European Journal of Chemistry 2020, 11(1), 30-36 | doi: https://doi.org/10.5155/eurjchem.11.1.30-36.1955 | Get rights and content






  OPEN ACCESS | PEER-REVIEWED | RESEARCH ARTICLE | DOWNLOAD PDF | VIEW FULL-TEXT PDF | TOTAL VIEWS

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


Mustapha Abdullahi (1,*) orcid , Adamu Uzairu (2) orcid , Gideon Adamu Shallangwa (3) orcid , David Ebuka Arthur (4) orcid , Bello Abdullahi Umar (5) orcid , Muhammad Tukur Ibrahim (6) orcid

(1) Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, 810107, Zaria, Nigeria
(2) Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, 810107, Zaria, Nigeria
(3) Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, 810107, Zaria, Nigeria
(4) Department of Chemistry, Baze University, 900108, Abuja, Nigeria
(5) Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, 810107, Zaria, Nigeria
(6) Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, 810107, Zaria, Nigeria
(*) Corresponding Author

Received: 27 Dec 2019 | Revised: 25 Jan 2020 | Accepted: 27 Jan 2020 | Published: 31 Mar 2020 | Issue Date: March 2020

Abstract


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.


Keywords


Protein; PLANTS; Docking; MolDock; Binding affinity; Scoring functions

Full Text:

PDF /    /


DOI: 10.5155/eurjchem.11.1.30-36.1955

Links for Article


| | | | | | |

| | | | | | |

Related Articles




Article Metrics

This Abstract was viewed 458 times | PDF Article downloaded 29 times

Funding information


The Physical Chemistry Unit, Department of Chemistry, Ahmadu Bello University Zaria, Zaria, Nigeria.

References

[1]. Zhai, W.; Wu, F.; Zhang, Y.; Fu, Y.; Liu, Z. Int. J. Mol. Sci. 2019, 20, 340, 1-18.
https://doi.org/10.3390/ijms20020340

[2]. Mabhula, A.; Singh, V. Med. Chem. Comm. 2019, 10, 1342-1360.
https://doi.org/10.1039/C9MD00057G

[3]. Ogbuabor, D. C.; Onwujekwe, O. E. Inf. Dis. Pov. 2019, 8, 1-11.
https://doi.org/10.1186/s40249-019-0556-2

[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.
https://doi.org/10.18052/www.scipress.com/IJPPE.2.5

[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.
https://doi.org/10.1016/j.jksus.2019.01.008

[7]. Cousins, K. R. J. Am. Chem. Soc. 2005, 127(11), 4115-4116.
https://doi.org/10.1021/ja0410237

[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.
https://doi.org/10.1039/B517914A

[9]. Thomsen, R.; Christensen, M. H. J. Med. Chem. 2006, 49(11), 3315-3321.
https://doi.org/10.1021/jm051197e

[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.
https://doi.org/10.1016/j.ejmech.2019.06.038

[12]. Abdullahi, M.; Shallangwa, G. A.; Ali, T.; Uzairu, A. J. Eng. Exact. Sci. 2019, 5(1), 63-78.
https://doi.org/10.18540/jcecvl5iss1pp0063-0078

[13]. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
https://doi.org/10.1063/1.464913

[14]. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
https://doi.org/10.1103/PhysRevB.37.785

[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.
https://doi.org/10.5155/eurjchem.10.4.358-366.1859

[17]. Piton, J.; Petrella, S.; Delarue, M.; Andre-Leroux, G.; Jarlier, V.; Aubry, A.; Mayer, C. PLoS ONE 2010, 5(8), e12245.
https://doi.org/10.1371/journal.pone.0012245

[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.
https://doi.org/10.31557/APJCP.2019.20.9.2681

[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.
https://doi.org/10.1016/j.jtusci.2014.04.007

[22]. Madhuri, M.; Prasad, C.; Avupati, V. R. Int. J. Comp. Appl. 2014, 95(6), 13-16.
https://doi.org/10.5120/16597-6403

[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.
https://doi.org/10.1080/07391102.2014.989408

