1
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Pliushcheuskaya P, Kesh S, Kaufmann E, Wucherpfennig S, Schwede F, Künze G, Nache V. Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain. ACS Chem Neurosci 2024; 15:1652-1668. [PMID: 38579109 PMCID: PMC11027099 DOI: 10.1021/acschemneuro.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
In treating retinitis pigmentosa, a genetic disorder causing progressive vision loss, selective inhibition of rod cyclic nucleotide-gated (CNG) channels holds promise. Blocking the increased Ca2+-influx in rod photoreceptors through CNG channels can potentially delay disease progression and improve the quality of life for patients. To find inhibitors for rod CNG channels, we investigated the impact of 16 cGMP analogues on both rod and cone CNG channels using the patch-clamp technique. Although modifications at the C8 position of the guanine ring did not change the ligand efficacy, modifications at the N1 and N2 positions rendered cGMP largely ineffective in activating retinal CNG channels. Notably, PET-cGMP displayed selective potential, favoring rod over cone, whereas Rp-cGMPS showed greater efficiency in activating cone over rod CNG channels. Ligand docking and molecular dynamics simulations on cyclic nucleotide-binding domains showed comparable binding energies and binding modes for cGMP and its analogues in both rod and cone CNG channels (CNGA1 vs CNGA3 subunits). Computational experiments on CNGB1a vs CNGB3 subunits showed similar binding modes albeit with fewer amino acid interactions with cGMP due to an inactivated conformation of their C-helix. In addition, no clear correlation could be observed between the computational scores and the CNG channel efficacy values, suggesting additional factors beyond binding strength determining ligand selectivity and potency. This study highlights the importance of looking beyond the cyclic nucleotide-binding domain and toward the gating mechanism when searching for selective modulators. Future efforts in developing selective modulators for CNG channels should prioritize targeting alternative channel domains.
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Affiliation(s)
- Palina Pliushcheuskaya
- Institute
for Drug Discovery, Medical Faculty, University
of Leipzig, Leipzig 04103, Germany
| | - Sandeep Kesh
- Institute
of Physiology II, University Hospital Jena, Friedrich Schiller University
Jena, Jena 07743, Germany
| | - Emma Kaufmann
- Institute
of Physiology II, University Hospital Jena, Friedrich Schiller University
Jena, Jena 07743, Germany
| | - Sophie Wucherpfennig
- Institute
of Physiology II, University Hospital Jena, Friedrich Schiller University
Jena, Jena 07743, Germany
| | - Frank Schwede
- BIOLOG
Life Science Institute GmbH & Co KG, Bremen 28199, Germany
| | - Georg Künze
- Institute
for Drug Discovery, Medical Faculty, University
of Leipzig, Leipzig 04103, Germany
- Interdisciplinary
Center for Bioinformatics, University of
Leipzig, Leipzig 04107, Germany
- Center
for Scalable Data Analytics and Artificial Intelligence, University of Leipzig, Leipzig 04105, Germany
| | - Vasilica Nache
- Institute
of Physiology II, University Hospital Jena, Friedrich Schiller University
Jena, Jena 07743, Germany
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2
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Lelle M, Otte M, Bonus M, Gohlke H, Benndorf K. Fluorophore-Labeled Cyclic Nucleotides as Potent Agonists of Cyclic Nucleotide-Regulated Ion Channels. Chembiochem 2020; 21:2311-2320. [PMID: 32227403 PMCID: PMC7497086 DOI: 10.1002/cbic.202000116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/26/2020] [Indexed: 12/22/2022]
Abstract
High-affinity fluorescent derivatives of cyclic adenosine and guanosine monophosphate are powerful tools for investigating their natural targets. Cyclic nucleotide-regulated ion channels belong to these targets and are vital for many signal transduction processes, such as vision and olfaction. The relation of ligand binding to activation gating is still challenging, and there is a need for fluorescent probes that enable the process to be broken down to the single-molecule level. This inspired us to prepare fluorophore-labeled cyclic nucleotides, which are composed of a bright dye and a nucleotide derivative with a thiophenol motif at position 8 that has already been shown to enable superior binding affinity. These bioconjugates were prepared by a novel cross-linking strategy that involves substitution of the nucleobase with a modified thiophenolate in good yield. Both fluorescent nucleotides are potent activators of different cyclic nucleotide-regulated ion channels with respect to the natural ligand and previously reported substances. Molecular docking of the probes excluding the fluorophore reveals that the high potency can be attributed to additional hydrophobic and cation-π interactions between the ligand and the protein. Moreover, the introduced substances have the potential to investigate related target proteins, such as cAMP- and cGMP-dependent protein kinases, exchange proteins directly activated by cAMP or phosphodiesterases.
