Abstract
Sunitinib is a potent anti-cancer scaffold that acts as a VEGFR-2 inhibitor. Although the scaffold exhibits potent anti-cancer activity, it is cardiotoxic and also induces hypothyroidism. The current research aims to optimize the Sunitinib for cardio-toxicity and thyro-toxicity by scaffold hopping approach using the admetSAR server. The server has optimized the physico-chemical properties of Sunitinib, which were contributing to the cardiotoxicity and thyro-toxicity. The library of the optimized compounds was further screened by the molecular docking studies and results were validated by the MD simulation and DFT analysis for VEGFR-2 inhibition. Compounds 163 and 432 exhibited the highest affinity to VEGFR-2 receptor with minimal cardiotoxicity and thyro-toxicity. These two compounds could be the starting point for the further discovery of angiogenic inhibitors.
Similar content being viewed by others
References
Amala M, Rajamanikandan S, Prabhu D, Surekha K, Jeyakanthan J (2019) Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: combined molecular docking and molecular dynamics approaches. J Biomol Struct Dyn 37(2):394–410. https://doi.org/10.1080/07391102.2018.1427633
Ammar YA, Sh El-Sharief AM, Belal A, Abbas SY, Mohamed YA, Mehany ABM, Ragab A (2018) Design, synthesis, antiproliferative activity, molecular docking and cell cycle analysis of some novel (morpholinosulfonyl) isatins with potential EGFR inhibitory activity. Eur J Med Chem 5(156):918–932. https://doi.org/10.1016/j.ejmech.2018.06.061
Arora A, Scholar EM (2005) Role of tyrosine kinase inhibitors in cancer therapy. J Pharmacol Exp Ther 315(3):971–979. https://doi.org/10.1124/jpet.105.084145
Ayllon J, Beuselinck B, Morel A, Barrascout E, Medioni J, Scotte F, Oudard S (2011) Long-term response and postsurgical complete remissions after treatment with sunitinib malate, an oral multitargeted receptor tyrosine kinase inhibitor, in patients with metastatic renal cell carcinoma. Cancer Invest 29(4):282–285. https://doi.org/10.3109/07357907.2011.568560
Bhowmick S, Al Faris NA, Al Tamimi JZ, Al Othman ZA, Aldayel TS, Wabaidur SM, Islam MA (2020) Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: multi-cheminformatics approaches for anticancer therapeutics. J Mol Struct. https://doi.org/10.1016/j.molstruc.2020.128316
Bochevarov AD, Harder E, Hughes TF, Greenwood JR, Braden DA, Philipp DM, Rinaldo D, Hall MD, Zhang J, Friesner RA (2013) Jaguar: a high-performance quantum chemistry software program with strengths in life and materials sciences. Int J Quantum Chem 113(18):2110–2142. https://doi.org/10.1002/qua.24481
Bono P, Rautiola J, Utriainen T, Joensuu H (2011) Hypertension as predictor of sunitinib treatment outcome in metastatic renal cell carcinoma. Acta Oncol 50(4):569–573. https://doi.org/10.3109/0284186X.2010.543696
Bruce D, Tan PH (2011) Blocking the interaction of vascular endothelial growth factor receptors with their ligands and their effector signaling as a novel therapeutic target for cancer: time for a new look? Expert Opin Investig Drugs 20(10):1413–1434. https://doi.org/10.1517/13543784.2011.611801
Buda-Nowak A, Kucharz J, Dumnicka P, Kuzniewski M, Herman RM, Zygulska AL, Kusnierz-Cabala B (2017) Sunitinib-induced hypothyroidism predicts progression-free survival in metastatic renal cell carcinoma patients. Med Oncol 34(4):68. https://doi.org/10.1007/s12032-017-0928-z
Casalvieri KA, Matheson CJ, Backos DS, Reigan P (2020) Molecular docking of substituted pteridinones and pyrimidines to the ATP-binding site of the N-terminal domain of RSK2 and associated MM/GBSA and molecular field datasets. Data Brief 29:105347. https://doi.org/10.1016/j.dib.2020.105347
Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ (2010) Virtual screening with AutoDock: theory and practice. Expert Opin Drug Discov 5(6):597–607. https://doi.org/10.1517/17460441.2010.484460
Cui W, Zhang ZJ, Hu SQ, Mak SH, Xu DP, Choi CL, Wang YQ, Tsim WK, Lee MY, Rong JH, Han YF (2014) Sunitinib produces neuroprotective effect via inhibiting nitric oxide overproduction. CNS Neurosci Ther 20(3):244–252. https://doi.org/10.1111/cns.12203
Debnath B, Ganguly S (2016) Synthesis, biological evaluation, in silico docking, and virtual ADME studies of 2-[2-Oxo-3-(arylimino) indolin-1-yl]-N-arylacetamides as potent anti-breast cancer agents. Monatsh Chem 147(3):565–574. https://doi.org/10.1007/s00706-015-1566-9
