requires drug regimens that can penetrate the multiple layers of complex pulmonary lesions. Drug distribution in the caseous cores of cavities and lesions is especially crucial because they harbor subpopulations of drug-tolerant bacteria also commonly referred to as persisters. Existing methods for the measurement of drug penetration in tuberculosis lesions involve costly and time-consuming in vivo pharmacokinetic studies coupled to bioanalytical or imaging techniques. The in vitro measurement of drug binding to caseum macromolecules was proposed as an alternative to such techniques since this binding hinders the passive diffusion of drug molecules through caseum. Rapid equilibrium dialysis is a fast and reliable system for performing plasma protein and tissue binding studies. In this protocol, we used a rapid equilibrium dialysis (RED) device to measure drug binding to homogenates of caseum that is excised from the lesions and cavities of tuberculosis-infected rabbits. The protocol also describes how to generate a surrogate matrix from lipid loaded THP-1 macrophages to use in place of caseum. This caseum/surrogate binding assay is an important tool in tuberculosis drug discovery and can be adapted to help study drug distribution in lesions or abscesses caused by other diseases.

Using this protocol, we have tested hundreds of tuberculosis drug development compounds for their predicted efficiency at penetrating caseum. Figure 1 visualizes the basic concepts of the RED assay. The dialysis membrane of the RED inserts allows for unbound small molecules to diffuse from the donor well to the receiver well, finally achieving an equilibrium between both compartments. Small molecules that are bound to macromolecules such as proteins or lipids are trapped ...

Watch this Scientific Journal Video about An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions at JoVE.com

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

Here we describe a rapid equilibrium dialysis (RED) method to measure drug binding to caseum from pulmonary tuberculosis lesions and cavities. The protocol is also used with a foamy macrophage-derived matrix that is an effective surrogate to caseum.

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

The eradication of tuberculosis disease requires drug regimens that can penetrate the multiple layers of complex pulmonary lesions. Drug distribution in ...

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11.8K Views.  Rutgers. Here we describe a rapid equilibrium dialysis (RED) method to measure drug binding to caseum from pulmonary tuberculosis lesions and cavities. The protocol is also used with a foamy macrophage-derived matrix that is an effective surrogate to caseum.

Video: An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

A Microscopic Phenotypic Assay for the Quantification of Intracellular Mycobacteria Adapted for High-throughput/High-content Screening

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since several decades, the sudden burst of multi- and extensively-drug resistant strains is a serious threat for the control of tuberculosis. Therefore, it is essential to identify new targets and pathways critical for the causative agent of the tuberculosis, Mycobacterium tuberculosis (Mtb) and to search for novel chemicals that could become TB drugs. One approach is to set&#160;up methods suitable for the genetic and chemical screens of large scale libraries enabling the search of a needle in a haystack. To this end, we developed a phenotypic assay relying on the detection of fluorescently labeled Mtb within fluorescently labeled host&#160;cells using automated confocal microscopy. This in vitro assay allows an image based quantification of the colonization process of Mtb&#160;into the host and was optimized for the 384-well microplate format, which is proper for screens of siRNA-, chemical compound- or Mtb mutant-libraries. The images are then processed for multiparametric analysis, which provides read&#160;out inferring on the pathogenesis of Mtb&#160;within host cells.

Here, we describe a phenotypic assay applicable to the High-throughput/High-content screens of small-interfering synthetic RNA (siRNA), chemical compound, and Mycobacterium tuberculosis mutant libraries. This method relies on the detection of fluorescently labeled Mycobacterium tuberculosis within fluorescently labeled host&#160;cell using automated confocal microscopy.

Despite the availability of therapy and vaccine, tuberculosis (TB) remains one of the most deadly and widespread bacterial infections in the world. Since ...

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There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the etiological agent of TB, is refractory to rapid and lasting chemotherapy due to the presence of bacilli exhibiting phenotypic drug resistance. The charcoal agar resazurin assay (CARA) was developed as a tool to characterize active molecules discovered by high-throughput screening campaigns against replicating and non-replicating M. tuberculosis. Inclusion of activated charcoal in bacteriologic agar medium helps mitigate the impact of compound carry-over, and eliminates the requirement to pre-dilute cells prior to spotting on CARA microplates. After a 7-10 day incubation period at 37 &#176;C, the reduction of resazurin by mycobacterial microcolonies growing on the surface of CARA microplate wells permits semi-quantitative assessment of bacterial numbers via fluorometry. The CARA detects approximately a 2-3 log10 difference in bacterial numbers and predicts a minimal bactericidal concentration leading to &#8805;99% bacterial kill (MBC&#8805;99). The CARA helps determine whether a molecule is active on bacilli that are replicating, non-replicating, or both. Pilot experiments using the CARA facilitate the identification of which concentration of test agent and time of compound exposure require further evaluation by colony forming unit (CFU) assays. In addition, the CARA can predict if replicating actives are bactericidal or bacteriostatic.

