Density Functional Theory, Molecular Dynamics, and AlteQ Studies of Baimantuoluoamide A and Baimantuoluoamide B to Identify Potential Inhibitors of Mpro Proteins: a Novel Target for the Treatment of SARS COVID-19
- Authors: Gurushankar K.1,2, Jeyaseelan S.C.3,4, Grishina M.1, Sisvanto I.5, Tiwari R.6, Puspaningsih N.N.7
-
Affiliations:
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080, Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, 626126, Krishnankoil, Tamilnadu, India
- Post Graduate & Research Department of Physics, N.M.S.S.V.N. College, 625019, Madurai, Tamilnadu, India
- Post Graduate Department of Physics, Mannar Thirumalai Naciker College, 625004, Madurai, Tamilnadu, India
- Bioinformatic Laboratory, UCoE Research Center for Bio-Molecule Engineering Universitas Airlangga, 60115, Surabaya, Indonesia
- Department of Physics, Coordinator Research and Development Cell, Dr CV Raman University, 495113, Kargi Kota, Bilaspur, CG, India
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, 60115, Surabaya, Indonesia
- Issue: Vol 117, No 9-10 (5) (2023)
- Pages: 783-793
- Section: Articles
- URL: https://journals.rcsi.science/0370-274X/article/view/145223
- DOI: https://doi.org/10.31857/S1234567823100117
- EDN: https://elibrary.ru/COEQLL
- ID: 145223
Cite item
Abstract
COVID-19 has resulted in epidemic conditions over the world. Despite efforts by scientists from all over the world to develop an effective vaccine against this virus, there is presently no recognized cure for COVID-19. The most succeed treatments for various ailments come from natural components found in medicinal plants, which are also crucial for the development of new medications. This study intends to understand the role of the baimantuoluoamide A and baimantuoluoamide B molecules in the treatment of Covid19. Initially, density functional theory (DFT) used to explore their electronic potentials along with the Becke3–Lee–Yang–Parr (B3LYP) 6-311 +
basis set. A number of characteristics, including the energy gap, hardness, local softness, electronegativity, and electrophilicity, have also been calculated to discuss the reactivity of molecules. Using natural bond orbital, the title compound’s bioactive nature and stability were investigated. Further, both compounds potential inhibitors with main protease (Mpro) proteins, molecular dynamics simulations and AlteQ investigations also studied.
About the authors
K. Gurushankar
Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080, Chelyabinsk, Russia; Department of Physics, Kalasalingam Academy of Research and Education, 626126, Krishnankoil, Tamilnadu, India
Email: gurushankar01051987@gmail.com
S. Ch. Jeyaseelan
Post Graduate & Research Department of Physics, N.M.S.S.V.N. College, 625019, Madurai, Tamilnadu, India; Post Graduate Department of Physics, Mannar Thirumalai Naciker College, 625004, Madurai, Tamilnadu, India
Email: gurushankar01051987@gmail.com
M. Grishina
Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080, Chelyabinsk, Russia
Email: gurushankar01051987@gmail.com
I. Sisvanto
Bioinformatic Laboratory, UCoE Research Center for Bio-Molecule Engineering Universitas Airlangga, 60115, Surabaya, Indonesia
Email: gurushankar01051987@gmail.com
R. Tiwari
Department of Physics, Coordinator Research and Development Cell, Dr CV Raman University, 495113, Kargi Kota, Bilaspur, CG, India
Email: gurushankar01051987@gmail.com
N. N.T Puspaningsih
Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, 60115, Surabaya, Indonesia
Author for correspondence.
Email: gurushankar01051987@gmail.com
References
- S. Boopathi, A.B. Poma, and P. Kolandaivel, J. Biomol. Struct. Dyn. 39, 3409 (2021).
- K. Dhama, K. Sharun, R. Tiwari, M. Dadar, Y. S. Malik, K.P. Singh, and W. Chaicumpa, Hum. Vaccin. Immunother. 16, 1232 (2020).
- M. Cascella, M. Rajnik, A. Aleem, S.C. Dulebohn, and R.D. Napoli, 2022 Oct. 13. in: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing (2022).
- S. Beyersted, E.B. Casaro, and E. B. Range, Eur. J. Clin. Microbiol. Infect. Dis. 40, 905 (2021).
