Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate

Alexandre V Ivachtchenko; S.M. Kovalenko; Dmitry V Kravchenko; OD Mitkin; VV Ivanov; Thierry Langer

doi:10.1107/S2056989019015986

Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate

Alexandre V Ivachtchenko
, S.M. Kovalenko
, Dmitry V Kravchenko
, OD Mitkin
, VV Ivanov
, Thierry Langer

Department of Pharmaceutical Sciences

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

The title compound, C15H22N4O5S, was prepared via alkylation of 3-(chloromethyl)-5-(pentan-3-yl)-1,2,4-oxadiazole in anhydrous dioxane in the presence of triethylamine. The thiadiazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxadiazole ring is inclined to the mean plane of the thiadiazine ring by 77.45 (11)°. In the crystal, molecules are linked by C—H...N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the intermolecular contacts present in the crystal. Molecular docking studies were use to evaluate the title compound as a potential system that interacts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.

Original language	English
Pages (from-to)	12-17
Number of pages	6
Journal	Acta Crystallographica. Section E: Crystallographic Communications
Volume	76
Issue number	1
Early online date	27 Nov 2019
DOIs	https://doi.org/10.1107/S2056989019015986
Publication status	Published - Jan 2020

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Austrian Fields of Science 2012

104021 Structural chemistry

Keywords

2H-1,2,6-thiadiazine 1,1-dioxide
DERIVATIVES
HBV
Hirshfeld surface analysis
crystal structure
hepatitis B
hydrogen bonding
molecular docking study

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Ivachtchenko, A. V., Kovalenko, S. M., Kravchenko, D. V., Mitkin, OD., Ivanov, VV., & Langer, T. (2020). Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate. Acta Crystallographica. Section E: Crystallographic Communications, 76(1), 12-17. https://doi.org/10.1107/S2056989019015986

Ivachtchenko, Alexandre V ; Kovalenko, S.M. ; Kravchenko, Dmitry V et al. / Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate. In: Acta Crystallographica. Section E: Crystallographic Communications. 2020 ; Vol. 76, No. 1. pp. 12-17.

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title = "Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-\{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl\}- 2H-1,2,6-thiadiazine-4-carboxylate",

abstract = "The title compound, C15H22N4O5S, was prepared via alkylation of 3-(chloromethyl)-5-(pentan-3-yl)-1,2,4-oxadiazole in anhydrous dioxane in the presence of triethylamine. The thiadiazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) {\AA} from the mean plane through the other five atoms. The planar 1,2,4-oxadiazole ring is inclined to the mean plane of the thiadiazine ring by 77.45 (11)°. In the crystal, molecules are linked by C—H...N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the intermolecular contacts present in the crystal. Molecular docking studies were use to evaluate the title compound as a potential system that interacts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.",

keywords = "2H-1,2,6-thiadiazine 1,1-dioxide, DERIVATIVES, HBV, Hirshfeld surface analysis, crystal structure, hepatitis B, hydrogen bonding, molecular docking study",

author = "Ivachtchenko, \{Alexandre V\} and S.M. Kovalenko and Kravchenko, \{Dmitry V\} and OD Mitkin and VV Ivanov and Thierry Langer",

year = "2020",

month = jan,

doi = "10.1107/S2056989019015986",

language = "English",

volume = "76",

pages = "12--17",

journal = "Acta Crystallographica. Section E: Crystallographic Communications",

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Ivachtchenko, AV, Kovalenko, SM, Kravchenko, DV, Mitkin, OD, Ivanov, VV & Langer, T 2020, 'Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate', Acta Crystallographica. Section E: Crystallographic Communications, vol. 76, no. 1, pp. 12-17. https://doi.org/10.1107/S2056989019015986

Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate. / Ivachtchenko, Alexandre V; Kovalenko, S.M.; Kravchenko, Dmitry V et al.
In: Acta Crystallographica. Section E: Crystallographic Communications, Vol. 76, No. 1, 01.2020, p. 12-17.

Publications: Contribution to journal › Article › Peer Reviewed

TY - JOUR

T1 - Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate

AU - Ivachtchenko, Alexandre V

AU - Kovalenko, S.M.

AU - Kravchenko, Dmitry V

AU - Mitkin, OD

AU - Ivanov, VV

AU - Langer, Thierry

PY - 2020/1

Y1 - 2020/1

N2 - The title compound, C15H22N4O5S, was prepared via alkylation of 3-(chloromethyl)-5-(pentan-3-yl)-1,2,4-oxadiazole in anhydrous dioxane in the presence of triethylamine. The thiadiazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxadiazole ring is inclined to the mean plane of the thiadiazine ring by 77.45 (11)°. In the crystal, molecules are linked by C—H...N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the intermolecular contacts present in the crystal. Molecular docking studies were use to evaluate the title compound as a potential system that interacts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.

AB - The title compound, C15H22N4O5S, was prepared via alkylation of 3-(chloromethyl)-5-(pentan-3-yl)-1,2,4-oxadiazole in anhydrous dioxane in the presence of triethylamine. The thiadiazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxadiazole ring is inclined to the mean plane of the thiadiazine ring by 77.45 (11)°. In the crystal, molecules are linked by C—H...N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the intermolecular contacts present in the crystal. Molecular docking studies were use to evaluate the title compound as a potential system that interacts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.

KW - 2H-1,2,6-thiadiazine 1,1-dioxide

KW - DERIVATIVES

KW - HBV

KW - Hirshfeld surface analysis

KW - crystal structure

KW - hepatitis B

KW - hydrogen bonding

KW - molecular docking study

UR - https://www.scopus.com/pages/publications/85077709277

U2 - 10.1107/S2056989019015986

DO - 10.1107/S2056989019015986

M3 - Article

SN - 2056-9890

VL - 76

SP - 12

EP - 17

JO - Acta Crystallographica. Section E: Crystallographic Communications

JF - Acta Crystallographica. Section E: Crystallographic Communications

IS - 1

ER -

Ivachtchenko AV, Kovalenko SM, Kravchenko DV, Mitkin OD, Ivanov VV, Langer T. Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate. Acta Crystallographica. Section E: Crystallographic Communications. 2020 Jan;76(1):12-17. Epub 2019 Nov 27. doi: 10.1107/S2056989019015986

Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo- 2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}- 2H-1,2,6-thiadiazine-4-carboxylate

Abstract

UN SDGs

Austrian Fields of Science 2012

Keywords

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