CiteScore: 4.9     h-index: 21

Document Type : Original Research Article

Authors

1 Department of Chemistry and Industrial Chemistry, Bowen University, Iwo, Osun State, Nigeria

2 School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China

3 Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria

4 Department of Chemistry, Ekiti State University, Ado-Ekiti, Nigeria

5 Department of Chemistry, Federal University, Oye-Ekiti, Nigeria

6 Department of Physics, University of Alberta, Edmonton, Canada

Abstract

The biological activity and properties of fourteen cyclic peptides were investigated using in silico approach. The predicted features for the studied compounds using 6-31G* via Spartan 14 software were lipophilicity, the highest occupied molecular orbital energy, the lowest occupied molecular orbital energy, HOMO/LUMO energy gap, dipole moment, molecular weight, and polar surface area. The descriptors obtained perfectly described the activities of the studied ligands. Likewise, the studied ligands were docked against sedoheptulose-7-phosphate isomerase [PDB id: 2x3y] and it was observed that all the ligands examined in this work have higher binding affinity than the ceftazidime (referenced drug) except compound 9 and 12. The predicted compounds proved to have higher binding affinities than the referenced compound and these were further confirmed using molecular dynamic simulation as well as pharmacokinetics studies.

Graphical Abstract

Molecular Modeling Insights into Bioactivities of Head-to-Tail Cyclic Peptides: Potential Sedoheptulose-7-Phosphate Isomerase Inhibitors

