250
Views
0
CrossRef citations to date
0
Altmetric
Research Article

QSAR study of tetrahydropteridin derivatives as polo-like kinase 1(PLK1) Inhibitors with molecular docking and dynamics study

, , & ORCID Icon
Pages 91-116 | Received 10 Nov 2022, Accepted 07 Jan 2023, Published online: 06 Feb 2023

References

  • G. de Cárcer, G. Manning, and M. Malumbres, From Plk1 to Plk5, Cell Cycle 10 (2011), pp. 2255–2262. doi:10.4161/cc.10.14.16494.
  • P.R. Duchowicz, Linear regression QSAR models for polo-like kinase-1 inhibitors, Cells 7 (2018), pp. 13. doi:10.3390/cells7020013.
  • S. Bhujbal, S. Keretsu, and S. Cho, A Combined molecular docking and 3D‐QSAR studies on tetrahydropteridin derivatives as PLK2 antagonists, Bull. Korean Chem. Soc. 40 (2019), pp. 796–802. doi:10.1002/bkcs.11824.
  • R. Shahin, N.N. Al-Hashimi, N.E.-H. Daoud, S. Aljamal, and O. Shaheen, QSAR-guided pharmacophoric modeling reveals important structural requirements for Polo kinase 1 (Plk1) inhibitors, J. Mol. Graph. Model. 109 (2021), pp. 108022. doi:10.1016/j.jmgm.2021.108022.
  • R. Chekkara, N. Kandakatla, V.R. Gorla, S.R. Tenkayala, and E. Susithra, Theoretical studies on benzimidazole and imidazo[1,2-a]pyridine derivatives as Polo-like kinase 1 (Plk1) inhibitors: Pharmacophore modeling, atom-based 3D-QSAR and molecular docking approach, J. Saudi Chem. Soc. 21 (2017), pp. S311–S321. doi:10.1016/j.jscs.2014.03.007.
  • Y. Kong and A. Yan, QSAR models for predicting the bioactivity of Polo-like Kinase 1 inhibitors, Chemom. Intell. Lab. Syst. 167 (2017), pp. 214–225. doi:10.1016/j.chemolab.2017.06.011.
  • Z. Li, L. Xu, L. Zhu, Y. Zhao, T. Hu, B. Yin, Y. Liu, and Y. Hou, Design, synthesis and biological evaluation of novel pteridinone derivatives possessing a hydrazone moiety as potent PLK1 inhibitors, Bioorg. Med. Chem. Lett. 30 (2020), pp. 127329. doi:10.1016/j.bmcl.2020.127329.
  • L. Li, W. Xue, Z. Shen, J. Liu, M. Hu, Z. Cheng, Y. Wang, Y. Chen, H. Chang, Y. Liu, B. Liu, and J. Zhao, A cereblon modulator CC-885 induces CRBN- and p97-dependent PLK1 degradation and synergizes with volasertib to suppress lung cancer, Mol. Ther. Oncol. 18 (2020), pp. 215–225. doi:10.1016/j.omto.2020.06.013.
  • S. Al-Assaf, A. Abuhammad, M. Hijjawi, and M. Taha, Structure-based discovery of new polo-like kinase 1 (PLK1) inhibitors as potential anticancer agents via docking-based comparative intermolecular contacts analysis (dbCICA), Med. Chem. Res. 30 (2021), pp. 1747–1766. doi:10.1007/s00044-021-02774-x.
  • J. Sun, P.-C. Lv, F.-J. Guo, X.-Y. Wang, X. Han, Y. Zhang, G.-H. Sheng, -S.-S. Qian, and H.-L. Zhu, Aromatic diacylhydrazine derivatives as a new class of polo-like kinase 1 (PLK1) inhibitors, Eur. J. Med. Chem. 81 (2014), pp. 420–426. doi:10.1016/j.ejmech.2014.05.026.
  • A. Joshi, H. Bhojwani, and U. Joshi, Strategies to select the best pharmacophore model: A case study in pyrazoloquinazoline class of PLK-1 inhibitors, Med. Chem. Res. 27 (2018), pp. 234–260. doi:10.1007/s00044-017-2057-9.
  • S. Lu, H.-C. Liu, Y.-D. Chen, H.-L. Yuan, S.-L. Sun, Y.-P. Gao, P. Yang, L. Zhang, and T. Lu, Combined pharmacophore modeling, docking, and 3D-QSAR studies of PLK1 inhibitors, Int. J. Mol. Sci. 12 (2011), pp. 8713–8739. doi:10.3390/ijms12128713.
