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Research Articles

Virtual high throughput screening of natural peptides against ErbB1 and ErbB2 to identify potential inhibitors for cancer chemotherapy

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Pages 5551-5574 | Received 13 Oct 2022, Accepted 13 Jun 2023, Published online: 30 Jun 2023

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
  • Aertgeerts, K., Skene, R., Yano, J., Sang, B.-C., Zou, H., Snell, G., Jennings, A., Iwamoto, K., Habuka, N., Hirokawa, A., Ishikawa, T., Tanaka, T., Miki, H., Ohta, Y., & Sogabe, S. (2011). Structural analysis of the mechanism of inhibition and allosteric activation of the kinase domain of HER2 protein. The Journal of Biological Chemistry, 286(21), 18756–18765. https://doi.org/10.1074/jbc.M110.206193
  • Agrawal, P., Bhalla, S., Usmani, S. S., Singh, S., Chaudhary, K., Raghava, G. P. S., & Gautam, A. (2016). CPPsite 2.0: A repository of experimentally validated cell-penetrating peptides. Nucleic Acids Research, 44(D1), D1098–103. https://doi.org/10.1093/nar/gkv1266
  • Ayyamperumal, S., Jade, D., Tallapaneni, V., Chandrasekar, M. J. N., & Nanjan, M. J. (2022). In silico screening of FDA approved drugs against ACE2 receptor: Potential therapeutics to inhibit the entry of SARS-CoV-2 to human cells. Journal of Biomolecular Structure and Dynamics, 40(21), 11383–11394. https://doi.org/10.1080/07391102.2021.1960892
  • Ayyamperumal, S., Jade, D., Tallapaneni, V., Mohan, S., Barge, S., Moola Joghee, N., & M J N, C. (2022). Structural and functional analysis of Chitinase-IV of Brassica juncea: Molecular modeling and dynamic simulation study. Journal of Biomolecular Structure & Dynamics, 40(4), 1830–1842. https://doi.org/10.1080/07391102.2020.1835723
  • Barge, S., Jade, D., Ayyamperumal, S., Manna, P., Borah, J., Nanjan, C. M. J., Nanjan, M. J., & Talukdar, N. C. (2022). Potential inhibitors for FKBP51: An in silico study using virtual screening, molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure & Dynamics, 40(24), 13799–13811. https://doi.org/10.1080/07391102.2021.1994877
  • Buonfiglio, R., Recanatini, M., & Masetti, M. (2015). Protein flexibility in drug discovery: From theory to computation. ChemMedChem, 10(7), 1141–1148. https://doi.org/10.1002/cmdc.201500086
  • Cancer. (2022). https://www.who.int/news-room/fact-sheets/detail/cancer
  • Chen, K., & Conti, P. S. (2010). Target-specific delivery of peptide-based probes for PET imaging. Advanced Drug Delivery Reviews, 62(11), 1005–1022. https://doi.org/10.1016/j.addr.2010.09.004
  • Cheng, A., & Dixon, S. L. (2003). In silico models for the prediction of dose-dependent human hepatotoxicity. Journal of Computer-Aided Molecular Design, 17(12), 811–823. https://doi.org/10.1023/b:Jcam.0000021834.50768.c6
  • Cheng, A., & Merz, K. M. (2003). Prediction of aqueous solubility of a diverse set of compounds using quantitative structure- property relationships. Journal of Medicinal Chemistry, 46(17), 3572–3580. https://doi.org/10.1021/jm020266b
  • Chen, K., Sun, X., Niu, G., Ma, Y., Yap, L.-P., Hui, X., Wu, K., Fan, D., Conti, P. S., & Chen, X. (2012). Evaluation of 64Cu labeled GX1: A phage display peptide probe for PET imaging of tumor vasculature. Molecular Imaging and Biology, 14(1), 96–105. https://doi.org/10.1007/s11307-011-0479-1
