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Research Article

Exploration of novel hydroxamate zinc binding group inhibitors against HDAC-1-3 enzymes by AI-based virtual screening: atomistic insights from steered molecular dynamics

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Received 09 Nov 2023, Accepted 24 Feb 2024, Published online: 08 Mar 2024

References

  • Abdi, H., & Williams, L. J. (2010). Principal component analysis. WIREs Computational Statistics, 2(4), 433–459. https://doi.org/10.1002/wics.101
  • Allouche, A. (2012). Gabedit—A graphical user interface for computational chemistry softwares. Journal of Computational Chemistry, 32(1), 174–182. https://doi.org/10.1002/jcc
  • Amendola, G., & Cosconati, S. (2021). PyRMD: A new fully automated AI-powered ligand-based virtual screening tool. Journal of Chemical Information and Modeling, 61(8), 3835–3845. https://doi.org/10.1021/acs.jcim.1c00653
  • Andreini, C., Banci, L., Bertini, I., & Rosato, A. (2006). Zinc through the three domains of life. Journal of Proteome Research, 5(11), 3173–3178. https://doi.org/10.1021/pr0603699
  • Anzellotti, A. I., & Farrell, N. P. (2008). Zinc metalloproteins as medicinal targets. Chemical Society Reviews, 37(8), 1629–1651. https://doi.org/10.1039/b617121b
  • Aramsangtienchai, P., Spiegelman, N. A., He, B., Miller, S. P., Dai, L., Zhao, Y., & Lin, H. (2016). HDAC8 catalyzes the hydrolysis of long chain fatty acyl lysine. ACS Chemical Biology, 11(10), 2685–2692. https://doi.org/10.1021/acschembio.6b00396
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
  • Baştuğ, T., Chen, P.-C., Patra, S. M., & Kuyucak, S. (2008). Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling. The Journal of Chemical Physics, 128(15), 155104. https://doi.org/10.1063/1.2904461
  • Beckers, T., Burkhardt, C., Wieland, H., Gimmnich, P., Ciossek, T., Maier, T., & Sanders, K. (2007). Distinct pharmacological properties of second generation HDAC inhibitors with the benzamide or hydroxamate head group. International Journal of Cancer, 121(5), 1138–1148. https://doi.org/10.1002/ijc.22751
  • Bertrand, P. (2010). Inside HDAC with HDAC inhibitors. European Journal of Medicinal Chemistry, 45(6), 2095–2116. https://doi.org/10.1016/j.ejmech.2010.02.030
  • Bondarev, A. D., Attwood, M. M., Jonsson, J., Chubarev, V. N., Tarasov, V. V., & Schiöth, H. B. (2021). Recent developments of HDAC inhibitors: Emerging indications and novel molecules. British Journal of Clinical Pharmacology, 87(12), 4577–4597. https://doi.org/10.1111/bcp.14889
  • Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
  • Cashen, A., Juckett, M., Jumonville, A., Litzow, M., Flynn, P. J., Eckardt, J., LaPlant, B., Laumann, K., Erlichman, C., & DiPersio, J. (2012). Phase II study of the histone deacetylase inhibitor belinostat (PXD101) for the treatment of myelodysplastic syndrome (MDS). Annals of Hematology, 91(1), 33–38. https://doi.org/10.1007/s00277-011-1240-1
  • Cheshmazar, N., Hemmati, S., Hamzeh-Mivehroud, M., Sokouti, B., Zessin, M., Schutkowski, M., Sippl, W., Charoudeh, H. N., & Dastmalchi, S. (2022). Development of new inhibitors of HDAC1 − 3 enzymes aided by in silico design strategies. Journal of Chemical Information and Modeling, 62(10), 2387–2397. https://doi.org/10.1021/acs.jcim.1c01557
  • Cornell, W. D., Cieplak, P., Bayly, C. I., & Kollman, P. A. (1993). Application of RESP charges. Journal of the American Chemical Society, 115(21), 9620–9631. https://doi.org/10.1021/ja00074a030
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
  • Das, B., Mathew, A. T., Baidya, A. T. K., Devi, B., Salmon, R. R., & Kumar, R. (2023). Artificial intelligence assisted identification of potential tau aggregation inhibitors: Ligand- and structure-based virtual screening, in silico ADME, and molecular dynamics study. Molecular Diversity, 1–19. https://doi.org/10.1007/s11030-023-10645-3
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Esther Rubavathy, S. M., Palanisamy, K., Priyankha, S., Thilagavathi, R., Prakash, M., & Selvam, C. (2022). Discovery of novel HDAC8 inhibitors from natural compounds by in silico high throughput screening. Journal of Biomolecular Structure & Dynamics, 41(19), 9492–9502. https://doi.org/10.1080/07391102.2022.2142668
