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Kandasamy M, Mak KK, Devadoss T, Thanikachalam PV, Sakirolla R, Choudhury H, Pichika MR. Construction of a novel quinoxaline as a new class of Nrf2 activator. BMC Chem 2019; 13:117. [PMID: 31572984 PMCID: PMC6760105 DOI: 10.1186/s13065-019-0633-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/10/2019] [Indexed: 01/10/2023] Open
Abstract
Background The transcription factor Nuclear factor erythroid-2-related factor 2 (NRF2) and its principal repressive regulator, Kelch-like ECH-associated protein 1 (KEAP1), are perilous in the regulation of inflammation, as well as maintenance of homeostasis. Thus, NRF2 activation is involved in cytoprotection against many inflammatory disorders. N′-Nicotinoylquinoxaline-2-carbohdyrazide (NQC) was structurally designed by the combination of important pharmacophoric features of bioactive compounds reported in the literature. Methods NQC was synthesised and characterised using spectroscopic techniques. The compound was tested for its anti-inflammatory effect using Lipopolysaccharide from Escherichia coli (LPSEc) induced inflammation in mouse macrophages (RAW 264.7 cells). The effect of NQC on inflammatory cytokines was measured using enzyme-linked immune sorbent assay (ELISA). The Nrf2 activity of the compound NQC was determined using ‘Keap1:Nrf2 Inhibitor Screening Assay Kit’. To obtain the insights on NQC’s activity on Nrf2, molecular docking studies were performed using Schrödinger suite. The metabolic stability of NQC was determined using mouse, rat and human microsomes. Results NQC was found to be non-toxic at the dose of 50 µM on RAW 264.7 cells. NQC showed potent anti-inflammatory effect in an in vitro model of LPSEc stimulated murine macrophages (RAW 264.7 cells) with an IC50 value 26.13 ± 1.17 µM. NQC dose-dependently down-regulated the pro-inflammatory cytokines [interleukin (IL)-1β (13.27 ± 2.37 μM), IL-6 (10.13 ± 0.58 μM) and tumor necrosis factor (TNF)-α] (14.41 ± 1.83 μM); and inflammatory mediator, prostaglandin E2 (PGE2) with IC50 values, 15.23 ± 0.91 µM. Molecular docking studies confirmed the favourable binding of NQC at Kelch domain of Keap-1. It disrupts the Nrf2 interaction with kelch domain of keap 1 and its IC50 value was 4.21 ± 0.89 µM. The metabolic stability studies of NQC in human, rat and mouse liver microsomes revealed that it is quite stable with half-life values; 63.30 ± 1.73, 52.23 ± 0.81, 24.55 ± 1.13 min; microsomal intrinsic clearance values; 1.14 ± 0.31, 1.39 ± 0.87 and 2.96 ± 0.34 µL/min/g liver; respectively. It is observed that rat has comparable metabolic profile with human, thus, rat could be used as an in vivo model for prediction of pharmacokinetics and metabolism profiles of NQC in human. Conclusion NQC is a new class of NRF2 activator with potent in vitro anti-inflammatory activity and good metabolic stability.
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Affiliation(s)
- Murugesh Kandasamy
- 1Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.,4Center for Bioactive Molecules & Drug Delivery, Institute for Research, Development & Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Kit-Kay Mak
- 1Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.,2School of Postgraduate Studies and Research, International Medical University, Kuala Lumpur, Malaysia.,4Center for Bioactive Molecules & Drug Delivery, Institute for Research, Development & Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Thangaraj Devadoss
- KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh India
| | | | | | - Hira Choudhury
- 3Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.,4Center for Bioactive Molecules & Drug Delivery, Institute for Research, Development & Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Mallikarjuna Rao Pichika
- 1Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.,4Center for Bioactive Molecules & Drug Delivery, Institute for Research, Development & Innovation, International Medical University, Kuala Lumpur, Malaysia
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Huard K, Ahn K, Amor P, Beebe DA, Borzilleri KA, Chrunyk BA, Coffey SB, Cong Y, Conn EL, Culp JS, Dowling MS, Gorgoglione MF, Gutierrez JA, Knafels JD, Lachapelle EA, Pandit J, Parris KD, Perez S, Pfefferkorn JA, Price DA, Raymer B, Ross TT, Shavnya A, Smith AC, Subashi TA, Tesz GJ, Thuma BA, Tu M, Weaver JD, Weng Y, Withka JM, Xing G, Magee TV. Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK). J Med Chem 2017; 60:7835-7849. [PMID: 28853885 DOI: 10.1021/acs.jmedchem.7b00947] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Increased fructose consumption and its subsequent metabolism have been implicated in hepatic steatosis, dyslipidemia, obesity, and insulin resistance in humans. Since ketohexokinase (KHK) is the principal enzyme responsible for fructose metabolism, identification of a selective KHK inhibitor may help to further elucidate the effect of KHK inhibition on these metabolic disorders. Until now, studies on KHK inhibition with small molecules have been limited due to the lack of viable in vivo pharmacological tools. Herein we report the discovery of 12, a selective KHK inhibitor with potency and properties suitable for evaluating KHK inhibition in rat models. Key structural features interacting with KHK were discovered through fragment-based screening and subsequent optimization using structure-based drug design, and parallel medicinal chemistry led to the identification of pyridine 12.
