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Rout M, Dey S, Mishra S, Panda S, Singh MK, Sinha R, Dehury B, Pati S. Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus. J Biomol Struct Dyn 2024; 42:3935-3948. [PMID: 37221882 DOI: 10.1080/07391102.2023.2216290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent to screen potential analogs of existing FDA approved drugs of MPXV against P37 using state-of-the-art machine learning and computational biophysical techniques. AlphaFold2 guided all-atoms molecular dynamics simulations optimized P37 structure is used for molecular docking and binding free energy calculations. Similar to members of Phospholipase-D family , the predicted P37 structure also adopts a β-α-β-α-β sandwich fold, harbouring strongly conserved HxKxxxxD motif. The binding pocket comprises of Tyr48, Lys86, His115, Lys117, Ser130, Asn132, Trp280, Asn240, His325, Lys327 and Tyr346 forming strong hydrogen bonds and dense hydrophobic contacts with the screened analogs and is surrounded by positively charged patches. Loops connecting the two domains and C-terminal region exhibit high degree of flexibility. In some structural ensembles, the partial disorderness in the C-terminal region is presumed to be due to its low confidence score, acquired during structure prediction. Transition from loop to β-strands (244-254 aa) in P37-Cidofovir and its analog complexes advocates the need for further investigations. MD simulations support the accuracy of the molecular docking results, indicating the potential of analogs as potent binders of P37. Taken together, our results provide preferable understanding of molecular recognition and dynamics of ligand-bound states of P37, offering opportunities for development of new antivirals against MPXV. However, the need of in vitro and in vivo assays for confirmation of these results still persists.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Bhubaneswar, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Rohan Sinha
- Computer Science, National Institute of Technology Patna, Patna, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Bhubaneswar, Odisha, India
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Tkachenko IM, Shiryaev VA, Klimochkin YN. Towards a qualitative understanding of the carbonyl reactivity of α-substituted ethyl 5-oxohomoadamantyl-4-carboxylates. Org Biomol Chem 2023. [PMID: 37377423 DOI: 10.1039/d3ob00777d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Substituted ethyl 5-oxohomoadamantane-4-carboxylates were subjected to reactions with several nucleophiles to establish some aspects of the carbonyl reactivity. However, only one example of the desired Claisen retro-reaction was observed as 3,7-disubstituted bicyclo[3.3.1]nonane formation. Most of the reactions yielded α-substituted homoadamantan-5-ones or some products of their further transformations. Reductive amination of substituted homoadamantane-5-ones gave several homoadamantane-fused nitrogen heterocycles, which could be considered as GABA- and/or ∂-aminovaleric acid analogues. Reduction products of several substituted ketones were observed as single products when treated with organomagnesium reagents. These deviations from the general chemical reactivity patterns are associated with steric factors and the geometry of the cage unit and could be a particular case, which is reflecting the overall specificity of the chemistry of cage carbonyl compounds.
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Affiliation(s)
- Ilya M Tkachenko
- Samara State Technical University, 244, Molodogvardeyskaya st, Samara, 443100, Russian Federation.
| | - Vadim A Shiryaev
- Samara State Technical University, 244, Molodogvardeyskaya st, Samara, 443100, Russian Federation.
| | - Yuri N Klimochkin
- Samara State Technical University, 244, Molodogvardeyskaya st, Samara, 443100, Russian Federation.
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Ivleva EA, Zaborskaya MS, Shiryaev VA, Klimochkin YN. One pot synthesis of bridgehead amino alcohols from diamantoid hydrocarbons. SYNTHETIC COMMUN 2023. [DOI: 10.1080/00397911.2023.2177173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Elena A. Ivleva
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Maria S. Zaborskaya
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Vadim A. Shiryaev
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
| | - Yuri N. Klimochkin
- Department of Organic Chemistry, Samara State Technical University, Samara, Russian Federation
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Synthesis and Biological Activity of N-acyl Anabasine and Cytisine Derivatives with Adamantane, Pyridine and 1,2-Azole Fragments. Molecules 2022; 27:molecules27217387. [DOI: 10.3390/molecules27217387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
A series of N-acyl derivatives of anabasine and cytisine were prepared, to discover novel, natural product-based medicinal agents. All synthesized compounds were tested for antimicrobial, antifungal, antiviral and analgesic activity. The most pronounced antibacterial activity was shown by the compounds with isoxazole fragments, while the adamantane derivatives showed the greatest antiviral effect. It was found that the majority of anabasine derivatives showed significant analgesic activity, reducing the pain response of animals to the irritating effect of acetic acid. The presence of a high level of antimicrobial and antiviral activity in newly synthesized compounds makes it possible to consider them promising for further study of their pharmacological properties.