Desmond Molecular Dynamics System (2017) D. E. Shaw Research, New York, NY, 2018-4. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2018-4
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739–1749. https://doi.org/10.1021/jm0306430
Ganesan MS, Raja KK, Murugesan S, Kumar BK, Rajagopal G, Thirunavukkarasu S (2020) Synthesis, biological evaluation, molecular docking, molecular dynamics and DFT studies of quinoline-fluoroproline amide hybrids. J Mol Struct. https://doi.org/10.1016/j.molstruc.2020.128360
Gingrich DE, Reddy DR, Iqbal MA, Singh J, Aimone LD, Angeles TS, Albom M, Yang S, Ator MA, Meyer SL, Robinson C, Ruggeri BA, Dionne CA, Vaught JL, Mallamo JP, Hudkins RL (2003) A new class of potent vascular endothelial growth factor receptor tyrosine kinase inhibitors: structure-activity relationships for a series of 9-alkoxymethyl-12-(3-hydroxypropyl)indeno[2,1-a]pyrrolo[3,4-c]carbazole-5-ones and the identification of CEP-5214 and its dimethylglycine ester prodrug clinical candidate CEP-7055. J Med Chem 46(25):5375–5388. https://doi.org/10.1021/jm0301641
Guillemont J, Meyer C, Poncelet A, Bourdrez X, Andries K (2011) Diarylquinolines, synthesis pathways and quantitative structure–activity relationship studies leading to the discovery of TMC207. Future Med Chem 3(11):1345–1360. https://doi.org/10.4155/fmc.11.79
Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47(7):1750–1759. https://doi.org/10.1021/jm030644s
https://www.rcsb.org/structure/4AGD. Accessed on 18th Apr 2021
Hui EP, Ma BBY, King AD, Mo F, Chan SL, Kam MKM, Loong HH, Ahuja AT, Zee BCY, Chan ATC (2011) Hemorrhagic complications in a phase II study of sunitinib in patients of nasopharyngeal carcinoma who has previously received high-dose radiation. Ann Oncol 22(6):1280–1287. https://doi.org/10.1093/annonc/mdq629
Isidori A, Lenzi A, Rizza L, Rota F, Giacinto PD (2017) Role of sunitinib-induced hypothyroidism in oncological patients. Endocrinol Metab Int J 5(4):00129. https://doi.org/10.1002/cncr.25422
Jiao Q, Bi L, Ren Y, Song S, Wang Q, Wang YS (2018) Advances in studies of tyrosine kinase inhibitors and their acquired resistance. Mol Cancer 17(1):36. https://doi.org/10.1186/s12943-018-0801-5
Jin Z, Wang Y, Yu XF, Tan QQ, Liang SS, Li T, Zhang H, Shaw PC, Wang J, Hu C (2020a) Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: molecular dynamics simulation and MM-GBSA calculation. Comput Biol Chem 85:107241. https://doi.org/10.1016/j.compbiolchem.2020.107-241
Jordaan MA, Ebenezer O, Damoyi N, Shapi M (2020) Virtual screening, molecular docking studies and DFT calculations of FDA approved compounds similar to the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz. Heliyon 6(8):04642. https://doi.org/10.1016/j.heliyon.2020.e04642
Kappers MH, van Esch JH, Sluiter W, Sleijfer S, Danser AH, van den Meiracker AH (2010) Hypertension induced by the tyrosine kinase inhibitor sunitinib is associated with increased circulating endothelin-1 levels. Hypertension 56(4):675–681. https://doi.org/10.1161/HYPERTENSIONAHA.109.149690
Le Tourneau C, Raymond E, Faivre S (2007) Sunitinib: a novel tyrosine kinase inhibitor. A brief review of its therapeutic potential in the treatment of renal carcinoma and gastrointestinal stromal tumors (GIST). Ther Clin Risk Manag 3(2):341–348. https://doi.org/10.2147/tcrm.2007.3.2.341
Mahmoud HK, Farghaly TA, Abdulwahab HG, Al-Qurashi NT, Shaaban MR (2020) Novel 2-indolinone thiazole hybrids as sunitinib analogues: design, synthesis, and potent VEGFR-2 inhibition with potential anti-renal cancer activity. Eur J Med Chem 15(208):112752. https://doi.org/10.1016/j.ejmech.2020.112752
Murray JS, Politzer P (2011) The electrostatic potential: an overview. Wiley Interdiscipl Rev Comput Mol Sci 1(2):153–163. https://doi.org/10.1002/wcms.19
Panwar U, Singh SK (2020) Atom-based 3D-QSAR, molecular docking, DFT, and simulation studies of acyl hydrazone, hydrazine, and diazene derivatives as IN-LEDGF/p75 inhibitors. Struct Chem. https://doi.org/10.1007/s11224-020-01628-3
Patel H, Sonawane Y, Jagtap R, Dhangar K, Thapliyal N, Surana S, Noolvi M, Shaikh MS, Rane RA, Karpoormath R (2015) Structural insight of glitazone for hepato-toxicity: resolving mystery by PASS. Bioorg Med Chem Lett 25(9):1938–1946. https://doi.org/10.1016/j.bmcl.2015.03.020
