Molecular dynamics and 3D-QSAR studies on indazole derivatives as HIF-1α inhibitors

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Albadari, N., Deng, S., & Li, W. (2019). The transcriptional factors hif-1 and hif-2 and their novel inhibitors in cancer therapy. Expert Opinion on Drug Discovery, 14(7), 667–682. https://doi.org/10.1080/17460441.2019.1613370
   PubMed Web of Science ®Google Scholar
• An, H., Kim, N. J., Jung, J. W., Jang, H., Park, J. W., & Suh, Y. G. (2011). Design, synthesis and insight into the structure-activity relationship of 1,3-disubstituted indazoles as novel HIF-1 inhibitors. Bioorganic & Medicinal Chemistry Letters, 21(21), 6297–6300. https://doi.org/10.1016/j.bmcl.2011.08.120
   PubMed Web of Science ®Google Scholar
• Angelova, V. T., Pencheva, T., Vassilev, N., Simeonova, R., Momekov, G., & Valcheva, V. (2019). New indole and indazole derivatives as potential antimycobacterial agents. Medicinal Chemistry Research, 28(4), 485–497. https://doi.org/10.1007/s00044-019-02293-w
   Web of Science ®Google Scholar
• Azam, M. A., Thathan, J., & Jupudi, S. (2020). Pharmacophore modeling, atom based 3d-qsar, molecular docking and molecular dynamics studies on Escherichia coli pare inhibitors. Computational Biology and Chemistry, 84, 107197. https://doi.org/10.1016/j.compbiolchem.2019.107197
   PubMed Web of Science ®Google Scholar
• Banjare, L., Singh, Y., Verma, S. K., Singh, A. K., Kumar, P., Kumar, S., Jain, A. K., & Thareja, S. (2021). Multifaceted 3d-qsar analysis for the identification of pharmacophoric features of biphenyl analogues as aromatase inhibitors. Journal of Biomolecular Structure and Dynamics, 40(5), 1–20. https://doi.org/10.1080/07391102.2021.2019122
   Web of Science ®Google Scholar
• Banjare, L., Verma, S. K., Jain, A. K., & Thareja, S. (2019). Structure guided molecular docking assisted alignment dependent 3dqsar study on steroidal aromatase inhibitors (sais) as anti-breast cancer agents. Letters in Drug Design & Discovery, 16(7), 808–817. https://doi.org/10.2174/1570180815666181010101024
   Web of Science ®Google Scholar
• Ben El Ayouchia, H., Anane, H., El Idrissi Moubtassim, M. L., Domingo, L. R., Julve, M., & Stiriba, S. E. (2016). A theoretical study of the relationship between the electrophilicity ω index and hammett constant σp in [3 + 2] cycloaddition reactions of aryl azide/alkyne derivatives. Molecules, 21(11), 1434. https://doi.org/10.3390/molecules21111434
   PubMed Web of Science ®Google Scholar
• Bitencourt-Ferreira, G., & de Azevedo, W. F. (2019). Docking screens for drug discovery. In W. F. de Azevedo Jr. (Ed.), Molegro virtual docker for docking. Springer (pp. 149-167).
