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Namasivayam V, Silbermann K, Pahnke J, Wiese M, Stefan SM. Scaffold fragmentation and substructure hopping reveal potential, robustness, and limits of computer-aided pattern analysis (C@PA). Comput Struct Biotechnol J 2021; 19:3269-3283. [PMID: 34141145 PMCID: PMC8193046 DOI: 10.1016/j.csbj.2021.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023] Open
Abstract
Computer-aided pattern analysis (C@PA) was recently presented as a powerful tool to predict multitarget ABC transporter inhibitors. The backbone of this computational methodology was the statistical analysis of frequently occurring molecular features amongst a fixed set of reported small-molecules that had been evaluated toward ABCB1, ABCC1, and ABCG2. As a result, negative and positive patterns were elucidated, and secondary positive substructures could be suggested that complemented the multitarget fingerprints. Elevating C@PA to a non-statistical and exploratory level, the concluded secondary positive patterns were extended with potential positive substructures to improve C@PA's prediction capabilities and to explore its robustness. A small-set compound library of known ABCC1 inhibitors with a known hit rate for triple ABCB1, ABCC1, and ABCG2 inhibition was taken to virtually screen for the extended positive patterns. In total, 846 potential broad-spectrum ABCB1, ABCC1, and ABCG2 inhibitors resulted, from which 10 have been purchased and biologically evaluated. Our approach revealed 4 novel multitarget ABCB1, ABCC1, and ABCG2 inhibitors with a biological hit rate of 40%, but with a slightly lower inhibitory power than derived from the original C@PA. This is the very first report about discovering novel broad-spectrum inhibitors against the most prominent ABC transporters by improving C@PA.
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Key Words
- ABC transporter, ATP-binding cassette transporter
- ABCB1 (P-gp)
- ABCC1 (MRP1)
- ABCG2 (BCRP)
- ATP, adenosine-triphosphate
- Alzheimer's disease (AD)
- BCRP, breast cancer resistance protein (ABCG2)
- C@PA, computer-aided pattern analysis
- F1–5, pharmacophore features 1–5
- IC50, half-maximal inhibition concentration
- MDR, multidrug resistance
- MOE, molecular operating environment
- MRP1, multidrug resistance-associated protein 1 (ABCC1)
- Multidrug resistance (MDR)
- Multitarget fingerprints
- P-gp, P-glycoprotein (ABCB1)
- Pan-ABC inhibition / antagonism / blockage (PANABC)
- Pattern analysis (C@PA)
- SEM, standard error of the mean
- SMILES, simplified molecular input line entry specification
- Tc, Tanimotto coefficient
- Triple / multitarget / broad-spectrum / promiscuous inhibitor / antagonist
- Under-studied ABC transporters (e.g., ABCA7)
- Well-studied ABC transporters
- calcein AM, calcein acetoxymethyl
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Affiliation(s)
- Vigneshwaran Namasivayam
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Katja Silbermann
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Jens Pahnke
- Department of Neuro-/Pathology, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
- LIED, University of Lübeck, Ratzenburger Allee 160, 23538 Lübeck, Germany
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Jelgavas iela 1, 1004 Rīga, Latvia
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Michael Wiese
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Sven Marcel Stefan
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
- Department of Neuro-/Pathology, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
- Cancer Drug Resistance and Stem Cell Program, University of Sydney, Kolling Builging, 10 Westbourne Street, Sydney, New South Wales 2065, Australia
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Akocak S, Lolak N, Bua S, Turel I, Supuran CT. Synthesis and biological evaluation of novel N,N'-diaryl cyanoguanidines acting as potent and selective carbonic anhydrase II inhibitors. Bioorg Chem 2018; 77:245-251. [PMID: 29421699 DOI: 10.1016/j.bioorg.2018.01.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 12/11/2022]
Abstract
A series of novel N,N''-diaryl cyanoguanidines were synthesized by reacting diphenyl N-cyanocarbonimidate with sulfanilamide followed by treatment of the obtained cyano-O-phenylisourea with substituted aromatic amines. The newly prepared N,N''-diaryl cyanoguanidines showed a very interesting inhibition profile against four selected human carbonic anhydrase (CA, EC 4.2.1.1) isoforms, hCA I and hCA II (cytosolic), hCA IV (membrane-bound), and hCA IX (transmembrane). All these compounds showed a potent inhibition against isoform hCA II,with inhibition constants in the low nanomolar range, as well as a high selectivity for hCA II over hCA I, IV and IX. Since hCA II is an important drug target for antiglaucoma agents, these isoform-selective inhibitors may be considered of interest for further medicinal/pharmacologic studies.
