Süleyman Demirel University Journal of Natural and Applied Sciences
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Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi

Year 2021, Volume 25, Issue 2, 401 - 409, 20.08.2021

Sefa ÇELİK Sevim AKYÜZ Ayşen ÖZEL

https://doi.org/10.19113/sdufenbed.881399

Abstract

Bu çalışmada HT-29, Hela ve MCF-7 hücre hatlarına karşı antikanser etki gösteren Cyclo(Tyr-Tyr) dipeptidinin olası en kararlı yedi konformasyonu tirozin aminoasilerinin χ yan zincir dihedral açılarına bağlı olarak konformasyon analizi yapılarak belirlenmiştir. Konformasyon analizi sonrasında belirlenen konformasyonlara ait geometrik yapılar, yan zincire ait dihedral açıdaki değişimler ve konformerlerin toplam ve bağıl enerjileri ile bu konformasyonların toplam enerjilerine katkı sağlayan van der Waals, elektrostatik, torsiyon enerji katkıları ayrı ayrı hesaplanmıştır. Ek olarak bu dipeptidin dimerik formu, kuantum kimyasal ab-initio hesaplamalarla optimize edilerek halka yapıya ait w, φ, Ψ dihedral açıları monomer form ile karşılaştırmalı olarak verilmiştir ve dimerik formu oluşturan moleküller arası hidrojen bağları belirlenmiştir.

Keywords

Cyclo(Tyr-Tyr), Dipeptit, Diketopiperazin, Konformasyon Analizi, Moleküler Modelleme