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Ivleva EA, Khamzina MR, Zaborskaya MS, Klimochkin YN. Nucleophilic Substitution Reactions of 1-Nitroxy-3-(nitroxymethyl)adamantanes. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022070065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Klimochkin YN, Ivleva EA. Synthesis and Chemical Transformations of N-Adamantylated Amides. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022050050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Quinine Esters with 1,2-Azole, Pyridine and Adamantane Fragments. Molecules 2022; 27:molecules27113476. [PMID: 35684414 PMCID: PMC9182173 DOI: 10.3390/molecules27113476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
An efficient method of producing quinine derivatives via reaction of acylation with 4,5-dichloroisothiazole-3-, 5-arylisoxazole-3-, adamantane- and hydrochlorides of pyridine-3- and pyridine-4-carbonyl chlorides was developed. All synthesized compounds were tested for antiviral, antimicrobial and analgesic activity. The most pronounced antibacterial activity was shown by the compounds 2e, 3b, 3c and 3e with isoxazole and pyridine fragments. It was found that most of the tested compounds showed significant analgesic activity reducing the pain response of animals to the irritating effect of acetic acid.
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Palchykov V, Manko N, Finiuk N, Stoika R, Obushak M, Pokhodylo N. Antimicrobial action of arylsulfonamides bearing (aza)norbornane and related motifs: evaluation of new promising anti-MRSA agents. Med Chem Res 2022. [DOI: 10.1007/s00044-021-02827-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Tertiary tetraols of adamantane (C10H16, Tricyclo[3.3.1.1(3,7)]decan) have been widely used for the synthesis of highly symmetric compounds with unique physical and chemical properties. The methods for one-stage simultaneously selective, deep, and cheap oxidation of adamantane to tetraols of different structures have not yet been developed. In this research, chemically simple, cheap, and environmentally friendly reagents are used and that is the first step in this direction. The conditions, under which the impact of a hydrogen peroxide water solution on adamantane dissolved in acetonitrile results in full conversion of adamantane and formation of a total 72% mixture of its tri-, tetra-, and penta-oxygenated products, predominantly poliols, have been found. Conversion and adamantane oxidation depth are shown to depend on the ratio of components of the water-acetonitrile solution and the method of oxidizer solution introduction when using the dimer form of 1:1 dimethylglyoxime and copper dichloride complex as a catalyst. Under the conditions of mass-spectrometry ionization by electrons (70 eV), fragmentation across three C–C bonds of the molecular ions framework of adamantane tertiary alcohols Ad(OH)n in the range n = 0–4 increases linearly with the rise of n.