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Affiliation(s)
- Suleyman Akocak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Adiyaman University, 02040 Adiyaman, Turkey.
| | - Nabih Lolak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Adiyaman University, 02040 Adiyaman, Turkey
| | - Silvia Bua
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Idris Turel
- Department of Pharmacology, Faculty of Pharmacy, Adiyaman University, 02040 Adiyaman, Turkey
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.
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Wangngae S, Pattarawarapan M, Phakhodee W. Ph3P/I2-Mediated Synthesis of N,N′,N″-Substituted Guanidines and 2-Iminoimidazolin-4-ones from Aryl Isothiocyanates. J Org Chem 2017; 82:10331-10340. [DOI: 10.1021/acs.joc.7b01794] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sirilak Wangngae
- Department
of Chemistry, Faculty of Science, ‡Graduate School, §Center of Excellence in Materials
Science and Technology, and ∥Center of Excellence for Innovation in Chemistry,
Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Mookda Pattarawarapan
- Department
of Chemistry, Faculty of Science, ‡Graduate School, §Center of Excellence in Materials
Science and Technology, and ∥Center of Excellence for Innovation in Chemistry,
Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wong Phakhodee
- Department
of Chemistry, Faculty of Science, ‡Graduate School, §Center of Excellence in Materials
Science and Technology, and ∥Center of Excellence for Innovation in Chemistry,
Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Pirotte B, Florence X, Goffin E, Medeiros MB, de Tullio P, Lebrun P. 4-Phenylureido/thioureido-substituted 2,2-dimethylchroman analogs of cromakalim bearing a bulky ‘carbamate’ moiety at the 6-position as potent inhibitors of glucose-sensitive insulin secretion. Eur J Med Chem 2016; 121:338-351. [DOI: 10.1016/j.ejmech.2016.05.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 11/25/2022]
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Lövborg H, Burman R, Gullbo J. Structure-activity relationship analysis of cytotoxic cyanoguanidines: selection of CHS 828 as candidate drug. BMC Res Notes 2009; 2:114. [PMID: 19563661 PMCID: PMC2709656 DOI: 10.1186/1756-0500-2-114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 06/29/2009] [Indexed: 11/24/2022] Open
Abstract
Background N-(6-(4-chlorophenoxy)hexyl)-N'-cyano-N''-4-pyridyl guanidine) (CHS 828) is the first candidate drug from a novel group of anti-tumour agents – the pyridyl cyanoguanidines, shown to be potent compounds interfering with cellular metabolism (inhibition of nicotinamide phosphoribosyl transferase) and NF-κB signalling. Substituted cyanoguanidines are also found in anti-hypertensive agents such as the potassium channel opener pinacidil (N-cyano-N'-(4-pyridyl)-N''-(1,2,2-trimethylpropyl)guanidine) and histamine-II receptor antagonists (e.g. cimetidine, N-cyano-N'-methyl-N''-[2-[[(5-methylimidazol-4-yl]methyl]thio]ethyl)guanidine). In animal studies, CHS 828 has shown very promising activity, and phase I and II studies resulted in further development of a with a water soluble prodrug. Findings To study the structural requirements for cyanoguanidine cytotoxicity a set of 19 analogues were synthesized. The cytotoxic effects were then studied in ten cell lines selected for different origins and mechanisms of resistance, using the fluorometric microculture cytotoxicity assay (FMCA). The compounds showed varying cytotoxic activity even though the dose-response curves for some analogues were very shallow. Pinacidil and cimetidine were found to be non-toxic in all ten cell lines. Starting with cyanoguanidine as the crucial core it was shown that 4-pyridyl substitution was more efficient than was 3-pyridyl substitution. The 4-pyridyl cyanoguanidine moiety should be linked by an alkyl chain, optimally a hexyl, heptyl or octyl chain, to a bulky end group. The exact composition of this end group did not seem to be of crucial importance; when the end group was a mono-substituted phenyl ring it was shown that the preferred position was 4-substitution, followed by 3- and, finally, 2-substitution as the least active. Whether the substituent was a chloro, nitro or methoxy substituent seemed to be of minor importance. Finally, the activity patterns in the ten cell lines were compared. Substances with similar structures correlated well, whilst substances with large differences in molecular structure demonstrated lower correlation coefficients. Conclusion According to this structure-activity relationship (SAR) study, CHS 828 meets the requirements for optimal cytotoxic activity for this class of compounds.
