Research Article
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Year 2024, Volume: 8 Issue: 3, 122 - 128, 19.09.2024
https://doi.org/10.33435/tcandtc.1385998

Abstract

Project Number

None

References

  • [1] K. Ansari & C. Lal. Synthesis and biological activity of some heterocyclic compounds containing benzimidazole and beta-lactam moiety. Journal of Chemical Sciences, 121 (2009) 1017-1025.
  • [2] C. Kus, G. Ayhan-Kilcigil, B. C. Eke, & M. Işcan. Synthesis and antioxidant properties of some novel benzimidazole derivatives on lipid peroxidation in the rat liver. Archives of pharmacal research, 27 (2004) 156-163.
  • [3] Z. Ateş-Alagöz, C. Kuş, & T. Çoban. Synthesis and antioxidant properties of novel benzimidazoles containing substituted indole or 1, 1, 4, 4-tetramethyl-1, 2, 3, 4-tetrahydro-naphthalene fragments. Journal of enzyme inhibition and medicinal chemistry, 20 (2005) 325-331.
  • [4] H. Göker, S. Özden, S. Yıldız, & D. W. Boykin. Synthesis and potent antibacterial activity against MRSA of some novel 1, 2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidines. European journal of medicinal chemistry, 40 (2005) 1062-1069.
  • [5] S. Tahlan, S. Kumar, & B. Narasimhan, Antimicrobial potential of 1H-benzo [d] imidazole scaffold: a review. BMC Chemistry, 13 (2019) 1-27.
  • [6] K. G. Desai & K. R. Desai. Green route for the heterocyclization of 2-mercaptobenzimidazole into β-lactum segment derivatives containing–CONH–bridge with benzimidazole: Screening in vitro antimicrobial activity with various microorganisms. Bioorganic & medicinal chemistry, 14 (2006) 8271-8279.
  • [7] A. Patil, S. Ganguly, & S. Surana. A systematic review of benzimidazole derivatives as an antiulcer agent. Rasayan Journal of Chemistry, 1 (2008) 447-60.
  • [8] S. R. Mathapati, A. H. Jadhav, M. B. Swami, & J. K. Dawle. Zinc Sulfamate Catalyzed Efficient Selective Synthesis of Benzimidazole Derivatives under Ambient Conditions, Letters in Organic Chemistry, 16 (2019) 740-749.
  • [9] P. Preston. In Benzimidazole and congeneric tricyclic compounds (eds) A Weissberger and EC Taylor," New York: John Wiley and Sons, 2 (1980) 63-147.
  • [10] K. Hoffman. In Imidazole and its derivatives (ed.) A Weissberger," The chemistry of heterocyclic compounds (New York: Interscience Publishers, Inc) 247-317 (1953).
  • [11] V. V. Fedotov, V. L. Rusinov, E. N. Ulomsky, E. M. Mukhin, E. B. Gorbunov, & O. N. Chupakhin. Pyrimido [1, 2-a] benzimidazoles: synthesis and perspective of their pharmacological use, Chemistry of Heterocyclic Compounds, 57 (2021) 383-409.
  • [12] E. Ortiz-Prado, K. Simbaña-Rivera, L. Gomez-Barreno, M. Rubio-Neira, L. P. Guaman, & N. C. Kyriakidis. Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review, Diagnostic microbiology and infectious disease, 98 (2020) 115094,
  • [13] C. T. Chasapis, P.-S. A. Ntoupa, C. A. Spiliopoulou, & M. E. Stefanidou. Recent aspects of the effects of zinc on human health, Archives of toxicology, 94 (2020) 1443-1460.
