ACOPLAMIENTO MOLECULAR. UNA BREVE REVISIÓN A LOS AVANCES RECIENTES SOBRE CÁNCER
DOI:
https://doi.org/10.32399/icuap.rdic.2448-5829.2022.23.807Resumen
Resumen
Dentro del campo de la química computacional, el acoplamiento molecular o molecular docking ha
sido una metodología con un amplio auge. Las problemáticas actuales, tales como los elevados costos que
involucran la investigación de nuevos fármacos, la gestión de residuos peligrosos o la remediación de espacios
contaminados, han elevado el interés en los métodos computacionales que ayudan a optimizar estos procesos.
Aunque la reducción de costos que ofrece el diseño asistido por computadora es alta, se debe considerar
que entre más complejos sean los sistemas que se evalúen, se incrementarán tanto el costo como el tiempo
que consumen los cálculos correspondientes para realizar una predicción adecuada, resultando en un efecto
inverso al buscado. Afortunadamente, tal y como fue predicho por la ley de Moore, la potencia de los nuevos
procesadores se duplica con respecto a sus predecesores cada determinado tiempo, resultando en equipos
con una capacidad de realizar más cálculos en menos tiempo y en nuevo software con menores limitaciones
para realizar tareas más complejas. Lo anterior también ha beneficiado la eficacia de las herramientas para
realizar acoplamiento molecular, con lo cual a medida que se incrementa el poder de cómputo, disminuye la
dificultad de evaluar sistemas más grandes y complejos.[1] El objetivo de este trabajo es proporcionar una
breve revisión de la teoría, así como de los avances realizados usando esta herramienta en la investigación
sobre cáncer.
Citas
Acharya, R., Chacko, S., Bose, P., Lapenna, A., & Pattanayak, S. (2019). Structure based multitargeted molecular
docking analysis of selected furanocoumarins against breast cancer. Scientific reports, 1-13.
Aly, A., Bräse, S., Hassan, A., Mohamed, N., Abd El-Haleem, L., Nieger, M., . . . Abdelhafez, E. (2020). New Paracyclophane
Thiazoles with Anti-Leukemia Activity: Design, Synthesis, Molecular Docking, and Mechanistic
Studies. Molecules, 3089.
Arjun, H. A., Rajan, R. K., Elancheran, R., Ramanathan, M., Bhattacharjee, A., & Kabilan, S. (2020). Crystal
structure, Hirshfeld surface analysis, DFT and molecular docking studies on benzohydrazide derivatives as potential
inhibitors of prostate cancer. Chemical Data Collections, 100350.
Bade, B., & Cruz, C. (2020). Lung cancer 2020: epidemiology, etiology, and prevention. Clinics in chest medicine,
1-24.
Berman, H. M., Westbrook J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. (2000).
The Protein Data Bank Nucleic Acids Research, 28: 235-242.
Brito, V., Santos, A. O., Almeida, P., & Silvestre, S. (2019). Novel 4-azaandrostenes as prostate cancer cell growth
inhibitors: synthesis, antiproliferative effects, and molecular docking studies. Comptes Rendus Chimie, 73-83.
Burotto, M., Chiou, V. L., Lee, J. M., & Kohn, E. C. (2014). The MAPK pathway across different malignancies: a
new perspective. Cancer, 3446-3456.
Centers for Medicare & Medicaid Services. (2022). 2022 ASP Drug Pricing Files. Retrieved from https://www.
cms.gov/medicare/medicare-part-b-drug-average-sales-price/2022-asp-drug-pricing-files.
Chen, H., & Boutros, P. C. (2011). VennDiagram: a package for the generation of highly-customizable Venn and
Euler diagrams in R. BMC bioinformatics, 12(1), 1-7.
Chen, Y. (2015). Beware of Docking! Trends in pharmacological sciences, 78-95.
del Águila, I., Mendiola, M. A., Pradhan, S., Sinha, C., & López-Torres, E. (2021). Synthesis, characterization,
in vitro cytotoxic activity and molecular docking of dinuclear gold (I) complexes with terephthalaldehyde bis
(thiosemicarbazones). Polyhedron, 115498.
DiMasi, J. A. (2020). Research and Development Costs of New Drugs. Journal of American Medical Association,
517-517.
Elia, S., Al-Karmalawy, A., Nasr, M., & Elsahl, M. (2022). Loperamide potentiates doxorubicin sensitivity in
triple‐negative breast cancer cells by targeting MDR1 and JNK and suppressing mTOR and Bcl‐2: In vitro and
molecular docking study. Journal of biochemical and molecular toxicology, p. e22938.