   Google Scholar
• Cappel, D., Dixon, S. L., Sherman, W., & Duan, J. (2015). Exploring conformational search protocols for ligand-based virtual screening and 3-d qsar modeling. Journal of Computer-Aided Molecular Design, 29(2), 165–182. https://doi.org/10.1007/s10822-014-9813-4
   PubMed Web of Science ®Google Scholar
• Cheekavolu, C., & Muniappan, M. (2016). In vivo and in vitro anti-inflammatory activity of indazole and its derivatives. Journal of Clinical and Diagnostic Research, 10(9), FF01–FF06. https://doi.org/10.7860/JCDR/2016/19338.8465
   PubMed Web of Science ®Google Scholar
• Chung, J. Y., Pasha, F., Cho, S. J., Won, M., Lee, J. J., & Lee, K. (2009). Pharmacophore-based 3d-qsar of hif-1 inhibitors. Archives of Pharmacal Research, 32(3), 317–323. https://doi.org/10.1007/s12272-009-1301-3
   PubMed Web of Science ®Google Scholar
• Du, S., Lu, H., Yang, D., Li, H., Gu, X., Wan, C., Jia, C., Wang, M., Li, X., & Qin, Z. (2015). Synthesis, antifungal activity and qsar of some novel carboxylic acid amides. Molecules (Basel, Switzerland), 20(3), 4071–4087. https://doi.org/10.3390/molecules20034071
   PubMed Web of Science ®Google Scholar
• Ertl, P. A. (2021). A Web Tool for Calculating Substituent Descriptors Compatible with Hammett Sigma Constants. ChemRxiv. http://doi.org/10.26434/chemrxiv.14215964.v1
   Google Scholar
• Gavhane, Y., Shete, A., Bhagat, A., Shinde, V., Bhong, K., Khairnar, G., & Yadav, A. (2011). Solid tumors: Facts, challenges and solutions. International Journal of Pharmaceutical Sciences and Research,2(1) 2–12. http://www.ijpsr.info/docs/IJPSR11-02-01-01.pdf
   Google Scholar
• Halder, A. K., Saha, A., Saha, K. D., & Jha, T. (2015). Stepwise development of structure–activity relationship of diverse parp-1 inhibitors through comparative and validated in silic o modeling techniques and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 33(8), 1756–1779. https://doi.org/10.1080/07391102.2014.969772
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). Lincs: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). Vmd: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27-38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Janardhanan, J. C., Mishra, R. K., Das, G., Sini, S., Jayamurthy, P., Suresh, C. H., Praveen, V. K., Manoj, N., & Babu, B. P. (2018). Functionalizable 1h‐indazoles by palladium catalyzed aza‐nenitzescu reaction: Pharmacophores to donor‐acceptor type multi‐luminescent fluorophores. Asian Journal of Organic Chemistry, 7(10), 2094–2104. https://doi.org/10.1002/ajoc.201800413
   Web of Science ®Google Scholar
• Jones, L. H., Allan, G., Barba, O., Burt, C., Corbau, R., Dupont, T., Knöchel, T., Irving, S., Middleton, D. S., Mowbray, C. E., Perros, M., Ringrose, H., Swain, N. A., Webster, R., Westby, M., & Phillips, C. (2009). Novel indazole non-nucleoside reverse transcriptase inhibitors using molecular hybridization based on crystallographic overlays. Journal of Medicinal Chemistry, 52(4), 1219–1223. https://doi.org/10.1021/jm801322h
   PubMed Web of Science ®Google Scholar
• Kumar Verma, S., Kant Sharma, S., & Thareja, S. (2015). Docking study of novel pyrrolidine derivatives as potential dipeptidyl peptidase-iv (dpp-iv) inhibitors. Letters in Drug Design & Discovery, 12(4), 284–291. https://doi.org/10.2174/1570180811666141016000752
   Web of Science ®Google Scholar
• Lee, F. Y., Lien, J. C., Huang, L. J., Huang, T. M., Tsai, S. C., Teng, C. M., Wu, C. C., Cheng, F. C., & Kuo, S. C. (2001). Synthesis of 1-benzyl-3-(5'-hydroxymethyl-2'-furyl)indazole analogues as novel antiplatelet agents. Journal of Medicinal Chemistry, 44(22), 3746–3749. https://doi.org/10.1021/jm010001h
   PubMed Web of Science ®Google Scholar