  • Z. Pei, J. Ning, N. Zhang, X. Zhang, H. Zhang, and R. Zhang, Genetic instability of lung induced by carbon black nanoparticles is related with Plk1 signals changes, NanoImpact 26 (2022), pp. 100400. doi:10.1016/j.impact.2022.100400.
  • B. Cholewa, M. Ndiaye, W. Huang, X. Liu, and N. Ahmad, Small molecule inhibition of polo-like kinase 1 by volasertib (BI 6727) causes significant melanoma growth delay and regression in vivo, Cancer Lett. 385 (2016), pp. 179–187. doi:10.1016/j.canlet.2016.10.025.
  • R. Affatato, L. Carrassa, R. Chilà, M. Lupi, V. Restelli, and G. Damia, Identification of PLK1 as a new therapeutic target in mucinous ovarian carcinoma, Cancers 12 (2020), pp. 672. doi:10.3390/cancers12030672.
  • S. Liu, H. Yosief, L. Dai, H. Huang, G. Dhawan, X. Zhang, A. Muthengi, J. Roberts, D. Buckley, J. Perry, L. Wu, J. Bradner, J. Qi, and W. Zhang, Structure-guided design and development of potent and selective dual bromodomain 4 (BRD4)/polo-like kinase 1 (PLK1) Inhibitors, J. Med. Chem. 61 (2018), pp. 7785–7795. doi:10.1021/acs.jmedchem.8b00765.
  • J. Fernández-Sainz, P.J. Pacheco-Liñán, J.M. Granadino-Roldán, I. Bravo, J. Rubio-Martínez, J. Albaladejo, and A. Garzón-Ruiz, Shedding light on the binding mechanism of kinase inhibitors BI-2536, Volasetib and Ro-3280 with their pharmacological target PLK1, J. Photochem. Photobiol. B: Biol. 232 (2022), pp. 112477. doi:10.1016/j.jphotobiol.2022.112477.
  • J. Tong, T. Wang, and Y. Feng, Drug design and molecular docking simulations of Polo-like kinase 1 inhibitors based on QSAR study, New J. Chem. 44 (2020), pp. 21134–21145. doi:10.1039/D0NJ04367B.
  • Z. Deng, G. Chen, S. Liu, Y. Li, J. Zhong, B. Zhang, H. Huang, Z. Wang, Q. Xu, and X. Deng, Discovery of Methyl 3-((2-((1-(dimethylglycyl)-5-methoxyindolin-6-yl)amino)-5-(trifluoro-methyl)pyrimidin-4-yl)amino)thiophene-2-carboxylate as a potent and selective polo-like Kinase 1 (PLK1) inhibitor for combating hepatocellular carcinoma, Eur. J. Med. Chem. 206 (2020), pp. 112697. doi:10.1016/j.ejmech.2020.112697.
  • S. Su, G. Chhabra, C.K. Singh, M.A. Ndiaye, and N. Ahmad, PLK1 inhibition-based combination therapies for cancer management, Transl. Oncol. 16 (2022), pp. 101332. doi:10.1016/j.tranon.2021.101332.
  • Y. Oh, H. Jung, H. Kim, J. Baek, J. Jun, H. Cho, D. Im, and J.-M. Hah, Design and synthesis of a novel PLK1 inhibitor scaffold using a hybridized 3D-QSAR model, Int. J. Mol. Sci. 22 (2021), pp. 3865. doi:10.3390/ijms22083865.
  • J. Tong, D. Luo, S. Bian, and X. Zhang, Structural investigation of tetrahydropteridin analogues as selective PLK1 inhibitors for treating cancer through combined QSAR techniques, molecular docking, and molecular dynamics simulations, J. Mol. Liq. 335 (2021), pp. 116235. doi:10.1016/j.molliq.2021.116235.
  • S. Ahmadi, S. Lotfi, S. Afshari, P. Kumar, and E. Ghasemi, CORAL: Monte Carlo based global QSAR modelling of Bruton tyrosine kinase inhibitors using hybrid descriptors, SAR QSAR Environ. Res. 32 (2021), pp. 1013–1031. doi:10.1080/1062936X.2021.2003429.
  • S. Ahmadi, S. Lotfi, and P. Kumar, A Monte Carlo method based QSPR model for prediction of reaction rate constants of hydrated electrons with organic contaminants, SAR QSAR Environ. Res. 31 (2020), pp. 935–950. doi:10.1080/1062936X.2020.1842495.
  • A. Kumar and P. Kumar, Prediction of power conversion efficiency of phenothiazine-based dye-sensitized solar cells using Monte Carlo method with index of ideality of correlation, SAR QSAR Environ. Res. 32 (2021), pp. 817–834. doi:10.1080/1062936X.2021.1973095.