Keywords

Main Subjects

[1] D. Dance, Int. J. Antimicrob. Agents, 2014, 43, 310-318. [CrossRef], [Google Scholar], [Publisher]
[2] C. Potisap, M.A.W. Khan, A. Boonmee, J.L. Rodrigues, S. Wongratanacheewin, R.W. Sermswan, AMB Expr., 2018, 8, 1-14. [CrossRef], [Google Scholar], [Publisher]
[3] D. Limmathurotsakul, S. Wongratanacheewin, N. Teerawattanasook, G. Wongsu- van, S. Chaisuksant, P. Chetchotisakd, W. Chaowagul, N.P. Day, S.J. Peacock, Am. J. Trop. Med. Hyg., 2010, 82, 1113–17. [CrossRef], [Google Scholar], [Publisher]
[4] O. Karatuna, D.A.B. Dance, E. Matuschek, J. Åhman, P. Turner, J. Hopkins, P. Amornchai, V. Wuthiekanun, T.-P. Cusack, R. Baird, J. Hennessy, R. Norton, M. Armstrong, S. Zange, L. Zoeller, T. Wahab, D. Jacob, R. Grunow, G. Kahlmeter. Clin. Microbiol. Infect., 2021, 27, 736e741. [CrossRef], [Google Scholar], [Publisher]
[5] Y.C. Chee, Radiol. Infect. Dis., 2020, 7, 31e34. [CrossRef], [Google Scholar], [Publisher]
[6] R. Seng, R. Phunpang, N. Saiprom, A. Dulsuk, C. Chewapreecha, J. Thaipadungpanit, EM. Batty, W. Chantratita, TE West, N Chantratita. Front. Microbiol. 2023, 14, 1103297. [CrossRef], [Google Scholar], [Publisher]
[7] V.K. Paul, A. Govindakarnavar, T. Meghan, L. Mark, S. Nalini, Asian Pac. J. Trop. Med., 2016, 9, 515–524. [CrossRef], [Google Scholar], [Publisher]
[8] M.S. Kim, D.H. Shin, Acta Crystallogr. F:Struct. Biol. Commun., 2009, 65, 1110-1112. [CrossRef], [Google Scholar], [Publisher]
[9] N.J. Harmer, J. Mol. Biol., 2010, 400, 379-392. [CrossRef], [Google Scholar], [Publisher]
[10] C. Potisap, M.A.W. Khan, A. Boonmee, J.L. Rodrigues, S. Wongratanacheewin, R.W. Sermswan, AMB Express, 2018, 8, 136. [CrossRef], [Google Scholar], [Publisher]
[11] P.L. Taylor, K.M. Blakely, G.P. De Leon, J.R. Walker, F. McArthur, E. Evdokimova, K. Zhang, M.A. Valvano, G.D. Wright, M.S. Junop, J. Biol. Chem., 2008, 283, 2835-2845. [CrossRef], [Google Scholar], [Publisher]
[12] M.J. Anderson, T.O. Crist, J.M. Chase, M. Vellend, B.D. Inouye, A.L. Freestone, N.J. Sanders, H.V. Cornell, L.S. Comita, K.F. Davies, Ecol. Lett., 2011, 14, 19-28. [CrossRef], [Google Scholar], [Publisher]
[13] P. Boottanun, C. Potisap, J.G. Hurdle, R.W. Sermswan, AMB express, 2017, 7, 16. [CrossRef], [Google Scholar], [Publisher]
[14] M.A. Abdalla, L.J. McGaw, Molecules, 2018, 23, 2080. [CrossRef], [Google Scholar], [Publisher]
[15] X. Jing, K. Jin, Med. Res. Rev., 2020, 40, 753–810. [CrossRef], [Google Scholar], [Publisher]
[16] T. Mogi, K. Kita, Cell. Mol. Life Sci. 2009, 66, 3821–3826. [CrossRef], [Google Scholar], [Publisher]
[17] F. Román-Hurtado, M. Sánchez-Hidalgo, J. Martín, F.J. Ortiz-López, D. Carretero-Molina, F. Reyes, O. Genilloud, Microorganisms, 2021, 9, 135. [CrossRef], [Google Scholar], [Publisher]
[18] N.J. Harmer, J. Mol. Biol., 2010, 400, 379. [CrossRef], [Google Scholar], [Publisher]
[19] G. Li, F. Yuan, B. Yao, Org. Lett. 2022, 24, 31, 5767–5771. [CrossRef], [Google Scholar], [Publisher]
[20] A.K. Oyebamiji, J.O. Babalola, K.A. Odelade, S.A. Akintelu, O.A. Nubi, H.O. Aworinde, E. Faboro, E.T. Akintayo, B. Semire, Eclét. Quím., 2023, 48, 54-80. [CrossRef], [Google Scholar], [Publisher]
[21] E. Pakizeh, M. Mohammadi, A. Mostafaei, Solid State Commun., 2023, 369, 115214. [CrossRef], [Google Scholar], [Publisher]
[22] M. Mohammadi, E. Pakizeh, Chin. J. Phys., 2023, In press. [CrossRef], [Google Scholar], [Publisher]
[23] M. Mohammadi, E. Pakizeh, Mater. Sci. Eng. B, 2023, 297, 116752. [CrossRef], [Google Scholar], [Publisher]
[24] D. Jacquemin, E.A. Perpe`te, I. Ciofini, C. Adamo, Acc. Chem. Res., 2008, 42, 326. [CrossRef], [Google Scholar], [Publisher]
[25] M. Pastore, E. Mosconi, F. de Angelis, M. Gratzel, J. Phys. Chem. C, 2010, 114, 7205-7212. [CrossRef], [Google Scholar], [Publisher]
[26] F. Iorhuna, A.A. Muhammad, T.A. Nyijime, M. Shuaibu. Adv. J. Chem. A, 2023, 6, 380-390. [CrossRef], [Publisher]
[27] S. Hadidi, M.H. Farzaei. Adv. J. Chem. A, 2023, 6, 123-140. [CrossRef], Publisher]
[28] J.P. Ameji, A.O. Ebune, I.W. Aderemi, A. Moyosore, G. Idah. Adv. J. Chem. A, 2023, 6, 92-104. [CrossRef], [Google Scholar], [Publisher]
[29] A.K. Oyebamiji, E.T. Akintayo, C.O. Akintayo, H.O. Aworinde, O.D. Adekunle, S.A. Akintelu, Ukr. Biochem. J. 2023, 95, 93-105. [CrossRef], [Google Scholar], [Publisher]
[30] B. Semire, A.K. Oyebamiji, O.A. Odunola, Sci. Afr., 2020, 7, e00287. [CrossRef], [Google Scholar], [Publisher]
[31] M. Abdul-Hammed, B. Semire, SA Adegboyega, AK Oyebamiji, T.A. Olowolafe. Phys. Chem. Res., 2020, 8, 296-310. [CrossRef], [Google Scholar], [Publisher]
[32] R.O. Oyewole, A.K. Oyebamiji, B. Semire, Heliyon, 2020, 6, e03926. [CrossRef], [Google Scholar], [Publisher]
[33] R.O. Adegoke, A.K. Oyebamiji, B. Semire, Data Brief, 2020, 31, 105963. [CrossRef], [Google Scholar], [Publisher]
[34] U.A. Çevik, I. Celik, A. Işık, R.R. Pillai, T.E. Tallei, R. Yadav, Y. Özkay, Z.A. Kaplancık, J. Mol. Struct. 2022, 1252, 132095. [CrossRef], [Google Scholar], [Publisher]
[35] H.A. Radwan, I. Ahmad, SR. Akand, M. Shaikh, R. Pawara, SN. Manjula, H. Patel, J. Mol. Struct. 2022, 1251, 131972. [CrossRef], [Google Scholar], [Publisher]
[36] D.R. Roe, T.E. Cheatham III, J. Chem. Theory Comput., 2013, 9, 3084–3095. [CrossRef], [Google Scholar], [Publisher]
[37]. M.D. Adeoye, A.K. Oyebamiji, M.A. Ashiru, R.A. Adigun, O.H. Olalere, B. Semire, Eclet. Quim. J., 2022, 47, 27-36. [CrossRef], [Google Scholar], [Publisher]
[38] S. A. Jamelah, H.A. Aljawhara, Y.S. Mary, Y.S. Mary, J. Mol. Struct., 2020, 1217, 128388. [CrossRef], [Google Scholar], [Publisher]
[39] B. Semire, A. Oyebamiji, M. Ahmad, Pak. J. Chem., 2012, 2, 166-173. [Google Scholar], [Publisher]
[40] E.A. Erazua, S.A. Akintelu, J.M. Adelowo, S.N. Odoemene, O.M. Josiah, S.F. Raheem, D.F. Latona, M.D. Adeoye, A.O. Esan, A.K. Oyebamiji, Trop. J. Nat. Prod. Res., 2021, 5, 2022-2029. [CrossRef], [Google Scholar]
[41] A.K. Oyebamiji, G.F. Tolufashe, O.M. Oyawoye, T.A. Oyedepo, B. Semire, J. Chem., 2020, 6735232. [CrossRef], [Google Scholar], [Publisher]