Ferlay, J., Colombet, M., Soerjomataram, I., Parkin, D., Piñeros, M., Znaor, A., & Bray, F. (2021). Cancer statistics
for the year 2020: An overview. International Journal of Cancer, 778-789.
Gao, X., Chen, G., Gao, C., Zhang, D. H., Kuan, S. F., Stabile, L., . . . Hu, J. (2017). MAP 4K4 is a novel MAPK/ERK
pathway regulator required for lung adenocarcinoma maintenance. Molecular Oncology, 628-639.
Goldstein, L. J. (1996). MDR1 gene expression in solid tumours. European Journal of Cancer, 1039-1050.
Grande, F., Rizzuti, B., Occhiuzzi, M., Ioele, G., Casacchia, T., Gelmini, F., . . . Statti, G. (2018). Identification by
Molecular Docking of Homoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors. Molecules,
894.
Groom, C. R., Bruno, I. J., Lightfoot, M. P., Ward, S. C. (2016). Acta Crystallographica Section B: Structural
Science, Crystal Engineering and Materials, 72(2), 171-179.
Huang, S., Grinter, S. Z., & Zou, X. (2010). Scoring functions and their evaluation methods for protein–ligand
docking: recent advances and future directions. Physical chemistry chemical physics, 12899-12908.
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky,
L., Zhang, J., & Bolton, E. E. (2019). PubChem in 2021: new data content and improved web interfaces. Nucleic
Acids Res., 49(D1), D1388-D1395. https://doi.org/10.1093/nar/gkaa971
Lemjabbar-Alaoui, H., Hassan, O. U., Yang, Y. W., & Buchanan, P. (2015). Lung cancer: Biology and treatment
options. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 189-210.
Li, X., Lin, B., Lin, Z., Ma, Y., Wang, Q., Zheng, Y., & Luo, L. (2021). Exploration in the mechanism of fucosterol
for the treatment of non-small cell lung cancer based on network pharmacology and molecular Docking. Scientific
reports, 1-20.
Lv, G., Zhang, D. L., Wang, D., Pan, L., & Liu, Y. (2019). Synthesis, crystal structure, anti-bone cancer activity
and molecular docking investigations of the heterocyclic compound 1-((2S, 3S)-2-(benzyloxy) pentan-3-yl)-4-
(4-(4-(4-hydroxyphenyl) piperazin-1-yl) phenyl)-1H-1, 2, 4-triazol-5 (4H)-one. Journal of Structural Chemistry,
1173-1179.
Mechchate, H., Costa de Oliveira, R., Es-safi, I., Vasconcelos Mourão, E., Bouhrim, M., Kyrylchuk, A., . . . Grafov,
A. (2021). Antileukemic Activity and Molecular Docking Study of a Polyphenolic Extract from Coriander Seeds.
Pharmaceuticals, 770.
Mehta, D., Jackson, R., Paul, G., & Shi, J. (2017). Why do trials for Alzheimer’s disease drugs keep failing? A dis
continued drug perspective for 2010–2015. Expert opinion on investigational drugs, 735-739.
Moore, G. E. (1965). Cramming more components onto integrated circuits. Electronics, 114-117.
Morris, G. M., & Lim-Wilby, M. (2008). Molecular Docking. In A. Kukol, Molecular Modeling of Proteins (pp.365-382). New Jersey: Springer.
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. J. (2009). Autodock4
and AutoDockTools4: automated docking with selective receptor flexiblity. Journal of Computational
Chemistry, 16: 2785-91.
Reitsma, M. B., Kendrick, P. J., Ababneh, E., Abbafati, C., Abbasi-Kangevari, M., Abdoli, A., & Gorini, G. (2021).
Spatial, temporal, and demographic patterns in prevalence of smoking tobacco use and attributable disease burden
in 204 countries and territories, 1990–2019: a systematic analysis from the Global Burden of Disease Study
2019. The Lancet, 2337-2360.
Safran, M., Rosen, N., Twik, M., BarShir, R., Stein, T. I., Dahary, D., ... & Lancet, D. (2021). The GeneCards Suite.
In Practical Guide to Life Science Databases, 27-56.
Shamsel-Din, H. A., Gizawy, M. A., & Abdelaziz, G. (2020). Molecular Docking and preliminary bioevaluation
of 99mTc-Thiadiazuron as a novel potential agent for cervical cancer imaging. Journal of Radioanalytical and
Nuclear Chemistry, 1375-1381.
Singh, U. C., & Kollman, P. A. (1984). An approach to computing electrostatic charges for molecules. Journal of
computational chemistry, 5(2), 129-145.