• Li, J., Xi, W., Li, X., Sun, H., & Li, Y. (2019). Advances in inhibition of protein-protein interactions targeting hypoxia-inducible factor-1 for cancer therapy. Bioorganic & Medicinal Chemistry, 27(7), 1145–1158. https://doi.org/10.1016/j.bmc.2019.01.042
   PubMed Web of Science ®Google Scholar
• López-Vallejo, F., Castillo, R., Yépez-Mulia, L., & Medina-Franco, J. L. (2011). Benzotriazoles and indazoles are scaffolds with biological activity against entamoeba histolytica. Journal of Biomolecular Screening, 16(8), 862–868. https://doi.org/10.1177/1087057111414902
   PubMedGoogle Scholar
• Molinari, A., Oliva, A., Arismendi-Macuer, M., Guzmán, L., Fuentealba, M., Knox, M., Vinet, R., & San Feliciano, A. (2015). New 1H-benzo[f]indazole-4,9-diones conjugated with C-protected amino acids and other derivatives: Synthesis and in vitro antiproliferative evaluation. Molecules (Basel, Switzerland), 20(12), 21924–21938. https://doi.org/10.3390/molecules201219809
   PubMed Web of Science ®Google Scholar
• Mooring, S. R., Jin, H., Devi, N. S., Jabbar, A. A., Kaluz, S., Liu, Y., Van Meir, E. G., & Wang, B. (2011). Design and synthesis of novel small-molecule inhibitors of the hypoxia inducible factor pathway. Journal of Medicinal Chemistry, 54(24), 8471–8489. https://doi.org/10.1021/jm201018g
   PubMed Web of Science ®Google Scholar
• Muz, B., de la Puente, P., Azab, F., & Azab, A. K. (2015). The role of hypoxia in cancer progression, angiogenesis, metastasis, and resistance to therapy. Hypoxia (Auckland, NZ), 3, 83–92. https://doi.org/10.2147/HP.S93413
   PubMed Web of Science ®Google Scholar
• Nemaysh, V., & Luthra, P. M. (2017). Computational analysis revealing that k634 and t681 mutations modulate the 3d-structure of pdgfr-β and lead to sunitinib resistance. RSC Advances, 7(60), 37612–37626. https://doi.org/10.1039/C7RA01305A
   Web of Science ®Google Scholar
• Ounissi, M., Kameli, A., Tigrine, C., & Rachedi, F. Z. (2018). Computer-aided identification of natural lead compounds as cyclooxygenase-2 inhibitors using virtual screening and molecular dynamic simulation. Computational Biology and Chemistry, 77, 1–16. 10.1016/j.compbiolchem.2018.07.005
   PubMed Web of Science ®Google Scholar
• Palakurti, R., & Vadrevu, R. (2017). Pharmacophore based 3d-qsar modeling, virtual screening and docking for identification of potential inhibitors of β-secretase. Computational Biology and Chemistry, 68, 107–117. https://doi.org/10.1016/j.compbiolchem.2017.03.001
   PubMed Web of Science ®Google Scholar
• Pinzi, L., & Rastelli, G. (2019). Molecular docking: Shifting paradigms in drug discovery. International Journal of Molecular Sciences, 20(18), 4331. https://doi.org/10.3390/ijms20184331
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). Prodrg: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Sheng, R., Li, S., Lin, G., Shangguan, S., Gu, Y., Qiu, N., Cao, J., He, Q., Yang, B., & Hu, Y. (2015). Novel potent hif-1 inhibitors for the prevention of tumor metastasis: Discovery and optimization of 3-aryl-5-indazole-1, 2, 4-oxadiazole derivatives. RSC Advances, 5(100), 81817–81830. https://doi.org/10.1039/C5RA15191K
   Web of Science ®Google Scholar
• Shenoy, N., Shrivastava, M., Sukrithan, V., Papaspyridi, D., & Darbinyan, K. (2015). The regulation and interactions of the hypoxia inducible factor pathway in carcinogenesis and potential cancer therapeutic strategies. Journal of Cancer Therapy, 06(06), 511–521. https://doi.org/10.4236/jct.2015.66055
   Google Scholar
• Shin, D. H., Kim, J. H., Jung, Y. J., Kim, K. E., Jeong, J. M., Chun, Y. S., & Park, J. W. (2007). Preclinical evaluation of yc-1, a hif inhibitor, for the prevention of tumor spreading. Cancer Letters, 255(1), 107–116. https://doi.org/10.1016/j.canlet.2007.03.026
   PubMed Web of Science ®Google Scholar