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Affiliation(s)
- Marco Lelle
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
| | - Maik Otte
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
| | - Michele Bonus
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstrasse 140225DüsseldorfGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstrasse 140225DüsseldorfGermany
- John von Neumann Institute for Computing (NIC)Jülich Supercomputing Centre (JSC) andInstitute of Biological Information Processing (IBI-7: Structural Biochemistry)Forschungszentrum Jülich GmbHWilhelm-Johnen-Strasse52425JülichGermany
| | - Klaus Benndorf
- Institute of Physiology IIUniversity Hospital JenaKollegiengasse 907743JenaGermany
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3
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Otte M, Schweinitz A, Lelle M, Thon S, Enke U, Yüksel S, Schmauder R, Bonus M, Gohlke H, Benndorf K. Novel Fluorescent Cyclic Nucleotide Derivatives to Study CNG and HCN Channel Function. Biophys J 2019; 116:2411-2422. [PMID: 31130235 DOI: 10.1016/j.bpj.2019.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/19/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022] Open
Abstract
A highly specific molecular interaction of diffusible ligands with their receptors belongs to the key processes in cellular signaling. Because an appropriate method to monitor the unitary binding events is still missing, most of our present knowledge is based on ensemble signals recorded from a big number of receptors, such as ion currents or fluorescence changes of suitably labeled receptors, and reasoning from these data to the ligand binding. To study the binding process itself, appropriately tagged ligands are required that fully activate the receptors and report the binding at the same time. Herein, we tailored a series of 18 novel fluorescent cyclic nucleotide derivatives by attaching 6 different dyes via different alkyl linkers to the 8-position of the purine ring of cGMP or cAMP. The biological activity was determined in inside-out macropatches containing either homotetrameric (CNGA2), heterotetrameric (CNGA2:CNGA4:CNGB1b), or hyperpolarization-activated cyclic nucleotide-modulated (HCN2) channels. All these novel fluorescent ligands are efficient to activate the channels, and the potency of most of them significantly exceeded that of the natural cyclic nucleotides cGMP or cAMP. Moreover, some of them showed an enhanced brightness when bound to the channels. The best of our derivatives bear great potential to systematically analyze the activation mechanism in CNG and HCN channels, at both the level of ensemble and single-molecule analyses.
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Affiliation(s)
- Maik Otte
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Andrea Schweinitz
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Marco Lelle
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Susanne Thon
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Uta Enke
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Sezin Yüksel
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Ralf Schmauder
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Michele Bonus
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing, Jülich Supercomputing Centre & Institute for Complex Systems Structural Biochemistry, Forschungszentrum Jülich, GmbH, Jülich, Germany
| | - Klaus Benndorf
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany.
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Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation. Sci Rep 2018; 8:14960. [PMID: 30297855 PMCID: PMC6175941 DOI: 10.1038/s41598-018-33050-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/19/2018] [Indexed: 01/01/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are tetrameric non-specific cation channels in the plasma membrane that are activated by either cAMP or cGMP binding to specific binding domains incorporated in each subunit. Typical apparent affinities of these channels for these cyclic nucleotides range from several hundred nanomolar to tens of micromolar. Here we synthesized and characterized novel cAMP and cGMP derivatives by substituting either hydrophobic alkyl chains or similar-sized more hydrophilic heteroalkyl chains to the 8-position of the purine ring with the aim to obtain full agonists of higher potency. The compounds were tested in homotetrameric CNGA2, heterotetrameric CNGA2:CNGA4:CNGB1b and homotetrameric HCN2 channels. We show that nearly all compounds are full agonists and that longer alkyl chains systematically increase the apparent affinity, at the best more than 30 times. The effects are stronger in CNG than HCN2 channels which, however, are constitutively more sensitive to cAMP. Kinetic analyses reveal that the off-rate is significantly slowed by the hydrophobic alkyl chains. Molecular dynamics simulations and free energy calculations suggest that an intricate enthalpy - entropy compensation underlies the higher apparent affinity of the derivatives with the longer alkyl chains, which is shown to result from a reduced loss of configurational entropy upon binding.