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Pavlov DI, Ryadun AA, Samsonenko DG, Fedin VP, Potapov AS. Synthesis, crystal structures, and luminescence properties of coordination polymers and a discrete complex of cadmium(ii) halides with 1-(1,2,4-triazol-1-yl)adamantane. Russ Chem Bull 2021. [DOI: 10.1007/s11172-021-3159-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Shiryaev VA, Skomorohov MY, Leonova MV, Bormotov NI, Serova OA, Shishkina LN, Agafonov AP, Maksyutov RA, Klimochkin YN. Adamantane derivatives as potential inhibitors of p37 major envelope protein and poxvirus reproduction. Design, synthesis and antiviral activity. Eur J Med Chem 2021; 221:113485. [PMID: 33965861 PMCID: PMC9533879 DOI: 10.1016/j.ejmech.2021.113485] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/07/2022]
Abstract
Currently, smallpox, caused by the variola virus belonging to the poxvirus family, has been completely eradicated according to the WHO. However, other representatives of poxviruses, such as vaccinia virus, cowpox virus, ectromelia virus, monkeypox virus, mousepox virus and others, remain in the natural environment and can infect both animals and humans. The pathogens of animal diseases, belonging to the category with a high epidemic risk, have already caused several outbreaks among humans, and can, in an unfavorable combination of circumstances, cause not only an epidemic, but also a pandemic. Despite the fact that there are protocols for the treatment of poxvirus infections, the targeted design of new drugs will increase their availability and expand the arsenal of antiviral chemotherapeutic agents. One of the potential targets of poxviruses is the p37 protein, which is a tecovirimat target. This protein is relatively small, has no homologs among proteins of humans and other mammals and is necessary for the replication of viral particles, which makes it attractive target for virtual screening. Using the I-TASSER modelling and molecular dynamics refinement the p37 orthopox virus protein model was obtained and its was confirmed by ramachandran plot analysis and superimposition of the model with the template protein with similar function. A virtual library of adamantane containing compounds was generated and a number of potential inhibitors were chosen from virtual library using molecular docking. Several compounds bearing adamantane moiety were synthesized and their biological activity was tested in vitro on vaccinia, cowpox and mousepox viruses. The new compounds inhibiting vaccinia virus replication with IC50 concentrations between 0.133 and 0.515 μM were found as a result of the research. The applied approach can be useful in the search of new inhibitors of orthopox reproduction. The proposed approach may be suitable for the design of new poxvirus inhibitors containing cage structural moiety.
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Affiliation(s)
- Vadim A Shiryaev
- Department of Organic Chemistry, Samara State Technical University, 244 Molodogvardeyskaya St., Samara, Samara Region, 443100, Russia.
| | - Michael Yu Skomorohov
- Department of Organic Chemistry, Samara State Technical University, 244 Molodogvardeyskaya St., Samara, Samara Region, 443100, Russia
| | - Marina V Leonova
- Department of Organic Chemistry, Samara State Technical University, 244 Molodogvardeyskaya St., Samara, Samara Region, 443100, Russia
| | - Nikolai I Bormotov
- State Research Centre of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Region, 630559, Russia
| | - Olga A Serova
- State Research Centre of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Region, 630559, Russia
| | - Larisa N Shishkina
- State Research Centre of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Region, 630559, Russia
| | - Alexander P Agafonov
- State Research Centre of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Region, 630559, Russia
| | - Rinat A Maksyutov
- State Research Centre of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk Region, 630559, Russia
| | - Yuri N Klimochkin
- Department of Organic Chemistry, Samara State Technical University, 244 Molodogvardeyskaya St., Samara, Samara Region, 443100, Russia
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12
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Nikerov DS, Ashatkina MA, Shiryaev VA, Tkachenko IM, Rybakov VB, Reznikov AN, Klimochkin YN. Synthesis of non-racemic dihydrofurans via Ni(II)-catalyzed asymmetric Michael addition. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Baleeva NS, Rybakov VB, Ivleva EA, Shiryaev VA, Klimochkin YN. Synthesis and Chemical Transformations of 7-Hydroxybicyclo[3.3.1]nonane-3-carbohydrazide. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428020110081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Klimochkin YN, Ivleva EA, Moiseev IK. Selective Nitroxylation of Adamantane Derivatives in the System Nitric Acid–Acetic Anhydride. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020090055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Shiryaev VA, Klimochkin YN. Heterocyclic Inhibitors of Viroporins in the Design of Antiviral Compounds. Chem Heterocycl Compd (N Y) 2020; 56:626-635. [PMID: 32836315 PMCID: PMC7366462 DOI: 10.1007/s10593-020-02712-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
Ion channels of viruses (viroporins) represent a common type of protein targets for drugs. The relative simplicity of channel architecture allows convenient computational modeling and enables virtual search for new inhibitors. In this review, we analyze the data published over the last 10 years on known ion channels of viruses that cause socially significant diseases. The effectiveness of inhibition by various types of heterocyclic compounds of the viroporins of influenza virus, hepatitis С virus, human immunodeficiency virus, human papillomaviruses, coronaviruses, and respiratory syncytial virus is discussed. The presented material highlights the promise held by the search for heterocyclic antiviral compounds that act by inhibition of viroporins.
