Penghambatan Senyawa di dalam Kopi terhadap Protein Fibronektin dan Protein Shroom: Kajian Gangguan Neurulasi Primer Secara in Silico

Novian Budi Santoso, Susanto Susanto, Hebert Adrianto, Viol Dhea Kharisma

Abstract


Coffee drinking habits exist in Indonesian culture. Coffee as the primary source of caffeine is here the effect of embryotoxicity on paralysis, wrong brain. The brain is going on so that the body is a curiosity. Fibronectin and shroom proteins play in the primary stacking cage, which is the seasoning of the nerve roof. This study aimed to predict molecular inhibition of compounds in coffee in fibronectin protein and shroom protein in silica. The research method used samples of ligands and target proteins from the PubChem database and protein databank, then analyzed using PyRx, Discovery Studio, and PyMol software. The results of the study of literature there are five compounds in coffee. As a result of molecular docking simulation analysis, caffeine compounds (CID 2519) had lower total binding energy (-9.9 kcal/mol) in other combinations in fibronectin and shroom proteins. There are six residues of the amino acid fibronectin and 5 in shroom with caffeine. There are chemical bonds provided for caffeine compounds consisting of hydrophobic, alkyl, Van der Waals, and electrostatic. Caffeine can inhibit fibronectin and shroom protein activity and in vitro and in vivo tests to validate bioinformatics results.


Keywords


Caffeine; Coffee; Fibronectin; In silico; Shroom.

Full Text:

PDF

References


Alfawaz, H. A., Khan, N., Yakout, S. M., Khattak, M., Alsaikhan, A. A., Almousa, A. A., Alsuwailem, T. A., Almjlad, T. M., Alamri, N. A., Alshammari, S. G., & Al-Daghri, N. M. (2020). Prevalence, Predictors, and awareness of coffee consumption and its trend among saudi female students. International Journal of Environmental Research and Public Health, 17(19), 1-17. https://doi.org/10.3390/ijerph17197020.

Almahdy, A., Almunawwarah, N.A., Fitria, N. (2013). Uji efek teratogen kakao bubuk pada fetus mencit putih. Indonesian Journal of Pharmaceutical Science and Technology, 2(1), 9-26. https://ejournal.stfi.ac.id/index.php/jstfi/article/view/22

Ban, T., Ohue, M., & Akiyama, Y. (2018). Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem. Computational biology and chemistry, 73, 139-146. https://doi.org/10.1016/j.compbiolchem.2018.02.008

Bebenek, E.B., Piórecka, B., Chadzinska, M.K.Z., Jagielski, P., Zawadzka, M.S. (2018). Evaluation of caffeine consumption among pregnant women from Southern Poland. Int. J. Environ. Res. Public Health 15 (2373), 1-9. https://doi.org/10.3390/ijerph15112373

Chu, C. W., Gerstenzang, E., Ossipova, O., & Sokol, S. Y. (2013). Lulu regulates Shroom-induced apical constriction during neural tube closure. PloS One, 8(11), 1-10. https://doi.org/10.1371/journal.pone.0081854

Dam, R. M., Hu, F. B., & Willett, W. C. (2020). Coffee, caffeine, and health. The New England Journal of Medicine, 383(4), 369-378. https://doi.org/10.1056/NEJMra1816604.

Demir, Y., Türkeş, C., & Beydemir, Ş. (2020). Molecular docking studies and inhibition properties of some antineoplastic agents against paraoxonase-I. Anticancer Agents Med Chem, 20(7), 887-896. https://doi.org/10.2174/1871520620666200218110645

Frary, C.D., Johnson, R.K., Wang, M.Q., (2005). Food sources and intakes of caffeine in the diets of persons in the United States. J. Am. Dietetic Assoc. 105(1), 110-113. https://doi.org/10.1016/j.jada.2004.10.027

Gao, Y. D., & Huang, J. F. (2011). An extension strategy of discovery Studio 2.0 for non-bonded interaction energy automatic calculation at the residue level. Zoological research, 32(3), 262-266. https://tspace.library.utoronto.ca/handle/1807/64665

Giordanetto, F., Tyrchan, C., & Ulander, J. (2017). Intramolecular hydrogen bond expectations in medicinal chemistry. ACS medicinal chemistry letters, 8(2), 139-142. https://pubs.acs.org/doi/full/10.1021/acsmedchemlett.7b00002

George, E.L., Georges-Labouesse, E.N., Patel-King, R.S., Rayburn, H., Hynes, R.O. (1993). Defects in mesoderm, neural tube and vascular development in mouse embryos lacking fibronectin. Development, 119 (4): 1079–109. https://doi.org/10.1242/dev.119.4.1079

Goederen, V., Vetter, R., McDole, K., Iber, D. (2022). Hinge point emergence in mammalian spinal neurulation. Proc Natl Acad Sci USA, 119(20), e2117075119. https://doi.org/10.1073/pnas.2117075119.