How to cite


Abdullahi, M.; Uzairu, A.; Shallangwa, G.; Arthur, D.; Umar, B.; Ibrahim, M. Eur. J. Chem. 2020, 11(1), 30-36. doi:10.5155/eurjchem.11.1.30-36.1955
Abdullahi, M.; Uzairu, A.; Shallangwa, G.; Arthur, D.; Umar, B.; Ibrahim, M. Virtual molecular docking study of some novel carboxamide series as new anti-tubercular agents. Eur. J. Chem. 2020, 11(1), 30-36. doi:10.5155/eurjchem.11.1.30-36.1955
Abdullahi, M., Uzairu, A., Shallangwa, G., Arthur, D., Umar, B., & Ibrahim, M. (2020). Virtual molecular docking study of some novel carboxamide series as new anti-tubercular agents. European Journal of Chemistry, 11(1), 30-36. doi:10.5155/eurjchem.11.1.30-36.1955
Abdullahi, Mustapha, Adamu Uzairu, Gideon Adamu Shallangwa, David Ebuka Arthur, Bello Abdullahi Umar, & Muhammad Tukur Ibrahim. "Virtual molecular docking study of some novel carboxamide series as new anti-tubercular agents." European Journal of Chemistry [Online], 11.1 (2020): 30-36. Web. 29 May. 2020
Abdullahi, Mustapha, Uzairu, Adamu, Shallangwa, Gideon, Arthur, David, Umar, Bello, AND Ibrahim, Muhammad. "Virtual molecular docking study of some novel carboxamide series as new anti-tubercular agents" European Journal of Chemistry [Online], Volume 11 Number 1 (31 March 2020)

The other citation formats (EndNote | Reference Manager | ProCite | BibTeX | RefWorks) for this article can be found online at: How to cite item


DOI Link: https://doi.org/10.5155/eurjchem.11.1.30-36.1955

| | | | | | |

| | | | | |

Save to Zotero Save to Mendeley



European Journal of Chemistry 2020, 11(1), 30-36 | doi: https://doi.org/10.5155/eurjchem.11.1.30-36.1955 | Get rights and content

Refbacks

  • There are currently no refbacks.




Copyright (c) 2020 Authors

Creative Commons License
This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at http://www.eurjchem.com/index.php/eurjchem/pages/view/terms and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License (http://creativecommons.org/licenses/by-nc/4.0). 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 (http://www.eurjchem.com/index.php/eurjchem/pages/view/terms) are administered by Atlanta Publishing House LLC (European Journal of Chemistry).


© Copyright 2010 - 2020  Atlanta Publishing House LLC All Right Reserved.

The opinions expressed in all articles published in European Journal of Chemistry are those of the specific author(s), and do not necessarily reflect the views of Atlanta Publishing House LLC, or European Journal of Chemistry, or any of its employees.

Copyright 2010-2020 Atlanta Publishing House LLC. All rights reserved. This site is owned and operated by Atlanta Publishing House LLC whose registered office is 2850 Smith Ridge Trce Peachtree Cor GA 30071-2636, USA. Registered in USA.

hatay escort hatay escort corlu escort corum escort burgaz escort giresun escort aydin escort ordu escort erzincan escort hatay escort sivas escort rize escort edirne escort aksaray escort kibris escort isparta escort erzurum escort tekirdag escort usak escort urfa escort kastamonu escort kibris escort manisa escort giresun escort urfa escort nevsehir escort sivas escort yalova escort ordu escort hatay escort yalova escort amasya escort kayseri escort ordu escort maras escort canakkale escort yalova escort balikesir escort manisa escort urfa escort mugla escort trabzon escort bolu escort corlu escort diyarbakir escort isparta escort kutahya escort elazig escort erzurum escort sakarya escort afyon escort kutahya escort konya escort agri escort cesme escort sinop escort sivas escort konya escort kibris escort adapazari escort luleburgaz escort adana escort kibris escort rize escort sakarya escort alanya escort isparta escort burdur escort konya escort bitlis escort canakkale escort sivas escort amasya escort mus escort aydin escort van escort yalova escort kastamonu escort mardin escort bolu escort afyon escort sakarya escort isparta escort tokat escort trakya escort bayburt escort urfa escort mardin escort