• Home
  • New Imidazo[4,5-a] Acridine: Synthesis and Studying the Molecular Dynamics Simulation of Its Interaction with the Topoisomerase Enzyme

Share To

Article Url


Manuscript ID : JCHR-2304-1724 (R2) Visit : 171 Page: 159 - 166

10.22034/jchr.2023.1984058.1724

Article Type: Original Research

New Imidazo[4,5-a] Acridine: Synthesis and Studying the Molecular Dynamics Simulation of Its Interaction with the Topoisomerase Enzyme

Subject Areas : Journal of Chemical Health Risks

Maryam Toosi 1 , Mehdi Pordel 2 , Mohammad Reza Bozorgmehr 3

1 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
2 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
3 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

Received: 2023-04-17 Accepted : 2023-09-09 Published : 2024-03-01

Keywords: Molecular modeling, aromaticity, Imidazo[4, 5-a]acridine, Topoisomerase,

Abstract :

Acridine and imidazole were combined and synthesized 3,8-disubstituted-propyl-3H-imidazo[4,5-a]acridine-11-carbonitrile, as a new derivative. The interaction of this new compound with the topoisomerase enzyme was studied by molecular dynamics simulation. The 3,8-disubstituted-3H-imidazo[4,5-a]acridine-11-carbonitrile structure has been optimized by the density functional theory method. According to the results obtained from the molecular dynamics simulation, Arg364, Lys532, Asp533, Tyr537, Arg590, Cys630, Asn631, Gln633 and Adenine11 interact with the ligand by hydrophobic interactions and Arg488 and Adenine12 interact with the ligand by hydrogen bond interactions. Due to the fact that some of these residues, Arg488 and Arg590 are located in the enzyme active site, the new ligand appears to be inhibitory effect. Also, the calculation of the Harmonic Oscillator Model for Aromaticity (HOMA) index showed that the 5-membered ring of ligand and the 6-membered ring attached to the 5-membered ring had more reactivity with the enzyme. The contribution of charged residues in the binding free energy of the ligand is greater than the uncharged residues.

References:


