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New 1,11-dimethyl-3,6,9-triazatricyclo[7.3.1.13,11]tetradecane-4,8,12-trione derivative as an allosteric modulator of the glutamatergic system. MENDELEEV COMMUNICATIONS 2023. [DOI: 10.1016/j.mencom.2023.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Golubeva EA, Lavrov MI, Radchenko EV, Palyulin VA. Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules 2022; 13:biom13010056. [PMID: 36671441 PMCID: PMC9856200 DOI: 10.3390/biom13010056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
L-Glutamic acid is the main excitatory neurotransmitter in the central nervous system (CNS). Its associated receptors localized on neuronal and non-neuronal cells mediate rapid excitatory synaptic transmission in the CNS and regulate a wide range of processes in the brain, spinal cord, retina, and peripheral nervous system. In particular, the glutamate receptors selective to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) also play an important role in numerous neurological disorders and attract close attention as targets for the creation of new classes of drugs for the treatment or substantial correction of a number of serious neurodegenerative and neuropsychiatric diseases. For this reason, the search for various types of AMPA receptor ligands and studies of their properties are attracting considerable attention both in academic institutions and in pharmaceutical companies around the world. This review focuses mainly on the advances in this area published since 2017. Particular attention is paid to the structural diversity of new chemotypes of agonists, competitive AMPA receptor antagonists, positive and negative allosteric modulators, transmembrane AMPA regulatory protein (TARP) dependent allosteric modulators, ion channel blockers as well as their binding sites. This review also presents the studies of the mechanisms of action of AMPA receptor ligands that mediate their therapeutic effects.
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Sedenkova KN, Zverev DV, Nazarova AA, Lavrov MI, Radchenko EV, Grishin YK, Gabrel’yan AV, Zamoyski VL, Grigoriev VV, Averina EB, Palyulin VA. Novel Nanomolar Allosteric Modulators of AMPA Receptor of Bis(pyrimidine) Series: Synthesis, Biotesting and SAR Analysis. Molecules 2022; 27:molecules27238252. [PMID: 36500341 PMCID: PMC9741252 DOI: 10.3390/molecules27238252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Positive allosteric modulators (PAMs) of AMPA receptors represent attractive candidates for the development of drugs for the treatment of cognitive and neurodegenerative disorders. Dimeric molecules have been reported to have an especially potent modulating effect, due to the U-shaped form of the AMPA receptor's allosteric binding site. In the present work, novel bis(pyrimidines) were studied as AMPA receptor modulators. A convenient and flexible preparative approach to bis(pyrimidines) containing a hydroquinone linker was elaborated, and a series of derivatives with varied substituents was obtained. The compounds were examined in the patch clamp experiments for their influence on the kainate-induced currents, and 10 of them were found to have potentiating properties. The best potency was found for 2-methyl-4-(4-((2-methyl-5,6,7,8-tetrahydroquinazolin-4-yl)oxy)phenoxy)-6,7,8,9-tetrahydro-5H-cyclohepta[d]pyrimidine, which potentiated the kainate-induced currents by up to 77% in all tested concentrations (10-12-10-6 M). The results were rationalized via the modeling of modulator complexes with the dimeric ligand binding domain of the GluA2 AMPA receptor, using molecular docking and molecular dynamics simulation. The prediction of ADMET, physicochemical, and PAINS properties of the studied bis(pyrimidines) confirmed that PAMs of this type may act as the potential lead compounds for the development of neuroprotective drugs.
