Main Article Content

Abstract

In present work, 1-methylnicotinamide (1-MNA) has been investigated theoretically by density functional theory approach and investigated its vibrational spectroscopy. To complete the structure optimization, determination of vibrational frequencies and other valuable parameters, B3LYP method used with the 6-311++G(d,p) basis set. Atoms in molecules theory (AIM) had been used to evaluate ellipticity, isosurface projection by electron localization function and binding energies. The IR and Raman spectra have also been calculated computationally. NBO analysis employed to determine interactions of donor and acceptor. Fukui functions and molecular electrostatic potential (MEP) showed reactive regions of the molecule. UV-vis spectrum calculated using TD-DFT/PCM methods with different solvents. Thermodynamic properties like free energy, enthalpy and entropy with various temperature were calculated. By the use of the electrophilicity index, the probability of the bioactive nature of the molecule was proved theoretically. Protein-ligand interactions calculated and established by molecular docking. The biological investigations for druglikeness also employed for the (1-MNA).

Keywords

1-Methylnicotinamide Density functional theory Natural bond orbital Molecular docking Ellipticity Molecular electrostatic potential.

Article Details

How to Cite
Kumar, M., Singh, S., Siddiqui, N., & Javed, S. (2021). Quantum Computational, Spectroscopic, NHO and Molecular Docking Studies on 1-Methyl-nicotinamide (MNA): An Antithrombotic, Anti-inflammatory, Gastroprotective and Vasoprotective Compound. Asian Journal of Organic & Medicinal Chemistry, 6(2), 128–140. https://doi.org/10.14233/ajomc.2021.AJOMC-P326