  • [14] A. Walsh, D. J. Payne, R. G. Egdell, & G. W. Watson. Stereochemistry of post-transition metal oxides: revision of the classical lone pair model, Chemical Society Reviews, 40 (2011) 4455-4463.
  • [15] S. Kotru, M. Klimuntowski, H. Ridha, Z. Uddin, A. A. Askhar, & G. Singh, Electrochemical sensing: A prognostic tool in the fight against COVID-19, Trends in Analytical Chemistry, 136 (2021) 116198.
  • [16] M. Islam, S. Akash, & F. Islam Aovi. The mental health impact of COVID-19 pandemic in Dhaka, Academia Letters, (2021). doi: https://doi.org/10.20935/AL253.
  • [17] S. Gurunathan, M. Qasim, Y. Choi, J. T. Do, C. Park, & K. Hong. Antiviral potential of nanoparticles-can nanoparticles fight against coronaviruses, Nanomaterials, 10 (2020) 1645.
  • [18] K. P. Kepp. Consistent descriptions of metal–ligand bonds and spin-crossover in inorganic chemistry, Coordination Chemistry Reviews, 257 (2013) 196-209.
  • [19] H. Chermette. Density functional theory: a powerful tool for theoretical studies in coordination chemistry, Coordination Chemistry Reviews, 178 (1998) 699-721.
  • [20] S. Ekins, J. Mestres, & B. Testa. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling, British j\Journal of Pharmacology, 152 (2007) 9-20.
  • [21] H.M. Berman, J. Westbrook, Z. Feng, G. Gillil, T.N. Bhat, H. Weissig, I.N. Shindyalov, & P.E. Bourne, The Protein Data Bank (2000) Nucleic Acids Research 28: 235-242.
  • [22] F. M. Mashood Ahmaed, Sampath Chinnam, C. Malathi, K. Gurushantha, Ajoy Kumer, & S. Jadoun. Molecular Dynamics Simulation, QSAR, DFT, Molecular Docking, ADMET, and Synthesis of Ethyl 3-((5-Bromopyridin-2-yl)Imino)Butanoate Analogues as Potential Inhibitors of SARS-CoV-2, Polycycl. Aromat. Cmpd., 44 (2024) 294-312.
  • [23] J. W. Bhagyashri, N. W. Sandip, A. C. Vivekananda, Y. Merve, Ismail Celik, Mithun Rudrapal, Johra Khan, Sampath Chinnam, A. G. Aniket, & Vishnu S.N. Design, docking, MD simulation and in-silco ADMET prediction studies of novel indolebased benzamides targeting estrogen receptor alfa positive for effective breast cancer therapy, Pharamcia, 70 (2023) 307-316.
  • [24] N. Aatika, D. Jyothis, Sampath Chinnam, K. Kavita, S. Sonam, F. Joy, Mithun Rudrapal. Synthesis, DFT and In Silico Anti-COVID Evaluation of Novel Tetrazole Analogues, Polycycl. Aromat. Cmpd., 43 (2023) 1941-1956.
  • [25] M. N. Manjunatha, A. G. Dikundwar, & K. R. Nagasundara. Zn(II), Cd(II) and Hg(II) complexes with 1-(p-methoxybenzyl)-2- (p-methoxyphenyl)benzimidazole: Syntheses, structures and luminescence, Polyhedron, 30 (2011) 1299-1304.
  • [26] S. Dallakyan & A. J. Olson. Small-molecule library screening by docking with PyRx, in Chemical biology, ed: Springer, (2015) 243-250.
  • [27] J. Eberhardt, D. Santos-Martins, A. F. Tillack, & S. Forli. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling and Trott, O., & Olson, A. J. (2010).

Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors

Year 2024, Volume: 8 Issue: 3, 122 - 128, 19.09.2024
https://doi.org/10.33435/tcandtc.1385998

Abstract

A new SARS-CoV-2 virus and its variants including omicron created a pandemic situation and caused more deaths in worldwide prompted many researchers to explore potential drug candidates. In this connection, we explored the first-of-its-kind report on computational studies such as molecular docking, and ADMET properties of Zn(II) complexes. The studies revealed the novel zinc complexes have high binding affinities with the SARS-CoV-2 spike glycoprotein (6vxx) alpha variant (7EKF), beta variant (7ekg), gamma variant (7EKC), delta variant (7V8B), and the omicron variant (7T9J). Molecular docking results of RMSD for SARS-CoV-2 beta variant (7ekg) and gamma variant (7EKC) are within excellent chemical stability in their protein-ligand complex state and should be effective in the biological system. ADME studies provided the better results with no adverse effect of toxicity related AMES along with absence of hepatotoxicity and skin sensitization when compared to Molnupiravir drug and it has a greater hepatotoxicity. This study could open further exploration of these novel zinc complexes for SARS-CoV-2 inhibition.

Ethical Statement

None

Supporting Institution

M.S. Ramaiah Institute of Technology, India

Project Number

None

Thanks

Thank you.

