Research Article
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Year 2020, Volume: 4 Issue: 1, 12 - 23, 15.06.2020
https://doi.org/10.33435/tcandtc.614263

Abstract

References

  • [1] H. Frankish, 15 Million new cancer cases per year by 2020, says WHO: Lancet. (2003) 361, 1278–1287, DOI: 10.1016/S0140-6736(03)13038-3.
  • [2] H.D. Nelson, M.E. Smith, J.C. Griffin, R. Fu, Use of medications to reduce risk for primary breast cancer: a systematic review for the U.S. Preventive Services Task Force. Annals of Internal Medicine 158 (2013) 604-14.
  • [3] M.N. Okobia, C.H. Bunker, F.E. Okonofua and U. Osime Knowledge, Attitude and Practice of Nigerian Women towards Breast Cancer: A Cross-Sectional Study. World Journal of Surgical Oncology. 4 (2006) 11–15.
  • [4] Rathod, Antifungal and Antibacterial activities of Imidazolyl pyrimidines derivatives and their QSAR Studies under Conventional and Microwave-assisted, Int J PharmTech Res. 3 (2011) 1942–1951.
  • [5] Y. Pommier, E. Leo, H. Zhang, and C. Marchand, DNA Topoisomerases and Their Poisoning by Anticancer and Antibacterial Drugs, Chem. Biol. 17 (2010) 421–433.
  • [6] Y. Pommier, Y. Sun, S.N. Huang, and J.L. Nitiss, Roles of Eukaryotic Topoisomerases in Transcription, Replication and Genomic Stability, Nat. Rev. Mol. Cell Biol. 17 (2016) 703–721.
  • [7] J.E. Deweese, and N. Osheroff, The DNA Cleavage Reaction of Topoisomerase II: Wolf in Sheep’s Clothing. Nucleic Acids Res. 37 (2009) 738–749.
  • [8] P. Forterre, and D. Gadelle, Phylogenomics of DNA Topoisomerases: Their Origin and Putative Roles in the Emergence of Modern Organisms, Nucleic Acids Res. 37 (2009) 679–692.
  • [9] B. Mukesh, and K. Rakesh, Molecular Docking: A Review. IJRAP, 2 (2011)1746-1751.
  • [10] I.A. Guedes, C.S. de Magalhães and L.E. Dardenne, Receptor–Ligand Molecular Docking: Biophysical Reviews. (2014) 6 75-87
  • [11] Albratty, M., El-Sharkawy, K. A., and Alam, S., (2017). Synthesis and Antitumor Activity of Some Novel Thiophene, Pyrimidine, Coumarine, Pyrazole and Pyridine Derivatives. Acta Pharm. 67, 15–33, DOI: 10.1515/acph-2017-0004.
  • [12] Z. Li, H. Wan, Y. Shi, P. Ouyang, Personal experience with four kinds of chemical structure drawing software: review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch, Journal of Chemical Information and Computer Sciences. 44 (2004) 1886–1890.
  • [13] C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical Review B. 37 (1988) 785.
  • [14] A.D. Becke, Becke’s three parameter hybrid method using the LYP correlation functional, J. Chem. Phys. 98 (1993) 5648– 5652.
  • [15] S.E. Adeniji, S. Uba, A. Uzairu, In Silico Study For Investigating and Predicting the activities of 1, 2, 4-triazole derivaties as potent anti-tubercular agents, The Journal of Engineering and Exact Sciences. 4 (2018) 246–254.
  • [16] P. Singh, Quantitative Structure-Activity Relationship Study of Substituted-[1, 2, 4] Oxadiazoles as S1P1 Agonists, Journal of Current Chemical and Pharmaceutical Sciences. 3 (2013) 334–345.
  • [17] G. Melagraki, A. Afantitis, K. Makridima, H. Sarimveis, O. Igglessi-Markopoulou, Prediction of toxicity using a novel RBF neural network training methodology, Journal of Molecular Modeling. 12 (2006) 297–305.
  • [18] A. Afantitis, G. Melagraki, H. Sarimveis, P.A. Koutentis, J. Markopoulos, O. IgglessiMarkopoulou, A novel QSAR model for predicting induction of apoptosis by 4-aryl4H-chromenes, Bioorganic & Medicinal Chemistry. 14 (2006) 6686–6694.
  • [19] A.K. Chakraborti, B. Gopalakrishnan, M.E. Sobhia, A. Malde, 3D-QSAR studies of indole derivatives as phosphodiesterase IV inhibitors, European Journal of Medicinal Chemistry. 38 (2003) 975–982.
  • [20] K.F. Khaled, Modeling corrosion inhibition of iron in acid medium by genetic function approximation method: A QSAR model, Corrosion Science. 53 (2011) 3457–3465.
  • [21] A. Tropsha, P. Gramatica, V.K. Gombar, The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. Mol. Inform. 22, 69-77, 2003, DOI: 10.1002/qsar.200390007.
  • [22] N. Minovski, Š. Župerl, V. Drgan, M. Novič, Assessment of applicability domain for multivariate counter-propagation artificial neural network predictive models by minimum Euclidean distance space analysis: a case study, Anal. Chim. Acta 759 (2013) 28–42.
  • [23] R. Veerasamy, H. Rajak, A. Jain, S. Sivadasan, C.P. Varghese, R.K. Agrawal, Validation of QSAR models-strategies and importance, International Journal of Drug Design & Discovery. 3 (2011) 511–519.
  • [24] A. Tropsha, P. Gramatica, V. K. Gombar, The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models, Molecular Informatics. 22 (2003) 69–77.
  • [25] http://www.rcsb.org/pdb/home/home.do
  • [26] S.E. Adeniji, S. Uba, A. Uzairu, QSAR Modeling and Molecular Docking Analysis of Some Active Compounds against Mycobacterium tuberculosis Receptor (Mtb CYP121), Journal of Pathogens. (2018) 1– 24.

QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent

Year 2020, Volume: 4 Issue: 1, 12 - 23, 15.06.2020
https://doi.org/10.33435/tcandtc.614263

Abstract

Quantitative Structure Activity Relationship
(QSAR) and molecular Docking studies were carried out on some novel compounds to
generate a good QSAR models that relate the anti-breast cancer activity values
with the molecular structure of the compounds. Genetic Function Algorithm (GFA)
and Multiple Linear Regression Analysis (MLRA) were used to select the
descriptors that were used to build the models. The best model built was found
to have statistical validation values of squared correlation coefficient (R2) = 0.999, adjusted squared
correlation coefficient (
 = 0.998, cross validation coefficient  = 0.998 and an external squared correlation coefficient
=
0.879 which was used to confirm the validation of the model. The docking results
showed that ligands 6 and 5 with binding energy (-9.2kcalmol-1 and
-9.0kcalmol-1) respectively have the highest binding affinity when
compared to the reference drug doxorubicin with binding energy (-6.8kcalmol-1).
The stability and robustness of the built model showed that new anti-breast
cancer agents can be design from these derivatives.

References

  • [1] H. Frankish, 15 Million new cancer cases per year by 2020, says WHO: Lancet. (2003) 361, 1278–1287, DOI: 10.1016/S0140-6736(03)13038-3.
  • [2] H.D. Nelson, M.E. Smith, J.C. Griffin, R. Fu, Use of medications to reduce risk for primary breast cancer: a systematic review for the U.S. Preventive Services Task Force. Annals of Internal Medicine 158 (2013) 604-14.
  • [3] M.N. Okobia, C.H. Bunker, F.E. Okonofua and U. Osime Knowledge, Attitude and Practice of Nigerian Women towards Breast Cancer: A Cross-Sectional Study. World Journal of Surgical Oncology. 4 (2006) 11–15.
  • [4] Rathod, Antifungal and Antibacterial activities of Imidazolyl pyrimidines derivatives and their QSAR Studies under Conventional and Microwave-assisted, Int J PharmTech Res. 3 (2011) 1942–1951.
  • [5] Y. Pommier, E. Leo, H. Zhang, and C. Marchand, DNA Topoisomerases and Their Poisoning by Anticancer and Antibacterial Drugs, Chem. Biol. 17 (2010) 421–433.
  • [6] Y. Pommier, Y. Sun, S.N. Huang, and J.L. Nitiss, Roles of Eukaryotic Topoisomerases in Transcription, Replication and Genomic Stability, Nat. Rev. Mol. Cell Biol. 17 (2016) 703–721.
  • [7] J.E. Deweese, and N. Osheroff, The DNA Cleavage Reaction of Topoisomerase II: Wolf in Sheep’s Clothing. Nucleic Acids Res. 37 (2009) 738–749.
  • [8] P. Forterre, and D. Gadelle, Phylogenomics of DNA Topoisomerases: Their Origin and Putative Roles in the Emergence of Modern Organisms, Nucleic Acids Res. 37 (2009) 679–692.
  • [9] B. Mukesh, and K. Rakesh, Molecular Docking: A Review. IJRAP, 2 (2011)1746-1751.
  • [10] I.A. Guedes, C.S. de Magalhães and L.E. Dardenne, Receptor–Ligand Molecular Docking: Biophysical Reviews. (2014) 6 75-87