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Affiliation(s)
- Henrik Lövborg
- Division of Clinical Pharmacology, Faculty of Health Sciences, Department of Medicine and Care, Linköping University, SE-581 85Linköping, Sweden.
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Possible role of an ischemic preconditioning-like response mechanism in KATP channel opener-mediated protection against streptozotocin-induced suppression of rat pancreatic islet function. Biochem Pharmacol 2008; 76:1748-56. [DOI: 10.1016/j.bcp.2008.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 09/03/2008] [Accepted: 09/03/2008] [Indexed: 11/18/2022]
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Marsault E, Benakli K, Beaubien S, Saint-Louis C, Déziel R, Fraser G. Potent macrocyclic antagonists to the motilin receptor presenting novel unnatural amino acids. Bioorg Med Chem Lett 2007; 17:4187-90. [PMID: 17533127 DOI: 10.1016/j.bmcl.2007.05.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 05/13/2007] [Accepted: 05/14/2007] [Indexed: 10/23/2022]
Abstract
Novel, potent small molecule motilin receptor antagonists are described. These peptidomimetic macrocycles are composed of a tripeptide cyclized backbone-to-backbone with a nonpeptidic tether and bear new unnatural amino acids containing basic side chains.
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Affiliation(s)
- Eric Marsault
- Tranzyme Pharma Inc. 3001, 12e av Nord, Sherbrooke, PQ, Canada J1H5N4.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo CP 780, CEP 13560-970, São Carlos, Brazil.
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Hamilton SK, Wilkinson DE, Hamilton GS, Wu YQ. Microwave-Assisted Synthesis ofN,N‘-Diaryl Cyanoguanidines. Org Lett 2005; 7:2429-31. [PMID: 15932215 DOI: 10.1021/ol050728q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] A mild, efficient, and high-yielding method for the synthesis of N,N'-diaryl cyanoguanidines from their corresponding thioureas under microwave-assisted conditions is described. A series of cyanoguanidines were synthesized containing both electron-donating and electron-withdrawing substituents. The reactions were facilitated by the use of polar solvents along with moderate temperatures.
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Affiliation(s)
- Sean K Hamilton
- Department of Research, Guilford Pharmaceuticals, Inc., Baltimore, Maryland 21224, USA
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Nielsen FE, Jacobsen P, Worsaae A, Arkhammar POG, Wahl P, Bondo Hansen J. 2-(4-Methoxyphenoxy)-5-nitro-N-(4-sulfamoylphenyl)benzamide activates Kir6.2/SUR1 K(ATP) channels. Bioorg Med Chem Lett 2005; 14:5727-30. [PMID: 15501029 DOI: 10.1016/j.bmcl.2004.09.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 09/21/2004] [Accepted: 09/21/2004] [Indexed: 11/26/2022]
Abstract
2-(4-Methoxyphenoxy)-5-nitro-N-(4-sulfamoylphenyl)benzamide and close analogues inhibit glucose stimulated insulin release through activation of Kir6.2/SUR1 K(ATP) channels of beta cells.
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