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5
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New cGMP analogues restrain proliferation and migration of melanoma cells. Oncotarget 2017; 9:5301-5320. [PMID: 29435180 PMCID: PMC5797051 DOI: 10.18632/oncotarget.23685] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022] Open
Abstract
Melanoma is one of the most aggressive cancers and displays high resistance to conventional chemotherapy underlining the need for new therapeutic strategies. The cGMP/PKG signaling pathway was detected in melanoma cells and shown to reduce migration, proliferation and to increase apoptosis in different cancer types. In this study, we evaluated the effects on cell viability, cell death, proliferation and migration of novel dimeric cGMP analogues in two melanoma cell lines (MNT1 and SkMel28). These new dimeric cGMP analogues, by activating PKG with limited effects on PKA, significantly reduced proliferation, migration and increased cell death. No decrease in cell viability was observed in non-tumor cells suggesting a tumor-specific effect. These effects observed in melanoma are possibly mediated by PKG2 activation based on the decreased toxic effects in tumor cell lines not expressing PKG2. Finally, PKG-associated phosphorylation of vasodilator-stimulated-phosphoprotein (VASP), linked to cell death, proliferation and migration was found increased and with a change of subcellular localization. Increased phosphorylation of RhoA induced by activation of PKG may also contribute to reduced migration ability of the SkMel28 melanoma cell line when treated with cGMP analogues. These findings suggest that the cGMP/PKG pathway can be envisaged as a therapeutic target of novel dimeric cGMP analogues for the treatment of melanoma.
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6
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Hoffmann D, Rentsch A, Vighi E, Bertolotti E, Comitato A, Schwede F, Genieser HG, Marigo V. New dimeric cGMP analogues reduce proliferation in three colon cancer cell lines. Eur J Med Chem 2017; 141:61-72. [PMID: 29028532 DOI: 10.1016/j.ejmech.2017.09.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/07/2017] [Accepted: 09/25/2017] [Indexed: 01/18/2023]
Abstract
Activation of the cGMP-dependent protein kinase G (PKG) can inhibit growth and/or induce apoptosis in colon cancer. In this study we evaluated the effects on cell viability, cell death and proliferation of novel dimeric cGMP analogues, compared to a monomeric compound. Three colon cancer cell lines, which only express isoform 2 of PKG, were treated with these novel cGMP analogues and responded with increased PKG activity. cGMP analogues reduced cell viability in the three cell lines and this was due to a cytostatic rather than cytotoxic effect. These findings suggest that activation of PKG2 can be a therapeutic target in the treatment of colon cancer and, most importantly, that dimeric cGMP analogues can further improve the beneficial effects previously observed with monomeric cGMP analogues.
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Affiliation(s)
- Dorit Hoffmann
- Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Andreas Rentsch
- BIOLOG Life Science Institute Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199 Bremen, Germany
| | - Eleonora Vighi
- Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Evelina Bertolotti
- Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Antonella Comitato
- Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Frank Schwede
- BIOLOG Life Science Institute Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199 Bremen, Germany
| | - Hans-Gottfried Genieser
- BIOLOG Life Science Institute Forschungslabor und Biochemica-Vertrieb GmbH, Flughafendamm 9a, 28199 Bremen, Germany
| | - Valeria Marigo
- Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy.
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7
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Fuchi Y, Obayashi H, Sasaki S. Development of new 1,3-diazaphenoxazine derivatives (thioG-grasp) to covalently capture 8-thioguanosine. Molecules 2015; 20:1078-87. [PMID: 25584836 PMCID: PMC6272678 DOI: 10.3390/molecules20011078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/07/2015] [Indexed: 11/16/2022] Open
Abstract
The derivatives of 8-thioguanosine are thought to be included in the signal transduction system related to 8-nitroguanosine. In this study, we attempted to develop new 1,3-diazaphenoxazine (G-clamp) derivatives to covalently capture 8-thioguanosine (thioG-grasp). It was expected that the chlorine atom at the end of the linker would be displaced by the nucleophilic attack by the sulfur atom of 8-thioguanosine via multiple hydrogen-bonded complexes. The thioG-grasp derivative with a propyl linker reacted efficiently with 8-thioguanosine to form the corresponding adduct.
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Affiliation(s)
- Yasufumi Fuchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Hideto Obayashi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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8
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Kirk SR, Andrade AL, Melich K, Jackson EP, Cuellar E, Karpen JW. Halogen substituents on the aromatic moiety of the tetracaine scaffold improve potency of cyclic nucleotide-gated channel block. Bioorg Med Chem Lett 2011; 21:6417-9. [DOI: 10.1016/j.bmcl.2011.08.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 08/19/2011] [Indexed: 11/28/2022]
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9
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Andrade AL, Melich K, Whatley GG, Kirk SR, Karpen JW. Cyclic nucleotide-gated channel block by hydrolysis-resistant tetracaine derivatives. J Med Chem 2011; 54:4904-12. [PMID: 21634421 DOI: 10.1021/jm200495g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To meet a pressing need for better cyclic nucleotide-gated (CNG) channel antagonists, we have increased the biological stability of tetracaine-based blockers by synthesizing amide and thioamide linkage substitutions of tetracaine (1) and a higher affinity octyl tail derivative (5). We report the apparent K(D) values, the mechanism of block, and the in vitro hydrolysis rates for these compounds. The ester linkage substitutions did not adversely affect CNG channel block; unexpectedly, thioamide substitution in 1 (compound 8) improved block significantly. Furthermore, the ester linkage substitutions did not appear to affect the mechanism of block in terms of the strong state preference for closed channels. All ester substituted compounds, especially the thioamide substitutions, were more resistant to hydrolysis by serum cholinesterase than their ester counterparts. These findings have implications for dissecting the physiological roles of CNG channels, treating certain forms of retinal degeneration, and possibly the current clinical uses of compound 1.