  1. Abd-Allah O., Abdelhamid A., Mohamed S., 2015. Synthesis and Anti-inflammatory Study of Novel N-substituted Hydro-acridine-1, 8-diones and Bis-hexahydroacridine-1, 8-dione Derivatives. Med Chem, S2:004.
    2.
  2. Mallu L., Thirumalai D., Asharani I.V., 2017. One‐pot cascade synthesis and in vitro evaluation of anti-inflammatory and antidiabetic activities of S methylphenyl substituted acridine‐1, 8‐diones. Chemical Biology & Drug Design. 90(4), 520-526.
    3.
  3. Daghigh L.R., Pordel M., Davoodnia A., Jajarmi M., 2015. Synthesis, antiviral, and cytotoxic investigation of imidazo [4, 5-a] acridones. Medicinal Chemistry Research. 24(11), 3912-3919.
    4.
  4. Kaya M., Yıldırır Y., Çelik G.Y., 2015. Synthesis, characterization, and in vitro antimicrobial and antifungal activity of novel acridines. Pharmaceutical Chemistry Journal. 48(11), 722-726.
    5.
  5. Nowak K., 2017. Chemical structures and biological activities of bis-and tetrakis-acridine derivatives: A review. Journal of Molecular Structure. 1146, 562-570.
    6.
  6. Fahrenholtz C.D., Ding S., Bernish B.W., Wright M.L., Zheng Y., Yang M., Yao X., Donati G.L., Gross M.D., Bierbach U., 2016. Design and cellular studies of a carbon nanotube-based delivery system for a hybrid platinum-acridine anticancer agent. Journal of Inorganic Biochemistry. 165, 170-180.
    7.
  7. Yu Z., Han M., Cowan J.A., 2015. Toward the Design of a Catalytic Metallodrug: Selective Cleavage of G Quadruplex Telomeric DNA by an Anticancer Copper–Acridine–ATCUN Complex. Angewandte Chemie. 127(6), 1921-1925.
    8.
  8. Hu Y., Shen Y., Wu X., Tu X., Wang G.X., 2018. Synthesis and biological evaluation of coumarin derivatives containing imidazole skeleton as potential antibacterial agents. European Journal of Medicinal Chemistry. 143, 958-969.
    9.
  9. Shankar B., Jalapathi P., Valeru A., Kumar A.K., Saikrishna B., rao Kudle K., 2017. Synthesis and biological evaluation of new 2-(6-alkyl-pyrazin-2-yl)-1H-benz [d] imidazoles as potent anti-inflammatory and antioxidant agents. Medicinal Chemistry Research. 26(9), 1835-1846.
    10.
  10. Posfai D., Eubanks A.L., Keim A.I., Lu K.Y., Wang G. Z., Hughes P.F., Kato N., Haystead T. A., Derbyshire E.R., 2018. Identification of Hsp90 inhibitors with anti-Plasmodium activity. Antimicrobial Agents and Chemotherapy. 62(4).
    11.
  11. Corcoran J., Lange A., Cumming R.I., Owen S.F., Ball J.S., Tyler C.R., Winter M.J., 2014. Bioavailability of the imidazole antifungal agent clotrimazole and its effects on key biotransformation genes in the common carp (Cyprinus carpio). Aquatic Toxicology. 152, 57-65.
    12.
  12. Ebadian B., Fathi A., Savoj M., 2021. In Vitro Evaluation of the Effect of Different Luting Cements and Tooth Preparation Angle on the Microleakage of Zirconia Crowns. International Journal of Dentistry. 8461579.
    13.
  13. Zechiedrich E.L., Osheroff N., 1990. Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers, The EMBO Journal. 9(13), 4555-4562.
    14.
  14. Abolhasani M., Givehchian P., Fathi A., Goudarzi S., 2021. Relationship of Life Satisfaction and Satisfaction with Fixed Implant-Supported Prostheses in the Elderly. Journal of Iranian Dental Association. 33(1), 17-21
    15.
  15. Champoux J.J., 2001. DNA topoisomerases: structure, function, and mechanism. Annual Review of Biochemistry. 70(1), 369-413.
    16.
  16. Khalil M.S., Ebrahim H.A., Pasalar P., Yaghmaei P., Hayati R.N., 2012. Reflection on design and testing of pancreatic alpha-amylase inhibitors: an in silico comparison between rat and rabbit enzyme models, DARU Journal of Pharmaceutical Science. 20,77
    17.
  17. Preston P.N., 1981Benzimidazoles and Cogeneric Tricyclic Compounds, Volume 40(1). Wiley: New Jersey,.
    18.
  18. Maroofi V., Pordel M., Chegini H., Ramezani S., 2015. Synthesis, Spectral Studies and Quantum-Chemical Investigations on the Powerful Fluorophores: Imidazo [4, 5-a] acridines. Journal of Fluorescence. 25(5), 1235-1243.
    19.
  19. Fathi A., Giti R., Farzin M., 2018. How different influential factors affect the color and translucency of Y-ZTP: A review of the literature. Annals of Dental Specialty. 6(3), 338-341.
    20.