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Affiliation(s)
- Kim Huard
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kay Ahn
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Paul Amor
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David A Beebe
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kris A Borzilleri
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Boris A Chrunyk
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Steven B Coffey
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yang Cong
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Edward L Conn
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey S Culp
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew F Gorgoglione
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jemy A Gutierrez
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D Knafels
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Erik A Lachapelle
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kevin D Parris
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sylvie Perez
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jeffrey A Pfefferkorn
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David A Price
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Brian Raymer
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Trenton T Ross
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Andre Shavnya
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Aaron C Smith
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Timothy A Subashi
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory J Tesz
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Benjamin A Thuma
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Meihua Tu
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D Weaver
- Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yan Weng
- Medicine Design, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jane M Withka
- Structural Biology and Biophysics, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gang Xing
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Thomas V Magee
- Internal Medicine, Pfizer Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
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Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJS. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. ACTA ACUST UNITED AC 2015; 20:788-800. [PMID: 25690569 DOI: 10.1177/1087057115570550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/02/2015] [Indexed: 01/25/2023]
Abstract
The ubiquitous AAA+ ATPase p97 functions as a dynamic molecular machine driving several cellular processes. It is essential in regulating protein homeostasis, and it represents a potential drug target for cancer, particularly when there is a greater reliance on the endoplasmic reticulum-associated protein degradation pathway and ubiquitin-proteasome pathway to degrade an overabundance of secreted proteins. Here, we report a case study for using fragment-based ligand design approaches against this large and dynamic hexamer, which has multiple potential binding sites for small molecules. A screen of a fragment library was conducted by surface plasmon resonance (SPR) and followed up by nuclear magnetic resonance (NMR), two complementary biophysical techniques. Virtual screening was also carried out to examine possible binding sites for the experimental hits and evaluate the potential utility of fragment docking for this target. Out of this effort, 13 fragments were discovered that showed reversible binding with affinities between 140 µM and 1 mM, binding stoichiometries of 1:1 or 2:1, and good ligand efficiencies. Structural data for fragment-protein interactions were obtained with residue-specific [U-(2)H] (13)CH3-methyl-labeling NMR strategies, and these data were compared to poses from docking. The combination of virtual screening, SPR, and NMR enabled us to find and validate a number of interesting fragment hits and allowed us to gain an understanding of the structural nature of fragment binding.
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Affiliation(s)
- Michael S Chimenti
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Thomas L James
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
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Meiby E, Simmonite H, le Strat L, Davis B, Matassova N, Moore JD, Mrosek M, Murray J, Hubbard RE, Ohlson S. Fragment Screening by Weak Affinity Chromatography: Comparison with Established Techniques for Screening against HSP90. Anal Chem 2013; 85:6756-66. [DOI: 10.1021/ac400715t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Elinor Meiby
- Department of Chemistry and Biomedical
Sciences, Linnaeus University, SE-391 82
Kalmar, Sweden
| | | | - Loic le Strat
- Vernalis, Granta Park, Cambridge CB21 6GB, United Kingdom
| | - Ben Davis
- Vernalis, Granta Park, Cambridge CB21 6GB, United Kingdom
| | | | | | - Michael Mrosek
- Vernalis, Granta Park, Cambridge CB21 6GB, United Kingdom
| | - James Murray
- Vernalis, Granta Park, Cambridge CB21 6GB, United Kingdom
| | - Roderick E. Hubbard
- Vernalis, Granta Park, Cambridge CB21 6GB, United Kingdom
- YSBL, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Sten Ohlson
- Department of Chemistry and Biomedical
Sciences, Linnaeus University, SE-391 82
Kalmar, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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