  • Deng, Y., & Li, J. (2017). Rational optimization of tumor suppressor-derived peptide inhibitor selectivity between oncogene tyrosine kinases ErbB1 and ErbB2. Archiv der Pharmazie, 350(12), 1700181. https://doi.org/10.1002/ardp.201700181
  • Dixon, S. L., & Merz, K. M. (2001). One-dimensional molecular representations and similarity calculations: Methodology and validation. Journal of Medicinal Chemistry, 44(23), 3795–3809. https://doi.org/10.1021/jm010137f
  • Egan, W. J., Merz, K. M., & Baldwin, J. J. (2000). Prediction of drug absorption using multivariate statistics. Journal of Medicinal Chemistry, 43(21), 3867–3877. https://doi.org/10.1021/jm000292e
  • Elmetwally, S. A., Saied, K. F., Eissa, I. H., & Elkaeed, E. B. (2019). Design, synthesis and anticancer evaluation of thieno [2, 3-d] pyrimidine derivatives as dual EGFR/HER2 inhibitors and apoptosis inducers. Bioorganic Chemistry, 88, 102944. https://doi.org/10.1016/j.bioorg.2019.102944
  • Farkhani, S. M., Valizadeh, A., Karami, H., Mohammadi, S., Sohrabi, N., & Badrzadeh, F. (2014). Cell penetrating peptides: Efficient vectors for delivery of nanoparticles, nanocarriers, therapeutic and diagnostic molecules. Peptides, 57, 78–94. https://doi.org/10.1016/j.peptides.2014.04.015
  • Ganesan, A. (2008). The impact of natural products upon modern drug discovery. Current Opinion in Chemical Biology, 12(3), 306–317. https://doi.org/10.1016/j.cbpa.2008.03.016
  • Gautam, A., Singh, H., Tyagi, A., Chaudhary, K., Kumar, R., Kapoor, P., & Raghava, G. P. S. (2012). CPPsite: A curated database of cell penetrating peptides. Database, 2012(0), bas015–bas015. https://doi.org/10.1093/database/bas015
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Grunwald, V., & Hidalgo, M. (2003). Developing inhibitors of the epidermal growth factor receptor for cancer treatment. Journal of the National Cancer Institute, 95(12), 851–867. https://doi.org/10.1093/jnci/95.12.851
  • Guardiola, S., Díaz-Lobo, M., Seco, J., García, J., Nevola, L., & Giralt, E. (2016). Peptides targeting EGF block the EGF–EGFR interaction. Chembiochem : A European Journal of Chemical Biology, 17(8), 702–711. https://doi.org/10.1002/cbic.201500525
  • Hodgson, J. (2001). ADMET—turning chemicals into drugs. Nature Biotechnology, 19(8), 722–726. https://doi.org/10.1038/90761
  • Hu, J.-B., Dong, M.-J., & Zhang, J. (2016). A holistic in silico approach to develop novel inhibitors targeting ErbB1 and ErbB2 kinases. Tropical Journal of Pharmaceutical Research, 15(2), 231–239. https://doi.org/10.4314/tjpr.v15i2.3
  • Huan, Y., Kong, Q., Mou, H., & Yi, H. (2020). Antimicrobial peptides: Classification, design, application and research progress in multiple fields. Frontiers in Microbiology, 11, 2559. https://doi.org/10.3389/fmicb.2020.582779
  • Jade, D., Ayyamperumal, S., Tallapaneni, V., Joghee Nanjan, C. M., Barge, S., Mohan, S., & Nanjan, M. J. (2021). Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PLPRO and 3CLPRO proteases. European Journal of Pharmacology, 901, 174082. https://doi.org/10.1016/j.ejphar.2021.174082
  • Jade, D. D., Pandey, R., Kumar, R., & Gupta, D. (2022). Ligand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics. Journal of Biomolecular Structure & Dynamics, 40(4), 1702–1718. https://doi.org/10.1080/07391102.2020.1831962