- R. Razali, H. Asis, and C. Budiman, Microorganisms 9, 2481 (2021).
- S.G. Katre, A. J. Asnani, K. Pratyush, N.G. Sakharkar, A.G. Bhope, K.T. Sawarkar, and V. S. Nimbekar, Futur. J. Pharm. Sci. 8, 36 (2022).
- C. Liu, Q. Zhou, Y. Li, L.V. Garner, S.P. Watkins, L. J. Carter, J. Smoot, A.C. Gregg, A.D. Daniels, S. Jervey, and D. Albaiu, ACS Cent. Sci. 25, 315 (2020).
- Z. Xu, C. Peng, Y. Shi, Z. Zhu, K. Mu, and X. Wang, https://doi.org/10.1101/2020.01.27.921627 (2020).
- N. Bohr, Dialectica 2, 312 (1948).
- H. Rimac, M.A. Grishina, and V.A. Potemkin, Future Med. Chem. 12, 1387 (2020).
- S. Kandagalla, H. Rimac, V.A. Potemkin, and M.A. Grishina, Future Med. Chem. 13, 863 (2021).
- H. Rimac, M. Grishina, and V. Potemkin, J. Chem. Inf. Model 61, 1801 (2021).
- N. Palko, M. Grishina, and V. Potemkin, Molecules 26, 3960 (2021).
- M. Akram, I.M. Tahir, S.M.A. Shah, Z. Mahmood, A. Altaf, K. Ahmad, N. Munir, M. Daniyal, S. Nasir, and H. Mehboob, Phytother. Res. 32, 811 (2018).
- Y. Zhao, Y. Wu, and M. Wang, in: Handbook of Food Chemistry, ed. by P. Cheung and B. Mehta, Springer, Berlin, Heidelberg (2015).
- V. Kumar, V. Bhatt, and N. Kumar, Studies in Natural Products Chemistry 56, 287 (2018).
- Y. Xiao, Y. Yan, L. Chang, H. Ji, H. Sun, S. Song, K. Feng, A. Nuermaimaiti, Z. Lu, and L. Wang, Antiviral Res. 212, 105558 (2023).
- K. Gurushankar, H. Rimac, V. Potemkin, and M. Grishina, J. Mol. Struct. 1230, 129925 (2021).
- B.R. Beck, B. Shin, Y. Choi, S. Park, and K. Kang, Comput. Struct. Biotechnol. J. 18, 784 (2020).
- A.A. Elfiky, Life Sci. 253, 117592e (2020).
- A. Belhassan, S. Chtita, H. Zaki, T. Lakhlifi, and M. Bouachrine, Bioinformation 16, 404 (2020).
- N. Muralidharan, R. Sakthivel, D. Velmurugan, and M.M. Gromiha, J. Biomol. Struct. Dyn. 39, 2673 (2021).
- S. Vardhan and S.K. Sahoo, Comput. Biol. Med. 124, 103936 (2020).
- P. Calligari, S. Bobone, G. Ricci, and A. Bocedi, Viruses 12, 445 (2020).
- L. S. Braga, D.H. Leal, K. Kuca, and T.C. Ramalho, Curr. Org. Chem. 24, 314 (2020).
- R. Sahu, R.K. Mohapatra, S. I. Al-Resayes, D. Das, P.K. Parhi, S. Rahman, L. Pintilie, M. Kumar, M. Azam, and A. Ansari, J. Saudi Chem. Soc. 25, 101193 (2021).
- F. Pereira, K. Xiao, D.A. Latino, C. Wu, Q. Zhang, and J. Aires-de-Sousa, J. Chem. Inf. Model 57, 11 (2017).
- A. Karuppasamy, K.G. Krishnan, M.P. Velayutham Pillai, and C. Ramalingan, J. Mol. Struct. 1128, 674 (2017).
- N. Rasool, F. Yasmin, S. Sahai, W. Hussain, H. Inam, and A. Arshad, Chem. Phys. Lett. 771, 138463 (2021).
- M.G. Khrenova, V.G. Tsirelson, and A.V. Nemukhin, Phys. Chem. Chem. Phys. 22, 19069 (2020).
- K. Arafet, N. Serrano-Aparicio, A. Lodola, A. J. Mulholland, F.V. Gonz'alez, K. 'Swiderek, and V. Moliner, Chem. Sci. 12, 1433 (2021).
