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Kappel S, Melek K, Ross-Kaschitza D, Hauert B, Gerber CE, Lochner M, Peinelt C. CBA (4-chloro-2-(2-chlorophenoxy)acetamido) benzoic acid) inhibits TMEM206 mediated currents and TMEM206 does not contribute to acid-induced cell death in colorectal cancer cells. Front Pharmacol 2024; 15:1369513. [PMID: 38515848 PMCID: PMC10955468 DOI: 10.3389/fphar.2024.1369513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/08/2024] [Indexed: 03/23/2024] Open
Abstract
Introduction: Upon activation at low pH, TMEM206 conducts Cl- ions across plasma and vesicular membranes. In a (patho)physiological context, TMEM206 was reported to contribute to acid-induced cell death in neurons, kidney and cervical epithelial cells. We investigated the role of TMEM206 in acid-induced cell death in colorectal cancer cells. In addition, we studied CBA as a new small molecule inhibitor for TMEM206. Methods: The role of TMEM206 in acid-induced cell death was studied with CRISPR/Cas9-mediated knockout and FACS analysis. The pharmacology of TMEM206 was determined with the patch clamp technique. Results: In colorectal cancer cells, TMEM206 is not a critical mediator of acid-induced cell death. CBA is a small molecule inhibitor of TMEM206 (IC50 = 9.55 µM) at low pH, at pH 6.0 inhibition is limited. Conclusion: CBA demonstrates effective and specific inhibition of TMEM206; however, its inhibitory efficacy is limited at pH 6.0. Despite this limitation, CBA is a potent inhibitor for functional studies at pH 4.5 and may be a promising scaffold for the development of future TMEM206 inhibitors.
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Affiliation(s)
| | | | | | | | | | | | - Christine Peinelt
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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2
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Malysz J, Maxwell SE, Petkov GV. Differential effects of TRPM4 channel inhibitors on Guinea pig urinary bladder smooth muscle excitability and contractility: Novel 4-chloro-2-[2-(2-chloro-phenoxy)-acetylamino]-benzoic acid (CBA) versus classical 9-phenanthrol. Pharmacol Res Perspect 2022; 10:e00982. [PMID: 35822549 PMCID: PMC9277609 DOI: 10.1002/prp2.982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/06/2022] Open
Abstract
Non-selective cation channels in urinary bladder smooth muscle (UBSM) are thought to mediate increases in cellular excitability and contractility. For transient receptor potential melastatin type-4 (TRPM4) channels, the evidence primarily relies on the inhibitor 9-phenanthrol, which exhibits pharmacological limitations. Recently, 4-chloro-2-[2-(2-chloro-phenoxy)-acetylamino]-benzoic acid (CBA) has been discovered as a novel TRPM4 channel blocker. We examined how, in comparison to 9-phenanthrol, CBA affects the excitability of freshly isolated guinea pig UBSM cells and the contractility of UBSM strips. Additionally, non-selective TRPM4 channel inhibitor flufenamic acid (FFA) and potentiator BTP2 (also known as YM-58483) were studied in UBSM cells. Unlike robust inhibition for 9-phenanthrol already known, CBA (up to 100 μM) displayed either no or a very weak reduction (<20%) in spontaneous phasic, 20 mM KCl-induced, and electrical field stimulated contractions. For 300 μM CBA, reductions were higher except for an increase in the frequency of KCl-induced contractions. In UBSM cells, examined under amphotericin B-perforated patch-clamp, CBA (30 μM) did not affect the membrane potential (I = 0) or voltage step-induced whole-cell cation currents, sensitive to 9-phenanthrol. The currents were not inhibited by FFA (100 μM), increased by BTP2 (10 μM), nor enhanced under a strongly depolarizing holding voltage of -16 or + 6 mV (vs. -74 mV). None of the three compounds affected the cell capacitance, unlike 9-phenanthrol. In summary, the novel inhibitor CBA and nonselective FFA did not mimic the inhibitory properties of 9-phenanthrol on UBSM function. These results suggest that TRPM4 channels, although expressed in UBSM, play a distinct role rather than direct regulation of excitability and contractility.
