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Title: Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors

Abstract

Inhibiting NAD biosynthesis by blocking the function of nicotinamide phosphoribosyl transferase (NAMPT) is an attractive therapeutic strategy for targeting tumor metabolism. However, the development of drug resistance commonly limits the efficacy of cancer therapeutics. This study identifies mutations in NAMPT that confer resistance to a novel NAMPT inhibitor, GNE-618, in cell culture and in vivo, thus demonstrating that the cytotoxicity of GNE-618 is on target. We determine the crystal structures of six NAMPT mutants in the apo form and in complex with various inhibitors and use cellular, biochemical and structural data to elucidate two resistance mechanisms. One is the surprising finding of allosteric modulation by mutation of residue Ser165, resulting in unwinding of an α-helix that binds the NAMPT substrate 5-phosphoribosyl-1-pyrophosphate (PRPP). The other mechanism is orthosteric blocking of inhibitor binding by mutations of Gly217. Furthermore, by evaluating a panel of diverse small molecule inhibitors, we unravel inhibitor structure activity relationships on the mutant enzymes. These results provide valuable insights into the design of next generation NAMPT inhibitors that offer improved therapeutic potential by evading certain mechanisms of resistance.

Authors:
 [1];  [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [1];  [1];  [3]
+ Show Author Affiliations
  1. Genentech, Inc., South San Francisco, CA (United States)
  2. Forma Therapeutics, Inc., Watertown, MA (United States)
  3. Univ. of Washington, Seattle, WA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1255305
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 9; Journal Issue: 10; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; Crystal structure; Enzyme structure; Enzyme inhibitors; Imidazole; Enzymes; Protein structure; Mutation detection; Nicotine

Citation Formats

Wang, Weiru, Elkins, Kristi, Oh, Angela, Ho, Yen-Ching, Wu, Jiansheng, Li, Hong, Xiao, Yang, Kwong, Mandy, Coons, Mary, Brillantes, Bobby, Cheng, Eric, Crocker, Lisa, Dragovich, Peter S., Sampath, Deepak, Zheng, Xiaozhang, Bair, Kenneth W., O'Brien, Thomas, Belmont, Lisa D., and Xu, Wenqing. Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors. United States: N. p., 2014. Web. doi:10.1371/journal.pone.0109366.
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Wang, Weiru, Elkins, Kristi, Oh, Angela, Ho, Yen-Ching, Wu, Jiansheng, Li, Hong, Xiao, Yang, Kwong, Mandy, Coons, Mary, Brillantes, Bobby, Cheng, Eric, Crocker, Lisa, Dragovich, Peter S., Sampath, Deepak, Zheng, Xiaozhang, Bair, Kenneth W., O'Brien, Thomas, Belmont, Lisa D., & Xu, Wenqing. Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors. United States. https://doi.org/10.1371/journal.pone.0109366
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Wang, Weiru, Elkins, Kristi, Oh, Angela, Ho, Yen-Ching, Wu, Jiansheng, Li, Hong, Xiao, Yang, Kwong, Mandy, Coons, Mary, Brillantes, Bobby, Cheng, Eric, Crocker, Lisa, Dragovich, Peter S., Sampath, Deepak, Zheng, Xiaozhang, Bair, Kenneth W., O'Brien, Thomas, Belmont, Lisa D., and Xu, Wenqing. Mon . "Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors". United States. https://doi.org/10.1371/journal.pone.0109366. https://www.osti.gov/servlets/purl/1255305.
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@article{osti_1255305,
title = {Structural Basis for Resistance to Diverse Classes of NAMPT Inhibitors},
author = {Wang, Weiru and Elkins, Kristi and Oh, Angela and Ho, Yen-Ching and Wu, Jiansheng and Li, Hong and Xiao, Yang and Kwong, Mandy and Coons, Mary and Brillantes, Bobby and Cheng, Eric and Crocker, Lisa and Dragovich, Peter S. and Sampath, Deepak and Zheng, Xiaozhang and Bair, Kenneth W. and O'Brien, Thomas and Belmont, Lisa D. and Xu, Wenqing},
abstractNote = {Inhibiting NAD biosynthesis by blocking the function of nicotinamide phosphoribosyl transferase (NAMPT) is an attractive therapeutic strategy for targeting tumor metabolism. However, the development of drug resistance commonly limits the efficacy of cancer therapeutics. This study identifies mutations in NAMPT that confer resistance to a novel NAMPT inhibitor, GNE-618, in cell culture and in vivo, thus demonstrating that the cytotoxicity of GNE-618 is on target. We determine the crystal structures of six NAMPT mutants in the apo form and in complex with various inhibitors and use cellular, biochemical and structural data to elucidate two resistance mechanisms. One is the surprising finding of allosteric modulation by mutation of residue Ser165, resulting in unwinding of an α-helix that binds the NAMPT substrate 5-phosphoribosyl-1-pyrophosphate (PRPP). The other mechanism is orthosteric blocking of inhibitor binding by mutations of Gly217. Furthermore, by evaluating a panel of diverse small molecule inhibitors, we unravel inhibitor structure activity relationships on the mutant enzymes. These results provide valuable insights into the design of next generation NAMPT inhibitors that offer improved therapeutic potential by evading certain mechanisms of resistance.},
doi = {10.1371/journal.pone.0109366},
journal = {PLoS ONE},
number = 10,
volume = 9,
place = {United States},
year = {Mon Oct 06 00:00:00 EDT 2014},
month = {Mon Oct 06 00:00:00 EDT 2014}
}
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https://doi.org/10.1371/journal.pone.0109366
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Fragment-Based Identification of Amides Derived from trans -2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)
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Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties
journal, June 2013

