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Platonov M, Maximyuk O, Rayevsky A, Hurmach V, Iegorova O, Naumchyk V, Bulgakov E, Cherninskyi A, Ozheredov D, Ryabukhin SV, Krishtal O, Volochnyuk DM. 4-(Azolyl)-Benzamidines as a Novel Chemotype for ASIC1a Inhibitors. Int J Mol Sci 2024; 25:3584. [PMID: 38612396 PMCID: PMC11011685 DOI: 10.3390/ijms25073584] [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: 11/26/2023] [Revised: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Acid-sensing ion channels (ASICs) play a key role in the perception and response to extracellular acidification changes. These proton-gated cation channels are critical for neuronal functions, like learning and memory, fear, mechanosensation and internal adjustments like synaptic plasticity. Moreover, they play a key role in neuronal degeneration, ischemic neuronal injury, seizure termination, pain-sensing, etc. Functional ASICs are homo or heterotrimers formed with (ASIC1-ASIC3) homologous subunits. ASIC1a, a major ASIC isoform in the central nervous system (CNS), possesses an acidic pocket in the extracellular region, which is a key regulator of channel gating. Growing data suggest that ASIC1a channels are a potential therapeutic target for treating a variety of neurological disorders, including stroke, epilepsy and pain. Many studies were aimed at identifying allosteric modulators of ASIC channels. However, the regulation of ASICs remains poorly understood. Using all available crystal structures, which correspond to different functional states of ASIC1, and a molecular dynamics simulation (MD) protocol, we analyzed the process of channel inactivation. Then we applied a molecular docking procedure to predict the protein conformation suitable for the amiloride binding. To confirm the effect of its sole active blocker against the ASIC1 state transition route we studied the complex with another MD simulation run. Further experiments evaluated various compounds in the Enamine library that emerge with a detectable ASIC inhibitory activity. We performed a detailed analysis of the structural basis of ASIC1a inhibition by amiloride, using a combination of in silico approaches to visualize its interaction with the ion pore in the open state. An artificial activation (otherwise, expansion of the central pore) causes a complex modification of the channel structure, namely its transmembrane domain. The output protein conformations were used as a set of docking models, suitable for a high-throughput virtual screening of the Enamine chemical library. The outcome of the virtual screening was confirmed by electrophysiological assays with the best results shown for three hit compounds.
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Affiliation(s)
- Maksym Platonov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Oleksandr Maximyuk
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Alexey Rayevsky
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Vasyl Hurmach
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Olena Iegorova
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Vasyl Naumchyk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
| | - Elijah Bulgakov
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Andrii Cherninskyi
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Danil Ozheredov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Serhiy V. Ryabukhin
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
| | - Oleg Krishtal
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Dmytro M. Volochnyuk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
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Abstract
Unusual amino acids are fundamental building blocks of modern medicinal chemistry. The combination of readily functionalized amine and carboxyl groups attached to a chiral central core along with one or two potentially diverse side chains provides a unique three-dimensional structure with a high degree of functionality. This makes them invaluable as starting materials for syntheses of complex molecules, highly diverse elements for SAR campaigns, integral components of peptidomimetic drugs, and potential drugs on their own. This Perspective highlights the diversity of unnatural amino acid structures found in hit-to-lead and lead optimization campaigns and clinical stage and approved drugs, reflecting their increasingly important role in medicinal chemistry.
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Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland Australia 4072
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Flemer S, Madalengoitia JS. On-resin synthesis of novel arginine-isostere peptides bearing substituted amidine headgroups. J Pept Sci 2011; 18:30-6. [PMID: 22034042 DOI: 10.1002/psc.1412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/02/2011] [Accepted: 08/11/2011] [Indexed: 11/12/2022]
Abstract
A methodology is presented for the facile synthesis of Arg-containing peptides modified at the guanidine headgroup as substituted amidine cores. This process allows for the iterative construction of these Arg isosteres while the peptide is being built out on the solid support, providing a high potential for diversity in substitution pattern in the resulting peptide. A series of N-Pmc-substituted thioamides were condensed with deprotected δ-N Orn-bearing peptides while attached to the solid support using Mukaiyama's reagent as coupling reagent, yielding isosteric Arg-containing analogs. Peptides were cleaved using trimethylsilyl trifluoromethanesulfonate/TFA and analyzed in their crude form in order to illustrate the amenability of this process toward production of peptide isolates in high crude purity. Arg-containing peptides having a single Arg isostere were utilized to show the general utility of this approach as well as a multiple-Arg-containing construct, illustrating the amenability of this method toward stepwise construction of differently substituted amidine headgroups within the same peptide.