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Affiliation(s)
- John Malysz
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
- Present address:
Department of Physiology and Cell BiologyUniversity of NevadaRenoNevadaUSA
| | - Sarah E. Maxwell
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Georgi V. Petkov
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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3
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Su A, Cheng Y, Xue H, She Y, Rajan K. Artificial intelligence informed toxicity screening of amine chemistries used in the synthesis of hybrid
organic–inorganic
perovskites. AIChE J 2022. [DOI: 10.1002/aic.17699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- An Su
- College of Chemical Engineering Zhejiang University of Technology Hangzhou China
- Department of Materials Design and Innovation University at Buffalo Buffalo New York USA
| | - Yingying Cheng
- College of Chemical Engineering Zhejiang University of Technology Hangzhou China
| | - Haotian Xue
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals Zhejiang University of Technology Hangzhou China
| | - Yuanbin She
- College of Chemical Engineering Zhejiang University of Technology Hangzhou China
| | - Krishna Rajan
- Department of Materials Design and Innovation University at Buffalo Buffalo New York USA
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Kovács ZM, Dienes C, Hézső T, Almássy J, Magyar J, Bányász T, Nánási PP, Horváth B, Szentandrássy N. Pharmacological Modulation and (Patho)Physiological Roles of TRPM4 Channel—Part 1: Modulation of TRPM4. Pharmaceuticals (Basel) 2022; 15:ph15010081. [PMID: 35056138 PMCID: PMC8781449 DOI: 10.3390/ph15010081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Transient receptor potential melastatin 4 is a unique member of the TRPM protein family and, similarly to TRPM5, is Ca2+-sensitive and permeable to monovalent but not divalent cations. It is widely expressed in many organs and is involved in several functions by regulating the membrane potential and Ca2+ homeostasis in both excitable and non-excitable cells. This part of the review discusses the pharmacological modulation of TRPM4 by listing, comparing, and describing both endogenous and exogenous activators and inhibitors of the ion channel. Moreover, other strategies used to study TRPM4 functions are listed and described. These strategies include siRNA-mediated silencing of TRPM4, dominant-negative TRPM4 variants, and anti-TRPM4 antibodies. TRPM4 is receiving more and more attention and is likely to be the topic of research in the future.
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Affiliation(s)
- Zsigmond Máté Kovács
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Csaba Dienes
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tamás Hézső
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - János Almássy
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
| | - János Magyar
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Division of Sport Physiology, Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tamás Bányász
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
| | - Péter P. Nánási
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Department of Dental Physiology and Pharmacology, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
| | - Balázs Horváth
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Norbert Szentandrássy
- Department of Physiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.M.K.); (C.D.); (T.H.); (J.A.); (J.M.); (T.B.); (P.P.N.); (B.H.)
- Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence:
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Investigation of Novel Small Molecular TRPM4 Inhibitors in Colorectal Cancer Cells. Cancers (Basel) 2021; 13:cancers13215400. [PMID: 34771564 PMCID: PMC8582472 DOI: 10.3390/cancers13215400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Transient receptor potential melastatin 4 (TRPM4) ion channel malfunction or aberrant expression is implicated in many diseases, including different cancers and cardiovascular diseases. Currently, there is a need for specific and potent TRPM4 inhibitors. They would allow to study the role of TRPM4 in disease models and to validate it as a potential target in therapies, including anti-cancer therapy. In colorectal cancer (CRC), TRPM4 is upregulated, and its conductivity plays a role in the regulation of viability and cell cycle of CRC cells. In this study, we tested three novel TRPM4 inhibitors, CBA, NBA, and LBA, in CRC cells. In HCT116 cells, we show that NBA inhibits TRPM4 currents in the micromolar range and alters proliferation and cell cycle. Furthermore, NBA decreases the viability of Colo205 cells. This makes NBA a promising candidate for further evaluation as a specific TRPM4 inhibitor in other cellular systems and disease models. Abstract (1) Background: Transient receptor potential melastatin (TRPM4) ion channel aberrant expression or malfunction contributes to different types of cancer, including colorectal cancer (CRC). However, TRPM4 still needs to be validated as a potential target in anti-cancer therapy. Currently, the lack of potent and selective TRPM4 inhibitors limits further studies on TRPM4 in cancer disease models. In this study, we validated novel TRPM4 inhibitors, CBA, NBA, and LBA, in CRC cells. (2) Methods: The potency to inhibit TRPM4 conductivity in CRC cells was assessed with the whole-cell patch clamp technique. Furthermore, the impact of TRPM4 inhibitors on cellular functions, such as viability, proliferation, and cell cycle, were assessed in cellular assays. (3) Results: We show that in CRC cells, novel TRPM4 inhibitors irreversibly block TRPM4 currents in a low micromolar range. NBA decreases proliferation and alters the cell cycle in HCT116 cells. Furthermore, NBA reduces the viability of the Colo205 cell line, which highly expresses TRPM4. (4) Conclusions: NBA is a promising new TRPM4 inhibitor candidate, which could be used to study the role of TRPM4 in cancer disease models and other diseases.