The charcoal agar resazurin assay (CARA) is a semi-quantitative, medium-throughput method to assess activity of test agents against mycobacteria that are replicating, non-replicating, or both. The CARA permits rapid evaluation of time- and concentration-dependent activity and identifies parameters to pursue by colony forming unit (CFU) assays.

There is an urgent need to discover and progress anti-infectives that shorten the duration of tuberculosis (TB) treatment. Mycobacterium tuberculosis, the ...

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread of multi drug-resistant TB (MDR-TB), there is a real urgency to develop new therapeutic strategies against M. tuberculosis infections. Traditionally, compounds are evaluated based on their antibacterial activity under in vitro growth conditions in broth; however, results are often misleading for intracellular pathogens like M. tuberculosis since in-broth phenotypic screening conditions are significantly different from the actual disease conditions within the human body. Screening for inhibitors that work inside macrophages has been traditionally difficult due to the complexity, variability in infection, and slow replication rate of M. tuberculosis. In this study, we report a new approach to rapidly assess the effectiveness of compounds on the viability of M. tuberculosis in a macrophage infection model. Using a combination of a cytotoxicity assay and an in-broth M. tuberculosis viability assay, we were able to create a screening system that generates a comprehensive analysis of compounds of interest. This system is capable of producing quantitative data at a low cost that is within reach of most labs and yet is highly scalable to fit large industrial settings.

System for Efficacy and Cytotoxicity Screening of Inhibitors Targeting Intracellular Mycobacterium tuberculosis

We have developed a modular high-throughput screening system for discovering novel compounds against Mycobacterium tuberculosis, targeting intracellular and in-broth growing bacteria as well as cytotoxicity against the mammalian host cell.

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a leading cause of morbidity and mortality worldwide. With the increased spread ...

A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis

The early drug development process for anti-tuberculosis drugs is hindered by the inefficient translation of compounds with in vitro activity to effectiveness in the clinical setting. This is likely due to a lack of consideration for the physiologically relevant cellular penetration barriers that exist in the infected host. We recently established an alternative infection model that generates large macrophage aggregate structures containing densely packed M. tuberculosis (Mtb) at its core, which was suitable for drug susceptibility testing. This infection model is inexpensive, rapid, and most importantly BSL-2 compatible. Here, we describe the experimental procedures to generate Mtb/macrophage aggregate structures that would produce macrophage-passaged Mtb for drug susceptibility testing. In particular, we demonstrate how this infection system could be directly adapted to the 96-well plate format showing throughput capability for the screening of compound libraries against Mtb. Overall, this assay is a valuable addition to the currently available Mtb drug discovery toolbox due to its simplicity, cost effectiveness, and scalability.

A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis

New models and assays that would improve the early drug development process for next-generation anti-tuberculosis drugs are highly desirable. Here, we describe a quick, inexpensive, and BSL-2 compatible assay to evaluate drug efficacy against Mycobacterium tuberculosis that can be easily adapted for high-throughput screening.

The early drug development process for anti-tuberculosis drugs is hindered by the inefficient translation of compounds with in vitro activity to ...

A Tuberculosis Molecular Bacterial Load Assay (TB-MBLA)

Tuberculosis is caused by Mycobacterium tuberculosis (Mtb), a pathogen classified by the United Nations (UN) as a dangerous category B biological substance. For the sake of the workers&#8217; safety, handling of all samples presumed to carry Mtb must be conducted in a containment level (CL) 3 laboratory. The TB molecular bacterial load assay (TB-MBLA) test is a reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) test that quantifies Mtb bacillary load using primers and dual-labelled probes for 16S rRNA. We describe the use of heat inactivation to render TB samples noninfectious while preserving RNA for the TB-MBLA. A 1 mL aliquot of the sputum sample in tightly closed 15 mL centrifuge tubes is boiled for 20 min at either 80 &#176;C, 85 &#176;C, or 95 &#176;C to inactivate Mtb bacilli. Cultivation of the heat inactivated and control (live) samples for 42 days confirmed the death of TB. The inactivated sample is then spiked with 100 &#181;L of the extraction control and RNA is extracted following the standard RNA isolation procedure. No growth was observed in the cultures of heat treated samples. The isolated RNA is subjected to real-time RT-qPCR, which amplifies a specific target in the Mtb 16S rRNA gene, yielding results in the form of quantification cycles (Cq). A standard curve is used to translate Cq into bacterial load, or estimated colony forming units per mL (eCFU/mL). There is an inverse relationship between Cq and the bacterial load of a sample. The limitation is that heat inactivation lyses some cells, exposing the RNA to RNases that cause a loss of &#60;1 log10eCFU/mL (i.e., &#60;10 CFU/mL). Further studies will determine the proportion of very low burden patients that cause false negative results due to heat inactivation.

