Interaksi Molekuler Peptida Antimikrobial Lendir Kulit Ikan Lele Kuning (Pelteobagrus fulvidraco) terhadap Penicillin-Binding Protein 3 (PBP3) pada Escherichia coli secara In silico
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Submitted
25 April 2020
25 April 2020
Published
30 June 2020
30 June 2020
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Abstract
Background: Lendir kulit ikan baru-baru ini dikenal sebagai sumber potensial peptida antimikrobial yang berfungsi untuk memberikan pertahanan pertama terhadap bakteri patogen, seperi Escherichia coli. Beberapa peptida antimikrobial yang dihasilkan oleh lendir kulit ikan lele kuning (Pelteobagrus fulvidraco) terbukti mampu menghambat Penicillin-Binding Protein 3 (PBP3) pada Escherichia coli, antara lain Pelteobagrin, Myxinidin, Pleurocidin, dan Pardaxin-P1. Metode: Penelitian ini bertujuan untuk melakukan identifikasi, evaluasi, dan eksplorasi terhadap interaksi molekuler antara molekul peptida antimikrobial dengan Penicillin-Binding Protein 3 (PBP3) pada Escherichia coli menggunakan motode penambatan molekuler berbasis protein-peptida. Sekuensing peptida antimikrobial terlebih dahulu dimodelkan ke dalam bentuk konformasi 3D menggunakan server PEP-FOLD. Konformasi terbaik hasil pemodelan dipilih untuk selanjutnya dilakukan studi interaksi terhadap makromolekul Penicillin-Binding Protein 3 (PBP3) pada Escherichia coli menggunakan perangkat lunak PatchDock. Interaksi yang terbentuk kemudian diamati lebih lanjut menggunakan perangkat lunak BIOVIA Discovery Studio 2020. Hasil: Hasil dari penambatan molekuler menunjukkan bahwa peptida Pardaxin-P1 memiliki afinitas paling baik, yaitu dengan ACE score −1402,39 kJ/mol. Kesimpulan: Dengan demikian, peptida antimikrobial tersebut diprediksi dapat dipilih sebagai kandidat antimikroba alami.
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References
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Patil, B. S., Krishnamurthy, G., Lokesh, M. R., Shashikumar, N. D., Bhojya Naik, H. S., Latthe, P. R., & Ghate, M. (2013). Synthesis of some novel 1,2,4-triazole and 1,3,4-oxadiazole derivatives of biological interest. Medicinal Chemistry Research. https://doi.org/10.1007/s00044-012-0332-3
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Senthilkumar, B., Meshachpaul, D., & Rajasekaran, R. (2016). Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs. Biochemistry Research International. https://doi.org/10.1155/2016/4101059
Sharma, S., Kumar, P., Chandra, R., Singh, S. P., Mandal, A., & Dondapati, R. S. (2019). Overview of BIOVIA materials studio, LAMMPS, and GROMACS. In Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs. https://doi.org/10.1016/B978-0-12-816954-4.00002-4
Shen, Y., Maupetit, J., Derreumaux, P., & Tuffery, P. (2014). Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction. Journal of Chemical Theory and Computation, 10, 4745–4758. https://doi.org/dx.doi.org/10.1021/ct500592m
Stöhr, A. C., Papp, T., & Marschang, R. E. (2016). Repeated Detection of an Invertebrate Iridovirus in Amphibians. Journal of Herpetological Medicine and Surgery. https://doi.org/10.5818/1529-9651-26.1-2.54
Su, Y. (2011). Isolation and identification of pelteobagrin, a novel antimicrobial peptide from the skin mucus of yellow catfish (Pelteobagrus fulvidraco). Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology. https://doi.org/10.1016/j.cbpb.2010.11.002
Thevenet, P., Shen, Y., Maupetit, J., Guyon, F., Derreumaux, P., & Tuffery, P. (2012). PEP-FOLD"¯: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Research, 40, 288–293. https://doi.org/10.1093/nar/gks419
Read More
íngeles Esteban, M. (2012). An Overview of the Immunological Defenses in Fish Skin. ISRN Immunology. https://doi.org/10.5402/2012/853470
Avci, F. G., Akbulut, B. S., & Ozkirimli, E. (2018). Membrane Active Peptides and Their Biophysical Characterization. Biomolecules, 8(77), 1–43. https://doi.org/10.3390/biom8030077
Bellini, D., Koekemoer, L., Newman, H., & Dowson, C. G. (2019). Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of β-Lactam Target-Mediated Resistance. Journal of Molecular Biology, 431(18), 3501–3519. https://doi.org/10.1016/j.jmb.2019.07.010
Brinchmann, M. F., Patel, D. P., Pinto, N., & Iversen, M. H. (2018). Functional Aspects of Fish Mucosal Lectins”Interaction with Non-Self Monica. Molecules, 23(1119), 1–12. https://doi.org/10.3390/molecules23051119
Dash, S., Das, S. K., Samal, J., & Thatoi, H. (2018). Epidermal mucus , a major determinant in fish health"¯: A review. Irianian Journal of Veterinary Research, 19(2), 72–81. https://doi.org/10.22099/ijvr.2018.4849
Gokhale, A. S., & Satyanarayanajois, S. (2014). Peptides and Peptidomimetics As Immunomodulators. Immunotherapy, 6(6), 755–774. https://doi.org/10.2217/IMT.14.37
Hedmon, O., Jacqueline, A., Koffi, K. T., Drago, K. C., & Engeu, O. P. (2018). Fish Mucus: A Neglected Reservoir for Antimicrobial Peptides. Asian Journal of Pharmaceutical Research and Development, 6(4), 6–11. https://doi.org/http://dx.doi.org/10.22270/ajprd.v6.i4.389
Irazazabal, L. N., Porto, W. F., Fensterseifer, I. C. M., Alves, E. S. F., Matos, C. O., Menezes, A. C. S., Felício, M. R., Gonçalves, S., Santos, N. C., Suzana, M., Humblot, V., Lií£o, L. M., Ladram, A., & Franco, L. (2018). Fast and Potent Bactericidal Membrane Lytic Activity Of Padbs1r1, A Novel Cationic Antimicrobial Peptide. Biochimica et Biophysica Acta - Biomembranes, 186(1), 178–190. https://doi.org/10.1016/j.bbamem.2018.08.001
Lei, J., Sun, L. C., Huang, S., Zhu, C., Li, P., He, J., Mackey, V., Coy, D. H., & He, Q. Y. (2019). The antimicrobial peptides and their potential clinical applications. In American Journal of Translational Research.