Sousa, S. F., Fernandes, P. A., & Ramos , M. J. (2006). Protein–Ligand Docking: Current Status and Future Challenges.
PROTEINS: Structure, Function, and Bioinformatics, 15-26.
Sterling, T., & Irwin, J. (2015). ZINC 15–ligand discovery for everyone. Journal of chemical information and
modeling, 2324-2337.
Thandra, K. C., Barsouk, A., Saginala, K., Aluru, J. S., & Barsouk, A. (2021). Epidemiology of lung cancer. , 25(1),
45. Contemporary Oncology, 45-52.
Thompson, K. L., Rosenzweig, B. A., Pine, P. S., Retief, J., Turpaz, Y., Afshari, C. A., ... & Sistare, F. D. (2005).
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats. Nucleic acids
research, 33(22), e187-e187.
UniProt Consortium. (2019). UniProt: a worldwide hub of protein knowledge. Nucleic acids research, 47(1),
506-515.
U.S. DEPARTMENT OF LABOR. (2022). State Minimum Wage Laws. Retrieved 04 03, 2022, from Wage and
Hour Division: https://www.dol.gov/agencies/whd/minimum-wage/state
Valarmathi, T., Premkumar, R., & Benial, A. M. (2020). Spectroscopic and molecular docking studies on 1-Hydroxyanthraquinone:
A potent ovarian cancer drug. Journal of Molecular Structure, 128163.
Waks, A., & Winer, E. (2019). Breast Cancer treatment: a review. Journal of American Medical Association, 288-300.
Wang, X., Chao, L., Li, X., Ma, G., Chen, L., Zang, Y., & Zhou, G. (2010). Elevated expression of phosphorylated
c-Jun NH2-terminal kinase in basal-like and “triple-negative” breast cancers. Human pathology, 401-406.
Wouters, O., McKee, M., & Luyten, J. (2020). Estimated Research and Development Investment Needed to Bring
a New Medicine to Market, 2009-2018. Journal of American Medical Association, 844-853.
Xu, D., Wang, X., Huang, D., Chen, B., Lin, X., Liu, A., & Huang, J. (2022). Disclosing targets and pharmacological
mechanisms of total bioflavonoids extracted from Selaginella doederleinii against non-small cell lung cancer
by combination of network pharmacology and proteomics. Journal of Ethnopharmacology, 114836.
Yousuf, Z., Iman, K., Iftikhar, N., & Mirza, M. (2017). Structure-based virtual screening and molecular Docking
for the identification of potential multi-targeted inhibitors against breast cancer. Breast Cancer: Targets and Therapy,
447-459.
Yunwu, Z., Yan, W., Yujia, W., Xinyao, S., Chaorui, L., Shiliang, S., & Quanyu, D. (2021). Using network pharmacology
and molecular Docking to explore the mechanism of Shan Ci Gu (Cremastra appendiculata) against
non-small cell lung cancer. Frontiers in Chemistry, 414.
docking analysis of selected furanocoumarins against breast cancer. Scientific reports, 1-13.
Aly, A., Bräse, S., Hassan, A., Mohamed, N., Abd El-Haleem, L., Nieger, M., . . . Abdelhafez, E. (2020). New Paracyclophane
Thiazoles with Anti-Leukemia Activity: Design, Synthesis, Molecular Docking, and Mechanistic
Studies. Molecules, 3089.
Arjun, H. A., Rajan, R. K., Elancheran, R., Ramanathan, M., Bhattacharjee, A., & Kabilan, S. (2020). Crystal
structure, Hirshfeld surface analysis, DFT and molecular docking studies on benzohydrazide derivatives as potential
inhibitors of prostate cancer. Chemical Data Collections, 100350.
Bade, B., & Cruz, C. (2020). Lung cancer 2020: epidemiology, etiology, and prevention. Clinics in chest medicine,
1-24.
Berman, H. M., Westbrook J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. (2000).
The Protein Data Bank Nucleic Acids Research, 28: 235-242.
Brito, V., Santos, A. O., Almeida, P., & Silvestre, S. (2019). Novel 4-azaandrostenes as prostate cancer cell growth
inhibitors: synthesis, antiproliferative effects, and molecular docking studies. Comptes Rendus Chimie, 73-83.
Burotto, M., Chiou, V. L., Lee, J. M., & Kohn, E. C. (2014). The MAPK pathway across different malignancies: a
new perspective. Cancer, 3446-3456.
Centers for Medicare & Medicaid Services. (2022). 2022 ASP Drug Pricing Files. Retrieved from https://www.
cms.gov/medicare/medicare-part-b-drug-average-sales-price/2022-asp-drug-pricing-files.