  • Jhoti, H., Williams, G., Rees, D. C., & Murray, C. W. (2013). The’rule of three’for fragment-based drug discovery: Where are we now? Nature Reviews. Drug Discovery, 12(8), 644–645. https://doi.org/10.1038/nrd3926-c1
  • Kang, T. H., Mao, C.-P., He, L., Tsai, Y.-C., Liu, K., La, V., Wu, T.-C., & Hung, C.-F. (2012). Tumor-targeted delivery of IL-2 by NKG2D leads to accumulation of antigen-specific CD8+ T cells in the tumor loci and enhanced anti-tumor effects. PLoS One, 7(4), e35141. https://doi.org/10.1371/journal.pone.0035141
  • Kapoor, P., Singh, H., Gautam, A., Chaudhary, K., Kumar, R., & Raghava, G. P. (2012). TumorHoPe: A database of tumor homing peptides. PLoS One, 7(4), e35187. https://doi.org/10.1371/journal.pone.0035187
  • Kumar, R., Jade, D., & Gupta, D. (2019). A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: Combination of 2D/3D similarity screening, molecular docking and molecular dynamics. Journal of Biomolecular Structure & Dynamics, 37(4), 931–943. https://doi.org/10.1080/07391102.2018.1444509
  • Kumari, R., Kumar, R., Consortium, O. S. D. D., & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Lau, J. L., & Dunn, M. K. (2018). Therapeutic peptides: Historical perspectives, current development trends, and future directions. Bioorganic & Medicinal Chemistry, 26(10), 2700–2707. https://doi.org/10.1016/j.bmc.2017.06.052
  • Lee, S., Xie, J., & Chen, X. (2010). Peptides and peptide hormones for molecular imaging and disease diagnosis. Chemical Reviews, 110(5), 3087–3111. https://doi.org/10.1021/cr900361p
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
  • Liu, L., Greger, J., Shi, H., Liu, Y., Greshock, J., Annan, R., Halsey, W., Sathe, G. M., Martin, A.-M., & Gilmer, T. M. (2009). Novel mechanism of lapatinib resistance in HER2-positive breast tumor cells: Activation of AXL. Cancer Research, 69(17), 6871–6878. https://doi.org/10.1158/0008-5472.CAN-08-4490
  • Marqus, S., Pirogova, E., & Piva, T. J. (2017). Evaluation of the use of therapeutic peptides for cancer treatment. Journal of Biomedical Science, 24(1), 15. https://doi.org/10.1186/s12929-017-0328-x
  • Minkiewicz, P., Dziuba, J., Iwaniak, A., Dziuba, M., & Darewicz, M. (2008). BIOPEP database and other programs for processing bioactive peptide sequences. Journal of AOAC International, 91(4), 965–980.
  • Mohan, S., Jade, D., Gupta, S., Ayyamperumal, S., Chandrasekar, M. N., & Nanjan, M. J. (2022). Virtual high-throughput screening: Potential inhibitors for the mycobacterial α-subunit of tryptophan synthase. Molecular Simulation, 48(4), 342–353. https://doi.org/10.1080/08927022.2021.2015069
  • Normanno, N., De Luca, A., Bianco, C., Strizzi, L., Mancino, M., Maiello, M. R., Carotenuto, A., De Feo, G., Caponigro, F., & Salomon, D. S. (2006). Epidermal growth factor receptor (EGFR) signaling in cancer. Gene, 366(1), 2–16. https://doi.org/10.1016/j.gene.2005.10.018
  • Patnaik, S. K., Chandrasekar, M. J. N., Nagarjuna, P., Ramamurthi, D., & Swaroop, A. K. (2022). Targeting of ErbB1, ErbB2, and their dual targeting using small molecules and natural peptides: Blocking EGFR cell signaling pathways in cancer: A mini review. Mini Reviews in Medicinal Chemistry, 22(22), 2831–46.
  • Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man, O., Beckmann, J. S., Silman, I., & Sussman, J. L. (2005). FoldIndex\copyright: A simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics (Oxford, England), 21(16), 3435–3438. https://doi.org/10.1093/bioinformatics/bti537
  • Quinn, R. J., Carroll, A. R., Pham, N. B., Baron, P., Palframan, M. E., Suraweera, L., Pierens, G. K., & Muresan, S. (2008). Developing a drug-like natural product library. Journal of Natural Products, 71(3), 464–468. https://doi.org/10.1021/np070526y
  • Rao, S. N., Head, M. S., Kulkarni, A., & LaLonde, J. M. (2007). Validation studies of the site-directed docking program LibDock. Journal of Chemical Information and Modeling, 47(6), 2159–2171. https://doi.org/10.1021/ci6004299
  • Roskoski, R. Jr (2014). The ErbB/HER family of protein-tyrosine kinases and cancer. Pharmacological Research, 79, 34–74. https://doi.org/10.1016/j.phrs.2013.11.002
  • Ryan, Q., Ibrahim, A., Cohen, M. H., Johnson, J., Ko, C-w., Sridhara, R., Justice, R., & Pazdur, R. (2008). FDA drug approval summary: Lapatinib in combination with capecitabine for previously treated metastatic breast cancer that overexpresses HER-2. The Oncologist, 13(10), 1114–1119. https://doi.org/10.1634/theoncologist.2008-0816
  • Schmid, N., Eichenberger, A. P., Choutko, A., Riniker, S., Winger, M., Mark, A. E., & van Gunsteren, W. F. (2011). Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal: EBJ, 40(7), 843–856. https://doi.org/10.1007/s00249-011-0700-9
  • Schr€odinger. (2019). Release 2019-4: LigPrep. Schr€odinger, LLC.
  • 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
  • Sever, B., Altıntop, M. D., Radwan, M. O., Özdemir, A., Otsuka, M., Fujita, M., & Ciftci, H. I. (2019). Design, synthesis and biological evaluation of a new series of thiazolyl-pyrazolines as dual EGFR and HER2 inhibitors. European Journal of Medicinal Chemistry, 182, 111648. https://doi.org/10.1016/j.ejmech.2019.111648
  • Sharma, S. V., Bell, D. W., Settleman, J., & Haber, D. A. (2007). Epidermal growth factor receptor mutations in lung cancer. Nature Reviews. Cancer, 7(3), 169–181. https://doi.org/10.1038/nrc2088
  • Shi, G., Kang, X., Dong, F., Liu, Y., Zhu, N., Hu, Y., Xu, H., Lao, X., & Zheng, H. (2022). DRAMP 3.0: An enhanced comprehensive data repository of antimicrobial peptides. Nucleic Acids Research, 50(D1), D488–D496. https://doi.org/10.1093/nar/gkab651
  • Siegel, R. L., Miller, K. D., & Jemal, A. (2016). CA: A cancer journal for clinicians. Cancer Stat, 66, 7–30.
  • Singh, S., Chaudhary, K., Dhanda, S. K., Bhalla, S., Usmani, S. S., Gautam, A., Tuknait, A., Agrawal, P., Mathur, D., & Raghava, G. P. S. (2016). SATPdb: A database of structurally annotated therapeutic peptides. Nucleic Acids Research, 44(D1), D1119–26. https://doi.org/10.1093/nar/gkv1114
  • Stamos, J., Sliwkowski, M. X., & Eigenbrot, C. (2002). Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. The Journal of Biological Chemistry, 277(48), 46265–46272. https://doi.org/10.1074/jbc.M207135200
  • Sun, M., Jia, J., Sun, H., & Wang, F. (2020). Design and synthesis of a novel class EGFR/HER2 dual inhibitors containing tricyclic oxazine fused quinazolines scaffold. Bioorganic & Medicinal Chemistry Letters, 30(9), 127045. https://doi.org/10.1016/j.bmcl.2020.127045
  • Susnow, R. G., & Dixon, S. L. (2003). Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition. Journal of Chemical Information and Computer Sciences, 43(4), 1308–1315. https://doi.org/10.1021/ci030283p
  • Tebbutt, N., Pedersen, M. W., & Johns, T. G. (2013). Targeting the ERBB family in cancer: Couples therapy. Nature Reviews. Cancer, 13(9), 663–673. https://doi.org/10.1038/nrc3559
  • Tyagi, A., Kapoor, P., Kumar, R., Chaudhary, K., Gautam, A., & Raghava, G. P. S. (2013). In silico models for designing and discovering novel anticancer peptides. Scientific Reports, 3(1), 8. https://doi.org/10.1038/srep02984
  • Tyagi, A., Tuknait, A., Anand, P., Gupta, S., Sharma, M., Mathur, D., Joshi, A., Singh, S., Gautam, A., & Raghava, G. P. S. (2015). CancerPPD: A database of anticancer peptides and proteins. Nucleic Acids Research, 43(Database issue), D837–43. https://doi.org/10.1093/nar/gku892
  • Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., et al. (2010). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31, 671–690.