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Affiliation(s)
- Kseniya N. Sedenkova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Denis V. Zverev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Anna A. Nazarova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Mstislav I. Lavrov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Eugene V. Radchenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Yuri K. Grishin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Alexey V. Gabrel’yan
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severny proezd 1, Chernogolovka, 142432 Moscow, Russia
| | - Vladimir L. Zamoyski
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severny proezd 1, Chernogolovka, 142432 Moscow, Russia
| | - Vladimir V. Grigoriev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Severny proezd 1, Chernogolovka, 142432 Moscow, Russia
| | - Elena B. Averina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
| | - Vladimir A. Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, 119991 Moscow, Russia
- Correspondence:
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Lavrov MI, Veremeeva PN, Golubeva EA, Radchenko EV, Zamoyski VL, Grigoriev VV, Palyulin VA. Positive and negative AMPA receptor modulators based on tricyclic bispidine derivative: Minor structural change inverts the type of activity. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Krut’ko DP, Medved’ko AV, Lyssenko KA, Churakov AV, Dalinger AI, Kalinin MA, Gudovannyy AO, Ponomarev KY, Suslov EV, Vatsadze SZ. Bispidine Platform as a Tool for Studying Amide Configuration Stability. Molecules 2022; 27:430. [PMID: 35056748 PMCID: PMC8779339 DOI: 10.3390/molecules27020430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this work, the solution conformations of seventeen 3,7-diacyl bispidines were studied by means of NMR spectroscopy including VT NMR experiments. The acyl groups included alkyl, alkenyl, aryl, hetaryl, and ferrocene moieties. The presence of syn/anti-isomers and their ratios were estimated, and some reasons explaining experimental facts were formulated. In particular, all aliphatic and heterocyclic units in the acylic R(CO) fragments led to an increased content of the syn-form in DMSO-d6 solutions. In contrast, only the anti-form was detected in DMSO-d6 and CDCl3 in the case when R = Ph, ferrocenyl, (R)-myrtenyl. In the case of a chiral compound derived from the natural terpene myrtene, a new dynamic process was found in addition to the expected inversion around the amide N-C(O) bond. Here, rotation around the CO-C=C bond in the acylic R fragment was detected, and its energy was estimated. For this compound, ΔG for amide N-C(O) inversion was found to be equal to 15.0 ± 0.2 kcal/mol, and for the rotation around the N(CO)-C2' bond, it was equal to 15.6 ± 0.3 kcal/mol. NMR analysis of the chiral bispidine-based bis-amide was conducted for the first time. Two X-ray structures are reported. For the first time, the unique syn-form was found in the crystal of an acyclic bispidine-based bis-amide. Quantum chemical calculations revealed the unexpected mechanism for amide bond inversion. It was found that the reaction does not proceed as direct N-C(O) bond inversion in the double-chair (CC) conformation but rather requires the conformational transformation into the chair-boat (CB) form first. The amide bond inversion in the latter requires less energy than in the CC form.
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Affiliation(s)
- Dmitry P. Krut’ko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | | | - Konstantin A. Lyssenko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry, 119991 Moscow, Russia;
| | - Alexander I. Dalinger
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Mikhail A. Kalinin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia;
| | - Alexey O. Gudovannyy
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- High Chemical College, Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
| | - Konstantin Y. Ponomarev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Eugeny V. Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Sergey Z. Vatsadze
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
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Vasilenko DA, Sadovnikov KS, Sedenkova KN, Karlov DS, Radchenko EV, Grishin YK, Rybakov VB, Kuznetsova TS, Zamoyski VL, Grigoriev VV, Palyulin VA, Averina EB. A Facile Approach to Bis(isoxazoles), Promising Ligands of the AMPA Receptor. Molecules 2021; 26:molecules26216411. [PMID: 34770819 PMCID: PMC8588558 DOI: 10.3390/molecules26216411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
A convenient synthetic approach to novel functionalized bis(isoxazoles), the promising bivalent ligands of the AMPA receptor, was elaborated. It was based on the heterocyclization reactions of readily available electrophilic alkenes with the tetranitromethane-triethylamine complex. The structural diversity of the synthesized compounds was demonstrated. In the electrophysiological experiments using the patch clamp technique on Purkinje neurons, the compound 1,4-phenylenedi(methylene)bis(5-aminoisoxazole-3-carboxylate) was shown to be highly potent positive modulator of the AMPA receptor, potentiating kainate-induced currents up to 70% at 10−11 M.