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Affiliation(s)
- Vadim A. Shiryaev
- Samara State Technical University, 244 Molodogvardeiskaya St, Samara, 443100 Russia
| | - Yuri N. Klimochkin
- Samara State Technical University, 244 Molodogvardeiskaya St, Samara, 443100 Russia
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16
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Palchykov VA, Gaponova RG, Omelchenko IV, Kasyan LI. Synthesis of new azapolycyclic scaffolds via the domino aminolysis of dicyclopentadiene diepoxide in water. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Ivleva EA, Grinʼ IS, Uchaev IS, Klimochkin YN. Oxidation of Deactivated Cage Substrates in the System
H2SO4–HNO3. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020030082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Tkachenko IM, Mankova PA, Rybakov VB, Golovin EV, Klimochkin YN. Wagner-Meerwein type rearrangement in 5-oxohomoadamantane series. Org Biomol Chem 2020; 18:465-478. [PMID: 31845947 DOI: 10.1039/c9ob02060h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Efficient methods for introducing various substituents into the α-position of ethyl 5-oxohomoadamantyl-4-carboxylate are reported. An unexpected acid-catalysed 1,2-alkyl shift in the series of synthesized α,α-bis-substituted 5-oxohomoadamantanes, and also in the hydroxy derivatives of homoadamantane was found. Such a retropinacol-like rearrangement leads to tetra- or pentacyclic mono- or bis-lactones containing a homoadamantane moiety. This new transformation opens access to the synthesis of previously unknown 2,4-di and 2,3,4-trisubstituted derivatives of homoadamantane. The resulting caged γ-butyro- and δ-valerolactones could be considered as potential synthetic or metabolic precursors of conformationally restricted GABA and δ-aminovaleric acid analogues.
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Affiliation(s)
- Ilya M Tkachenko
- Samara State Technical University, 244, Molodogvardeyskaya st., Samara, 443100, Russian Federation.
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Canseco-González D, O JLRDL, Herbert-Pucheta JE. Combined XRD-paramagnetic 13C NMR spectroscopy of 1,2,3-triazoles for revealing copper traces in a Huisgen click-chemistry cycloaddition. A model case. HETEROCYCL COMMUN 2019. [DOI: 10.1515/hc-2019-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractCopper-catalyzed Alkyne-Azide Cycloaddition (CuAAC) click chemistry robustness has been demonstrated over recent years to produce 1,2,3-triazoles with excellent yields at mild conditions with simple purification methods. However, the consequences of having copper paramagnetic traces in final products, which complicate spectroscopic assignments and can produce inaccurate conclusions, has been scarcely discussed. Herein we present a strategy that combines X-Ray Diffraction (XRD) with 13C- paramagnetic Nuclear Magnetic Resonance spectroscopy, in order to demonstrate the presence of paramagnetic metal traces at standard Huisgen synthesis and purification conditions. We also demonstrate that the derivatization of 1,4-disubstituted-1,2,3-triazoles to produce 1,3,4,-trisubstituted-1,2,3.triazolium salts, promotes an efficient removal of Cu(II/I) moieties. Evidence of paramagnetic metal moieties is given using XRD structural analysis of abnormalities in torsional angles between substituents and the 1,2,3-triazole center, in parallel to 13C- paramagnetic NMR chemical shift and line width analysis. As model systems to demonstrate the importance of characterizing paramagnetic traces, we present the synthesis of novel 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-1H-1,2,3-triazole and its derivatized 1-((3s,5s,7s)-adamantan-1-yl)-4-cyclopropyl-3-methyl-1H-[1,2,3]-triazol-3-ium triflate salt.