Hildebrand, J. D., Leventry, A. D., Aideyman, O. P., Majewski, J. C., Haddad, J. A., Bisi, D. C., & Kaufmann, N. (2021). A modifier screen identifies regulators of cytoskeletal architecture as mediators of Shroom-dependent changes in tissue morphology. Biology Open, 10(2). https://doi.org/10.1242/bio.055640

Ilham, M.I., Haniarti, Usman. (2019). Hubungan pola konsumsi kopi terhadap kejadian gastristis pada mahasiswa muhammadiyah parepare. Jurnal Ilmiah Manusia dan Kesehatan, 2(3), 433-446. https://doi.org/10.31850/makes.v2i3.189

Iriani, O.S., dan Ulfah. (2019). Hubungan kebiasaan meminum teh dan kopi dengan kejadian anemia pada ibu hamil di BPM Bidan “E” Desa Ciwangi Kecamatan Balubur Limbangan Kabupaten Garut. Jurnal Sehat Masada, 13(2), 68-72. https://doi.org/10.38037/jsm.v13i2.108

Irnidayanti, Y., Darmanto, W., & Abadi, A. (2010). Ekspresi level gen mRNA protein ekstraseluler otak embrio mencit black-6 uk-12 akibat induksi 2-methoxyethanol: analisis secara real time RT-PCR. Berkala Penelitian Hayati, 15(2), 171-179. https://berkalahayati.org/index.php/jurnal/article/view/272

Kharisma, V.D., Ansori, A.N.M., Widyananda, M.H., Utami, S.L., Nugraha, A.P. (2020) The potency of conserved region on E6 HPV-16 as a binding target of black tea compounds against cervical cancer. Biochem. Cell. Arch, 20 (1), 2795-2802.

Kumar, A., Kaur, H., Jain, A., Nair, D. T., & Salunke, D. M. (2018). Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens. Scientific reports, 8(1), 1-12. https://doi.org/10.1038/s41598-017-18733-9

Lashein, F. E.M., Seleem, A.A., Ahmed, A.A. (2016). Effect of caffeine and retinoic acid on skeleton of mice embryos. The Journal of Basic & Applied Zoology, 75(2016), 36-45. https://doi.org/10.1016/j.jobaz.2016.06.003

Lee, C., Le, M.P., Wallingford, J.B. (2009). The shroom family proteins play broad roles in the morphogenesis of thickened epithelial sheets. Dev Dyn, 238(6), 1480-91. https://doi.org/10.1002/dvdy.21942

Liveina dan Artini, I.G.A. (2014). Pola konsumsi dan efek samping minuman mengandung kafein pada mahasiswa program studi Pendidikan Dokter Fakultas Kedokteran Universitas Udayana. Jurnal Medika Udayana, 3(4), 1-12. https://ojs.unud.ac.id/index.php/eum/article/view/8507

Luqman, A., Kharisma, V. D., Ruiz, R. A., and Götz, F. (2020). In silico and in vitrostudy of trace amines (TA) and dopamine (DOP) interaction with human alpha1-adrenergic receptor and the bacterial adrenergic receptor QseC. Cell. Physiol. Biochem, 54, 888-898. https://doi.org/10.33594/000000276

Magenis, M. L., Damiani, A. P., Franca, I. B., de Marcos, P. S., Effting, P. S., Muller, A. P., de Bem Silveira, G., Borges Correa, M., Medeiros, E. B., Silveira, P., Budni, J., Boeck, C. R., & de Andrade, V. M. (2022). Behavioral, genetic and biochemical changes in the brain of the offspring of female mice treated with caffeine during pregnancy and lactation. Reproductive Toxicology, 112 (2022), 119–135. https://doi.org/10.1016/j.reprotox.2022.07.005

Moreira, A., Nunes, F. M., Simões, C., Maciel, E., Domingues, P., Domingues, M., & Coimbra, M. A. (2017). Data on coffee composition and mass spectrometry analysis of mixtures of coffee related carbohydrates, phenolic compounds and peptides. Data in Brief, 13, 145-161. https://doi.org/10.1016/j.dib.2017.05.027

Nikolopoulou, E., Galea, G. L., Rolo, A., Greene, N. D., & Copp, A. J. (2017). Neural tube closure: cellular, molecular and biomechanical mechanisms. Development (Cambridge, England), 144(4), 552-566. https://doi.org/10.1242/dev.145904

O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3 (33), 1-14. https://doi.org/10.1186/1758-2946-3-33

Oktafarel, K.M., Mario, Augusta, D.N., Arifin, A., Ekomadyo, A.S., Susanto, V. (2021). Coffee culture and heritage: (demystifying the heritage value of coffee shops inside historical buildings in Jakarta and Bandung. Local Wisdom, 13 (1), 51-66. https://doi.org/10.26905/lw.v13i1.5088

Pubchem. (2021). National Center for Biotechnology Information. https://pubchem.ncbi.nlm.nih.gov.