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Borgström A, Peinelt C, Stokłosa P. TRPM4 in Cancer-A New Potential Drug Target. Biomolecules 2021; 11:biom11020229. [PMID: 33562811 PMCID: PMC7914809 DOI: 10.3390/biom11020229] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Transient receptor potential melastatin 4 (TRPM4) is widely expressed in various organs and associated with cardiovascular and immune diseases. Lately, the interest in studies on TRPM4 in cancer has increased. Thus far, TRPM4 has been investigated in diffuse large B-cell lymphoma, prostate, colorectal, liver, breast, urinary bladder, cervical, and endometrial cancer. In several types of cancer TRPM4 is overexpressed and contributes to cancer hallmark functions such as increased proliferation and migration and cell cycle shift. Hence, TRPM4 is a potential prognostic cancer marker and a promising anticancer drug target candidate. Currently, the underlying mechanism by which TRPM4 contributes to cancer hallmark functions is under investigation. TRPM4 is a Ca2+-activated monovalent cation channel, and its ion conductivity can decrease intracellular Ca2+ signaling. Furthermore, TRPM4 can interact with different partner proteins. However, the lack of potent and specific TRPM4 inhibitors has delayed the investigations of TRPM4. In this review, we summarize the potential mechanisms of action and discuss new small molecule TRPM4 inhibitors, as well as the TRPM4 antibody, M4P. Additionally, we provide an overview of TRPM4 in human cancer and discuss TRPM4 as a diagnostic marker and anticancer drug target.
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7
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Jimenez I, Prado Y, Marchant F, Otero C, Eltit F, Cabello-Verrugio C, Cerda O, Simon F. TRPM Channels in Human Diseases. Cells 2020; 9:E2604. [PMID: 33291725 PMCID: PMC7761947 DOI: 10.3390/cells9122604] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
The transient receptor potential melastatin (TRPM) subfamily belongs to the TRP cation channels family. Since the first cloning of TRPM1 in 1989, tremendous progress has been made in identifying novel members of the TRPM subfamily and their functions. The TRPM subfamily is composed of eight members consisting of four six-transmembrane domain subunits, resulting in homomeric or heteromeric channels. From a structural point of view, based on the homology sequence of the coiled-coil in the C-terminus, the eight TRPM members are clustered into four groups: TRPM1/M3, M2/M8, M4/M5 and M6/M7. TRPM subfamily members have been involved in several physiological functions. However, they are also linked to diverse pathophysiological human processes. Alterations in the expression and function of TRPM subfamily ion channels might generate several human diseases including cardiovascular and neurodegenerative alterations, organ dysfunction, cancer and many other channelopathies. These effects position them as remarkable putative targets for novel diagnostic strategies, drug design and therapeutic approaches. Here, we review the current knowledge about the main characteristics of all members of the TRPM family, focusing on their actions in human diseases.
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Affiliation(s)
- Ivanka Jimenez
- Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; (I.J.); (Y.P.); (F.M.); (C.C.-V.)
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile;
| | - Yolanda Prado
- Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; (I.J.); (Y.P.); (F.M.); (C.C.-V.)
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile;
| | - Felipe Marchant
- Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; (I.J.); (Y.P.); (F.M.); (C.C.-V.)
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile;
| | - Carolina Otero
- Faculty of Medicine, School of Chemistry and Pharmacy, Universidad Andrés Bello, Santiago 8370186, Chile;
| | - Felipe Eltit
- Vancouver Prostate Centre, Vancouver, BC V6Z 1Y6, Canada;
- Department of Urological Sciences, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Claudio Cabello-Verrugio
- Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; (I.J.); (Y.P.); (F.M.); (C.C.-V.)
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago 7560484, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago 8370146, Chile
| | - Oscar Cerda
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile;
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Felipe Simon
- Faculty of Life Science, Universidad Andrés Bello, Santiago 8370186, Chile; (I.J.); (Y.P.); (F.M.); (C.C.-V.)