  20. Stewart L., Redinbo M.R., Qiu X., Hol W.G., Champoux J.J., 1998. A model for the mechanism of human topoisomerase I. Science. 279(5356), 1534-1541.
    21.
  21. Chillemi G., Redinbo M., Bruselles A., Desideri A., 2004. Role of the linker domain and the 203–214 N-terminal residues in the human topoisomerase I DNA complex dynamics. Biophysical Journal. 87(6), 4087-4097.
    22.
  22. Fathi A., Farzin M., Giti R., Kalantari M.H., 2019. Effects of number of firings and veneer thickness on the color and translucency of 2 different zirconia-based ceramic systems. The Journal of Prosthetic Dentistry. 122(6), 565-571.
    23.
  23. Afshar m., Ranjineh K.R., Ahmadi R., Nakhaei M.M., 2021. In Silico Adsorption of Lomustin anticancer drug on the surface of Boron Nitride nanotube. Chem Rev Lett. 4, 178-184.
    24.
  24. Ghasemi E., Fathi A. H., Parvizinia S., 2019. Effect of three disinfectants on dimensional changes of different impression materials. Journal of Iranian Dental Association. 31(3), 169-176.
    25.
  25. Schmidt M.W., Baldridge K. K., Boatz J. A., Elbert S. T., Gordon M. S., Jensen J. H., Koseki S., Matsunaga N., Nguyen K. A., Su S., 1993. General atomic and molecular electronic structure system. Journal of Computational Chemistry. 14(11), 1347-1363.
    26.
  26. Zoete V., Cuendet M.A., Grosdidier A., Michielin O., 2011. SwissParam: a fast force field generation tool for small organic molecules. Journal of Computational Chemistry. 32(11), 2359-2368.
    27.
  27. Luenberger D.G., Ye Y., 1984. Linear and nonlinear programming., Springer: New York.
    28.
  28. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G., 1995. A smooth particle mesh Ewald method. The Journal of Chemical Physics. 103(19), 8577-8593.
    29.
  29. Kaviani R., 2022. Use Bioethanol as a Clean and Cost-Effective Fuel. Journal of Engineering in Industrial Research. 3(2), 147-152.
    30.
  30. Hess B., Bekker H., Berendsen H.J., Fraaije J.G., 1997. LINCS: a linear constraint solver for molecular simulations. Journal of Computational Chemistry. 18(12), 1463-1472.
    31.
  31. Jedariforoughi A., 2022. Bioreactor based cancer therapy. Doctmedico Journal. 2(2), 201-206.
    32.
  32. Miyamoto S., Kollman P.A., 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry. 13(8), 952-962.
    33.
  33. Bussi G., Donadio D., Parrinello M., 2007. Canonical sampling through velocity rescaling. The Journal of chemical physic. 126(1), 014101.
    34.
  34. Monirifard R., Abolhasani M., Tahani B., Fathi A., Choobdaran A., 2019. Relationship of Personality Traits and Patient Satisfaction with Fixed Implant Prosthodontic Treatments. Journal of Iranian Dental Association. 31(4), 182-188.
    35.
  35. Lei H., Wu C., Liu H., Duan Y., 2007. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proceedings of the National Academy of Sciences. 104(12), 4925-4930.
    36.
  36. Wallace A.C., Laskowski R.A., Thornton J.M., 1995. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection. 8(2), 127-134.
    37.
  37. Shirzadi P., Vaziri P., Lo Han K., Johnson A., 2022. Investigating the Impact of Energy on Iran's National Security. Journal of Engineering in Industrial Research. 3(2), 161-167.
    38.
  38. Kruszewski J., Krygowski T., 1972. Definition of aromaticity basing on the harmonic oscillator model. Tetrahedron Letters. 13(36), 3839-3842.
    39.
  39. Krygowski T.M., 1993. Crystallographic studies of inter-and intramolecular interactions reflected in aromatic character of pi-electron systems. Journal of Chemical Information and Computer sciences. 33(1), 70-78.
    40.
  40. Shirzadi P., 2022. Optimization and Simulation of Process Unit in the Chemical Industry. Journal of Engineering in Industrial Research. 3(2), 153-160.
    41.
  41. Lu T., Chen F., 2012. Multiwfn: a multifunctional wavefunction analyzer. Journal of Computational Chemistry. 33(5), 580-592.
    42.
  42. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33(12), 889-897.
    43.
  43. Kumari R., Kumar R., Consortium O.S.D.D., Lynn A., 2014. g_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling. 54(7), 1951-1962.
    44.

Related articles

The rights to this website are owned by the Raimag Press Management System.
Copyright © 2021-2024

Home| Login| About Us| Contact Us|
[فارسی] [العربية] [fa] [ar]