Chen, H., & Boutros, P. C. (2011). VennDiagram: a package for the generation of highly-customizable Venn and
Euler diagrams in R. BMC bioinformatics, 12(1), 1-7.
Chen, Y. (2015). Beware of Docking! Trends in pharmacological sciences, 78-95.
del Águila, I., Mendiola, M. A., Pradhan, S., Sinha, C., & López-Torres, E. (2021). Synthesis, characterization,
in vitro cytotoxic activity and molecular docking of dinuclear gold (I) complexes with terephthalaldehyde bis
(thiosemicarbazones). Polyhedron, 115498.
DiMasi, J. A. (2020). Research and Development Costs of New Drugs. Journal of American Medical Association,
517-517.
Elia, S., Al-Karmalawy, A., Nasr, M., & Elsahl, M. (2022). Loperamide potentiates doxorubicin sensitivity in
triple‐negative breast cancer cells by targeting MDR1 and JNK and suppressing mTOR and Bcl‐2: In vitro and
molecular docking study. Journal of biochemical and molecular toxicology, p. e22938.
Ferlay, J., Colombet, M., Soerjomataram, I., Parkin, D., Piñeros, M., Znaor, A., & Bray, F. (2021). Cancer statistics
for the year 2020: An overview. International Journal of Cancer, 778-789.
Gao, X., Chen, G., Gao, C., Zhang, D. H., Kuan, S. F., Stabile, L., . . . Hu, J. (2017). MAP 4K4 is a novel MAPK/ERK
pathway regulator required for lung adenocarcinoma maintenance. Molecular Oncology, 628-639.
Goldstein, L. J. (1996). MDR1 gene expression in solid tumours. European Journal of Cancer, 1039-1050.
Grande, F., Rizzuti, B., Occhiuzzi, M., Ioele, G., Casacchia, T., Gelmini, F., . . . Statti, G. (2018). Identification by
Molecular Docking of Homoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors. Molecules,
894.
Groom, C. R., Bruno, I. J., Lightfoot, M. P., Ward, S. C. (2016). Acta Crystallographica Section B: Structural
Science, Crystal Engineering and Materials, 72(2), 171-179.
Huang, S., Grinter, S. Z., & Zou, X. (2010). Scoring functions and their evaluation methods for protein–ligand
docking: recent advances and future directions. Physical chemistry chemical physics, 12899-12908.
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky,
L., Zhang, J., & Bolton, E. E. (2019). PubChem in 2021: new data content and improved web interfaces. Nucleic
Acids Res., 49(D1), D1388-D1395. https://doi.org/10.1093/nar/gkaa971
Lemjabbar-Alaoui, H., Hassan, O. U., Yang, Y. W., & Buchanan, P. (2015). Lung cancer: Biology and treatment
options. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 189-210.
Li, X., Lin, B., Lin, Z., Ma, Y., Wang, Q., Zheng, Y., & Luo, L. (2021). Exploration in the mechanism of fucosterol
for the treatment of non-small cell lung cancer based on network pharmacology and molecular Docking. Scientific
reports, 1-20.
Lv, G., Zhang, D. L., Wang, D., Pan, L., & Liu, Y. (2019). Synthesis, crystal structure, anti-bone cancer activity
and molecular docking investigations of the heterocyclic compound 1-((2S, 3S)-2-(benzyloxy) pentan-3-yl)-4-
(4-(4-(4-hydroxyphenyl) piperazin-1-yl) phenyl)-1H-1, 2, 4-triazol-5 (4H)-one. Journal of Structural Chemistry,
1173-1179.
Mechchate, H., Costa de Oliveira, R., Es-safi, I., Vasconcelos Mourão, E., Bouhrim, M., Kyrylchuk, A., . . . Grafov,
A. (2021). Antileukemic Activity and Molecular Docking Study of a Polyphenolic Extract from Coriander Seeds.
Pharmaceuticals, 770.
Mehta, D., Jackson, R., Paul, G., & Shi, J. (2017). Why do trials for Alzheimer’s disease drugs keep failing? A dis
continued drug perspective for 2010–2015. Expert opinion on investigational drugs, 735-739.
Moore, G. E. (1965). Cramming more components onto integrated circuits. Electronics, 114-117.
Morris, G. M., & Lim-Wilby, M. (2008). Molecular Docking. In A. Kukol, Molecular Modeling of Proteins (pp.365-382). New Jersey: Springer.