  • [11] Albratty, M., El-Sharkawy, K. A., and Alam, S., (2017). Synthesis and Antitumor Activity of Some Novel Thiophene, Pyrimidine, Coumarine, Pyrazole and Pyridine Derivatives. Acta Pharm. 67, 15–33, DOI: 10.1515/acph-2017-0004.
  • [12] Z. Li, H. Wan, Y. Shi, P. Ouyang, Personal experience with four kinds of chemical structure drawing software: review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch, Journal of Chemical Information and Computer Sciences. 44 (2004) 1886–1890.
  • [13] C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical Review B. 37 (1988) 785.
  • [14] A.D. Becke, Becke’s three parameter hybrid method using the LYP correlation functional, J. Chem. Phys. 98 (1993) 5648– 5652.
  • [15] S.E. Adeniji, S. Uba, A. Uzairu, In Silico Study For Investigating and Predicting the activities of 1, 2, 4-triazole derivaties as potent anti-tubercular agents, The Journal of Engineering and Exact Sciences. 4 (2018) 246–254.
  • [16] P. Singh, Quantitative Structure-Activity Relationship Study of Substituted-[1, 2, 4] Oxadiazoles as S1P1 Agonists, Journal of Current Chemical and Pharmaceutical Sciences. 3 (2013) 334–345.
  • [17] G. Melagraki, A. Afantitis, K. Makridima, H. Sarimveis, O. Igglessi-Markopoulou, Prediction of toxicity using a novel RBF neural network training methodology, Journal of Molecular Modeling. 12 (2006) 297–305.
  • [18] A. Afantitis, G. Melagraki, H. Sarimveis, P.A. Koutentis, J. Markopoulos, O. IgglessiMarkopoulou, A novel QSAR model for predicting induction of apoptosis by 4-aryl4H-chromenes, Bioorganic & Medicinal Chemistry. 14 (2006) 6686–6694.
  • [19] A.K. Chakraborti, B. Gopalakrishnan, M.E. Sobhia, A. Malde, 3D-QSAR studies of indole derivatives as phosphodiesterase IV inhibitors, European Journal of Medicinal Chemistry. 38 (2003) 975–982.
  • [20] K.F. Khaled, Modeling corrosion inhibition of iron in acid medium by genetic function approximation method: A QSAR model, Corrosion Science. 53 (2011) 3457–3465.
  • [21] A. Tropsha, P. Gramatica, V.K. Gombar, The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. Mol. Inform. 22, 69-77, 2003, DOI: 10.1002/qsar.200390007.
  • [22] N. Minovski, Š. Župerl, V. Drgan, M. Novič, Assessment of applicability domain for multivariate counter-propagation artificial neural network predictive models by minimum Euclidean distance space analysis: a case study, Anal. Chim. Acta 759 (2013) 28–42.
  • [23] R. Veerasamy, H. Rajak, A. Jain, S. Sivadasan, C.P. Varghese, R.K. Agrawal, Validation of QSAR models-strategies and importance, International Journal of Drug Design & Discovery. 3 (2011) 511–519.
  • [24] A. Tropsha, P. Gramatica, V. K. Gombar, The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models, Molecular Informatics. 22 (2003) 69–77.
  • [25] http://www.rcsb.org/pdb/home/home.do
  • [26] S.E. Adeniji, S. Uba, A. Uzairu, QSAR Modeling and Molecular Docking Analysis of Some Active Compounds against Mycobacterium tuberculosis Receptor (Mtb CYP121), Journal of Pathogens. (2018) 1– 24.
There are 26 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