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Affiliation(s)
- Daniel Canseco-González
- Consejo Nacional de Ciencia y Tecnología – Laboratorio Nacional de Investigación y Servicio Agroalimentario y Forestal, Universidad Autónoma Chapingo, Km. 38.5 Carretera México-Texcoco, Chapingo 56230, Estado de México, México
| | - José Luis Rodríguez de la O
- Academia de Genética, Departamento de Fitotecnia, Universidad Autónoma Chapingo, Km. 38.5 Carretera México-Texcoco, Chapingo 56230, Estado de México, México
| | - José Enrique Herbert-Pucheta
- Consejo Nacional de Ciencia y Tecnología – Laboratorio Nacional de Investigación y Servicio Agroalimentario y Forestal, Universidad Autónoma Chapingo, Km. 38.5 Carretera México-Texcoco, Chapingo 56230, Estado de México, México
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Khaziev R, Shtyrlin N, Pavelyev R, Nigmatullin R, Gabbasova R, Grishaev D, Shtro A, Galochkina A, Nikolaeva Y, Vinogradova T, Manicheva O, Dogonadze M, Gnezdilov O, Sokolovich E, Yablonskiy P, Balakin K, Shtyrlin Y. Synthesis and Antimicrobial Activity of Adamantyl Substituted Pyridoxine Derivatives. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666190911150705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Adamantane derivatives possess multiple pharmacological activities such
as antiviral, anticancer, antimycobacterial, antidiabetic, antiparkinsonian and others. The interest of
medicinal chemists in adamantane compounds is due to their unique spatial structure, high lipophilicity,
and carbon cage rigidity. As a result, these molecules can easily penetrate biological lipid
membranes and often have unique target-specific activity profile. Another pharmacophore studied in
this work is pyridoxine (vitamin B6). Pyridoxine plays highly important roles in living cells as a key
cofactor of many enzymes. On the other hand, its molecular scaffold is a valuable structural platform
which has led to the development of several launched drugs (Pyritinol, Pirisudanol, Cycletanine,
Mangafodipir) and a wide number of preclinical and clinical drug candidates.
Objective:
The objective of this study is a synthesis of pyridoxine-adamantane and pyridoxinecyclooctane
dipharmacophore molecules. The underlying idea was to assess the antibacterial and
antiviral potential of such dipharmacophores, based on multiple examples of promising antiinfective
agents which have in their structures adamantane and pyridoxine moieties. Another specific reason
was to explore the ability of pyridoxine pharmacophore to suppress the potential of microbial pathogens
to develop resistance to drug molecules.
Methods:
In this study, a series of pyridoxine-adamantane and pyridoxine-cyclooctane dipharmacophore
molecules were synthesized based on reactions of three different cycloalkyl amines with the
corresponding electrophilic derivatives of pyridoxine aldehydes, chlorides and acetates. All synthesized
compounds have been tested for their in vitro activity against M. tuberculosis H37Rv strain and
H3N2 (A/Aichi/2/68) influenza virus.
Results:
Series of pyridoxine-adamantane and pyridoxine-cyclooctane dipharmacophore molecules
were synthesized based on reactions of three different cycloalkylamines with the corresponding
electrophilic derivatives of pyridoxine aldehydes, chlorides and acetates. Reaction of cycloalkylamines
with pyridoxine derivatives, in which meta-hydroxyl and ortho-hydroxymethyl groups are
protected by acetyl groups, represents a useful alternative to reductive amination of aldehydes and
nucleophilic substitution of alkyl halides. According to a tentative mechanism, it proceeds via paraand
ortho-pyridinone methides which readily react with nucleophiles. None of the synthesized dipharmacophore
compounds showed activity against M. tuberculosis H37Rv strain. At the same time,
three compounds demonstrated some antiviral activity against H3N2 (A/Aichi/2/68) influenza virus
(EC50 52-88 µg/mL) that was comparable to the activity of Amantadine, though lower than the activity
of Rimantadine. The results of this work can be useful in the design of physiologically active
derivatives of pyridoxine and adamantane.
Conclusion:
The results of this work can be useful in the design of physiologically active derivatives
of pyridoxine and adamantane.