Patel HM, Shaikh M, Ahmad I, Lokwani D, Surana SJ (2021a) BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non-small cell lung cancer (NSCLC). J Biomol Struct Dyn 39(8):2838–2856. https://doi.org/10.1080/07391102.2020.1754918
Patel HM, Ahmad I, Pawara R, Shaikh M, Surana S (2021b) In silico search of triple mutant T790M/C797S allosteric inhibitors to conquer acquired resistance problem in non-small cell lung cancer (NSCLC): a combined approach of structure-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 39(4):1491–1505. https://doi.org/10.1080/07391102.2020.1734092
Peng FW, Liu DK, Zhang QW, Xu YG, Shi L (2017) VEGFR-2 inhibitors and the therapeutic applications thereof: a patent review (2012–2016). Expert Opin Ther Pat 27(9):987–1004. https://doi.org/10.1080/13543776.2017.1344215
Schrödinger Release (2008) Protein preparation wizard. Epik, Schrödinger, LLC, New York
Santos IS, Guerra FS, Bernardino LF, Fernandes PD, Hamerski L, Silva BV (2019) A facile synthesis of novel isatinspirooxazine derivatives and potential in vitro anti-proliferative activity. J Braz Chem Soc 30(1):198. https://doi.org/10.21577/0103-5053.20180153
Shah S, Lee C, Choi H, Gautam J, Jang H, Kim GJ, Lee YJ, Chaudhary CL, Park SW, Nam TG, Kim JA, Jeong BS (2016) 5-Hydroxy-7-azaindolin-2-one, a novel hybrid of pyridinol and sunitinib: design, synthesis and cytotoxicity against cancer cells. Org Biomol Chem 14(21):4829–4841. https://doi.org/10.1039/c6ob00406g
Simons M (2012) An inside view: VEGF receptor trafficking and signaling. Physiology (bethesda) 27(4):213–222. https://doi.org/10.1152/physiol.00016.2012
Singh P, Kaur M, Holzer W (2010) Synthesis and evaluation of indole, pyrazole, chromone and pyrimidine based conjugates for tumor growth inhibitory activities—development of highly efficacious cytotoxic agents. Eur J Med Chem 45(11):4968–4982. https://doi.org/10.1016/j.ejmech.2010.08.004
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F (2021) Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 71(3):209–249. https://doi.org/10.3322/caac.21660
Vijayakumar B, Parasuraman S, Raveendran R, Velmurugan D (2014) Identification of natural inhibitors against angiotensin I converting enzyme for cardiac safety using induced fit docking and MM-GBSA studies. Pharmacogn Mag 10(Suppl 3):S639–S644. https://doi.org/10.4103/0973-1296.139809
Vistoli G, Pedretti A, Testa B (2008) Assessing drug-likeness–what are we missing? Drug Discov Today 13(7–8):285–294. https://doi.org/10.1016/j.drudis.2007.11.007
Wang F, Wang L, Li Y, Wang N, Wang Y, Cao Q, Gong P, Yang J, Wu C (2018) PAC-1 and its derivative WF-210 inhibit angiogenesis by inhibiting VEGF/VEGFR pathway. Eur J Pharmacol 821:29–38. https://doi.org/10.1016/j.ejphar.2017.12.035
Zhang L, Zheng Q, Yang Y, Zhou H, Gong X, Zhao S, Fan C (2014) Synthesis and in vivo SAR study of indolin-2-one-based multi-targeted inhibitors as potential anticancer agents. Eur J Med Chem 82:139–151. https://doi.org/10.1016/j.ejmech.2014.05.051
Zhao Y, Adjei AA (2015) Targeting angiogenesis in cancer therapy: moving beyond vascular endothelial growth factor. Oncologist 20(6):660–673. https://doi.org/10.1634/theoncologist.2014-0465
Acknowledgements
Authors are thankful to Principal, BVDU Poona College of Pharmacy, Pune and Principal, Vice Principal for conducting collaborative research work R. C. Patel Institute of Pharmaceutical Education and Research, authors are also thankful to Dr. Harun Patel, Division of Computer-Aided Drug Design for contributing for designing and carrying out research work at CADD division at R. C. Patel Institute of Pharmaceutical Education and Research.
Funding
The author(s) received no financial aid or support in any form for this research work.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
Authors have no conflict of interest to declare.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Chaudhari, B., Patel, H., Thakar, S. et al. Optimizing the Sunitinib for cardio-toxicity and thyro-toxicity by scaffold hopping approach. In Silico Pharmacol. 10, 10 (2022). https://doi.org/10.1007/s40203-022-00125-1
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s40203-022-00125-1