References

  • [1] Uthuppan, J., Soni, K. 2013. Conformational analysis: a review. International Journal of Pharmaceutical Sciences and Research, 4(1), 34-41.
  • [2] Udenfriend, S., Meienhofer, J., Hruby, V. J. 2014. Conformation in Biology and Drug Design: The Peptides: Analysis, Synthesis, Biology, 7, Elsevier.
  • [3] Ström, K., Sjögren, J., Broberg, A., Schnürer, J. 2002. Lactobacillus plantarum MiLAB 393 produces the antifungal cyclic dipeptides cyclo (L-Phe-L-Pro) and cyclo (L-Phe-trans-4-OH-L-Pro) and 3-phenyllactic acid. Applied and Environmental Microbiology, 68(9), 4322-4327.
  • [4] Yamazaki, T., Nunami, K. I., Goodman, M. 1991. Cyclic retro–inverso dipeptides with two aromatic side chains. II. Conformational analysis. Biopolymers: Original Research on Biomolecules, 31(13), 1513-1528.
  • [5] Ovchinnikov, Y. A., Ivanov, V. T. 1982. The Proteins. ss 307-642. Neurath, H., Hill, R. L. ed. 1982. Academic Press, New York.
  • [6] Karanam, G., Arumugam, M. K. 2020. Reactive oxygen species generation and mitochondrial dysfunction for the initiation of apoptotic cell death in human hepatocellular carcinoma HepG2 cells by a cyclic dipeptide Cyclo (-Pro-Tyr). Molecular Biology Reports, 47(5), 3347-3359.
  • [7] Zainullina, L. F., Ivanova, T. V., Gudasheva, T. A., Vakhitova, Y. V., Seredenin, S. B. 2020. Effect of Neuropeptide Cyclo-L-Prolylglycine on Cell Proliferative Activity. Bulletin of Experimental Biology and Medicine, 169(3), 347-350.
  • [8] Şimşek, A., Kılıç, B. 2016. Et kaynaklı biyoaktif peptitler ve fonksiyonel özellikleri. Gıda, 41(4), 267-274.
  • [9] Gao, X., Li, X., Yan, P., Sun, R., Kan, G., Zhou, Y. 2018. Identification and functional mechanism of novel angiotensin I converting enzyme inhibitory dipeptides from Xerocomus badius cultured in shrimp processing waste medium. BioMed Research International, ID: 5089270.
  • [10] Wu, H., He, H. L., Chen, X. L., Sun, C. Y., Zhang, Y. Z., Zhou, B. C. 2008. Purification and identification of novel angiotensin-I-converting enzyme inhibitory peptides from shark meat hydrolysate. Process Biochemistry, 43(4), 457-461.
  • [11] Nakashima, Y., Arihara, K., Sasaki, A., Mio, H., Ishikawa, S., Itoh, M. 2002. Antihypertensive activities of peptides derived from porcine skeletal muscle myosin in spontaneously hypertensive rats. Journal of Food Science, 67(1), 434-437.
  • [12] Lee, S. H., Qian, Z. J., Kim, S. K. 2010. A novel angiotensin I converting enzyme inhibitory peptide from tuna frame protein hydrolysate and its antihypertensive effect in spontaneously hypertensive rats. Food Chemistry, 118(1), 96-102.
  • [13] de la Torre, B. G., Albericio, F. 2020. Peptide Therapeutics 2.0. Molecules, 25(10), 2293.
  • [14] Kilian, G., Jamie, H., Brauns, S. C. A., Dyason, K., Milne, P. J. 2005. Biological activity of selected tyrosine-containing 2,5-diketopiperazines. Die Pharmazie-An International Journal of Pharmaceutical Sciences, 60(4), 305-309.
  • [15] Rajput, S., McLean, K. J., Poddar, H., Selvam, I. R., Nagalingam, G., Triccas, J. A., Levy, C. W., Munro, A. W., Hutton, C. A. 2019. Structure–activity relationships of cyclo (L-tyrosyl-L-tyrosine) derivatives binding to Mycobacterium tuberculosis CYP121: iodinated analogues promote shift to high-spin adduct. Journal of Medicinal Chemistry, 62(21), 9792-9805.
  • [16] IUPAC-IUB. 1971. Commission on Biochemical Nomenclature, Biochim. Biochimica et Biophysica Acta, 121.
  • [17] Maksumov, I. S., Ismailova, L. I., Godjaev, N. M. 1983. The program for semiempirical calculation of conformations of the molecular complexes. Journal of Structural Chemistry, 24(4), 647-648.
  • [18] Popov, E. M. 1985. An approach to the problem of the structuro-functional organization of natural peptides. Molekuliarnaia Biologiia, 19(4), 1107-1138.
  • [19] Popov, E. M., Godjaev, N. M., Ismailova, L. I., Musaev, S. M., Aliev, R. E., Akhmedov, N. A., Maksumov, I. S. 1982. A-Priori calculation of spatial structure of bovine pancreatic trypsin-inhibitor. Bioorganicheskaya Khimiya, 8(6), 776-816.
  • [20] Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Replogle, J. A. 2003. Software for Computational Chemistry; Gaussian Inc.: Pittsburgh, PA, USA.
  • [21] Becke, A. D. 1993. Density-functional thermochemistry, III. The role ofexact exchange. The Journal of Chemical Physics, 98(7), 5648–5652.
  • [22] Sundius, T. 1990. Molvib –A flexible program for force field calculations. Journal of Molecular Structure, 218, 321–326.
  • [23] Sundius, T. 2002. Scaling of ab initio force fields by MOLVIB. Vibrational Spectroscopy, 29, 89–95.
  • [24] Istvan, K. 2002. Simirra, A program for simulation of IR and Raman Spectra. Chemical Research Center.,Budapeşte.
  • [25] Corey, R. B. 1938. The crystal structure of diketopiperazine. Journal of the American Chemical Society, 60(7), 1598-1604.
  • [26] Degeilh, R., Marsh, R. E. 1959. A refinement of the crystal structure of diketopiperazine (2,5-piperazinedione). Acta Crystallographica, 12(12), 1007-1014.
  • [27] Dorset, D. L. 2010. Direct methods and refinement in electron and X-ray crystallography–diketopiperazine revisited. Zeitschrift für Kristallographie International Journal for Structural, Physical, and Chemical Aspects of Crystalline Materials, 225(2-3), 86-93.
  • [28] Mendham, A. P., Dines, T. J., Snowden, M. J., Withnall, R., Chowdhry, B. Z. 2009. IR/Raman spectroscopy and DFT calculations of cyclic diamino acid peptides. Part III: Comparison of solid state and solution structures of cyclo (L-Ser-L-Ser). Journal of Raman Spectroscopy, 40(11), 1508-1520.
  • [29] Celik, S., Yilmaz, G., Ozel, A. E., Akyuz, S. 2020. Structural and spectral analysis of anticancer active cyclo (Ala–His) dipeptide. Journal of Biomolecular Structure and Dynamics, 1-13.
  • [30] Celik, S., Ozel, A. E., Akyuz, S. 2016. Comparative study of antitumor active cyclo (Gly-Leu) dipeptide: a computational and molecular modeling study. Vibrational Spectroscopy, 83, 57-69.
  • [31] Mendham, A. P., Dines, T. J., Snowden, M. J., Chowdhry, B. Z., Withnall, R. 2009. Vibrational spectroscopy and DFT calculations of di-aminoacid cyclic peptides. Part I: Cyclo(Gly–Gly), cyclo(L-Ala–L-Ala) and cyclo(L-Ala–Gly) in the solid state and in aqueous solution. Journal of Raman Spectroscopy, 40(11), 1478–1497.