References

  1. J. Gebicki, A. Sysa-Jedrzejowska, J. Adamus, A. Wozniacka, M. Rybak and J. Zielonka, 1-Methylnicotinamide: A Potent Anti-inflammatory Agent of Vitamin Origin, Pol. J. Pharmacol., 55, 109 (2003).
  2. S. Chlopicki, J. Swies, A. Mogielnicki, W. Buczko, M. Bartus, M. Lomnicka, J. Adamus and J. Gebicki, 1-Methylnicotinamide (MNA), A Primary Metabolite of Nicotinamide, Exerts Anti-thrombotic Activity Mediated by a Cyclooxygenase-2/Prostacyclin Pathway, Br. J. Pharmacol., 152, 230 (2000); https://doi.org/10.1038/sj.bjp.0707383
  3. K. Bryniarski, R. Biedron, A. Jakubowski, J. Marcinkiewicz and S. Chlopicki, Anti-inflammatory Effect of 1-Methylnicotinamide in Contact Hypersensitivity to Oxazolone in Mice; Involvement of Prostacyclin, Eur. J. Pharmacol., 578, 332 (2008); https://doi.org/10.1016/j.ejphar.2007.09.011
  4. T.B. Domagala, A. Szeffler, L.W. Dobrucki, J. Dropinski, S. Polanski, M. Leszczynska-Wiloch, K. Kotula-Horowitz, J. Wojciechowski, L. Wojnowski, A. Szczeklik and L. Kalinowski, Nitric Oxide Production and Endothelium-Dependent Vasorelaxation Ameliorated by N1-Methylnicotinamide in Human Blood Vessels, Hypertension, 59, 825 (2012); https://doi.org/10.1161/HYPERTENSIONAHA.111.183210
  5. K. Strom, D.M. Alamo, F. Ottosson, A. Edlund, L. Hjort, S.W. Jörgensen, P. Almgren, Y. Zhou, M. Martin-Rincon, C. Ekman, A. Pérez-López, O. Ekström, I. Perez-Suarez, M. Mattiasson, P. de Pablos-Velasco, N. Oskolkov, E. Ahlqvist, N. Wierup, L. Eliasson, A. Vaag, L. Groop, K.G. Stenkula, C. Fernandez, J.A.L. Calbet, H.-C. Holmberg and O. Hansson, N1-Methylnicotinamide is a Signalling Molecule Produced in Skeletal Muscle Coordinating Energy Metabolism, Sci. Rep., 8, 3016 (2018); https://doi.org/10.1038/s41598-018-21099-1
  6. M. Bartus, M. Fomnicka, R.B. Kostogrys, P. Kazmierczak, C. Watala, E.M. Slominska, R.T. Smoleñski, P.M. Pisulewski, J. Adamus, J. Gêbicki and S. Chlopicki, 1-Methylnicotinamide (MNA) Prevents Endothelial Dysfunction in Hypertriglyceridemic and Diabetic Rats, Pharmacol. Rep., 60, 127 (2008).
  7. A. Blazejczyk, M. Switalska, S. Chlopicki, A. Marcinek, J. Gebicki, M. Nowak, A. Nasulewicz-Goldeman and J. Wietrzyk, 1-Methyl-nicotinamide and its Structural Analog 1,4-dimethylpyridine for the Prevention of Cancer Metastasis, J. Exp. Clin. Cancer Res., 35, 110 (2016); https://doi.org/10.1186/s13046-016-0389-9
  8. J. Schmeisser, Mansfeld, D. Kuhlow, S. Weimer, S. Priebe, I. Heiland, M. Birringer, M. Groth, A. Segref, Y. Kanfi, N.L. Price, S. Schmeisser, S. Schuster, A.F.H. Pfeiffer, R. Guthke, M. Platzer, T. Hoppe, H.Y. Cohen, K. Zarse, D.A. Sinclair and M. Ristow, Role of Sirtuins in Lifespan Regulation is Linked to Methylation of Nicotinamide, Nat. Chem. Biol., 9, 693 (2013); https://doi.org/10.1038/nchembio.1352
  9. Menavitin Produkte, die das Molekül 1-MNA beinhalten: das Novel Food mit natürlicher Intelligenz, Startup Valley (in German) (2020).
  10. G.A. Petersson, A. Bennett, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley and J. Mantzaris, A Complete Basis Set Model Chemistry. I. The Total Energies of Closed-shell Atoms and Hydrides of the First-Row Elements, J. Chem. Phys., 89, 2193 (1988); https://doi.org/10.1063/1.455064
  11. G.A. Petersson and M.A. Al-Laham, A Complete Basis Set Model Chemistry. II. Open-Shell Systems and the Total Energies of the First-Row Atoms, J. Chem. Phys., 94, 6081 (1991); https://doi.org/10.1063/1.460447
  12. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria and M.A. Robb, R. Cheeseman, J. Montgomer, T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W.Wong, C. Gonzalez, J.A. Pople, Gaussian 03, Revision C. 02, Gaussian Inc., Wallingford, CT (2004).
  13. F. Neese, The ORCA Program System, WIREs Comput. Mol. Sci., 2, 73 (2012); https://doi.org/10.1002/wcms.81
