Computational chemistry as a tool to understand chemical and biochemical processes at a molecular level
Main Article Content
Abstract
As technology advances, computational chemistry has become a key part of scientific research. Nowadays, computational chemistry has been able to obtain methods and algorithms capable of reducing errors in the prediction of properties and simulation of chemical events being comparable with results obtained experimentally. Being able to understand different chemical processes from a molecular point of view, which sometimes is impossible to achieve through experimentation, makes computational chemistry a powerful tool. In this sense, processes such as drug discovery have ceased to depend on serendipity to become a more efficient and rational process; therefore, reducing the time to put a drug in clinical trials by half. In this review, some examples of how computational chemistry has helped to get a better understanding of chemical processes are examined. Studies getting new insights into the Vicarious nucleophilic substitution, interaction of silver nanoparticles with organic molecules, and the reaction mechanism of lignin biodegradation in the presence of lignin peroxidase are reviewed. Also, investigations on the possible mechanism of action of drugs such as acetaminophen or antimicrobial peptides extracted from frog exudate are presented.
Downloads
Article Details
- The authors agree to respect the academic information of other authors, and to assign the copyrights to the journal infoANALÍTICA, so that the article can be edited, published and distributed.
- The content of the scientific articles and the publications that appear in the journal is the exclusive responsibility of their authors. The distribution of the articles published in the infoANALÍTICA Journal is done under a Creative Commons Reconocimiento-CompartirIgual 4.0 Internacional License.
References
Bell, S., Dines, T. J., Chowdhry, B. Z., & Withnall, R. (2007). Computational chemistry using modern electronic structure methods. Journal of Chemical Education, 84(8), 1364–1370. https://doi.org/10.1021/ed084p1364
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Zardecki, C. (2002). The protein data bank. Acta Crystallographica Section D: Biological Crystallography, 28, 235–242. https://doi.org/10.1107/S0907444902003451
Botting, R., & Ayoub, S. S. (2005). COX-3 and the mechanism of action of paracetamol/acetaminophen. Prostaglandins Leukotrienes and Essential Fatty Acids, 72, 85–87. https://doi.org/10.1016/j.plefa.2004.10.005
Conlon, J. M. (2012). The potential of frog skin antimicrobial peptides for development into therapeutically valuable anti-infective agents. In ACS Symposium Series (Vol. 1095, pp. 47–60). American Chemical Society. https://doi.org/10.1021/bk-2012-1095.ch003
Cuesta, S.; Arias, J.; Gallegos, F.; Alzate-Morales, J.; Meneses, L. (2018). On the Reaction Mechanism of the 3,4-Dimethoxybenzaldehyde Formation from 1-(3′,4′-Dimethoxyphenyl)Propene. Molecules, 23(2), E412. https://doi.org/10.3390/molecules23020412
Cuesta H., S., Arias de P., J., Gallegos P., F., Proaño B., C., Blasco-Zúñiga, A., Rivera I., M., & Meneses O., L. (2019a). Modelamiento molecular de la dermaseptina SP2 extraída de Agalychnis spurrelli. InfoANALÍTICA, 7(1), 41. https://doi.org/10.26807/ia.v7i1.95
Cuesta, S., Gallegos, F., Arias, J., Pilaquinga, F., Blasco-Zúñiga, A., Proaño-Bolaños, C., … Meneses, L. (2019b). Molecular modeling of four Dermaseptin-related peptides of the gliding tree frog Agalychnis spurrelli. Journal of Molecular Modeling, 25(9). https://doi.org/10.1007/s00894-019-4141-1
Cuesta, S., Vela, C., & Meneses, L. (2017). Modelación molecular de la interacción del paracetamol y el 4-aminofenol con las enzimas Ciclooxigenasa 1 y 2. Revista Ecuatoriana de Medicina y Ciencias Biológicas. https://doi.org/10.26807/remcb.v38i2.546
Dashtban, M., Schraft, H., Syed, T. A., & Qin, W. (2010). Fungal biodegradation and enzymatic modification of lignin. International Journal of Biochemistry and Molecular Biology.