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. J. (2009). Autodock4
and AutoDockTools4: automated docking with selective receptor flexiblity. Journal of Computational
Chemistry, 16: 2785-91.
Reitsma, M. B., Kendrick, P. J., Ababneh, E., Abbafati, C., Abbasi-Kangevari, M., Abdoli, A., & Gorini, G. (2021).
Spatial, temporal, and demographic patterns in prevalence of smoking tobacco use and attributable disease burden
in 204 countries and territories, 1990–2019: a systematic analysis from the Global Burden of Disease Study
2019. The Lancet, 2337-2360.
Safran, M., Rosen, N., Twik, M., BarShir, R., Stein, T. I., Dahary, D., ... & Lancet, D. (2021). The GeneCards Suite.
In Practical Guide to Life Science Databases, 27-56.
Shamsel-Din, H. A., Gizawy, M. A., & Abdelaziz, G. (2020). Molecular Docking and preliminary bioevaluation
of 99mTc-Thiadiazuron as a novel potential agent for cervical cancer imaging. Journal of Radioanalytical and
Nuclear Chemistry, 1375-1381.
Singh, U. C., & Kollman, P. A. (1984). An approach to computing electrostatic charges for molecules. Journal of
computational chemistry, 5(2), 129-145.
Sousa, S. F., Fernandes, P. A., & Ramos , M. J. (2006). Protein–Ligand Docking: Current Status and Future Challenges.
PROTEINS: Structure, Function, and Bioinformatics, 15-26.
Sterling, T., & Irwin, J. (2015). ZINC 15–ligand discovery for everyone. Journal of chemical information and
modeling, 2324-2337.
Thandra, K. C., Barsouk, A., Saginala, K., Aluru, J. S., & Barsouk, A. (2021). Epidemiology of lung cancer. , 25(1),
45. Contemporary Oncology, 45-52.
Thompson, K. L., Rosenzweig, B. A., Pine, P. S., Retief, J., Turpaz, Y., Afshari, C. A., ... & Sistare, F. D. (2005).
Use of a mixed tissue RNA design for performance assessments on multiple microarray formats. Nucleic acids
research, 33(22), e187-e187.
UniProt Consortium. (2019). UniProt: a worldwide hub of protein knowledge. Nucleic acids research, 47(1),
506-515.
U.S. DEPARTMENT OF LABOR. (2022). State Minimum Wage Laws. Retrieved 04 03, 2022, from Wage and
Hour Division: https://www.dol.gov/agencies/whd/minimum-wage/state
Valarmathi, T., Premkumar, R., & Benial, A. M. (2020). Spectroscopic and molecular docking studies on 1-Hydroxyanthraquinone:
A potent ovarian cancer drug. Journal of Molecular Structure, 128163.
Waks, A., & Winer, E. (2019). Breast Cancer treatment: a review. Journal of American Medical Association, 288-300.
Wang, X., Chao, L., Li, X., Ma, G., Chen, L., Zang, Y., & Zhou, G. (2010). Elevated expression of phosphorylated
c-Jun NH2-terminal kinase in basal-like and “triple-negative” breast cancers. Human pathology, 401-406.
Wouters, O., McKee, M., & Luyten, J. (2020). Estimated Research and Development Investment Needed to Bring
a New Medicine to Market, 2009-2018. Journal of American Medical Association, 844-853.
Xu, D., Wang, X., Huang, D., Chen, B., Lin, X., Liu, A., & Huang, J. (2022). Disclosing targets and pharmacological
mechanisms of total bioflavonoids extracted from Selaginella doederleinii against non-small cell lung cancer
by combination of network pharmacology and proteomics. Journal of Ethnopharmacology, 114836.
Yousuf, Z., Iman, K., Iftikhar, N., & Mirza, M. (2017). Structure-based virtual screening and molecular Docking
for the identification of potential multi-targeted inhibitors against breast cancer. Breast Cancer: Targets and Therapy,
447-459.
Yunwu, Z., Yan, W., Yujia, W., Xinyao, S., Chaorui, L., Shiliang, S., & Quanyu, D. (2021). Using network pharmacology
and molecular Docking to explore the mechanism of Shan Ci Gu (Cremastra appendiculata) against
non-small cell lung cancer. Frontiers in Chemistry, 414.
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Publicado
2022-06-20
Cómo citar
Ramírez-Contreras, D. (2022). ACOPLAMIENTO MOLECULAR. UNA BREVE REVISIÓN A LOS AVANCES RECIENTES SOBRE CÁNCER. RD-ICUAP, 8(23), 68–85. https://doi.org/10.32399/icuap.rdic.2448-5829.2022.23.807
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