  14. M.H. Jomroz, Vibrational Energy Distribution Analysis, VEDA4, Warsaw (2004).
  15. A. Daina, O. Michielin and V. Zoete, SwissADME: A Free Web Tool to Evaluate Pharmacokinetics, Drug-likeness and Medicinal Chemistry Friendliness of Small Molecules, Sci. Rep., 7, 42717 (2017); https://doi.org/10.1038/srep42717
  16. T. Lu and F. Chen, Multiwfn: A Multifunctional Wavefunction Analyzer, J. Comput. Chem., 33, 580 (2012); https://doi.org/10.1002/jcc.22885
  17. Origin 8.0, OriginLab Corp., Northampton, MA (2007).
  18. C.S. Abraham, J.C. Prasana, S. Muthu, F. Rizwana B and M. Raja, Quantum Computational Studies, Spectroscopic (FT-IR, FT-Raman and UV–Vis) Profiling, Natural Hybrid Orbital and Molecular Docking Analysis on 2,4-Dibromoaniline, J. Mol. Struct., 1160, 393 (2018); https://doi.org/10.1016/j.molstruc.2018.02.022
  19. G. Socrates, Infrared and Raman Characteristic Group Frequencies, Table and Charts, Wiley: Chichester, Ed. 3 (2001).
  20. L.J. Bellamy, The Infrared Spectra of Complex Molecules, Chapman and Hall: London, vol. 2 (1980).
  21. M. Tsuboi, 15N Isotope Effects on the Vibrational Frequencies of Aniline and Assignments of the Frequencies of its nh2 Group, Spectrochim. Acta, 16A, 505 (1960); https://doi.org/10.1016/0371-1951(60)80046-X
  22. G. Varsanyi, Assignments for Vibrational Spectra of Seven Hundred Benzene Derivatives, Academia Kiado: Budapest, vols. 1 and 2 (1973).
  23. G. Varsanyi, Vibrational Spectra of Seven Hundred Benzene Derivatives, Academic Press: New York (1969).
  24. L.J. Bellamy, The Infrared Spectra of Complex Molecules, John Wiley: New York (1959).
  25. A.J. Barnes, M.A. Majid, M.A. Stuckey, P. Gregory and C.V. Stead, The Resonance Raman Spectra of Orange II and Para Red: Molecular Structure and Vibrational Assignment, Spectrochim. Acta A Mol. Biomol. Spectrosc., 41, 629 (1985); https://doi.org/10.1016/0584-8539(85)80050-7
  26. S. Pinchas, D. Samuel and M. Weiss-Broday, The Infrared Absorption of 18O-labelled Benzamide, J. Chem. Soc., 1688 (1961); https://doi.org/10.1039/jr9610001688
  27. J.S. Murry and K. Sen, Molecular Electrostatic Potential Concepts and Applications, Elsevier: Amesterdam (1996).
  28. O. Haji-Ghassemi, R.J. Blackler, N.M. Young and S.V. Evans, Antibody Recognition of Carbohydrate Epitopes, Glycobiology, 25, 920 (2015); https://doi.org/10.1093/glycob/cwv037
  29. J. Poater, M. Duran, M. Solà and B. Silvi, Theoretical Evaluation of Electron Delocalization in Aromatic Molecules by Means of Atoms in Molecules (AIM) and Electron Localization Function (ELF) Topological Approaches, Chem. Rev., 105, 3911 (2005); https://doi.org/10.1021/cr030085x
  30. H. Sekino and R.J. Bartlett, Hyperpolarizabilities of the Hydrogen Fluoride Molecule: A Discrepancy Between Theory and Experiment?, J. Chem. Phys., 84, 2726 (1986); https://doi.org/10.1063/1.450348
  31. J. Henriksson, T. Saue and P. Norman, Quadratic Response Functions in the Relativistic Four-component Kohn-Sham Approximation, J. Chem. Phys., 128, 024105 (2008); https://doi.org/10.1063/1.2816709
  32. J.P. Hermann, D. Ricard and J. Ducuing, Optical Nonlinearities in Conjugated Systems: b-Carotene, Appl. Phys. Lett., 23, 178 (1973); https://doi.org/10.1063/1.1654850
  33. S. Debrus, H. Ratajczak, J. Venturini, N. Pincon, J. Baran, J. Barycki, T. Glowiak and A. Pietraszko, Novel Nonlinear Optical Crystals of Noncentrosymmetric Structure Based on Hydrogen Bonds Interactions Between Organic and Inorganic Molecules, Synth. Met., 127, 99 (2002); https://doi.org/10.1016/S0379-6779(01)00607-5
  34. C. Cassidy, J.M. Halbout, W. Donaldson and C.L. Tang, Nonlinear Optical Properties of Urea, Opt. Commun., 29, 243 (1979); https://doi.org/10.1016/0030-4018(79)90027-0