A Tuberculosis Molecular Bacterial Load Assay TB-MBLA

We describe a tuberculosis molecular bacterial load assay test performed after heat inactivation of sputum. Heat inactivation renders sputum samples noninfectious and obviates the need for containment level 3 laboratories for tuberculosis molecular tests.

Tuberculosis is caused by Mycobacterium tuberculosis (Mtb), a pathogen classified by the United Nations (UN) as a dangerous category B biological ...

Spatial Quantification of Drugs in Pulmonary Tuberculosis Lesions by Laser Capture Microdissection Liquid Chromatography Mass Spectrometry (LCM-LC/MS)

Tuberculosis is still a leading cause of morbidity and mortality worldwide. Improvements to existing drug regimens and the development of novel therapeutics are urgently required. The ability of dosed TB drugs to reach and sterilize bacteria within poorly-vascularized necrotic regions (caseum) of pulmonary granulomas is crucial for successful therapeutic intervention. Effective therapeutic regimens must therefore contain drugs with favorable caseum penetration properties. Current LC/MS methods for quantifying drug levels in biological tissues have limited spatial resolution capabilities, making it difficult to accurately determine absolute drug concentrations within small tissue compartments such as those found within necrotic granulomas. Here we present a protocol combining laser capture microdissection (LCM) of pathologically-distinct tissue regions with LC/MS quantification. This technique provides absolute quantification of drugs within granuloma caseum, surrounding cellular lesion and uninvolved lung tissue and, therefore, accurately determines whether bactericidal concentrations are being achieved. In addition to tuberculosis research, the technique has many potential applications for spatially-resolved quantification of drugs in diseased tissues.

Spatial Quantification of Drugs in Pulmonary Tuberculosis Lesions by Laser Capture Microdissection Liquid Chromatography Mass Spectrometry LCM-LC/MS

Here, we describe a protocol using laser capture microdissection coupled with LC/MS analysis to spatially-quantify drug distributions within pulmonary tuberculosis granulomas. The approach has broad applicability to quantifying drug concentrations within tissues at high spatial detail.

Tuberculosis is still a leading cause of morbidity and mortality worldwide. Improvements to existing drug regimens and the development of novel ...

Medicine

An Automated Culture System for Use in Preclinical Testing of Host-Directed Therapies for Tuberculosis

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), was the most significant infectious disease killer globally until the advent of COVID-19. Mtb has evolved to persist in its intracellular environment, evade host defenses, and has developed resistance to many anti-tubercular drugs. One approach to solving resistance is identifying existing&#160;approved drugs that will boost the host immune response to Mtb. These drugs could then be repurposed as adjunctive host-directed therapies (HDT) to shorten treatment time and help overcome antibiotic resistance.
Quantification of intracellular Mtb growth in macrophages is a crucial aspect of assessing potential HDT. The gold standard for measuring Mtb growth is counting colony-forming units (CFU) on agar plates. This is a slow, labor-intensive assay that does not lend itself to rapid screening of drugs. In this protocol, an automated, broth-based culture system, which is more commonly used to detect Mtb in clinical specimens, has been adapted for preclinical screening of host-directed therapies. The capacity of the liquid culture assay system to investigate intracellular Mtb growth in macrophages treated with HDT was evaluated. The HDTs tested for their ability to inhibit Mtb growth were all-trans Retinoic acid (AtRA), both in solution and encapsulated in poly(lactic-co-glycolic acid) (PLGA) microparticles and the combination of interferon-gamma and linezolid. The advantages of this automated liquid culture-based technique over the CFU method include simplicity of setup, less labor-intensive preparation, and faster time to results (5-12 days compared to 21 days or more for agar plates).

Rapid and efficient quantification of intracellular M. tuberculosis growth is crucial for pursuing improved therapies against tuberculosis (TB). This protocol describes a broth-based colorimetric detection assay using an automated liquid culture system to quantify Mtb growth in macrophages treated with candidate host-directed therapies.

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), was the most significant infectious disease killer globally until the advent ...