Theoretical IR, Raman and Molecular Structure Analysis of Cyclo (Tyr-Tyr) Dipeptide

Year 2021, Volume 25, Issue 2, 401 - 409, 20.08.2021

Sefa ÇELİK Sevim AKYÜZ Ayşen ÖZEL

https://doi.org/10.19113/sdufenbed.881399

Abstract

In this study, the most stable seven conformations of the Cyclo (Tyr-Tyr) dipeptide, which shows anticancer effect against HT-29, Hela, and MCF-7 cell lines, were determined by conformational analysis based on χ side-chain dihedral angles of the two tyrosine amino acids. The geometric structures of the conformations, determined after the conformation analysis, the changes in the dihedral angle of the side-chain, the total and relative energies of the conformers, and the van der Waals, electrostatic and torsion energy contributions, that contribute to the total energies, were calculated separately. The most stable conformer, determined by conformation analysis, was then optimized using density functional theory (DFT), B3LYP functional and the 6-31++G(d,p) basis set by using Gaussian03 program, and the fundamental vibrational wavenumbers of the optimized structure were calculated at the same level of theory. In addition, IR intensities, Raman activities, potential energy distributions were determined using the MOLVIB program, and the scaled Raman activities scaled were transformed into Raman intensities by Simirra program. Furthermore, the dimeric form of the dipeptide was created and optimized at the DFT/B3LYP/6-31G(d,p) level of theory. The w, φ, Ψ dihedral angles of the ring structure were given comparatively with the monomer form calculated with the same basis sets. The intermolecular hydrogen bonds that play role in the formation of the dimeric structure have been determined.

Keywords

Cyclo(Tyr-Tyr), Dipeptide, Diketopiperazine, Conformational analysis, Molecular modeling