Egwim, E. C., Kabiru, A. Y., & Tola, A. J. (2015). Partial characterization of lignin peroxidase expressed by bacterial and fungal isolates from termite gut. Biokemistri, 27(1), 33–38. Retrieved from http://www.bioline.org.br/bk
Fabara, A., Cuesta, S., Pilaquinga, F., & Meneses, L. (2018). Computational Modeling of the Interaction of Silver Nanoparticles with the Lipid Layer of the Skin. Journal of Nanotechnology, 2018. https://doi.org/10.1155/2018/4927017
Foresman, J. B. (2001). Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems By David Young (Cytoclonal Pharmaceutics Inc.). Wiley-Interscience: New York. 2001. xxvi + 382 pp. $69.95. ISBN: 0-471-33368-9. Journal of the American Chemical Society, 123(41), 10142–10143. https://doi.org/10.1021/ja015246y
Fourches, D., Muratov, E., & Tropsha, A. (2010, July 26). Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research. Journal of Chemical Information and Modeling. https://doi.org/10.1021/ci100176x
Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.;Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenber, D. J. (2009). Gaussian 09. Gaussian, Inc. Wallingford CT.
Graham, G. G., Davies, M. J., Day, R. O., Mohamudally, A., & Scott, K. F. (2013). The modern pharmacology of paracetamol: Therapeutic actions, mechanism of action, metabolism, toxicity and recent pharmacological findings. Inflammopharmacology, 21, 201–232. https://doi.org/10.1007/s10787-013-0172-x
Graham, G. G., & Scott, K. F. (2005). Mechanism of action of paracetamol. American Journal of Therapeutics, 12, 46–55. https://doi.org/10.1097/00045391-200501000-00008
Harada, A., Sasaki, K., & Kaneta, T. (2016). Direct determination of lignin peroxidase released from Phanerochaete chrysosporium by in-capillary enzyme assay using micellar electrokinetic chromatography. Journal of Chromatography A, 1440, 145–149. https://doi.org/10.1016/j.chroma.2016.02.062
Hassan, M., Brown, R. D., Varma-O’Brien, S., & Rogers, D. (2006, August). Cheminformatics analysis and learning in a data pipelining environment. Molecular Diversity. https://doi.org/10.1007/s11030-006-9041-5
Holthausen, D. J., Lee, S. H., Kumar, V. T., Bouvier, N. M., Krammer, F., Ellebedy, A. H., … Jacob, J. (2017). An Amphibian Host Defense Peptide Is Virucidal for Human H1 Hemagglutinin-Bearing Influenza Viruses. Immunity, 46(4), 587–595. https://doi.org/10.1016/j.immuni.2017.03.018
Holtje, H. D., Folkers, G., & Luzar, A. (1998). Molecular Modeling, Basic Principles and Applications. Computers in Physics, 12(1), 41. https://doi.org/10.1063/1.168645
Jozwiak-Bebenista, M., & Nowak, J. Z. (2014). Paracetamol: Mechanism of action, applications and safety concern. Acta Poloniae Pharmaceutica - Drug Research, 71(1), 11–23.
Karlström, G., Lindh, R., Malmqvist, P. Å., Roos, B. O., Ryde, U., Veryazov, V., … Seijo, L. (2003). MOLCAS: A program package for computational chemistry. In Computational Materials Science (Vol. 28, pp. 222–239). https://doi.org/10.1016/S0927-0256(03)00109-5
Khindaria, A., Yamazaki, I., & Aust, S. D. (1995). Veratryl Alcohol Oxidation by Lignin Peroxidase. Biochemistry, 34(51), 16860–16869. https://doi.org/10.1021/bi00051a037
Kis, B., Snipes, A., Bari, F., & Busija, D. W. (2004). Regional distribution of cyclooxygenase-3 mRNA in the rat central nervous system. Molecular Brain Research, 126, 78–80. https://doi.org/10.1016/j.molbrainres.2004.03.015
Kis, B., Snipes, J. A., & Busija, D. W. (2005). Acetaminophen and the cyclooxygenase-3 puzzle: Sorting out facts, fictions, and uncertainties. Journal of Pharmacology and Experimental Therapeutics, 315, 1–7. https://doi.org/10.1124/jpet.105.085431
Kudo, S., Harada, A., Kubota, H., Sasaki, K., & Kaneta, T. (2017). Simultaneous Determination of Manganese Peroxidase and Lignin Peroxidase by Capillary Electrophoresis Enzyme Assays. ACS Omega, 2(10), 7329–7333. https://doi.org/10.1021/acsomega.7b00998
Lacombe, C., Piesse, C., Sagan, S., Combadière, C., Rosenstein, Y., & Auvynet, C. (2015). Pachymodulin, a new functional formyl peptide receptor 2 peptidic ligand isolated from frog skin has janus-like immunomodulatory capacities. Journal of Medicinal Chemistry, 58(3), 1089–1099. https://doi.org/10.1021/jm501018q