  • P. Kumar and A. Kumar, In silico enhancement of azo dye adsorption affinity for cellulose fibre through mechanistic interpretation under guidance of QSPR models using Monte Carlo method with index of ideality correlation, SAR QSAR Environ. Res. 31 (2020), pp. 697–715. doi:10.1080/1062936X.2020.1806105.
  • P. Kumar, A. Kumar, and J. Sindhu, In silico design of diacylglycerol acyltransferase-1 (DGAT1) inhibitors based on SMILES descriptors using Monte-Carlo method, SAR QSAR Environ. Res. 30 (2019), pp. 525–541. doi:10.1080/1062936X.2019.1629998.
  • P. Kumar, A. Kumar, and J. Sindhu, Design and development of novel focal adhesion kinase (FAK) inhibitors using Monte Carlo method with index of ideality of correlation to validate QSAR, SAR QSAR Environ. Res. 30 (2019), pp. 63–80. doi:10.1080/1062936X.2018.1564067.
  • P. Kumar, R. Singh, A. Kumar, A.P. Toropova, A.A. Toropov, M. Devi, S. Lal, J. Sindhu, and D. Singh, Identifications of good and bad structural fragments of hydrazone/2,5-disubstituted-1,3,4-oxadiazole hybrids with correlation intensity index and consensus modelling using Monte Carlo based QSAR studies, their molecular docking and ADME analysis, SAR QSAR Environ. Res. 33 (2022), pp. 677–700. doi:10.1080/1062936X.2022.2120068.
  • M.S. Chauhan, P. Kumar, and A. Kumar, Development of prediction model for fructose-1,6- bisphosphatase inhibitors using the Monte Carlo method, SAR QSAR Environ. Res. 30 (2019), pp. 145–159. doi:10.1080/1062936X.2019.1568299.
  • X.-Y. Wang, Y.-H. Wang, Z. Song, X.-Y. Hu, J.-P. Wei, J. Zhang, and H.-S. Wang, Recent progress in functional peptides designed for tumor-targeted imaging and therapy, J. Mater. Chem. C 9 (2021), pp. 3749–3772. doi:10.1039/D0TC05405D.
  • A. Nath, P. De, and K. Roy, In silico modelling of acute toxicity of 1, 2, 4-triazole antifungal agents towards zebrafish (Danio rerio) embryos: Application of the small dataset modeller tool, Toxicol. In Vitro 75 (2021), pp. 105205. doi:10.1016/j.tiv.2021.105205.
  • M. Duhan, J. Sindhu, P. Kumar, M. Devi, R. Singh, R. Kumar, S. Lal, A. Kumar, S. Kumar, and K. Hussain, Quantitative structure activity relationship studies of novel hydrazone derivatives as α-amylase inhibitors with index of ideality of correlation, J. Biomol. Struct. Dyn. 40 (2022), pp. 4933–4953. doi:10.1080/07391102.2020.1863861.
  • S.C. Peter, J.K. Dhanjal, V. Malik, N. Radhakrishnan, M. Jayakanthan, and D. Sundar, Quantitative structure-activity relationship (QSAR): Modeling approaches to biological applications, in Encyclopedia of Bioinformatics and Computational Biology, S. Ranganathan, M. Gribskov, K. Nakai, and C. Schonbach, eds., Academic Press, Oxford, 2019, pp. 661–676. doi:10.1016/B978-0-12-809633-8.20197-0.
  • M. Babu Singh, P. Jain, J. Tomar, V. Kumar, I. Bahadur, D.K. Arya, and P. Singh, An In Silico investigation for Acyclovir and its derivatives to fight the COVID-19: Molecular docking, DFT calculations, ADME and td-molecular dynamics simulations, J. Indian Chem. Soc. 99 (2022), pp. 100433. doi:10.1016/j.jics.2022.100433.
  • G. Zhang, N. Li, Y. Zhang, J. Pan, and D. Gong, Binding mechanism of 4−octylphenol with human serum albumin: Spectroscopic investigations, molecular docking and dynamics simulation, Spectrochim. Acta A: Mol. Biomol. Spectrosc. 255 (2021), pp. 119662. doi:10.1016/j.saa.2021.119662.
  • -M.-M. Zhan, Y. Yang, J. Luo, -X.-X. Zhang, X. Xiao, S. Li, K. Cheng, Z. Xie, Z. Tu, and C. Liao, Design, synthesis, and biological evaluation of novel highly selective polo-like kinase 2 inhibitors based on the tetrahydropteridin chemical scaffold, Eur. J. Med. Chem. 143 (2018), pp. 724–731. doi:10.1016/j.ejmech.2017.11.058.
