European Journal of Chemistry

Virtual molecular docking study of some novel carboxamide series as new anti-tubercular agents


Main Article Content

Mustapha Abdullahi
Adamu Uzairu
Gideon Adamu Shallangwa
David Ebuka Arthur
Bello Abdullahi Umar
Muhammad Tukur Ibrahim


A virtual docking simulation study was performed on thirty-five newly discovered compounds of N-(2-phenoxy) ethyl imidazo[1,2-a] pyridine-3-carboxamide (IPA), to explore their theoretical binding energy and pose with the active sites of the Mycobacterium tuberculosis target (DNA gyrase). The chemical structures of the compounds were drawn correctly with ChemDraw Ultra software, and then geometrically optimized at DFT level of theory with Spartan 14 software package. Consequently, the docking analysis was carried out using Molegro Virtual Docker (MVD). Five complexes (Complex 5, 24, 25, 33 and 35) with high binding energy were selected to examine their binding pose with the active sites of the protein. The docking results suggested a good MolDock score (≥ -90 kcal/mol) and Protein-Ligand ANT System (PLANTS) score (≥ -60 kcal/mol) which depicted that the compounds can efficiently bind with the active sites of the target. However, compound 5 has the best binding pose with the MolDock score of -140.476 kcal/mol which formed three hydrogen bond interactions with the Gln 538, Ala 531, and Ala 533 amino acid residues. This research gives a firsthand theoretical knowledge to improve the binding efficiency of these compounds with the target.

icon graph This Abstract was viewed 2137 times | icon graph Article PDF downloaded 649 times

How to Cite
Abdullahi, M.; Uzairu, A.; Shallangwa, G. A.; Arthur, D. E.; Umar, B. A.; Ibrahim, M. T. Virtual Molecular Docking Study of Some Novel Carboxamide Series As New Anti-Tubercular Agents. Eur. J. Chem. 2020, 11, 30-36.

Article Details

Crossref - Scopus - Google - European PMC

[1]. Zhai, W.; Wu, F.; Zhang, Y.; Fu, Y.; Liu, Z. Int. J. Mol. Sci. 2019, 20, 340, 1-18.

[2]. Mabhula, A.; Singh, V. Med. Chem. Comm. 2019, 10, 1342-1360.

[3]. Ogbuabor, D. C.; Onwujekwe, O. E. Inf. Dis. Pov. 2019, 8, 1-11.

[4]. Zhaoyang, W.; Yu, L.; Linhu, L.; Rui, Z.; Bin, W.; Kai, L.; Mingliang, L.; Xuefu, Y. ACS Med. Chem. Lett. 2016, 7(12), 1130-1133.

[5]. Lanez, T.; Lanez, E. Int. J. Pharmacol. Phytochem. Ethnomed. 2016, 2, 5-12.

[6]. Abdullahi, M.; Uzairu, A.; Shallangwa, G. A.; Mamza, P.; Arthur, D. E.; Ibrahim, M. T. J. King Saudi Uni. Sci. 2019, 32(1), 770-779.

[7]. Cousins, K. R. J. Am. Chem. Soc. 2005, 127(11), 4115-4116.

[8]. Shao, Y.; Molnar, L. F.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; DiStasio, R. A.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Van Voorhis, T.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C. P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. L.; Zhang, W.; ell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F.; Kong, J.; Krylov, A. I.; Gill, P. M. W.; Head-Gordon, M. (Spartan, Wavefunction Inc. , Irvine, CA, USA). Phys. Chem. Chem. Phys. 2006, 8, 3172-3191.

[9]. Thomsen, R.; Christensen, M. H. J. Med. Chem. 2006, 49(11), 3315-3321.

[10]. Biovia, D. S. CA, USA: San Diego, Discovery studio visualizer, 2017.

[11]. Wang, A.; Lv, K.; Li, L.; Liu, H.; Tao, Z.; Wang, B.; Liu, M.; Ma, C.; Ma, X.; Han, B.; Wang, A.; Lu, Y. Eur. J. Med. Chem. 2019, 178, 715-725.

[12]. Abdullahi, M.; Shallangwa, G. A.; Ali, T.; Uzairu, A. J. Eng. Exact. Sci. 2019, 5(1), 63-78.

[13]. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.

[14]. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.

[15]. Mustapha, A.; Shallangwa, G.; Ibrahim, M. T.; Bello, A. U.; Ebuka, D. A.; Uzairu, A.; Mamza, P. J. Turk. Chem. Soc. Chem. 2018, 5(3), 1387-1398.

[16]. Murtaza, S.; Altaf, A. A.; Hamayun, M.; Iftikhar, K.; Tahir, M. N.; Tariq, J.; Faiz, K. Eur. J. Chem. 2019, 10(4), 358-366.

[17]. Piton, J.; Petrella, S.; Delarue, M.; Andre-Leroux, G.; Jarlier, V.; Aubry, A.; Mayer, C. PLoS ONE 2010, 5(8), e12245.

[18]. Kusumaningrum, S.; Budianto, E.; Kosela, S.; Sumaryono, W.; Juniarti, F. J. App. Phar. Sci. 2014, 4(11), 47-53.

[19]. Yadav, M.; Khandelwal, R.; Urvy, M.; Srinitha. S.; Khandekar, N.; Nayarisseri, A.; Sugunakar, V.; Sanjeev, K. S. Asian Pac. J. Cancer Prev. 2019, 20(9), 2681-2692.

[20]. Torktaz, I.; Mohamadhashem, F.; Esmaeili, A.; Behjati, M.; Sharifzadeh, S. Bioimpacts. 2013, 3(3), 141-144.

[21]. Mishra, V.; Kashyap, S.; Hasija, Y. J. Taibah Univ. Sci. 2015, 9(1), 20-26.

[22]. Madhuri, M.; Prasad, C.; Avupati, V. R. Int. J. Comp. Appl. 2014, 95(6), 13-16.

[23]. Giacoppo, J. O. S.; Franca, T. C. C.; Kuca, K.; Cunha, E. F. F.; Abagyan, R.; Mancini, D. T.; Ramalho, T. C. J. Biom. Struc. Dyn. 2015, 33(9), 2048-2058.

Most read articles by the same author(s)

Dimensions - Altmetric - scite_ - PlumX

Downloads and views


Download data is not yet available.


Metrics Loading ...
License Terms

License Terms


Copyright © 2024 by Authors. This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License ( By accessing the work, you hereby accept the Terms. This is an open access article distributed under the terms and conditions of the CC BY NC License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited without any further permission from Atlanta Publishing House LLC (European Journal of Chemistry). No use, distribution, or reproduction is permitted which does not comply with these terms. Permissions for commercial use of this work beyond the scope of the License ( are administered by Atlanta Publishing House LLC (European Journal of Chemistry).