References

  • [1] Uthuppan, J., Soni, K. 2013. Conformational analysis: a review. International Journal of Pharmaceutical Sciences and Research, 4(1), 34-41.
  • [2] Udenfriend, S., Meienhofer, J., Hruby, V. J. 2014. Conformation in Biology and Drug Design: The Peptides: Analysis, Synthesis, Biology, 7, Elsevier.
  • [3] Ström, K., Sjögren, J., Broberg, A., Schnürer, J. 2002. Lactobacillus plantarum MiLAB 393 produces the antifungal cyclic dipeptides cyclo (L-Phe-L-Pro) and cyclo (L-Phe-trans-4-OH-L-Pro) and 3-phenyllactic acid. Applied and Environmental Microbiology, 68(9), 4322-4327.
  • [4] Yamazaki, T., Nunami, K. I., Goodman, M. 1991. Cyclic retro–inverso dipeptides with two aromatic side chains. II. Conformational analysis. Biopolymers: Original Research on Biomolecules, 31(13), 1513-1528.
  • [5] Ovchinnikov, Y. A., Ivanov, V. T. 1982. The Proteins. ss 307-642. Neurath, H., Hill, R. L. ed. 1982. Academic Press, New York.
  • [6] Karanam, G., Arumugam, M. K. 2020. Reactive oxygen species generation and mitochondrial dysfunction for the initiation of apoptotic cell death in human hepatocellular carcinoma HepG2 cells by a cyclic dipeptide Cyclo (-Pro-Tyr). Molecular Biology Reports, 47(5), 3347-3359.
  • [7] Zainullina, L. F., Ivanova, T. V., Gudasheva, T. A., Vakhitova, Y. V., Seredenin, S. B. 2020. Effect of Neuropeptide Cyclo-L-Prolylglycine on Cell Proliferative Activity. Bulletin of Experimental Biology and Medicine, 169(3), 347-350.
  • [8] Şimşek, A., Kılıç, B. 2016. Et kaynaklı biyoaktif peptitler ve fonksiyonel özellikleri. Gıda, 41(4), 267-274.
  • [9] Gao, X., Li, X., Yan, P., Sun, R., Kan, G., Zhou, Y. 2018. Identification and functional mechanism of novel angiotensin I converting enzyme inhibitory dipeptides from Xerocomus badius cultured in shrimp processing waste medium. BioMed Research International, ID: 5089270.
  • [10] Wu, H., He, H. L., Chen, X. L., Sun, C. Y., Zhang, Y. Z., Zhou, B. C. 2008. Purification and identification of novel angiotensin-I-converting enzyme inhibitory peptides from shark meat hydrolysate. Process Biochemistry, 43(4), 457-461.
  • [11] Nakashima, Y., Arihara, K., Sasaki, A., Mio, H., Ishikawa, S., Itoh, M. 2002. Antihypertensive activities of peptides derived from porcine skeletal muscle myosin in spontaneously hypertensive rats. Journal of Food Science, 67(1), 434-437.
  • [12] Lee, S. H., Qian, Z. J., Kim, S. K. 2010. A novel angiotensin I converting enzyme inhibitory peptide from tuna frame protein hydrolysate and its antihypertensive effect in spontaneously hypertensive rats. Food Chemistry, 118(1), 96-102.
  • [13] de la Torre, B. G., Albericio, F. 2020. Peptide Therapeutics 2.0. Molecules, 25(10), 2293.
  • [14] Kilian, G., Jamie, H., Brauns, S. C. A., Dyason, K., Milne, P. J. 2005. Biological activity of selected tyrosine-containing 2,5-diketopiperazines. Die Pharmazie-An International Journal of Pharmaceutical Sciences, 60(4), 305-309.
  • [15] Rajput, S., McLean, K. J., Poddar, H., Selvam, I. R., Nagalingam, G., Triccas, J. A., Levy, C. W., Munro, A. W., Hutton, C. A. 2019. Structure–activity relationships of cyclo (L-tyrosyl-L-tyrosine) derivatives binding to Mycobacterium tuberculosis CYP121: iodinated analogues promote shift to high-spin adduct. Journal of Medicinal Chemistry, 62(21), 9792-9805.
  • [16] IUPAC-IUB. 1971. Commission on Biochemical Nomenclature, Biochim. Biochimica et Biophysica Acta, 121.
  • [17] Maksumov, I. S., Ismailova, L. I., Godjaev, N. M. 1983. The program for semiempirical calculation of conformations of the molecular complexes. Journal of Structural Chemistry, 24(4), 647-648.
  • [18] Popov, E. M. 1985. An approach to the problem of the structuro-functional organization of natural peptides. Molekuliarnaia Biologiia, 19(4), 1107-1138.
  • [19] Popov, E. M., Godjaev, N. M., Ismailova, L. I., Musaev, S. M., Aliev, R. E., Akhmedov, N. A., Maksumov, I. S. 1982. A-Priori calculation of spatial structure of bovine pancreatic trypsin-inhibitor. Bioorganicheskaya Khimiya, 8(6), 776-816.
  • [20] Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Replogle, J. A. 2003. Software for Computational Chemistry; Gaussian Inc.: Pittsburgh, PA, USA.
  • [21] Becke, A. D. 1993. Density-functional thermochemistry, III. The role ofexact exchange. The Journal of Chemical Physics, 98(7), 5648–5652.
  • [22] Sundius, T. 1990. Molvib –A flexible program for force field calculations. Journal of Molecular Structure, 218, 321–326.
  • [23] Sundius, T. 2002. Scaling of ab initio force fields by MOLVIB. Vibrational Spectroscopy, 29, 89–95.
  • [24] Istvan, K. 2002. Simirra, A program for simulation of IR and Raman Spectra. Chemical Research Center.,Budapeşte.
  • [25] Corey, R. B. 1938. The crystal structure of diketopiperazine. Journal of the American Chemical Society, 60(7), 1598-1604.
  • [26] Degeilh, R., Marsh, R. E. 1959. A refinement of the crystal structure of diketopiperazine (2,5-piperazinedione). Acta Crystallographica, 12(12), 1007-1014.
  • [27] Dorset, D. L. 2010. Direct methods and refinement in electron and X-ray crystallography–diketopiperazine revisited. Zeitschrift für Kristallographie International Journal for Structural, Physical, and Chemical Aspects of Crystalline Materials, 225(2-3), 86-93.
  • [28] Mendham, A. P., Dines, T. J., Snowden, M. J., Withnall, R., Chowdhry, B. Z. 2009. IR/Raman spectroscopy and DFT calculations of cyclic diamino acid peptides. Part III: Comparison of solid state and solution structures of cyclo (L-Ser-L-Ser). Journal of Raman Spectroscopy, 40(11), 1508-1520.
  • [29] Celik, S., Yilmaz, G., Ozel, A. E., Akyuz, S. 2020. Structural and spectral analysis of anticancer active cyclo (Ala–His) dipeptide. Journal of Biomolecular Structure and Dynamics, 1-13.
  • [30] Celik, S., Ozel, A. E., Akyuz, S. 2016. Comparative study of antitumor active cyclo (Gly-Leu) dipeptide: a computational and molecular modeling study. Vibrational Spectroscopy, 83, 57-69.
  • [31] Mendham, A. P., Dines, T. J., Snowden, M. J., Chowdhry, B. Z., Withnall, R. 2009. Vibrational spectroscopy and DFT calculations of di-aminoacid cyclic peptides. Part I: Cyclo(Gly–Gly), cyclo(L-Ala–L-Ala) and cyclo(L-Ala–Gly) in the solid state and in aqueous solution. Journal of Raman Spectroscopy, 40(11), 1478–1497.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Articles
Authors