Lewars, E. G., & Lewars, E. G. (2016a). An Outline of What Computational Chemistry Is All About. In Computational Chemistry (pp. 1–8). Springer International Publishing. https://doi.org/10.1007/978-3-319-30916-3_1
Lewars, E. G., & Lewars, E. G. (2016b). Introduction to Quantum Mechanics in Computational Chemistry. In Computational Chemistry (pp. 101–191). Springer International Publishing. https://doi.org/10.1007/978-3-319-30916-3_4
Lewars, E. G., & Lewars, E. G. (2016c). Molecular Mechanics. In Computational Chemistry (pp. 51–99). Springer International Publishing. https://doi.org/10.1007/978-3-319-30916-3_3
Lewinski, N., Colvin, V., & Drezek, R. (2008, January). Cytotoxicity of nanopartides. Small. https://doi.org/10.1002/smll.200700595
Li, R., Chen, R., Chen, P., Wen, Y., Ke, P. C., & Cho, S. S. (2013). Computational and experimental characterizations of silver nanoparticle-apolipoprotein biocorona. Journal of Physical Chemistry B, 117(43), 13451–13456. https://doi.org/10.1021/jp4061158
MacDonald, J., Goacher, R. E., Abou-Zaid, M., & Master, E. R. (2016). Comparative analysis of lignin peroxidase and manganese peroxidase activity on coniferous and deciduous wood using ToF-SIMS. Applied Microbiology and Biotechnology, 100(18), 8013–8020. https://doi.org/10.1007/s00253-016-7560-2
Mąkosza, M. (2010). Nucleophilic substitution of hydrogen in electron-deficient arenes, a general process of great practical value. Chemical Society Reviews, 39(8), 2855–2868. https://doi.org/10.1039/b822559c
Ma̧kosza, M., Lemek, T., Kwast, A., & Terrier, F. (2002). Elucidation of the vicarious nucleophilic substitution of hydrogen mechanism via studies of competition between substitution of hydrogen, deuterium, and fluorine. Journal of Organic Chemistry, 67(2), 394–400. https://doi.org/10.1021/jo010590z
Ma̧kosza, M., & Wojciechowski, K. (2004). Nucleophilic substitution of hydrogen in heterocyclic chemistry. Chemical Reviews, 104(5), 2631–2666. https://doi.org/10.1021/cr020086+
Mallet, C., Daulhac, L., Bonnefont, J., Ledent, C., Etienne, M., Chapuy, E., … Eschalier, A. (2008). Endocannabinoid and serotonergic systems are needed for acetaminophen-induced analgesia. Pain, 139, 190–200. https://doi.org/10.1016/j.pain.2008.03.030
Manzo, G., Casu, M., Rinaldi, A. C., Montaldo, N. P., Luganini, A., Gribaudo, G., & Scorciapino, M. A. (2014). Folded structure and insertion depth of the frog-skin antimicrobial peptide esculentin-1b(1-18) in the presence of differently charged membrane-mimicking micelles. Journal of Natural Products, 77(11), 2410–2417. https://doi.org/10.1021/np5004406
Marani, M. M., Dourado, F. S., Quelemes, P. V., De Araujo, A. R., Perfeito, M. L. G., Barbosa, E. A., … Leite, J. R. S. A. (2015). Characterization and Biological Activities of Ocellatin Peptides from the Skin Secretion of the Frog Leptodactylus pustulatus. Journal of Natural Products, 78(7), 1495–1504. https://doi.org/10.1021/np500907t
Martinez, L.-L. L., & Orrantia Borunda, E. (2016). DFT Chemical Reactivity Analysis of Biological Molecules in the Presence of Silver Ion. Organic Chemistry: Current Research, 04(04). https://doi.org/10.4172/2161-0401.1000153
Meneses, L., Morocho, S., Castellanos, A., & Cuesta, S. (2017). Computational study of vicarious nucleophilic substitution reactions. Journal of Molecular Modeling, 23(10). https://doi.org/10.1007/s00894-017-3464-z
Ottani, A., Leone, S., Sandrini, M., Ferrari, A., & Bertolini, A. (2006). The analgesic activity of paracetamol is prevented by the blockade of cannabinoid CB1 receptors. European Journal of Pharmacology, 531, 280–281. https://doi.org/10.1016/j.ejphar.2005.12.015
Parr, R. G. (1980). Density Functional Theory of Atoms and Molecules. In Horizons of Quantum Chemistry. https://doi.org/10.1007/978-94-009-9027-2_2
Parr, R. G., Szentpály, L. V., & Liu, S. (1999). Electrophilicity index. Journal of the American Chemical Society, 121(9), 1922–1924. https://doi.org/10.1021/ja983494x