Pintican, D., Strilciuc, S., Armean, S.M., Mihu, D. (2019). Effects of ethanol, nicotine and caffeine gestational exposure of female rats on lung and brain tissues infetuses: morphological and biological study. Rom J Morphol Embryol, 60(2), 643–651. https://europepmc.org/article/med/31658339

Prihiyantoro, E., Darmanto, W., Wibowo, S., Sagi, M., & Soedjono, S. K. (2008). Gangguan pembentukan atap bumbung neural embrio mencit akibat induksi 2-ME yang bertepatan dengan masa neurulasi primer. Berkala Penelitian Hayati, 13(2), 163-172. https://www.berkalahayati.org/index.php/jurnal/article/view/365

Protein Data Bank. (2021). RCSB Protein Data Bank. United States. https://www.rcsb.org/

Qian, J., Zhang, Y., Qu, Y., Zhang, L., Shi, J., Zhang, X., … Zhang, Y. (2018). Caffeine consumption during early pregnancy impairs oviductal embryo transport, embryonic development and uterine receptivity in mice. Biology of Reproduction, 99(6), 1266-1275. DOI: https://doi.org/10.1093/biolre/ioy155

Rashidi F, Mahabady MK, Ranjbar R, and Najafzadeh VH. (2012). The effects of caffeine and carvedilol on skeletal system of rat embryos in prenatal period. African Journal of Pharmacy and Pharmacology, 6(29), 2229-2234. https://academicjournals.org/journal/AJPP/article-full-text-pdf/BA2C24933116

Rigsby, R. E., & Parker, A. B. (2016). Using the PyMOL application to reinforce visual understanding of protein structure. Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 44(5), 433-437. https://doi.org/10.1002/bmb.20966

Santoso, H. B. (2006). Struktur mikroskopis kartilago epifisialis tibia fetus mencit (Mus musculus L.) dari induk dengan perlakuan kafein. Berkala Penelitian Hayati, 12(1), 69-74. https://berkalahayati.org/index.php/jurnal/article/view/401

Schmidt, R.J., Romitti, P.A., Burns, T.L., Browne, M.L., Druschel, C.M., Olney, R.S. (2009). National birth defects prevention study. maternal caffeine consumption and risk of neural tube defects. Birth Defects Res A Clin Mol Teratol., 85(11), 879-89. https://doi.org/10.1002/bdra.20624

Sugiono, E., Arief, M., Santoso, A. (2013). Habitual coffee consumption does not correlate with blood pressure, Inflammation and Endothelial Dysfunction but Partially Correlates with Oxidative Stress. Indones Biomed J, 5(1), 51-58. https://doi.org/10.18585/inabj.v5i1.51.

Sulistyoningrum, E., dan Pribadi, F.W., 2014. Pengaruh pemberian kafein selama kehamilan terhadap berat lahir dan gambaran histologis uterus dan plasenta tikus putih (Rattus norvegicus). Journal of Holistic Nursing Science, 1(2), 17-24. http://journal.unimma.ac.id/index.php/nursing/article/view/436

Uslu, S., Emon, S. T., Alaca, N., Kocaturk, D. C., Uslu, U., & Uysal, A. (2022). Effects of dexamethasone exposure on neural crest cells and primary and secondary neurulation in chick embryos. Turkish neurosurgery, 32(3), 412-419. https://doi.org/10.5137/1019-5149.JTN.34904-21.2

Yue, Y., Li, W., Tang, J., Zeng, Y., Xiong, T., Qiu, X., … Mu, D. (2020). Maternal intake of caffeinated products and birth defects: a systematic review and meta-analysis of observational studies. Critical Reviews in Food Science and Nutrition, 61(22), 3756-3770. https://doi.org/10.1080/10408398.2020.1806200




DOI: https://doi.org/10.26630/jk.v13i2.2641

Refbacks

  • There are currently no refbacks.


Published by: Poltekkes Kemenkes Tanjung Karang

Alamat: Jl. Soekarno-Hatta No. 6 Bandar Lampung
Telepon: 0721-783852 Fax: 0721-773918, emai: jk@poltekkes-tjk.ac.id
 

Jurnal Kesehatan is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.