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Affiliation(s)
- Adriana L Andrade
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon 97239, United States
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10
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Francis SH, Sekhar KR, Ke H, Corbin JD. Inhibition of cyclic nucleotide phosphodiesterases by methylxanthines and related compounds. Handb Exp Pharmacol 2011:93-133. [PMID: 20859794 DOI: 10.1007/978-3-642-13443-2_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Naturally occurring methylxanthines were the first inhibitors of cyclic nucleotide (cN) phosphodiesterases (PDEs) to be discovered. To improve potency and specificity for inhibition of various PDEs in research and for treatment of diseases, thousands of compounds with related structures have now been synthesized. All known PDE inhibitors contain one or more rings that mimic the purine in the cN substrate and directly compete with cN for access to the catalytic site; this review focuses on inhibitors that contain a nucleus that is closely related to the xanthine ring of theophylline and caffeine and the purine ring of cNs. The specificity and potency of these compounds for blocking PDE action have been improved by appending groups at positions on the rings as well as by modification of the number and distribution of nitrogens and carbons in those rings. Several of these inhibitors are highly selective for particular PDEs; potent and largely selective PDE5 inhibitors are used clinically for treatment of erectile dysfunction [sildenafil (Viagra™), tadalafil (Cialis™) and vardenafil (Levitra™)] and pulmonary hypertension [sildenafil (Revatio™) and tadalafil (Adenocirca)]. Related compounds target other PDEs and show therapeutic promise for a number of maladies.
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Affiliation(s)
- Sharron H Francis
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232-0615, USA.
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11
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Abstract
The first cGMP-dependent protein kinase (PKG) modulators were described nearly 30 years ago and since then more than 200 compounds have been synthesized and tested, but only a small subset of these compounds has found widespread application. The aim of this review is to suggest a framework for evaluating and using PKG activators and inhibitors and to explore and interpret PKG signal transduction in cell culture-based model systems. Therefore, cross-reactivity of cGMP-analogs with other classes of cyclic nucleotide binding proteins, as well as the advantages and problems of newly designed PKG inhibitors, are discussed. Additional information and a search option are available at www.cyclic-nucleotides.org
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12
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Epac signaling is required for hippocampus-dependent memory retrieval. Proc Natl Acad Sci U S A 2008; 105:11993-7. [PMID: 18687890 DOI: 10.1073/pnas.0804172105] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previously we uncovered a critical role for norepinephrine and beta(1)-adrenergic signaling in hippocampus-dependent memory retrieval. Because the beta(1) receptor couples to G(s), we examine here whether cAMP is also required for contextual memory retrieval. Using pharmacologic and genetic approaches to manipulate cAMP and downstream signaling, we demonstrate that cAMP and two of its targets, protein kinase A (PKA) and exchange protein activated by cAMP (Epac), are both required for retrieval. These findings demonstrate that cAMP signaling through Epac (as well as PKA) plays an essential role in cognition.
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13
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Strassmaier T, Kirk SR, Banerji T, Karpen JW. Block of cyclic nucleotide-gated channels by tetracaine derivatives: role of apolar interactions at two distinct locations. Bioorg Med Chem Lett 2007; 18:645-9. [PMID: 18055205 DOI: 10.1016/j.bmcl.2007.11.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 11/16/2007] [Accepted: 11/19/2007] [Indexed: 11/19/2022]
Abstract
A series of new tetracaine derivatives was synthesized to explore the effects of hydrophobic character on blockade of cyclic nucleotide-gated (CNG) channels. Increasing the hydrophobicity at either of two positions on the tetracaine scaffold, the tertiary amine or the butyl tail, yields blockers with increased potency. However, shape also plays an important role. While gradual increases in length of the butyl tail lead to increased potency, substitution of the butyl tail with branched alkyl or cyclic groups is deleterious.
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Affiliation(s)
- Timothy Strassmaier
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, USA
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