• Singh, S. P., Deb, C. R., Ahmed, S. U., Saratchandra, Y., & Konwar, B. K. (2016). Molecular docking simulation analysis of the interaction of dietary flavonols with heat shock protein 90. Journal of Biomedical Research, 30(1), 67–74. https://doi.org/10.7555/JBR.29.20130158
   Google Scholar
• Soni, S., & Padwad, Y. S. (2017). Hif-1 in cancer therapy: Two decade long story of a transcription factor. Acta Oncologica (Stockholm, Sweden), 56(4), 503–515. https://doi.org/10.1080/0284186X.2017.1301680
   PubMed Web of Science ®Google Scholar
• Sung, H., Ferlay, J., Siegel, R. L., 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: A Cancer Journal for Clinicians, 71(3), 209–249. https://doi.org/10.3322/caac.21660
   PubMed Web of Science ®Google Scholar
• Takeuchi, A., Hori, M., Sato, S., Ban, H. S., Kuchimaru, T., Kizaka-Kondoh, S., Yamori, T., & Nakamura, H. (2012). Synthesis and biological activity of furanylindazoles as inhibitors of hypoxia inducible factor (hif)-1 transcriptional activity. MedChemComm, 3(11), 1455–1461. https://doi.org/10.1039/c2md20134h
   Web of Science ®Google Scholar
• Thareja, S., Rajpoot, T., & Verma, S. K. (2015). Generation of comparative pharmacophoric model for steroidal 5α-reductase i and ii inhibitors: A 3d-qsar study on 6-azasteroids. Steroids, 95–96, 103. https://doi.org/10.1016/j.steroids.2015.01.001
   Web of Science ®Google Scholar
• Tzvetkov, N. T., Hinz, S., Küppers, P., Gastreich, M., & Müller, C. E. (2014). Indazole- and indole-5-carboxamides: Selective and reversible monoamine oxidase B inhibitors with subnanomolar potency. Journal of Medicinal Chemistry, 57(15), 6679–6703. https://doi.org/10.1021/jm500729a
   PubMed Web of Science ®Google Scholar
• Verma, S. K., & Thareja, S. (2016). Molecular docking assisted 3d-qsar study of benzylidene-2, 4-thiazolidinedione derivatives as ptp-1b inhibitors for the management of type-2 diabetes mellitus. RSC Advances, 6(40), 33857–33867. https://doi.org/10.1039/C6RA03067J
   Web of Science ®Google Scholar
• Verma, S. K., & Thareja, S. (2017). Structure based comprehensive modelling, spatial fingerprints mapping and adme screening of curcumin analogues as novel alr2 inhibitors. PLoS One, 12(4), e0175318. https://doi.org/10.1371/journal.pone.0175318
   PubMed Web of Science ®Google Scholar
• Verma, S. K., Kumar, N., & Thareja, S. (2021). Gaussian field-based comparative 3d qsar modelling for the identification of favourable pharmacophoric features of chromene derivatives as selective inhibitors of alr2 over alr1. Structural Chemistry, 32(3), 1289–1298. https://doi.org/10.1007/s11224-020-01714-6
   Web of Science ®Google Scholar
• Vernekar, S. K. V., Hallaq, H. Y., Clarkson, G., Thompson, A. J., Silvestri, L., Lummis, S. C., & Lochner, M. (2010). Toward biophysical probes for the 5-ht3 receptor: Structure-activity relationship study of granisetron derivatives. Journal of Medicinal Chemistry, 53(5), 2324–2328. https://doi.org/10.1021/jm901827x
   PubMed Web of Science ®Google Scholar
• Wan, Y., He, S., Li, W., & Tang, Z. (2018). Indazole derivatives: Promising anti-tumor agents. Anti-Cancer Agents in Medicinal Chemistry, 18(9), 1228–1234. https://doi.org/10.2174/1871520618666180510113822
   PubMed Web of Science ®Google Scholar
• Yadav, D. K., Sharma, P., Misra, S., Singh, H., Mancera, R. L., Kim, K., Jang, C., Kim, M-h., Pérez-Sánchez, H., & Choi, E. H. (2018). Studies of the benzopyran class of selective cox-2 inhibitors using 3d-qsar and molecular docking. Archives of Pharmacal Research, 41 (12), 1178–1189. https://doi.org/10.1007/s12272-017-0945-7
   PubMed Web of Science ®Google Scholar
• Zhang, Q., Yan, Q., Yang, H., & Wei, W. (2019). Oxygen sensing and adaptability won the 2019 nobel prize in physiology or medicine. Genes & Diseases, 6(4), 328–332. https://doi.org/10.1016/j.gendis.2019.10.006
   PubMed Web of Science ®Google Scholar