Parr, R. G., & Yang, W. (1984). Density Functional Approach to the Frontier-Electron Theory of Chemical Reactivity. Journal of the American Chemical Society, 106(14), 4049–4050. https://doi.org/10.1021/ja00326a036
Patz, M., Mayr, H., Maruta, J., & Fukuzumi, S. (1995). Reactions of Carbocations with π Nucleophiles: Polar Mechanism and No Outer Sphere Electron Transfer. Angewandte Chemie International Edition in English, 34(11), 1225–1227. https://doi.org/10.1002/anie.199512251
Pérez, P., Domingo, L. R., Aurell, M. J., & Contreras, R. (2003). Quantitative characterization of the global electrophilicity pattern of some reagents involved in 1,3-dipolar cycloaddition reactions. Tetrahedron, 59(17), 3117–3125. https://doi.org/10.1016/S0040-4020(03)00374-0
Rai, N., Yadav, M., & Singh Yadav, H. (2016). Enzymatic Characterisation of Lignin Peroxidase from Luffa aegyptiaca Fruit Juice. American Journal of Plant Sciences, 07(03), 649–656. https://doi.org/10.4236/ajps.2016.73057
Romann, J., Wei, J., & Pileni, M. P. (2015). Computational matching of surface plasmon resonance: Interactions between silver nanoparticles and ligands. Journal of Physical Chemistry C, 119(20), 11094–11099. https://doi.org/10.1021/jp511859p
Saion, E., Gharibshahi, E., & Naghavi, K. (2013). Size-controlled and optical properties of monodispersed silver nanoparticles synthesized by the radiolytic reduction method. International Journal of Molecular Sciences, 14(4), 7880–7896. https://doi.org/10.3390/ijms14047880
Schindele, C., Houk, K. N., & Mayr, H. (2002). Relationships between carbocation stabilities and electrophilic reactivity parameters, E: Quantum mechanical studies of benzhydryl cation structures and stabilities. Journal of the American Chemical Society, 124(37), 11208–11214. https://doi.org/10.1021/ja020617b
Scorciapino, M. A., Manzo, G., Rinaldi, A. C., Sanna, R., Casu, M., Pantic, J. M., … Conlon, J. M. (2013). Conformational analysis of the frog skin peptide, plasticin-L1, and its effects on production of proinflammatory cytokines by macrophages. Biochemistry, 52(41), 7231–7241. https://doi.org/10.1021/bi4008287
Shah, M. M., Grover, T. A., Barr, D. P., & Aust, S. D. (1992). On the mechanism of inhibition of the veratryl alcohol oxidase activity of lignin peroxidase H2 by EDTA. Journal of Biological Chemistry, 267(30), 21564–21569.
Snipes, J. A., Kis, B., Shelness, G. S., Hewett, J. A., & Busija, D. W. (2005). Cloning and characterization of cyclooxygenase-1b (putative cyclooxygenase-3) in rat. Journal of Pharmacology and Experimental Therapeutics, 313(2), 668–676. https://doi.org/10.1124/jpet.104.079533
Stutz, K., Müller, A. T., Hiss, J. A., Schneider, P., Blatter, M., Pfeiffer, B., … Schneider, G. (2017). Peptide-Membrane Interaction between Targeting and Lysis. ACS Chemical Biology, 12(9), 2254–2259. https://doi.org/10.1021/acschembio.7b00504
Ten Have, R., Franssen, M. C. R., & Field, J. A. (2015). Lignin peroxidase initiates O2-dependent self-propagating chemical reactions which accelerate the consumption of 1-(3′,4′-dimethoxyphenyl)propene. Biochemical Journal, 347(2), 585–591. https://doi.org/10.1042/bj3470585
Vollhardt, P., & Schore, N. (2014). Organic Chemistry. Organic Chemistry. Macmillan Learning. https://doi.org/10.1007/978-1-319-19197-9
Winiarski, J., & Makosza, M. (1987). Vicarious Nucleophilic Substitution of Hydrogen. Accounts of Chemical Research, 20(8), 282–289. https://doi.org/10.1021/ar00140a003
Wu, J., Fu, Y., He, Z., Han, Y., Zheng, L., Zhang, J., & Li, W. (2012). Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: A DFT study. Journal of Physical Chemistry B, 116(5), 1655–1665. https://doi.org/10.1021/jp206251v
You, C., Han, C., Wang, X., Zheng, Y., Li, Q., Hu, X., & Sun, H. (2012, September). The progress of silver nanoparticles in the antibacterial mechanism, clinical application and cytotoxicity. Molecular Biology Reports. https://doi.org/10.1007/s11033-012-1792-8
Zhao, Y., & Truhlar, D. G. (2008). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoretical Chemistry Accounts, 120(1–3), 215–241. https://doi.org/10.1007/s00214-007-0310-x