Masso-silva, J. A., & Diamond, G. (2014). Antimicrobial Peptides from Fish. Pharmaceuticals, 7(3), 265–310. https://doi.org/10.3390/ph7030265
Ozboyaci, M., Kokh, D. B., Corni, S., & Wade, R. C. (2016). Modeling and simulation of protein-surface interactions: Achievements and challenges. In Quarterly Reviews of Biophysics. https://doi.org/10.1017/S0033583515000256
Papp, T., & Marschang, R. E. (2019). Detection and Characterization of Invertebrate Iridoviruses Found in Reptiles and Prey Insects in Europe over the Past Two Decades. Viruses, 11(600), 1–25.
Patil, B. S., Krishnamurthy, G., Lokesh, M. R., Shashikumar, N. D., Bhojya Naik, H. S., Latthe, P. R., & Ghate, M. (2013). Synthesis of some novel 1,2,4-triazole and 1,3,4-oxadiazole derivatives of biological interest. Medicinal Chemistry Research. https://doi.org/10.1007/s00044-012-0332-3
Pushpanathan, M., Gunasekaran, P., & Rajendhran, J. (2013). Antimicrobial peptides: Versatile biological properties. International Journal of Peptides. https://doi.org/10.1155/2013/675391
Rakers, S., Niklasson, L., Steinhagen, D., Kruse, C., Sundell, K., & Paus, R. (2013). Antimicrobial Peptides ( AMPs ) from Fish Epidermis"¯: Perspectives for Investigative Dermatology. Journal of Investigative Dermatology, 133(5), 1140–1149. https://doi.org/10.1038/jid.2012.503
Reverter, M., Tapissier-bontemps, N., Lecchini, D., Banaigs, B., & Sasal, P. (2018). Biological and Ecological Roles of External Fish Mucus"¯: A Review. Fishes, 3(41), 1–19. https://doi.org/10.3390/fishes3040041
Rizvi, S. M. D., Shakil, S., & Haneef, M. (2013). A simple click by click protocol to perform docking: Autodock 4.2 made easy for non-bioinformaticians. EXCLI Journal. https://doi.org/10.17877/DE290R-11534
Senthilkumar, B., Meshachpaul, D., & Rajasekaran, R. (2016). Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs. Biochemistry Research International. https://doi.org/10.1155/2016/4101059
Sharma, S., Kumar, P., Chandra, R., Singh, S. P., Mandal, A., & Dondapati, R. S. (2019). Overview of BIOVIA materials studio, LAMMPS, and GROMACS. In Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs. https://doi.org/10.1016/B978-0-12-816954-4.00002-4
Shen, Y., Maupetit, J., Derreumaux, P., & Tuffery, P. (2014). Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction. Journal of Chemical Theory and Computation, 10, 4745–4758. https://doi.org/dx.doi.org/10.1021/ct500592m
Stöhr, A. C., Papp, T., & Marschang, R. E. (2016). Repeated Detection of an Invertebrate Iridovirus in Amphibians. Journal of Herpetological Medicine and Surgery. https://doi.org/10.5818/1529-9651-26.1-2.54
Su, Y. (2011). Isolation and identification of pelteobagrin, a novel antimicrobial peptide from the skin mucus of yellow catfish (Pelteobagrus fulvidraco). Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology. https://doi.org/10.1016/j.cbpb.2010.11.002
Thevenet, P., Shen, Y., Maupetit, J., Guyon, F., Derreumaux, P., & Tuffery, P. (2012). PEP-FOLD"¯: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Research, 40, 288–293. https://doi.org/10.1093/nar/gks419
Authors
Fakih, T. M., & Dewi, M. L. (2020). Interaksi Molekuler Peptida Antimikrobial Lendir Kulit Ikan Lele Kuning (Pelteobagrus fulvidraco) terhadap Penicillin-Binding Protein 3 (PBP3) pada Escherichia coli secara In silico. BIOEDUSCIENCE, 4(1), 48–55. https://doi.org/10.29405/j.bes/4148-554951
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