Sefa ÇELİK (Primary Author)
İSTANBUL ÜNİVERSİTESİ
0000-0001-6216-1297
Türkiye

Sevim AKYÜZ
İSTANBUL KÜLTÜR ÜNİVERSİTESİ
0000-0003-3313-6927
Türkiye

Ayşen ÖZEL
İSTANBUL ÜNİVERSİTESİ
0000-0002-8680-8830
Türkiye

Supporting Institution İstanbul Üniversitesi Bilimsel Araştırma Projeleri Yürütücü Sekreterliği
Project Number ÖNAP-2423
Thanks Bu çalışma, İstanbul Üniversitesi Bilimsel Araştırma Projeleri Yürütücü Sekreterliğinin ÖNAP-2423 numaralı projesi ile desteklenmiştir.
Publication Date August 20, 2021
Published in Issue Year 2021, Volume 25, Issue 2

Cite

Bibtex @research article { sdufenbed881399, journal = {Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi}, issn = {}, eissn = {1308-6529}, address = {}, publisher = {Süleyman Demirel University}, year = {2021}, volume = {25}, pages = {401 - 409}, doi = {10.19113/sdufenbed.881399}, title = {Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi}, key = {cite}, author = {Çelik, Sefa and Akyüz, Sevim and Özel, Ayşen} }
APA Çelik, S. , Akyüz, S. & Özel, A. (2021). Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi . Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi , 25 (2) , 401-409 . DOI: 10.19113/sdufenbed.881399
MLA Çelik, S. , Akyüz, S. , Özel, A. "Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi" . Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25 (2021 ): 401-409 <https://dergipark.org.tr/en/pub/sdufenbed/issue/64441/881399>
Chicago Çelik, S. , Akyüz, S. , Özel, A. "Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi". Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25 (2021 ): 401-409
RIS TY - JOUR T1 - Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi AU - Sefa Çelik , Sevim Akyüz , Ayşen Özel Y1 - 2021 PY - 2021 N1 - doi: 10.19113/sdufenbed.881399 DO - 10.19113/sdufenbed.881399 T2 - Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi JF - Journal JO - JOR SP - 401 EP - 409 VL - 25 IS - 2 SN - -1308-6529 M3 - doi: 10.19113/sdufenbed.881399 UR - https://doi.org/10.19113/sdufenbed.881399 Y2 - 2021 ER -
EndNote %0 Süleyman Demirel University Journal of Natural and Applied Sciences Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi %A Sefa Çelik , Sevim Akyüz , Ayşen Özel %T Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi %D 2021 %J Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi %P -1308-6529 %V 25 %N 2 %R doi: 10.19113/sdufenbed.881399 %U 10.19113/sdufenbed.881399
ISNAD Çelik, Sefa , Akyüz, Sevim , Özel, Ayşen . "Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi". Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25 / 2 (August 2021): 401-409 . https://doi.org/10.19113/sdufenbed.881399
AMA Çelik S. , Akyüz S. , Özel A. Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi. SDÜ Fen Bil Enst Der. 2021; 25(2): 401-409.
Vancouver Çelik S. , Akyüz S. , Özel A. Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi. 2021; 25(2): 401-409.
IEEE S. Çelik , S. Akyüz and A. Özel , "Cyclo(Tyr-Tyr) Dipeptidinin Teorik IR, Raman ve Moleküler Yapı Analizi", Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, vol. 25, no. 2, pp. 401-409, Aug. 2021, doi:10.19113/sdufenbed.881399
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