  • Gunzner-Toste, Janet; Zhao, Guiling; Bauer, Paul
  • Bioorganic & Medicinal Chemistry Letters, Vol. 23, Issue 12
  • DOI: 10.1016/j.bmcl.2013.04.040

Target enzyme mutations are the molecular basis for resistance towards pharmacological inhibition of nicotinamide phosphoribosyltransferase
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Fragment-Based Identification of Amides Derived from trans -2-(Pyridin-3-yl)cyclopropanecarboxylic Acid as Potent Inhibitors of Human Nicotinamide Phosphoribosyltransferase (NAMPT)
journal, January 2014

  • Giannetti, Anthony M.; Zheng, Xiaozhang; Skelton, Nicholas J.
  • Journal of Medicinal Chemistry, Vol. 57, Issue 3
  • DOI: 10.1021/jm4015108

The Secret Life of NAD + : An Old Metabolite Controlling New Metabolic Signaling Pathways
journal, April 2010

  • Houtkooper, Riekelt H.; Cantó, Carles; Wanders, Ronald J.
  • Endocrine Reviews, Vol. 31, Issue 2
  • DOI: 10.1210/er.2009-0026
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    Works referencing / citing this record:

    Identification of a novel NAMPT inhibitor by CRISPR/Cas9 chemogenomic profiling in mammalian cells
    text, January 2017

    Cancer cell metabolic plasticity allows resistance to NAMPT inhibition but invariably induces dependence on LDHA
    journal, March 2018

    • Thongon, Natthakan; Zucal, Chiara; D’Agostino, Vito Giuseppe
    • Cancer & Metabolism, Vol. 6, Issue 1
    • DOI: 10.1186/s40170-018-0174-7

    Extracellular nicotinamide phosphoribosyltransferase, a new cancer metabokine
    journal, June 2016

    • Grolla, Ambra A.; Travelli, Cristina; Genazzani, Armando A.
    • British Journal of Pharmacology, Vol. 173, Issue 14
    • DOI: 10.1111/bph.13505

    Cross resistance to diverse anticancer nicotinamide phosphoribosyltransferase inhibitors induced by FK866 treatment
    journal, March 2018

    Nicotinamide phosphoribosyltransferase (Nampt) in carcinogenesis: new clinical opportunities
    journal, June 2016

    New strategies to maximize therapeutic opportunities for NAMPT inhibitors in oncology
    journal, June 2015

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