European Journal of Chemistry 2022, 13(4), 440-450 | doi: https://doi.org/10.5155/eurjchem.13.4.440-450.2303 | Get rights and content

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Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide


Suganya Murugan (1) orcid , Prasanth Gunasekaran (2) orcid , Jayasudha Nehru (3) orcid , Anaglit Catherine Paul (4) orcid , Necmi Dege (5) orcid , Emine Berrin Cinar (6) orcid , Savaridasson Jose Kavitha (7) orcid , Kasthuri Balasubramani (8) orcid , Kaliyaperumal Thanigaimani (9) orcid , Venkatachalam Rajakannan (10) orcid , Madhukar Hemamalini (11,*) orcid

(1) Department of Chemistry, Faculty of Science, Mother Teresa Women’s University, Kodaikanal, 624101, India
(2) Centre of Advanced Study in Crystallography and Biophysics, Faculty of Science, University of Madras, Chennai, 600025, India
(3) Department of Chemistry, Faculty of Science, Mother Teresa Women’s University, Kodaikanal, 624101, India
(4) Department of Chemistry, Faculty of Science, Mother Teresa Women’s University, Kodaikanal, 624101, India
(5) Department of Physics, Faculty of Science, Ondokuz Mayis University, Samsun, 55200, Turkey
(6) Department of Physics, Faculty of Science, Ondokuz Mayis University, Samsun, 55200, Turkey
(7) Department of Chemistry, Faculty of Science, Mother Teresa Women’s University, Kodaikanal, 624101, India
(8) Department of Chemistry, Faculty of Science, Government Arts College (Autonomous), Thanthonrimalai, Karur, 639005, India
(9) Department of Chemistry, Faculty of Science, Government Arts College, Trichy, 620022, India
(10) Centre of Advanced Study in Crystallography and Biophysics, Faculty of Science, University of Madras, Chennai, 600025, India
(11) Department of Chemistry, Faculty of Science, Mother Teresa Women’s University, Kodaikanal, 624101, India
(*) Corresponding Author

Received: 08 Jul 2022 | Revised: 01 Sep 2022 | Accepted: 09 Sep 2022 | Published: 31 Dec 2022 | Issue Date: December 2022

Abstract


In this work, N-(2-methoxy-benzyl)-acetamide (2MBA) was synthesized from an amide derivative and it was characterized by FT-IR and NMR spectroscopy techniques. The crystal structure of 2MBA was also validated via single-crystal X-ray diffraction analysis. Crystal data for C10H13NO2 for 2MBA: Monoclinic, space group P21/n (no. 14), a = 9.1264(6) Å, b = 9.3375(7) Å, c = 11.9385(8) Å, β = 95.745(5)°, = 1012.26(12) Å3, Z = 4, μ(MoKα) = 0.082 mm-1, Dcalc = 1.176 g/cm3, 5632 reflections measured (5.368° ≤ 2Θ ≤ 51.992°), 1990 unique (Rint = 0.0377, Rsigma = 0.0314) which were used in all calculations. The final R1 was 0.0583 (I > 2σ(I)) and wR2 was 0.1444 (all data).  The intermolecular interactions in 2MBA were theoretically examined by Hirshfeld surface analysis and 2D fingerprint plots. Moreover, the HOMO and LUMO energy gaps of 2MBA was calculated by DFT calculation with the B3LYP/6-311G++(d,p) method. The electron-withdrawing and donating sites of the 2MBA were confirmed via molecular electrostatic potential surface analysis. The present study discusses the title compound not only highlighted the crystallographic data but also revealed good molecular interactions together with an anticancer drug target, which is a targeting PARP protein, which was an important drug target in the treatment of breast cancer.


Keywords


PARP protein; Crystal structure; Molecular docking; Density functional theory; Hirshfeld surface analysis; Molecular electrostatic potential

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DOI: 10.5155/eurjchem.13.4.440-450.2303

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Funding information


The Science and Engineering Research Board Science, International Research Experience (SERB-IRE) (SIR/2022/000011) and Mother Teresa Women’s University, Tamil Nadu, India.

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Murugan, S.; Gunasekaran, P.; Nehru, J.; Paul, A.; Dege, N.; Cinar, E.; Kavitha, S.; Balasubramani, K.; Thanigaimani, K.; Rajakannan, V.; Hemamalini, M. Eur. J. Chem. 2022, 13(4), 440-450. doi:10.5155/eurjchem.13.4.440-450.2303
Murugan, S.; Gunasekaran, P.; Nehru, J.; Paul, A.; Dege, N.; Cinar, E.; Kavitha, S.; Balasubramani, K.; Thanigaimani, K.; Rajakannan, V.; Hemamalini, M. Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide. Eur. J. Chem. 2022, 13(4), 440-450. doi:10.5155/eurjchem.13.4.440-450.2303
Murugan, S., Gunasekaran, P., Nehru, J., Paul, A., Dege, N., Cinar, E., Kavitha, S., Balasubramani, K., Thanigaimani, K., Rajakannan, V., & Hemamalini, M. (2022). Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide. European Journal of Chemistry, 13(4), 440-450. doi:10.5155/eurjchem.13.4.440-450.2303
Murugan, Suganya, Prasanth Gunasekaran, Jayasudha Nehru, Anaglit Catherine Paul, Necmi Dege, Emine Berrin Cinar, Savaridasson Jose Kavitha, Kasthuri Balasubramani, Kaliyaperumal Thanigaimani, Venkatachalam Rajakannan, & Madhukar Hemamalini. "Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide." European Journal of Chemistry [Online], 13.4 (2022): 440-450. Web. 5 Feb. 2023
Murugan, Suganya, Gunasekaran, Prasanth, Nehru, Jayasudha, Paul, Anaglit, Dege, Necmi, Cinar, Emine, Kavitha, Savaridasson, Balasubramani, Kasthuri, Thanigaimani, Kaliyaperumal, Rajakannan, Venkatachalam, AND Hemamalini, Madhukar. "Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide" European Journal of Chemistry [Online], Volume 13 Number 4 (31 December 2022)

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