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Affiliation(s)
- Rail Khaziev
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Nikita Shtyrlin
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Roman Pavelyev
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Raushan Nigmatullin
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Raylya Gabbasova
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Denis Grishaev
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anna Shtro
- Laboratory for Chemotherapy of Viral Infections, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russian Federation
| | - Anastasia Galochkina
- Laboratory for Chemotherapy of Viral Infections, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russian Federation
| | - Yulia Nikolaeva
- Laboratory for Chemotherapy of Viral Infections, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russian Federation
| | - Tatiana Vinogradova
- Saint Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg, Russian Federation
| | - Olga Manicheva
- Saint Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg, Russian Federation
| | - Marine Dogonadze
- Saint Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg, Russian Federation
| | - Oleg Gnezdilov
- Zavoisky Physical- Technical Institute, FRC Kazan Scientific Center, RAS, Kazan, Russia; 5Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Evgenii Sokolovich
- Saint Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg, Russian Federation
| | - Petr Yablonskiy
- Saint Petersburg Research Institute of Phthisiopulmonology, Saint Petersburg, Russian Federation
| | - Konstantin Balakin
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Yurii Shtyrlin
- Scientific and Educational Center of Pharmaceutics, Kazan (Volga Region) Federal University, Kazan, Russian Federation
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Shishkina SV, Isaiev IA, Urzhuntseva VV, Palchykov VA. The formation of the salt and neutral molecule cocrystal from equimolar solution of heliamine and bicyclo[2.2.1]hept-5-ene-endo-2,3-dicarboxylic acid. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:192-200. [PMID: 32830744 DOI: 10.1107/s205252061900115x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/22/2019] [Indexed: 06/11/2023]
Abstract
The possible interaction of 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline (heliamine) with bicyclo[2.2.1]hept-5-ene-endo-2,3-dicarboxylic acid anhydride has been studied. Instead of the reaction with heliamine, the acid anhydride was hydrolyzed into the appropriate dicarboxylic acid. An equimolar mixture of unreacted heliamine and in-situ-generated dicarboxylic acid crystallized in space group P21/c. The comprehensive study of the obtained crystals shows that the peculiarities of the crystallization process lead to the formation of the salt-cocrystal structure where the dianion interacts simultaneously with two cations forming a chain as the primary structural motif. The neutral molecules of dicarboxylic acid link the dianions of the neighbouring chains, forming a layer as the secondary structural motif. As a result, the stronger hydrogen bonds formed by the neutral molecules play a secondary role in the crystal structure formation.
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Affiliation(s)
- Svitlana V Shishkina
- SSI `Institute for Single Crystals', NAS of Ukraine, 60 Nauky Avenue, Kharkiv, 61001, Ukraine
| | - Ivan A Isaiev
- Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv, 61077, Ukraine
| | - Viktoriya V Urzhuntseva
- Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv, 61077, Ukraine
| | - Vitalii A Palchykov
- Department of Organic Chemistry, Oles Honchar Dnipro National University, 72 Gagarina Street, Dnipro, 49010, Ukraine
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Leonova MV, Belaya NV, Baimuratov MR, Klimochkin YN. Synthesis and Transformations of 2-(Adamantan-1-yl)aziridine. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428018110040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Savel’eva SA, Leonova MV, Baimuratov MR, Klimochkin YN. Synthesis and Transformations of Aryl-Substituted Alkenes of the Adamantane Series. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1070428018070047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Ivleva EA, Pogulyaiko AV, Klimochkin YN. Synthesis of (3-Hydroxyadamantan-1-yl)methanols. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s107042801809004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Tkachenko IV, Tarabara IN, Omelchenko IV, Palchykov VA. Grignard Reagents and Their N
-analogues in the Synthesis of Tricyclic and Tetracyclic Cage-like Lactams. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | - Irina V. Omelchenko