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago 8380453, Chile;
- Millennium Institute on Immunology and Immunotherapy, Santiago 8370146, Chile
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8
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Small Molecular Inhibitors Block TRPM4 Currents in Prostate Cancer Cells, with Limited Impact on Cancer Hallmark Functions. J Mol Biol 2020; 433:166665. [PMID: 33058873 DOI: 10.1016/j.jmb.2020.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/14/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022]
Abstract
Transient receptor potential melastatin 4 (TRPM4) is a broadly expressed Ca2+ activated monovalent cation channel that contributes to the pathophysiology of several diseases. For this study, we generated stable CRISPR/Cas9 TRPM4 knockout (K.O.) cells from the human prostate cancer cell line DU145 and analyzed the cells for changes in cancer hallmark functions. Both TRPM4-K.O. clones demonstrated lower proliferation and viability compared to the parental cells. Migration was also impaired in the TRPM4-K.O. cells. Additionally, analysis of 210 prostate cancer patient tissues demonstrates a positive association between TRPM4 protein expression and local/metastatic progression. Moreover, a decreased adhesion rate was detected in the two K.O. clones compared to DU145 cells. Next, we tested three novel TRPM4 inhibitors with whole-cell patch clamp technique for their potential to block TRPM4 currents. CBA, NBA and LBA partially inhibited TRPM4 currents in DU145 cells. However, none of these inhibitors demonstrated any TRPM4-specific effect in the cellular assays. To evaluate if the observed effect of TRPM4 K.O. on migration, viability, and cell cycle is linked to TRPM4 ion conductivity, we transfected TRPM4-K.O. cells with either TRPM4 wild-type or a dominant-negative mutant, non-permeable to Na+. Our data showed a partial rescue of the viability of cells expressing functional TRPM4, while the pore mutant was not able to rescue this phenotype. For cell cycle distribution, TRPM4 ion conductivity was not essential since TRPM4 wild-type and the pore mutant rescued the phenotype. In conclusion, TRPM4 contributes to viability, migration, cell cycle shift, and adhesion; however, blocking TRPM4 ion conductivity is insufficient to prevent its role in cancer hallmark functions in prostate cancer cells.
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Poirier M, Pujol-Giménez J, Manatschal C, Bühlmann S, Embaby A, Javor S, Hediger MA, Reymond JL. Pyrazolyl-pyrimidones inhibit the function of human solute carrier protein SLC11A2 (hDMT1) by metal chelation. RSC Med Chem 2020; 11:1023-1031. [PMID: 33479694 PMCID: PMC7649969 DOI: 10.1039/d0md00085j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Solute carrier proteins (SLCs) control fluxes of ions and molecules across biological membranes and represent an emerging class of drug targets. SLC11A2 (hDMT1) mediates intestinal iron uptake and its inhibition might be used to treat iron overload diseases such as hereditary hemochromatosis. Here we report a micromolar (IC50 = 1.1 μM) pyrazolyl-pyrimidone inhibitor of radiolabeled iron uptake in hDMT1 overexpressing HEK293 cells acting by a non-competitive mechanism, which however does not affect the electrophysiological properties of the transporter. Isothermal titration calorimetry, competition with calcein, induced precipitation of radioactive iron and cross inhibition of the unrelated iron transporter SLC39A8 (hZIP8) indicate that inhibition is mediated by metal chelation. Mapping the chemical space of thousands of pyrazolo-pyrimidones and similar 2,2'-diazabiaryls in ChEMBL suggests that their reported activities might partly reflect metal chelation. Such metal chelating groups are not listed in pan-assay interference compounds (PAINS) but should be checked when addressing SLCs.
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Affiliation(s)
- Marion Poirier
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Jonai Pujol-Giménez
- Institute of Biochemistry and Molecular Medicine , University of Bern , Bühlstrasse 28 , 3012 Bern , Switzerland
- Membrane Transport Discovery Lab , Department of Nephrology and Hypertension , Inselspital , University of Bern Kinderklinik , Freiburgstrasse 15 , 3010 Bern , Switzerland .
- Department of Biomedical Research , University of Bern , Murtenstrasse 35 , 3008 Bern , Switzerland
| | - Cristina Manatschal
- Department of Biochemistry , University of Zürich , Winterthurerstrasse 190 , Zürich , Switzerland
| | - Sven Bühlmann
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Ahmed Embaby
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Sacha Javor
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine , University of Bern , Bühlstrasse 28 , 3012 Bern , Switzerland
- Membrane Transport Discovery Lab , Department of Nephrology and Hypertension , Inselspital , University of Bern Kinderklinik , Freiburgstrasse 15 , 3010 Bern , Switzerland .
- Department of Biomedical Research , University of Bern , Murtenstrasse 35 , 3008 Bern , Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland .
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10
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Alkorta I, Elguero J. Theoretical studies of conformational analysis and intramolecular dynamic phenomena. Struct Chem 2019. [DOI: 10.1007/s11224-019-01370-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Capecchi A, Awale M, Probst D, Reymond JL. PubChem and ChEMBL beyond Lipinski. Mol Inform 2019; 38:e1900016. [PMID: 30844149 DOI: 10.1002/minf.201900016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022]
Abstract
Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP and NLC (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Daniel Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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