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Affiliation(s)
- Dmitry A. Vasilenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Kirill S. Sadovnikov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Kseniya N. Sedenkova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Dmitry S. Karlov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Eugene V. Radchenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Yuri K. Grishin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Victor B. Rybakov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Tamara S. Kuznetsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
| | - Vladimir L. Zamoyski
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, 142432 Moscow, Russia;
| | - Vladimir V. Grigoriev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, 142432 Moscow, Russia;
| | - Vladimir A. Palyulin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
- Correspondence: (V.A.P.); (E.B.A.)
| | - Elena B. Averina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.V.); (K.S.S.); (K.N.S.); (D.S.K.); (E.V.R.); (Y.K.G.); (V.B.R.); (T.S.K.); (V.V.G.)
- Correspondence: (V.A.P.); (E.B.A.)
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Borozdenko DA, Ezdoglian AA, Shmigol TA, Gonchar DI, Lyakhmun DN, Tarasenko DV, Golubev YV, Cherkashova EA, Namestnikova DD, Gubskiy IL, Lagunin AA, Gubsky LV, Chekhonin VP, Borisevich SS, Gureev MA, Shagina AD, Kiseleva NM, Negrebetsky VV, Baukov YI. A Novel Phenylpyrrolidine Derivative: Synthesis and Effect on Cognitive Functions in Rats with Experimental Ishemic Stroke. Molecules 2021; 26:molecules26206124. [PMID: 34684709 PMCID: PMC8541353 DOI: 10.3390/molecules26206124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
We performed an in silico, in vitro, and in vivo assessment of a potassium 2-[2-(2-oxo-4-phenylpyrrolidin-1-yl) acetamido]ethanesulfonate (compound 1) as a potential prodrug for cognitive function improvement in ischemic brain injury. Using in silico methods, we predicted the pharmacological efficacy and possible safety in rat models. In addition, in silico data showed neuroprotective features of compound 1, which were further supported by in vitro experiments in a glutamate excitotoxicity-induced model in newborn rat cortical neuron cultures. Next, we checked whether compound 1 is capable of crossing the blood-brain barrier in intact and ischemic animals. Compound 1 improved animal behavior both in intact and ischemic rats and, even though the concentration in intact brains was low, we still observed a significant anxiety reduction and activity escalation. We used molecular docking and molecular dynamics to support our hypothesis that compound 1 could affect the AMPA receptor function. In a rat model of acute focal cerebral ischemia, we studied the effects of compound 1 on the behavior and neurological deficit. An in vivo experiment demonstrated that compound 1 significantly reduced the neurological deficit and improved neurological symptom regression, exploratory behavior, and anxiety. Thus, here, for the first time, we show that compound 1 can be considered as an agent for restoring cognitive functions.
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Affiliation(s)
- Denis A. Borozdenko
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Aiarpi A. Ezdoglian
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Tatiana A. Shmigol
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Darya I. Gonchar
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Dmitri N. Lyakhmun
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Dmitri V. Tarasenko
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Yaroslav V. Golubev
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Elvira A. Cherkashova
- Department of Neurology, Neurosurgery and Medical Genetics, Faculty of Medicine Federal State Budgetary Institution, Federal Center of Brain Research and Neurotechnologies, Federal Medical Bio-logical Agency, 117997 Moscow, Russia; (E.A.C.); (D.D.N.); (I.L.G.)
| | - Daria D. Namestnikova
- Department of Neurology, Neurosurgery and Medical Genetics, Faculty of Medicine Federal State Budgetary Institution, Federal Center of Brain Research and Neurotechnologies, Federal Medical Bio-logical Agency, 117997 Moscow, Russia; (E.A.C.); (D.D.N.); (I.L.G.)
| | - Ilya L. Gubskiy
- Department of Neurology, Neurosurgery and Medical Genetics, Faculty of Medicine Federal State Budgetary Institution, Federal Center of Brain Research and Neurotechnologies, Federal Medical Bio-logical Agency, 117997 Moscow, Russia; (E.A.C.); (D.D.N.); (I.L.G.)