References

  • [1] K. Ansari & C. Lal. Synthesis and biological activity of some heterocyclic compounds containing benzimidazole and beta-lactam moiety. Journal of Chemical Sciences, 121 (2009) 1017-1025.
  • [2] C. Kus, G. Ayhan-Kilcigil, B. C. Eke, & M. Işcan. Synthesis and antioxidant properties of some novel benzimidazole derivatives on lipid peroxidation in the rat liver. Archives of pharmacal research, 27 (2004) 156-163.
  • [3] Z. Ateş-Alagöz, C. Kuş, & T. Çoban. Synthesis and antioxidant properties of novel benzimidazoles containing substituted indole or 1, 1, 4, 4-tetramethyl-1, 2, 3, 4-tetrahydro-naphthalene fragments. Journal of enzyme inhibition and medicinal chemistry, 20 (2005) 325-331.
  • [4] H. Göker, S. Özden, S. Yıldız, & D. W. Boykin. Synthesis and potent antibacterial activity against MRSA of some novel 1, 2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidines. European journal of medicinal chemistry, 40 (2005) 1062-1069.
  • [5] S. Tahlan, S. Kumar, & B. Narasimhan, Antimicrobial potential of 1H-benzo [d] imidazole scaffold: a review. BMC Chemistry, 13 (2019) 1-27.
  • [6] K. G. Desai & K. R. Desai. Green route for the heterocyclization of 2-mercaptobenzimidazole into β-lactum segment derivatives containing–CONH–bridge with benzimidazole: Screening in vitro antimicrobial activity with various microorganisms. Bioorganic & medicinal chemistry, 14 (2006) 8271-8279.
  • [7] A. Patil, S. Ganguly, & S. Surana. A systematic review of benzimidazole derivatives as an antiulcer agent. Rasayan Journal of Chemistry, 1 (2008) 447-60.
  • [8] S. R. Mathapati, A. H. Jadhav, M. B. Swami, & J. K. Dawle. Zinc Sulfamate Catalyzed Efficient Selective Synthesis of Benzimidazole Derivatives under Ambient Conditions, Letters in Organic Chemistry, 16 (2019) 740-749.
  • [9] P. Preston. In Benzimidazole and congeneric tricyclic compounds (eds) A Weissberger and EC Taylor," New York: John Wiley and Sons, 2 (1980) 63-147.
  • [10] K. Hoffman. In Imidazole and its derivatives (ed.) A Weissberger," The chemistry of heterocyclic compounds (New York: Interscience Publishers, Inc) 247-317 (1953).
  • [11] V. V. Fedotov, V. L. Rusinov, E. N. Ulomsky, E. M. Mukhin, E. B. Gorbunov, & O. N. Chupakhin. Pyrimido [1, 2-a] benzimidazoles: synthesis and perspective of their pharmacological use, Chemistry of Heterocyclic Compounds, 57 (2021) 383-409.
  • [12] E. Ortiz-Prado, K. Simbaña-Rivera, L. Gomez-Barreno, M. Rubio-Neira, L. P. Guaman, & N. C. Kyriakidis. Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review, Diagnostic microbiology and infectious disease, 98 (2020) 115094,
  • [13] C. T. Chasapis, P.-S. A. Ntoupa, C. A. Spiliopoulou, & M. E. Stefanidou. Recent aspects of the effects of zinc on human health, Archives of toxicology, 94 (2020) 1443-1460.
  • [14] A. Walsh, D. J. Payne, R. G. Egdell, & G. W. Watson. Stereochemistry of post-transition metal oxides: revision of the classical lone pair model, Chemical Society Reviews, 40 (2011) 4455-4463.
  • [15] S. Kotru, M. Klimuntowski, H. Ridha, Z. Uddin, A. A. Askhar, & G. Singh, Electrochemical sensing: A prognostic tool in the fight against COVID-19, Trends in Analytical Chemistry, 136 (2021) 116198.
  • [16] M. Islam, S. Akash, & F. Islam Aovi. The mental health impact of COVID-19 pandemic in Dhaka, Academia Letters, (2021). doi: https://doi.org/10.20935/AL253.
  • [17] S. Gurunathan, M. Qasim, Y. Choi, J. T. Do, C. Park, & K. Hong. Antiviral potential of nanoparticles-can nanoparticles fight against coronaviruses, Nanomaterials, 10 (2020) 1645.
  • [18] K. P. Kepp. Consistent descriptions of metal–ligand bonds and spin-crossover in inorganic chemistry, Coordination Chemistry Reviews, 257 (2013) 196-209.
  • [19] H. Chermette. Density functional theory: a powerful tool for theoretical studies in coordination chemistry, Coordination Chemistry Reviews, 178 (1998) 699-721.
  • [20] S. Ekins, J. Mestres, & B. Testa. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling, British j\Journal of Pharmacology, 152 (2007) 9-20.
  • [21] H.M. Berman, J. Westbrook, Z. Feng, G. Gillil, T.N. Bhat, H. Weissig, I.N. Shindyalov, & P.E. Bourne, The Protein Data Bank (2000) Nucleic Acids Research 28: 235-242.
  • [22] F. M. Mashood Ahmaed, Sampath Chinnam, C. Malathi, K. Gurushantha, Ajoy Kumer, & S. Jadoun. Molecular Dynamics Simulation, QSAR, DFT, Molecular Docking, ADMET, and Synthesis of Ethyl 3-((5-Bromopyridin-2-yl)Imino)Butanoate Analogues as Potential Inhibitors of SARS-CoV-2, Polycycl. Aromat. Cmpd., 44 (2024) 294-312.
  • [23] J. W. Bhagyashri, N. W. Sandip, A. C. Vivekananda, Y. Merve, Ismail Celik, Mithun Rudrapal, Johra Khan, Sampath Chinnam, A. G. Aniket, & Vishnu S.N. Design, docking, MD simulation and in-silco ADMET prediction studies of novel indolebased benzamides targeting estrogen receptor alfa positive for effective breast cancer therapy, Pharamcia, 70 (2023) 307-316.
  • [24] N. Aatika, D. Jyothis, Sampath Chinnam, K. Kavita, S. Sonam, F. Joy, Mithun Rudrapal. Synthesis, DFT and In Silico Anti-COVID Evaluation of Novel Tetrazole Analogues, Polycycl. Aromat. Cmpd., 43 (2023) 1941-1956.
  • [25] M. N. Manjunatha, A. G. Dikundwar, & K. R. Nagasundara. Zn(II), Cd(II) and Hg(II) complexes with 1-(p-methoxybenzyl)-2- (p-methoxyphenyl)benzimidazole: Syntheses, structures and luminescence, Polyhedron, 30 (2011) 1299-1304.
  • [26] S. Dallakyan & A. J. Olson. Small-molecule library screening by docking with PyRx, in Chemical biology, ed: Springer, (2015) 243-250.
  • [27] J. Eberhardt, D. Santos-Martins, A. F. Tillack, & S. Forli. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling and Trott, O., & Olson, A. J. (2010).
There are 27 citations in total.