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Affiliation(s)
- Stevenson Flemer
- Department of Chemistry, University of Vermont, A232 Cook Physical Sciences Building, 82 University Place, Burlington, VT 05405, USA
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Reiner JE, Siev DV, Araldi GL, Cui JJ, Ho JZ, Reddy KM, Mamedova L, Vu PH, Lee KSS, Minami NK, Gibson TS, Anderson SM, Bradbury AE, Nolan TG, Semple JE. Non-covalent thrombin inhibitors featuring P(3)-heterocycles with P(1)-monocyclic arginine surrogates. Bioorg Med Chem Lett 2002; 12:1203-8. [PMID: 11934589 DOI: 10.1016/s0960-894x(02)00129-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Investigations on P(2)-P(3)-heterocyclic dipeptide surrogates directed towards identification of an orally bioavailable thrombin inhibitor led us to pursue novel classes of achiral, non-covalent P(1)-arginine derivatives. The design, synthesis, and biological activity of inhibitors NC1-NC30 that feature three classes of monocyclic P(1)-arginine surrogates will be disclosed: (1) (hetero)aromatic amidines, amines and hydroxyamidines, (2) 2-aminopyrazines, and (3) 2-aminopyrimidines and 2-aminotetrahydropyrimidines.
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Affiliation(s)
- John E Reiner
- Department of Medicinal Chemistry, Corvas International, Inc., 3030 Science Park Road, San Diego, CA 92121, USA
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Narasimhan LS, Rubin JR, Holland DR, Plummer JS, Rapundalo ST, Edmunds JE, St-Denis Y, Siddiqui MA, Humblet C. Structural basis of the thrombin selectivity of a ligand that contains the constrained arginine mimic (2S)-2-amino-(3S)-3-(1-carbamimidoyl- piperidin-3-yl)-propanoic acid at P1. J Med Chem 2000; 43:361-8. [PMID: 10669563 DOI: 10.1021/jm990216f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the thrombin and trypsin complexed structures of a pair of peptidomimetic thrombin inhibitors, containing different P1 fragments. The first has arginine as its P1 fragment, and the second contains the constrained arginine mimic (2S)-2-amino-(3S)-3-(1-carbamimidoyl-piperidin-3-yl)-propano ic acid (SAPA), a fragment known to enhance thrombin/trypsin selectivity of inhibitors. On the basis of an analysis of the nonbonded interactions present in the structures of the trypsin and thrombin complexes of the two inhibitors, the calculated accessible surfaces of the enzymes and inhibitors in the four complexes, data on known structures of trypsin complexes of inhibitors, and factor Xa inhibitory potency of these compounds, we conclude that the ability of this arginine mimic to increase thrombin selectivity of an inhibitor is mediated by its differential interaction with the residue at position 192 (chymotrypsinogen numbering). Thrombin has a glutamic acid at residue 192, and trypsin has a glutamine. The analysis also suggests that this constrained arginine mimic, when present in an inhibitor, might enhance selectivity against other trypsin-like enzymes that have a glutamine at residue position 192.
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Affiliation(s)
- L S Narasimhan
- Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, 2800 Plymouth Road, Ann Arbor, Michigan 48105, USA.
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Abstract
Thrombin and factor Xa (fXa) are the only serine proteases for which small, potent, selective, noncovalent inhibitors have been developed, which are ultimately intended as drug development candidates (in this case as anticoagulants). Noncovalent inhibitors may be more selective and chemically and metabolically less reactive than covalent inhibitors. In addition, noncovalent inhibitors are more likely to have fast-binding kinetics which is particularly important in the development of thrombin inhibitors. TAME derived noncovalent thrombin inhibitors argatroban, napsagatran, and UK 156,406 have entered clinical trials as anticoagulants, the latter as an orally active agent. Serine trap deletion from substrate-like peptides led to the development of inogatran and melagatran, both of which have entered clinical trials as intravenous agents. The use of 3-aminopyridinone and pyrazinone acetamide peptidomimetic templates has resulted in the development of L-375,378 which has been chosen for clinical development as an orally active anticoagulant. Recently, compounds which do not have the conventional hydrogen bonding capabilities of peptides have begun to appear in the thrombin literature. Publications on noncovalent fXa inhibitors cover this type of peptidomimetic almost exclusively.
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Affiliation(s)
- P E Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA
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