  • Wang, Y. (2010). Breast cancer metastasis driven by ErbB2 and 14-3-3ξ: A division of labor. Cell Adhesion & Migration, 4(1), 7–9. https://doi.org/10.4161/cam.4.1.10497
  • Wang, X., Xu, L., Lao, Y., Zhang, H., & Xu, H. (2018). Natural products targeting EGFR signaling pathways as potential anticancer drugs. Current Protein & Peptide Science, 19(4), 380–388. https://doi.org/10.2174/1389203718666170106104211
  • Wang, J., Yin, T., Xiao, X., He, D., Xue, Z., Jiang, X., & Wang, Y. (2018). StraPep: A structure database of bioactive peptides. Database, 2018 https://doi.org/10.1093/database/bay038
  • Wee, P., & Wang, Z. (2017). Epidermal growth factor receptor cell proliferation signaling pathways. Cancers, 9(5), 52. https://doi.org/10.3390/cancers9050052
  • Wood, E. R., Truesdale, A. T., McDonald, O. B., Yuan, D., Hassell, A., Dickerson, S. H., Ellis, B., Pennisi, C., Horne, E., Lackey, K., Alligood, K. J., Rusnak, D. W., Gilmer, T. M., & Shewchuk, L. (2004). A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Research, 64(18), 6652–6659. https://doi.org/10.1158/0008-5472.CAN-04-1168
  • Woodburn, J. R. (1999). The epidermal growth factor receptor and its inhibition in cancer therapy. Pharmacology & Therapeutics, 82(2-3), 241–250. https://doi.org/10.1016/s0163-7258(98)00045-x
  • Wu, D., Gao, Y., Qi, Y., Chen, L., Ma, Y., & Li, Y. (2014). Peptide-based cancer therapy: Opportunity and challenge. Cancer Letters, 351(1), 13–22. https://doi.org/10.1016/j.canlet.2014.05.002
  • Xiao, Y.-F., Jie, M.-M., Li, B.-S., Hu, C.-J., Xie, R., Tang, B., & Yang, S.-M. (2015). Peptide-based treatment: A promising cancer therapy. Journal of Immunology Research, 2015, 1–13. https://doi.org/10.1155/2015/761820
  • Xie, M., Liu, D., & Yang, Y. (2020). Anti-cancer peptides: Classification, mechanism of action, reconstruction and modification. Open Biology, 10(7), 200004. https://doi.org/10.1098/rsob.200004
  • Yang, L., Li, Y., Bhattacharya, A., & Zhang, Y. (2016). Dual inhibition of ErbB1 and ErbB2 in cancer by recombinant human prolidase mutant hPEPD-G278D. Oncotarget, 7(27), 42340–42352. https://doi.org/10.18632/oncotarget.9851
  • Zhang, X., Gureasko, J., Shen, K., Cole, P. A., & Kuriyan, J. (2006). An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell, 125(6), 1137–1149. https://doi.org/10.1016/j.cell.2006.05.013

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