İdris Momohjimoh Ovaku 0000-0002-1075-6341

Abechi Stephehe Eyije This is me

Shallangwa Gideon Adamu This is me

Uzairu Adamu This is me 0000-0002-6973-6361

Publication Date June 15, 2020
Submission Date September 2, 2019
Published in Issue Year 2020 Volume: 4 Issue: 1

Cite

APA Momohjimoh Ovaku, İ., Stephehe Eyije, A., Gideon Adamu, S., Adamu, U. (2020). QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent. Turkish Computational and Theoretical Chemistry, 4(1), 12-23. https://doi.org/10.33435/tcandtc.614263
AMA Momohjimoh Ovaku İ, Stephehe Eyije A, Gideon Adamu S, Adamu U. QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent. Turkish Comp Theo Chem (TC&TC). June 2020;4(1):12-23. doi:10.33435/tcandtc.614263
Chicago Momohjimoh Ovaku, İdris, Abechi Stephehe Eyije, Shallangwa Gideon Adamu, and Uzairu Adamu. “QSAR and Molecular Docking Studies of Novel Thiophene, Pyrimidine, Coumarin, Pyrazole and Pyridine Derivatives As Potential Anti-Breast Cancer Agent”. Turkish Computational and Theoretical Chemistry 4, no. 1 (June 2020): 12-23. https://doi.org/10.33435/tcandtc.614263.
EndNote Momohjimoh Ovaku İ, Stephehe Eyije A, Gideon Adamu S, Adamu U (June 1, 2020) QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent. Turkish Computational and Theoretical Chemistry 4 1 12–23.
IEEE İ. Momohjimoh Ovaku, A. Stephehe Eyije, S. Gideon Adamu, and U. Adamu, “QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent”, Turkish Comp Theo Chem (TC&TC), vol. 4, no. 1, pp. 12–23, 2020, doi: 10.33435/tcandtc.614263.
ISNAD Momohjimoh Ovaku, İdris et al. “QSAR and Molecular Docking Studies of Novel Thiophene, Pyrimidine, Coumarin, Pyrazole and Pyridine Derivatives As Potential Anti-Breast Cancer Agent”. Turkish Computational and Theoretical Chemistry 4/1 (June 2020), 12-23. https://doi.org/10.33435/tcandtc.614263.
JAMA Momohjimoh Ovaku İ, Stephehe Eyije A, Gideon Adamu S, Adamu U. QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent. Turkish Comp Theo Chem (TC&TC). 2020;4:12–23.
MLA Momohjimoh Ovaku, İdris et al. “QSAR and Molecular Docking Studies of Novel Thiophene, Pyrimidine, Coumarin, Pyrazole and Pyridine Derivatives As Potential Anti-Breast Cancer Agent”. Turkish Computational and Theoretical Chemistry, vol. 4, no. 1, 2020, pp. 12-23, doi:10.33435/tcandtc.614263.
Vancouver Momohjimoh Ovaku İ, Stephehe Eyije A, Gideon Adamu S, Adamu U. QSAR and Molecular Docking Studies of novel thiophene, pyrimidine, coumarin, pyrazole and pyridine derivatives as Potential Anti-Breast Cancer Agent. Turkish Comp Theo Chem (TC&TC). 2020;4(1):12-23.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)