Details

Primary Language English
Subjects Molecular Imaging
Journal Section Research Article
Authors

Maralavadi Nagaraju Manjunatha This is me 0000-0001-7228-9147

Sampath Chinnam 0000-0002-5334-9076

Malathi Challa This is me 0000-0002-8985-9166

Sushmitha Nandakumar 0009-0002-8603-9725

Sridevi Chigurupati This is me 0000-0002-1081-2964

Harika Patnala This is me 0000-0002-8239-479X

Swetha Madamala This is me 0000-0002-3297-7647

Viola Fernandes This is me 0009-0002-7394-4785

Project Number None
Early Pub Date April 18, 2024
Publication Date September 19, 2024
Submission Date November 6, 2023
Acceptance Date March 3, 2024
Published in Issue Year 2024 Volume: 8 Issue: 3

Cite

APA Manjunatha, M. N., Chinnam, S., Challa, M., Nandakumar, S., et al. (2024). Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors. Turkish Computational and Theoretical Chemistry, 8(3), 122-128. https://doi.org/10.33435/tcandtc.1385998
AMA Manjunatha MN, Chinnam S, Challa M, Nandakumar S, Chigurupati S, Patnala H, Madamala S, Fernandes V. Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors. Turkish Comp Theo Chem (TC&TC). September 2024;8(3):122-128. doi:10.33435/tcandtc.1385998
Chicago Manjunatha, Maralavadi Nagaraju, Sampath Chinnam, Malathi Challa, Sushmitha Nandakumar, Sridevi Chigurupati, Harika Patnala, Swetha Madamala, and Viola Fernandes. “Molecular Docking Study, and ADMET Analysis for the Synthesized Novel Zn(II) Complexes As Potential SARS-CoV-2 Inhibitors”. Turkish Computational and Theoretical Chemistry 8, no. 3 (September 2024): 122-28. https://doi.org/10.33435/tcandtc.1385998.
EndNote Manjunatha MN, Chinnam S, Challa M, Nandakumar S, Chigurupati S, Patnala H, Madamala S, Fernandes V (September 1, 2024) Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors. Turkish Computational and Theoretical Chemistry 8 3 122–128.
IEEE M. N. Manjunatha, S. Chinnam, M. Challa, S. Nandakumar, S. Chigurupati, H. Patnala, S. Madamala, and V. Fernandes, “Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors”, Turkish Comp Theo Chem (TC&TC), vol. 8, no. 3, pp. 122–128, 2024, doi: 10.33435/tcandtc.1385998.
ISNAD Manjunatha, Maralavadi Nagaraju et al. “Molecular Docking Study, and ADMET Analysis for the Synthesized Novel Zn(II) Complexes As Potential SARS-CoV-2 Inhibitors”. Turkish Computational and Theoretical Chemistry 8/3 (September 2024), 122-128. https://doi.org/10.33435/tcandtc.1385998.
JAMA Manjunatha MN, Chinnam S, Challa M, Nandakumar S, Chigurupati S, Patnala H, Madamala S, Fernandes V. Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors. Turkish Comp Theo Chem (TC&TC). 2024;8:122–128.
MLA Manjunatha, Maralavadi Nagaraju et al. “Molecular Docking Study, and ADMET Analysis for the Synthesized Novel Zn(II) Complexes As Potential SARS-CoV-2 Inhibitors”. Turkish Computational and Theoretical Chemistry, vol. 8, no. 3, 2024, pp. 122-8, doi:10.33435/tcandtc.1385998.
Vancouver Manjunatha MN, Chinnam S, Challa M, Nandakumar S, Chigurupati S, Patnala H, Madamala S, Fernandes V. Molecular docking study, and ADMET analysis for the synthesized novel Zn(II) complexes as potential SARS-CoV-2 inhibitors. Turkish Comp Theo Chem (TC&TC). 2024;8(3):122-8.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)