- State Scientific Institution “Institute for Single Crystals”; National Academy of Sciences of Ukraine; Kharkiv 61001 Ukraine
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Shiryaev VA, Radchenko EV, Palyulin VA, Zefirov NS, Bormotov NI, Serova OA, Shishkina LN, Baimuratov MR, Bormasheva KM, Gruzd YA, Ivleva EA, Leonova MV, Lukashenko AV, Osipov DV, Osyanin VA, Reznikov AN, Shadrikova VA, Sibiryakova AE, Tkachenko IM, Klimochkin YN. Molecular design, synthesis and biological evaluation of cage compound-based inhibitors of hepatitis C virus p7 ion channels. Eur J Med Chem 2018; 158:214-235. [PMID: 30218908 DOI: 10.1016/j.ejmech.2018.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/04/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022]
Abstract
The hepatitis C caused by the hepatitis C virus (HCV) is an acute and/or chronic liver disease ranging in severity from a mild brief ailment to a serious lifelong illness that affects up to 3% of the world population and imposes significant and increasing social, economic, and humanistic burden. Over the past decade, its treatment was revolutionized by the development and introduction into clinical practice of the direct acting antiviral (DAA) agents targeting the non-structural viral proteins NS3/4A, NS5A, and NS5B. However, the current treatment options still have important limitations, thus, the development of new classes of DAAs acting on different viral targets and having better pharmacological profile is highly desirable. The hepatitis C virus p7 viroporin is a relatively small hydrophobic oligomeric viral ion channel that plays a critical role during virus assembly and maturation, making it an attractive and validated target for the development of the cage compound-based inhibitors. Using the homology modeling, molecular dynamics, and molecular docking techniques, we have built a representative set of models of the hepatitis C virus p7 ion channels (Gt1a, Gt1b, Gt1b_L20F, Gt2a, and Gt2b), analyzed the inhibitor binding sites, and identified a number of potential broad-spectrum inhibitor structures targeting them. For one promising compound, the binding to these targets was additionally confirmed and the binding modes and probable mechanisms of action were clarified by the molecular dynamics simulations. A number of compounds were synthesized, and the tests of their antiviral activity (using the BVDV model) and cytotoxicity demonstrate their potential therapeutic usefulness and encourage further more detailed studies. The proposed approach is also suitable for the design of broad-spectrum ligands interacting with other multiple labile targets including various viroporins.
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Affiliation(s)
- Vadim A Shiryaev
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia.
| | - Eugene V Radchenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Nikolay S Zefirov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russia
| | - Nikolay I Bormotov
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Olga A Serova
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Larisa N Shishkina
- State Research Center of Virology and Biotechnology 'Vector', Koltsovo, Novosibirsk Region, 630559, Russia
| | - Marat R Baimuratov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Kseniya M Bormasheva
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Yulia A Gruzd
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Elena A Ivleva
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Marina V Leonova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Anton V Lukashenko
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Dmitry V Osipov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Vitaliy A Osyanin
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Alexander N Reznikov
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Vera A Shadrikova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Anastasia E Sibiryakova
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Ilya M Tkachenko
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
| | - Yuri N Klimochkin
- Department of Organic Chemistry, Samara State Technical University, Molodogvardeyskaya 244, Samara, 443100, Russia
