Molecular Docking Study of Four Chromene Derivatives as Novel HIV-1 Integrase Inhibitors

Year 2019, Volume: 6 Issue: 2, 133 - 142, 15.06.2019

Nevin Arslan

https://doi.org/10.18596/jotcsa.478772

Cited By: 3

Abstract

Four ligands based on chromene derivatives have been docked into integrase of prototype foamy virus, which has a quite similar structural similarity with that of HIV-1 integrase using Autodock Vina (Vina). The docking scores for the derivatives are -7.3 kcal/mol, -7.5 kcal/mol, -6.9 kcal/mol, and -7.2 kcal/mol, respectively, which are comparable with that for Raltegravir (-10.7 kcal/mol). The docking results provide a detailed evidence for the interactions of four chromene derivatives. The results may lead to the design and development of new drug candidates against AIDS

Keywords

molecular docking

References

• 1) Borkotoky S. Docking Studies onHIV Integrase Inhibitors Based On Potential Ligand Binding Sites IJBB. 2012;2(3):21-29.
• 2) Ercan S. Docking and Molecular Dynamics Calculations of Some Previously Studied and Newly Designed Ligands to Catalytic Core Domain of HIV-1 Integrase and an Investigation to Effects of Conformational Changes of Protein on Docking Results. JOTCSA. 2017; 4(1): 243-270.
• 3) Vandamme A-M, Van Vaerenbergh K, De Clercq E. Anti-human immunodeficiency virus drug combination strategies. Antivir. Chem. Chemother.1998 ;9 :187-203.
• 4) Delelis O, Carayon K, Saïb A, Deprez E, Mouscadet J-F. Integrase and integration: biochemical activities of HIV-1 integrase. Retrovirology.2008 5:114.
• 5) Chen Julian C, Krucinski J, Miercke Larry J, Finer-Moore Janet S, Tang Ann H, Leavitt Andrew D, Stroud Robert M. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc. Natl. Acad. Sci U S A. 2000;97(15):8233-8.
• 6) Thomas M, Brady L. HIV integrase: A Target for AIDS therapeutics. Trends Biotechnol. 1997; 15: 167–172.
• 7) Islama Ataul Md, Pillay Tahir S. Structural requirements for potential HIV-integrase inhibitors identified using pharmacophore-based virtual screening and molecular dynamics studies. Mol. BioSyst. 2016; 12: 982-993.
• 8) Shaw-Reid Cathryn A, Munshi V, Graham P, Wolfe A, Witmer M, Danzeisen R, Olsen David B, Carrol Steven S, Embrey M, Wai John S, Miller Michael D, Cole James L, Hazuda Daria J. Inhibition of HIV-1 ribonuclease H by a novel diketo acid, 4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid. J. Biol Chem.2003; 278:2777–2780.
• 9) Grobler Jay A, Stillmock K, Hu B, Witmer M, Felock P, Espeseth Amy S, Wolfe A, Egbertson M, Bourgeois M, Melamed J, Wai John S, Young S, Vacca J, Hazuda Daria J .Diketo acid inhibitor mechanism and HIV-1 integrase: implications for metal binding in the active site of phosphotransferase enzymes. Proc. Natl. Acad. Sci USA. 2002; 99:6661–6666.
• 10) Rowley M.The discovery of Raltegravir, an integrase inhibitor for the treatment of HIV infection. Prog. Med. Chem .2008;46:1–28.
• 11) Summa V, Petrocchi A, Bonelli F, Crescenzi B, Donghi M, Ferrara M, Fiore F, Gardelli C, Gonzalez Paz O, Hazuda Daria J, Jones P, Kinzel O, Laufer R, Monteagudo E, Muraglia E, Nizi E, Orvieto F, Pace P, Pescatore G, Scarpelli R, Stillmock K, Witmer MV, Rowley M. Discovery of Raltegravir, a potent, selective orally bioavailable HIV-integrase inhititor for the treatment of HIV-AIDS infection. J. Med. Chem.2008 ;51:5843–5855.
• 12 ) Kumara Sivakumar P,.Patelb Chirag N, Jha Prakash C ,.Pandyab Himanshu A. Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding. Comp. Biol. Chem. 2017;71:117-128.
• 13) Sangeetha B, Muthukumaran R, Amutha R Pharmacophore modelling and electronic feature analysis of hydroxamic acid derivatives, the HIV integrase inhibitors. SAR QSAR Environ. Res. 2013; 24:753–771.
• 14) Bhatt H , Patel P, Pannecouque C. Discovery of HIV‐1 Integrase Inhibitors: Pharmacophore Mapping, Virtual Screening, Molecular Docking, Synthesis, and Biological Evaluation .Chem. Biol. Drug. Des.,2014;83:154–166.
• 15) Reddy Konda K, Singh Kumar S, Dessalew N, Tripathi Kumar S, Selvaraj C. Pharmacophore modelling and atom-based 3D-QSAR studies on N -methyl pyrimidones as HIV-1 integrase inhibitors. J. Enzyme Inhib. Med. Chem.2012; 27:339–347.
• 16) Telvekar Vikar N, Patel Kavitkumar N. Chem. Biol. Drug Des., 2011;78:150–160.
• 17) Gupta P, Sharma A, Garg P, Roy N QSAR study of curcumine derivatives as HIV-1 integrase inhibitors. Curr.Comput. Aided.Drug. Des.2013;9(1):141–150.
• 18)Frisch.M.J. , G.W. Trucks, H.B. Schlegel, G.E. Scuderia, M.A. Robb, J.R. Cheeseman, G.Scalmani, V. Barone, B. Mennucci, G.A. Petersson, et al.Gaussian 09, Revision a. 02.Gaussian Inc, Wallingford, CT, USA (2009).
• 19)Case Davi A, . Cheatham III Thomas E, Darden T, Gohlke H, Luo R, Merz Jr Kenneth M, Onufriev A, Simmerling C, Wang B and Woods R. The Amber biomolecular simulation programs. J. Computat. Chem. 2005;26, 1668-1688.
• 20) Trott O, Olson Arthur J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J.Com.Chem. 2010;31: 455–461
• 21) Daina A, Michielin O, Zoete V. a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 2017.3;7:42717
• 22) Hare S , Vos Ann M, Clayton Reginald F, Thuring Jan W, Cummings Maxwell D, Cherepanov P. Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.PNAS.2010.16;107(46):20057-62.