- C.M. Coleman, J.M. Sisk, R.M. Mingo, E.A. Nelson, J.M. White, and M. B. Frieman, J. Virol. 90, 8924 (2016).
- R. Dennington, T. Keith, and J. Milam, Shawnee Mission KS, 2009. Version 5.
- N.M. O'Boyle, A. L. Tenderholt, and K.M. Langner, J. Compt. Chem. 29, 839 (2008).
- K. Gholivand, F. Mohammadpanah, M. Pooyan, and R. Roohzadeh, Journal of Molecular Structure 1248, 131481 (2022).
- H. S. Sumrra, A.U. Hassan, M. Imran, M. Khalid, E.U. Mughal, M.N. Zafar, M.N. Tahir, M.A. Raza, and A.A.C. Braga, Appl. Organomet. Chem. 34, e5623 (2020).
- A. Ali, M. Khalid, S. Abid, J. Iqbal, M.N. Tahir, A.R. Raza, J. Zukerman-Schpector, and M.W. Paixao, Appl. Organomet Chem. 34, e5399 (2020).
- Y. S. Mary, G. Yalcin, Y. S. Mary, K. S. Resmi, R. Thomas, T. �Onkol, E.N. Kasap, and I. Yildiz, Chemical Papers 74, 1957 (2020).
- S. Christopher Jeyaseelan and A. Milton Franklin Benial, J. Mol. Recognit. 34, e2872 (2021).
- M. Pradeep Kumar, K. Kranthi Raj, D. Ramachandran, M.N. S. Pavan Kumar, Radha Vaddavalli, and P. Jhansi Lakshmi, J. Proteomics Bioinform. 3, 305 (2010).
- A. Kumari, V. S. Rajput, P. Nagpal, H. Kukrety, S. Grover, and A. Grover, J. Biomol. Struct. Dyn. 40, 4987 (2022).
- B. Nutho, S. Pengthaisong, A. Tankrathok, V. S. Lee, J.R.K. Cairns, T. Rungrotmongkol, and S. Hannongbua, Biomolecules 10, 1 (2020).
- A. Bornot, C. Etchebest, and A.G. De Brevern, Proteins Struct. Funct. Bioinforma. 79, 839 (2011).
- T. Joshi, T. Joshi, P. Sharma, S. Chandra, and V. Pande, J. Biomol. Struct. Dyn. 39, 823 (2021).
- B. Nutho, P. Mahalapbutr, K. Hengphasatporn, N.C. Pattaranggoon, N. Simanon, Y. Shigeta, S. Hannongbua, and T. Rungrotmongkol, Biochemistry 59, 1769 (2020).
- R. Suno, S. Lee, S. Maeda, S. Yasuda, K. Yamashita, K. Hirata, S. Horita, M. S. Tawaramoto, H. Tsujimoto, T. Murata, M. Kinoshita, M. Yamamoto, B.K. Kobilka, N. Vaidehi, S. Iwata, and T. Kobayashi, Nat. Chem. Biol. 14, 1150 (2018).
- P. Mahalapbutr, N. Darai, W. Panman, A. Opasmahakul, N. Kungwan, S. Hannongbua, and T. Rungrotmongkol, Sci. Rep. 9, 1 (2019).
- B.R. Miller, T.D. McGee, J.M. Swails, N. Homeyer, H. Gohlke, and A.E. Roitberg, J. Chem. Theory Comput. 8, 3314 (2012).
- C. Wang, D. Greene, L. Xiao, R. Qi, and R. Luo, Front. Mol. Biosci. 4, 1 (2018).
- U. Ryde and P. Soderhjelm, Chem. Rev. 116, 5520 (2016).
- V.A. Potemkin and M.A. Grishina, J. Comput. Aided Mol. Des. 22, 489 (2008).
- M. Grishina, O. Bolshakov, A. Potemkin, and V. Potemkin, Comput. Theor. Chem. 1091, 122 (2016).
- R. F.W. Bader, Chem. Rev. 91, 893 (1991).
- V. Naumovich, M. Grishina, J. Novak, P. Pathak, V. Potemkin, M. Shahbaaz, and M.H. Abdellattif, J. Biomol. Struct. Dyn. 40, 4775 (2022).