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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024. [PMID: 38577994 DOI: 10.1021/acsinfecdis.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V Krieger
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Ethan Clary
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Natalie Thornton
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Paolo A Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron Therapeutics, 55 Chapel Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen Therapeutics, 12 Gill Street, Woburn, Massachusetts 01801, United States
| | - Christopher D Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO Therapeutics, 150 Cambridgepark Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T S Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix Pharmaceuticals, 222 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Anthony D Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
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Wu Z, Graybill TL, Zeng X, Platchek M, Zhang J, Bodmer VQ, Wisnoski DD, Deng J, Coppo FT, Yao G, Tamburino A, Scavello G, Franklin GJ, Mataruse S, Bedard KL, Ding Y, Chai J, Summerfield J, Centrella PA, Messer JA, Pope AJ, Israel DI. Cell-Based Selection Expands the Utility of DNA-Encoded Small-Molecule Library Technology to Cell Surface Drug Targets: Identification of Novel Antagonists of the NK3 Tachykinin Receptor. ACS Comb Sci 2015; 17:722-31. [PMID: 26562224 DOI: 10.1021/acscombsci.5b00124] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded small-molecule library technology has recently emerged as a new paradigm for identifying ligands against drug targets. To date, this technology has been used with soluble protein targets that are produced and used in a purified state. Here, we describe a cell-based method for identifying small-molecule ligands from DNA-encoded libraries against integral membrane protein targets. We use this method to identify novel, potent, and specific inhibitors of NK3, a member of the tachykinin family of G-protein coupled receptors (GPCRs). The method is simple and broadly applicable to other GPCRs and integral membrane proteins. We have extended the application of DNA-encoded library technology to membrane-associated targets and demonstrate the feasibility of selecting DNA-tagged, small-molecule ligands from complex combinatorial libraries against targets in a heterogeneous milieu, such as the surface of a cell.
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Affiliation(s)
- Zining Wu
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Todd L. Graybill
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xin Zeng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Platchek
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jean Zhang
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Vera Q. Bodmer
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David D. Wisnoski
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jianghe Deng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Frank T. Coppo
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Gang Yao
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Alex Tamburino
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Genaro Scavello
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - G. Joseph Franklin
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Katie L. Bedard
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jing Chai
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jennifer Summerfield
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jeffrey A. Messer
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Andrew J. Pope
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David I. Israel
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
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