  • X. Lv, X. Yang, -M.-M. Zhan, P. Cao, S. Zheng, R. Peng, J. Han, Z. Xie, Z. Tu, and C. Liao, Structure-based design and SAR development of novel selective polo-like kinase 1 inhibitors having the tetrahydropteridin scaffold, Eur. J. Med. Chem. 184 (2019), pp. 111769. doi:10.1016/j.ejmech.2019.111769.
  • R.L. Bakal, R.D. Jawarkar, J.V. Manwar, M.S. Jaiswal, A. Ghosh, A. Gandhi, M.E.A. Zaki, S. Al-Hussain, A. Samad, V.H. Masand, N. Mukerjee, S. Nasir Abbas Bukhari, P. Sharma, and I. Lewaa, Identification of potent aldose reductase inhibitors as antidiabetic (Anti-hyperglycemic) agents using QSAR based virtual screening, molecular docking, MD simulation and MMGBSA approaches, Saudi Pharm. 30 (2022), pp. 693–710. doi:10.1016/j.jsps.2022.04.003.
  • S. Pramanik and K. Roy, Modeling bioconcentration factor (BCF) using mechanistically interpretable descriptors computed from open source tool “PaDEL-Descriptor”, Environ. Sci. Pollut. Res. 21 (2013), pp. 2955–2965. doi:10.1007/s11356-013-2247-z.
  • C.W. Yap, PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints, J. Comput. Chem. 32 (2011), pp. 1466–1474. doi:10.1002/jcc.21707.
  • V.H. Masand, N.N.E. El-Sayed, M.U. Bambole, V.R. Patil, and S.D. Thakur, Multiple quantitative structure-activity relationships (QSARs) analysis for orally active trypanocidal N-myristoyltransferase inhibitors, J. Mol. Struct. 1175 (2019), pp. 481–487. doi:10.1016/j.molstruc.2018.07.080.
  • V.H. Masand, N.N.E. El-Sayed, D.T. Mahajan, A.G. Mercader, A.M. Alafeefy, and I.G. Shibi, QSAR modeling for anti-human African trypanosomiasis activity of substituted 2-Phenylimidazopyridines, J. Mol. Struct. 1130 (2017), pp. 711–718. doi:10.1016/j.molstruc.2016.11.012.
  • A. Seth and K. Roy, QSAR modeling of algal low level toxicity values of different phenol and aniline derivatives using 2D descriptors, Aquat. Toxicol. 228 (2020), pp. 105627. doi:10.1016/j.aquatox.2020.105627.
  • D.E. Arthur, M.E.S. Soliman, S.E. Adeniji, O. Adedirin, and F. Peter, QSAR and molecular docking study of gonadotropin-releasing hormone receptor inhibitors, Sci. Afr. 17 (2022), pp. e01291.
  • P. Gopinath and M.K. Kathiravan, Molecular insights of oxadiazole benzene sulfonamides as human carbonic anhydrase IX inhibitors: Combined molecular docking, molecular dynamics, and 3D QSAR studies, J. Indian Chem. Soc. 99 (2022), pp. 100339. doi:10.1016/j.jics.2022.100339
  • A. Golbraikh and A. Tropsha, Beware of q2!, J. Mol. Graph. Model. 20 (2002), pp. 269–276. doi:10.1016/S1093-3263(01)00123-1.
  • G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, and A.J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, J. Comput. Chem. 30 (2009), pp. 2785–2791. doi:10.1002/jcc.21256.
  • S. Yuan, H.C.S. Chan, and Z. Hu, Using PyMOL as a platform for computational drug design, WIREs Comput. Mol. Sci. 7 (2017), pp. e1298. doi:10.1002/wcms.1298.
  • E. Pettersen, T. Goddard, C. Huang, G. Couch, D. Greenblatt, E. Meng, and T. Ferrin, UCSF chimera – A visualization system for exploratory research and analysis, J. Comput. Chem. 25 (2004), pp. 1605–1612. doi:10.1002/jcc.20084.
  • P. Rani, K.S. Chahal, P.R. Kataria, P. Kumar, S. Kumar, and J. Sindhu, Unravelling the thermodynamics and binding interactions of bovine serum albumin (BSA) with thiazole based carbohydrazide: Multi-spectroscopic, DFT and molecular dynamics approach, J. Mol. Struct. 1270 (2022), pp. 133939. doi:10.1016/j.molstruc.2022.133939.