  35. C.S. Abraham, J.C. Prasana and S. Muthu, Quantum Mechanical, Spectroscopic and Docking Studies of 2-Amino-3-bromo-5-nitro-pyridine by Density Functional Method, Spectrochim. Acta A Mol. Biomol. Spectrosc., 181, 153 (2017); https://doi.org/10.1016/j.saa.2017.03.045
  36. F. Weinhold and L.C. Randis, Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective, Cambridge University Press (2005).
  37. C. James, A.A. Raj, R. Reghunathan, V.S. Jayakumar and I.H. Joe, Structural Conformation and Vibrational Spectroscopic Studies of 2,6-bis(p-N,N-Dimethyl benzylidene)cyclohexanone using Density Functional Theory, J. Raman Spectrosc., 37, 1381 (2006); https://doi.org/10.1002/jrs.1554
  38. J. Liu, Z. Chen and S. Yuan, Study on the Prediction of Visible Absorption Maxima of Azobenzene Compounds, J. Zhejiang Univ. Sci., 6, 584 (2005); https://doi.org/10.1631/jzus.2005.B0584
  39. G. Varsanyi, Vibrational Spectra of Benzene Derivatives, Academic Press: New York, NY, USA (1969).
  40. K. Fukui, Role of Frontier Orbitals in Chemical Reactions, Science, 218, 747 (1982); https://doi.org/10.1126/science.218.4574.747
  41. S. Balachandar and M. Dhandapani, Biological Action of Molecular Adduct Pyrazole:Trichloroacetic Acid on Candida albicans and ctDNA - A Combined Experimental, Fukui Functions Calculation and Molecular Docking Analysis, J. Mol. Struct., 1184, 129 (2019); https://doi.org/10.1016/j.molstruc.2019.02.006
  42. N.M. O’boyle, A.L. Tenderholt and K.M. Langner, cclib: A Library for Package-Independent Computational Chemistry Algorithms, J. Comput. Inside Chem., 29, 839 (2008); https://doi.org/10.1002/jcc.20823
  43. S. Xavier and S. Periandy, Spectroscopic (FT-IR, FT-Raman, UV and NMR) Investigation on 1-Phenyl-2-nitropropene by Quantum Computational Calculations, Spectrochim. Acta A Mol. Biomol. Spectrosc., 149, 216 (2015); https://doi.org/10.1016/j.saa.2015.04.055
  44. A. Shalini, H. Tandon and T. Chakraborty, Molecular Electrophilicity Index - A Promising Descriptor for Predicting Toxicological Property, J. Bioequiv. Bioavailab., 9, 528 (2017); https://doi.org/10.4172/jbb.1000356
  45. R. Parthasarathi, V. Subramanian, D.R. Roy and P.K. Chattaraj, Electrophilicity Index as a Possible Descriptor of Biological Activity, Bioorg. Med. Chem., 12, 5533 (2004); https://doi.org/10.1016/j.bmc.2004.08.013
  46. D.R. Roy, R. Parthasarathi, B. Maiti, V. Subramanian and P.K. Chattaraj, Electrophilicity as a Possible Descriptor for Toxicity Prediction, Bioorg. Med. Chem., 13, 3405 (2005); https://doi.org/10.1016/j.bmc.2005.03.011
  47. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng and T.E. Ferrin, UCSF Chimera-A Visualization System for Exploratory Research and Analysis, J. Comput. Chem., 25, 1605 (2004); https://doi.org/10.1002/jcc.20084
  48. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell and A.J. Olson, AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility, J. Comput. Chem., 30, 2785 (2009); https://doi.org/10.1002/jcc.21256
  49. A. Daina, O. Michielin and V. Zoete, iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design using the GB/SA Approach, J. Chem. Inf. Model., 54, 3284 (2014); https://doi.org/10.1021/ci500467k
  50. C.A. Lipinski, F. Lombardo, B.W. Dominy and P.J. Feeney, Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings, Adv. Drug Deliv. Rev., 23, 3 (1997); https://doi.org/10.1016/S0169-409X(96)00423-1
  51. S. Aayisha, T.S. Renuga Devi, S. Janani, S. Muthu, M. Raja and S. Sevvanthi, DFT, Molecular Docking and Experimental FT-IR, FT-Raman, NMR Inquisitions on 4-Chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-6-methoxy-2-methylpyrimidin-5-amine: Alpha-2-imidazoline Receptor Agonist Antihypertensive Agent, J. Mol. Struct., 1186, 468 (2019); https://doi.org/10.1016/j.molstruc.2019.03.056

Most read articles by the same author(s)