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Konovalov AI, Antipin IS, Burilov VA, Madzhidov TI, Kurbangalieva AR, Nemtarev AV, Solovieva SE, Stoikov II, Mamedov VA, Zakharova LY, Gavrilova EL, Sinyashin OG, Balova IA, Vasilyev AV, Zenkevich IG, Krasavin MY, Kuznetsov MA, Molchanov AP, Novikov MS, Nikolaev VA, Rodina LL, Khlebnikov AF, Beletskaya IP, Vatsadze SZ, Gromov SP, Zyk NV, Lebedev AT, Lemenovskii DA, Petrosyan VS, Nenaidenko VG, Negrebetskii VV, Baukov YI, Shmigol’ TA, Korlyukov AA, Tikhomirov AS, Shchekotikhin AE, Traven’ VF, Voskresenskii LG, Zubkov FI, Golubchikov OA, Semeikin AS, Berezin DB, Stuzhin PA, Filimonov VD, Krasnokutskaya EA, Fedorov AY, Nyuchev AV, Orlov VY, Begunov RS, Rusakov AI, Kolobov AV, Kofanov ER, Fedotova OV, Egorova AY, Charushin VN, Chupakhin ON, Klimochkin YN, Osyanin VA, Reznikov AN, Fisyuk AS, Sagitullina GP, Aksenov AV, Aksenov NA, Grachev MK, Maslennikova VI, Koroteev MP, Brel’ AK, Lisina SV, Medvedeva SM, Shikhaliev KS, Suboch GA, Tovbis MS, Mironovich LM, Ivanov SM, Kurbatov SV, Kletskii ME, Burov ON, Kobrakov KI, Kuznetsov DN. Modern Trends of Organic Chemistry in Russian Universities. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s107042801802001x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Antipin IS, Kazymova MA, Kuznetsov MA, Vasilyev AV, Ishchenko MA, Kiryushkin AA, Kuznetsova LM, Makarenko SV, Ostrovskii VA, Petrov ML, Solod OV, Trishin YG, Yakovlev IP, Nenaidenko VG, Beloglazkina EK, Beletskaya IP, Ustynyuk YA, Solov’ev PA, Ivanov IV, Malina EV, Sivova NV, Negrebetskii VV, Baukov YI, Pozharskaya NA, Traven’ VF, Shchekotikhin AE, Varlamov AV, Borisova TN, Lesina YA, Krasnokutskaya EA, Rogozhnikov SI, Shurov SN, Kustova TP, Klyuev MV, Khelevina OG, Stuzhin PA, Fedorov AY, Gushchin AV, Dodonov VA, Kolobov AV, Plakhtinskii VV, Orlov VY, Kriven’ko AP, Fedotova OV, Pchelintseva NV, Charushin VN, Chupakhin ON, Klimochkin YN, Klimochkina AY, Kuryatnikov VN, Malinovskaya YA, Levina AS, Zhuravlev OE, Voronchikhina LI, Fisyuk AS, Aksenov AV, Aksenov NA, Aksenova IV. Organic chemistry. History and mutual relations of universities of Russia. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1070428017090019] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Synthesis and Biological Evaluations of NO-Donating Oxa- and Aza-Pentacycloundecane Derivatives as Potential Neuroprotective Candidates. Molecules 2018; 23:molecules23020308. [PMID: 29385098 PMCID: PMC6017363 DOI: 10.3390/molecules23020308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 11/17/2022] Open
Abstract
In order to utilize the neuroprotective properties of polycyclic cage compounds, and explore the NO-donating ability of nitrophenyl groups, an array of compounds was synthesized where the different nitrophenyl groups were appended on oxa and aza-bridged cage derivatives. Biological evaluations of the compounds were done for cytotoxicity, neuroprotective abilities, the inhibition of N-methyl-d-aspartate (NMDA)-mediated Ca2+ influx, the inhibition of voltage-mediated Ca2+ influx, and S-nitrosylation abilities. All of the compounds showed low toxicity. With a few exceptions, most of the compounds displayed good neuroprotection and showed inhibitory activity for NMDA-mediated and voltage-gated calcium influx, ranging from high (>70%) to low (20–39%) inhibition. In the S-nitrosylation assay, the compounds with the nitro moiety as the NO-donating group exhibited low to good nitrosylation potency compared to the positive controls. From the biological evaluation of the tested compounds, it was not possible to obtain a simple correlation that could explain the results across all of the biological study domains. This can be ascribed to the independent processes evaluated in the different assays, which reiterate that neuroprotection is a result of multifactorial biochemical mechanisms and interactions. However, these results signify the important aspects of the pentacylcoundecylamine neuroprotectants across different biological study realms.
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Baimuratov MR, Leonova MV, Shiryaev VA, Klimochkin YN. Reactions of tetracyclic γ-sultones with N-nucleophiles. Novel synthesis of 3,4-disubstituted homoadamantanes. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ivleva EA, Tkachenko IM, Klimochkin YN. Synthesis of adamantane functional derivatives basing on N-[(adamantan-1-yl)alkyl]acetamides. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1070428016110026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shadrikova VA, Golovin EV, Kuznetsova EA, Rostova MY, Klimochkin YN. Synthesis of substituted 1-[2-(adamantan-1-yl)ethyl]piperidines. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016100146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Osipov DV, Demidov MR, Osyanin VA, Skomorokhov MY, Klimochkin YN. Adamantylation of hydantoin. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016060257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ivleva EA, Gavrilova VS, Klimochkin YN. Synthesis of hydroxy derivatives from adamantanecarboxylic acids in the system MnO2–H2SO4. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016060051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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