  • S. Genheden and U. Ryde, The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities, Expert Opin. Drug Discov. 10 (2015), pp. 449–461. doi:10.1517/17460441.2015.1032936.
  • D.L. Beveridge and F.M. DiCapua, Free energy via molecular simulation: Applications to chemical and biomolecular systems, Annu. Rev. Biophys. Biophys. Chem. 18 (1989), pp. 431–492. doi:10.1146/annurev.bb.18.060189.002243.
  • C. Jarzynski, Nonequilibrium equality for free energy differences, Phys. Rev. Lett. 78 (1997), pp. 2690–2693. doi:10.1103/PhysRevLett.78.2690.
  • R.A. Friesner, R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, and D.T. Mainz, Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes, J. Med. Chem. 49 (2006), pp. 6177–6196. doi:10.1021/jm051256o.
  • S. Ahmed, M.C. Ali, R.A. Ruma, S. Mahmud, G.K. Paul, M.A. Saleh, M.M. Alshahrani, A.J. Obaidullah, S.K. Biswas, M.M. Rahman, M.M. Rahman, and M.R. Islam, Molecular docking and dynamics simulation of natural compounds from betel leaves (Piper betle L.) for investigating the potential inhibition of alpha-amylase and alpha-glucosidase of type 2 diabetes, Molecules 27 (2022), pp. 4526. doi:10.3390/molecules27144526.
  • S. Sirin, D.A. Pearlman, and W. Sherman, Physics-based enzyme design: Predicting binding affinity and catalytic activity, Proteins: Struct. Funct. Bioinform. 82 (2014), pp. 3397–3409. doi:10.1002/prot.24694.
  • R. Pingaew, V. Prachayasittikul, A. Worachartcheewan, A. Thongnum, S. Prachayasittikul, S. Ruchirawat, and V. Prachayasittikul, Anticancer activity and QSAR study of sulfur-containing thiourea and sulfonamide derivatives, Heliyon 8 (2022), pp. e10067. doi:10.1016/j.heliyon.2022.e10067.
  • T. Puzyn, J. Leszczynski, and M.T. Cronin, Recent Advances in QSAR Studies: Methods and Applications, Vol. 8, Springer Science & Business Media, London, 2010.
  • B. Hollas, An analysis of the autocorrelation descriptor for molecules, J. Math. Chem. 33 (2003), pp. 91–101. doi:10.1023/A:1023247831238.
  • Danishuddin and A.U. Khan, Descriptors and their selection methods in QSAR analysis: Paradigm for drug design, Drug Discov. Today 21 (2016), pp. 1291–1302. doi:10.1016/j.drudis.2016.06.013.
  • L.H. Hall and L.B. Kier, Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information, J. Chem. Inf. Comput. Sci. 35 (1995), pp. 1039–1045. doi:10.1021/ci00028a014.
  • L. Saíz-Urra, M. González, and M. Teijeira, 2D-autocorrelation descriptors for predicting cytotoxicity of naphthoquinone ester derivatives against oral human epidermoid carcinoma, Bioorg. Med. Chem. 15 (2007), pp. 3565–3571. doi:10.1016/j.bmc.2007.02.032.
  • H.M. Kasralikar, S.C. Jadhavar, S.V. Goswami, N.S. Kaminwar, and S.R. Bhusare, Design, synthesis and molecular docking of pyrazolo [3,4d] thiazole hybrids as potential anti-HIV-1 NNRT inhibitors, Bioorg. Chem. 86 (2019), pp. 437–444. doi:10.1016/j.bioorg.2019.02.006.
  • W. Gao, X. Ma, H. Yang, Y. Luan, and H. Ai, Molecular engineering and activity improvement of acetylcholinesterase inhibitors: Insights from 3D-QSAR, docking, and molecular dynamics simulation studies, J. Mol. Graph. Model. 116 (2022), pp. 108239. doi:10.1016/j.jmgm.2022.108239.
  • S. Jana, S. Dalapati, S. Ghosh, and N. Guchhait, Binding interaction between plasma protein bovine serum albumin and flexible charge transfer fluorophore: A spectroscopic study in combination with molecular docking and molecular dynamics simulation, J. Photochem. Photobiol. A: Chem. 231 (2012), pp. 19–27. doi:10.1016/j.jphotochem.2011.12.002.
  • L. Li, C.E. Peng, Y. Wang, C. Xiong, Y. Liu, C. Wu, and J. Wang, Identify promising IKK-β inhibitors: A docking-based 3D-QSAR study combining molecular design and molecular dynamics simulation, Arab. J. Chem. 15 (2022), pp. 103786. doi:10.1016/j.arabjc.2022.103786.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.