| | - Alexey A. Lagunin
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Leonid V. Gubsky
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
- Department of Neurology, Neurosurgery and Medical Genetics, Faculty of Medicine Federal State Budgetary Institution, Federal Center of Brain Research and Neurotechnologies, Federal Medical Bio-logical Agency, 117997 Moscow, Russia; (E.A.C.); (D.D.N.); (I.L.G.)
| | - Vladimir P. Chekhonin
- Department of Medical Nanobiotechnologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Sophia S. Borisevich
- Laboratory of Physical Chemistry, Ufa Institute of Chemistry UFRS RAS, pr. Oktyabrya 71, 450054 Ufa, Russia;
| | - Maxim A. Gureev
- Laboratory of Bioinformatics, Research Center “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov University, 119991 Moscow, Russia;
- Laboratory of Bioinformatics and Computational Modelling of Biological Systems, Department of Computational Biology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasia D. Shagina
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Nina M. Kiseleva
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Vadim V. Negrebetsky
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
| | - Yuri I. Baukov
- Department of Medicinal Chemistry and Toxicology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (D.A.B.); (A.A.E.); (T.A.S.); (D.I.G.); (D.N.L.); (D.V.T.); (Y.V.G.); (A.A.L.); (L.V.G.); (A.D.S.); (N.M.K.); (V.V.N.)
- Correspondence:
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Titov IY, Stroylov VS, Rusina P, Svitanko IV. Preliminary modelling as the first stage of targeted organic synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; calculations based on experimentally obtained structural information about the target; and dynamic simulation of the target – ligand complex and the reaction mechanism with calculation of the free energy of the reaction. The review is meant for synthetic chemists to be used as a guide for building an algorithm for preliminary modelling and synthesis of structures with specified properties.
The bibliography includes 353 references.
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Radchenko EV, Tarakanova AS, Karlov DS, Lavrov MI, Palyulin VA. [Ligands of the AMPA-subtype glutamate receptors: mechanisms of action and novel chemotypes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2021; 67:187-200. [PMID: 34142526 DOI: 10.18097/pbmc20216703187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ionotropic glutamate receptors of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype play a key role in synaptic plasticity representing one of the mechanisms for learning and memory formation. They can also serve as targets for the development of novel classes of pharmaceuticals for the treatment or substantive correction of many serious neurodegenerative and psychoneurological disorders. The search and studies of various types of AMPA receptor ligands attract considerable attention from academic organizations and pharmaceutical companies all over the world. This review mainly focuses on recent advances in this field. The architecture and operational mechanism of the receptor as well as its major binding sites and ligand types are considered. Special attention is paid to the studies of mechanisms of action and novel chemotypes of AMPA receptor agonists and competitive antagonists, positive and negative allosteric modulators, auxiliary protein-dependent allosteric modulators, and ion channel blockers.
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Affiliation(s)
| | | | - D S Karlov
- Lomonosov Moscow State University, Moscow, Russia
| | - M I Lavrov
- Lomonosov Moscow State University, Moscow, Russia
| | - V A Palyulin
- Lomonosov Moscow State University, Moscow, Russia
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Churakov AV, Medved’ko AV, Prikhodchenko PV, Krut’ko DP, Vatsadze SZ. First example of peroxosolvate of iodine-containing organic molecule. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Churakov AV, Medved’ko AV, Prikhodchenko PV, Krut’ko DP, Vatsadze SZ. First example of peroxosolvate of iodine-containing organic molecule. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Temnyakova NS, Vasilenko DA, Lavrov MI, Karlov DS, Grishin YK, Zamoyski VL, Grigoriev VV, Averina EB, Palyulin VA. New nanomolar negative modulators of AMPA receptors. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Temnyakova NS, Vasilenko DA, Lavrov MI, Karlov DS, Grishin YK, Zamoyski VL, Grigoriev VV, Averina EB, Palyulin VA. Novel bivalent positive allosteric AMPA receptor modulator of bis-amide series. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Vatsadze SZ, Medved’ko AV, Bodunov AA, Lyssenko KA. Bispidine-based bis-azoles as a new family of supramolecular receptors: the theoretical approach. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.05.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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