High-Throughput Screening Assay for Mycobacterium abscessus Using Dual Reporters

Assay Development for High-Throughput Drug Screening Against Mycobacteria

Mycobacterium abscessus (Mab) infections are challenging to treat due to high intrinsic drug resistance, comparable to multidrug-resistant tuberculosis. Treatments are extremely ineffective and based on a multi-drug regimen, resulting in low patient compliance. Consequently, the scientific community is urged to identify new and effective drugs to treat these infections. One of the strategies employed to this end is drug repurposing - the process of identifying new therapeutic opportunities for existing drugs in the market, circumventing the time required to establish pharmacokinetic and safety profiles of new drugs. With most studies on drug development against Mab relying on traditional and time-consuming methods, an assay for high-throughput drug screening was developed against mycobacteria using an in house developed double-reporter strain of Mab. Using liquid-handling robotics, automated microscopy, and analysis, alongside in house developed double reporter strains, bacterial viability can be rapidly measured using two different readouts, luminescence and fluorescence, without adding reagents or performing any extra steps. This reduces time and variability between assays, a major advantage for high-throughput screenings. The described protocol was validated by screening a library of 1280 compounds. The obtained results were corroborated by the literature, with efficient detection of active compounds. Thus, this work fulfilled the aim of supplying the field with a new tool to help fight this extremely drug-resistant bacteria.

Author Spotlight: Scalable Drug Screening Protocol for Efficient Discovery of M. abscessus Treatments

This study developed an assay for high-throughput screening against Mycobacterium abscessus with a&#160;recently created double reporter strain, using fluorescence and luminescence to assess bacterial viability quickly. This protocol will be relevant for researchers aiming to screen new drugs against this drug-resistant bacteria.

Mycobacterium abscessus (Mab) infections are challenging to treat due to high intrinsic drug resistance, comparable to multidrug-resistant tuberculosis. ...

Accelerating Tuberculosis Determination Using the Micro-CFU Method

Micro-Colony Forming Unit Assay for Efficacy Evaluation of Vaccines Against Tuberculosis

Tuberculosis (TB), the leading cause of death worldwide by an infectious agent, killed 1.6 million people in 2022, only being surpassed by COVID-19 during the 2019-2021 pandemic. The disease is caused by the bacterium Mycobacterium tuberculosis (M.tb). The Mycobacterium bovis strain Bacillus Calmette-Gu&#233;rin (BCG), the only TB vaccine, is the oldest licensed vaccine in the world, still in use. Currently, there are 12 vaccines in clinical trials and dozens of vaccines under pre-clinical development. The method of choice used to assess the efficacy of TB vaccines in pre-clinical studies is the enumeration of bacterial colonies by the colony-forming units (CFU) assay. This time-consuming assay takes 4 to 6 weeks to conclude, requires substantial laboratory and incubator space, has high reagent costs, and is prone to contamination. Here we describe an optimized method for colony enumeration, the micro-CFU (mCFU), that offers a simple and rapid solution to analyze M.tb vaccine efficacy results. The mCFU assay requires tenfold fewer reagents, reduces the incubation period threefold, taking 1 to 2 weeks to conclude, reduces lab space and reagent cost, and minimizes the health and safety risks associated with working with large numbers of M.tb. Moreover, to evaluate the efficacy of a TB vaccine, samples may be obtained from a variety of sources, including tissues from vaccinated animals infected with Mycobacteria. We also describe an optimized method to produce a unicellular, uniform, and high-quality mycobacterial culture for infection studies. Finally, we propose that these methods should be universally adopted for pre-clinical studies of vaccine efficacy determination, ultimately leading to time reduction in the development of vaccines against TB.

Author Spotlight: Optimizing CFU Determination for Efficient Assessment of TB Vaccine Efficacy and Antigen Presentation Analysis 

The determination of colony-forming units (CFU) is the gold-standard technique for quantifying bacteria, including Mycobacterium tuberculosis which can take weeks to form visible colonies. Here we describe a micro-CFU for CFU determination with increased time efficiency, reduced lab space and reagent cost, and scalability to medium and high throughput experiments.

Tuberculosis (TB), the leading cause of death worldwide by an infectious agent, killed 1.6 million people in 2022, only being surpassed by COVID-19 during ...

An Assay to Evaluate Drug Efficacy against a Mycobacterium tuberculosis Infection Model

Source: Schaaf, K., et al. <a href="https://app.jove.com/v/55453">A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis.</a> J. Vis. Exp. (2017)
This video demonstrates an assay to evaluate the efficacy of drugs against Mycobacterium tuberculosis (Mtb) infection. An in vitro infection model containing Mtb/macrophage aggregates is generated that mimics in vivo infection. Upon introducing suitable antibiotics, their efficacy is tested via resuzarin assay to monitor the survival of bacteria with increasing drug concentrations.

Test do oceny skuteczności leku przeciwko modelowi zakażenia Mycobacterium tuberculosis

1. Culture Conditions for Green Fluorescent Protein Expressing M. tuberculosis mc26206 (Mtb-GFP)
NOTE: The M. tuberculosis H37Rv derived auxotroph strain ...

An In Vitro Caseum Binding Assay that Predicts Drug Penetration in Tuberculosis Lesions

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