  • Ferreira, L. L. G., & Andricopulo, A. D. (2019). ADMET modeling approaches in drug discovery. Drug Discovery Today, 24(5), 1157–1165. https://doi.org/10.1016/j.drudis.2019.03.015
  • Ganai, S. A., Abdullah, E., Rashid, R., & Altaf, M. (2017). Combinatorial in silico strategy towards identifying potential hotspots during inhibition of structurally identical HDAC1 and HDAC2 enzymes for effective chemotherapy against neurological disorders. Frontiers in Molecular Neuroscience, 10(November), 357. https://doi.org/10.3389/fnmol.2017.00357
  • Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., & Overington, J. P. (2012). ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40(Database issue), D1100–D1107. https://doi.org/10.1093/nar/gkr777
  • Gong, W. (2015). Computational simulations of inhibition mechanism for zinc dependent histone deacetylases (Order No. 3740744). ProQuest Dissertations & Theses Global: The Sciences and Engineering Collection (1754416542). Retrieved from https://www.proquest.com/dissertations-theses/computational-simulations-inhibition-mechanism/docview/1754416542/se-2
  • Gurboga, M., Kugu, G., Kamberaj, H., & Mutlu, O. (2021). Identification of benzamide inhibitors of histone deacetylase 1 from Babesia and Theileria species via high-throughput virtual screening and molecular dynamics simulations. Parasitology Research, 120(6), 2175–2187. https://doi.org/10.1007/s00436-021-07158-z
  • Hassan, M. M., Israelian, J., Nawar, N., Ganda, G., Manaswiyoungkul, P., Raouf, Y. S., Armstrong, D., Sedighi, A., Olaoye, O. O., Erdogan, F., Cabral, A. D., Angeles, F., Altintas, R., De Araujo, E. D., & Gunning, P. T. (2020). Characterization of conformationally constrained benzanilide scaffolds for potent and selective HDAC8 targeting. Journal of Medicinal Chemistry, 63(15), 8634–8648. https://doi.org/10.1021/acs.jmedchem.0c01025
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. 10.1002/(SICI)1096-987X(199709)18:12
  • Ho, T. C. S., Chan, A. H. Y., & Ganesan, A. (2020). Thirty years of HDAC inhibitors: 2020 insight and hindsight. Journal of Medicinal Chemistry, 63(21), 12460–12484. https://doi.org/10.1021/acs.jmedchem.0c00830
  • Huo, D., Sun, Z., Wang, M., & Yan, A. (2023). Ligand and structure based hierarchical virtual screening cascade for finding novel epidermal growth factor receptor inhibitors. Chemical Biology & Drug Design, 103(1), e14375. https://doi.org/10.1111/cbdd.14375
  • Isralewitz, B., Gao, M., & Schulten, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology, 11(2), 224–230. https://doi.org/10.1016/s0959-440x(00)00194-9
  • Izrailev, S., Stepaniants, S., Isralewitz, B., Kosztin, D., Lu, H., Molnar, F., Wriggers, W., & Schulten, K. (1999). Steered molecular dynamics. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, & R. D. Skeel (Eds.), Computational molecular dynamics: Challenges, methods, ideas. Proceedings of the 2nd international symposium on algorithms for macromolecular modelling, Berlin, May 21–24, 1997, vol. 4 (pp. 39–65). Springer. https://doi.org/10.1007/978-3-642-58360-5_2
  • Kelly, W. K., & Marks, P. A. (2005). Drug insight: Histone deacetylase inhibitors - Development of the new targeted anticancer agent suberoylanilide hydroxamic acid. Nature Clinical Practice. Oncology, 2(3), 150–157. https://doi.org/10.1038/ncponc0106
  • Kumari, R., Kumar, R., & Lynn, A., Open Source Drug Discovery Consortium. (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
  • Lemkul, J., Genheden, S., Ryde, U., Hou, T., Wang, J., Li, Y., Wang, W., Kumari, R., Kumar, R., Lynn, A., Genheden, S., & Ryde, U. (2015). Assessing the performance of the MM_PBSA and MM_GBSA methods. 1. The Accuracy.pdf. Journal of Chemical Information and Modeling, 10(7), 449–461. http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf
  • Macchiagodena, M., Pagliai, M., Andreini, C., Rosato, A., & Procacci, P. (2019). Upgrading and validation of the AMBER force field for histidine and cysteine zinc(II)-binding residues in sites with four protein ligands. Journal of Chemical Information and Modeling, 59(9), 3803–3816. https://doi.org/10.1021/acs.jcim.9b00407
  • Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
  • Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
  • Marks, P. A., & Xu, W. S. (2009). Histone deacetylase inhibitors: Potential in cancer therapy. Journal of Cellular Biochemistry, 107(4), 600–608. https://doi.org/10.1002/jcb.22185
  • Mason, T. G., Freeman, B. D., & Izgorodina, E. I. (2023). Influencing molecular dynamics simulations of ion-exchange membranes by considering comonomer propagation. Macromolecules, 56(3), 1263–1277. https://doi.org/10.1021/acs.macromol.2c01743
  • Mukherjee, A., Zamani, F., & Suzuki, T. (2023). Evolution of slow-binding inhibitors targeting histone deacetylase isoforms. Journal of Medicinal Chemistry, 66(17), 11672–11700. https://doi.org/10.1021/acs.jmedchem.3c01160
  • Nerukh, D., Okimoto, N., Suenaga, A., & Taiji, M. (2012). Ligand diffusion on protein surface observed in molecular dynamics simulation. The Journal of Physical Chemistry Letters, 3(23), 3476–3479. https://doi.org/10.1021/jz301635h
  • Ngo, S. T., Vu, K. B., Bui, L. M., & Vu, V. V. (2019). Effective estimation of ligand-binding affinity using biased sampling method. ACS Omega, 4(2), 3887–3893. https://doi.org/10.1021/acsomega.8b03258
  • Pao, P. C., & Tsai, L. H. (2022). Histone deacetylases 1 and 2 in memory function. ACS Chemical Neuroscience, 13(7), 848–858. https://doi.org/10.1021/acschemneuro.1c00775
  • Patel, J. S., Berteotti, A., Ronsisvalle, S., Rocchia, W., & Cavalli, A. (2014). Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. Journal of Chemical Information and Modeling, 54(2), 470–480. https://doi.org/10.1021/ci4003574
  • Peters, M. B., Yang, Y., Wang, B., Füsti-Molnár, L., Weaver, M. N., & Merz, K. M. (2010). Structural survey of zinc-containing proteins and development of the zinc AMBER force field (ZAFF). Journal of Chemical Theory and Computation, 6(9), 2935–2947. https://doi.org/10.1021/ct1002626
  • Roberts, B. P., Scanlon, M. J., Krippner, G. Y., & Chalmers, D. K. (2009). Molecular dynamics of poly(L-lysine) dendrimers with naphthalene disulfonate caps. Macromolecules, 42(7), 2775–2783. https://doi.org/10.1021/ma802154e
  • Robertson, M. J., Tirado-Rives, J., & Jorgensen, W. L. (2016). Performance of protein-ligand force fields for the flavodoxin-flavin mononucleotide system. The Journal of Physical Chemistry Letters, 7(15), 3032–3036. https://doi.org/10.1021/acs.jpclett.6b01229
  • Salvador, L. A., Park, H., Al-Awadhi, F. H., Liu, Y., Kim, B., Zeller, S. L., Chen, Q. Y., Hong, J., & Luesch, H. (2014). Modulation of activity profiles for largazole-based HDAC inhibitors through alteration of prodrug properties. ACS Medicinal Chemistry Letters, 5(8), 905–910. https://doi.org/10.1021/ml500170r
  • Shetty, M. G., Pai, P., Deaver, R. E., Satyamoorthy, K., & Babitha, K. S. (2021). Histone deacetylase 2 selective inhibitors: A versatile therapeutic strategy as next generation drug target in cancer therapy. Pharmacological Research, 170(May), 105695. https://doi.org/10.1016/j.phrs.2021.105695
  • Shi, Y., Fu, Y., Zhang, X., Zhao, G., Yao, Y., Guo, Y., Ma, G., Bai, S., & Li, H. (2021). Romidepsin (FK228) regulates the expression of the immune checkpoint ligand PD-L1 and suppresses cellular immune functions in colon cancer. Cancer Immunology, Immunotherapy: CII, 70(1), 61–73. https://doi.org/10.1007/s00262-020-02653-1
  • Sundar Raman, S., Parthasarathi, R., Subramanian, V., & Ramasami, T. (2006). Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation. The Journal of Physical Chemistry. B, 110(41), 20678–20685. https://doi.org/10.1021/jp0625715
  • Van Gunsteren, W. F., & Berendsen, H. J. C. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3), 173–185. https://doi.org/10.1080/08927028808080941
  • Wang, C., Greene, D., Xiao, L., Qi, R., & Luo, R. (2018). Recent developments and applications of the MMPBSA method. Frontiers in Molecular Biosciences, 4(Jan), 87. https://doi.org/10.3389/fmolb.2017.00087
  • Watson, P. J., Fairall, L., Santos, G. M., & Schwabe, J. W. R. (2012). Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature, 481(7381), 335–340. https://doi.org/10.1038/nature10728
  • Wu, R., Lu, Z., Cao, Z., & Zhang, Y. (2011). Zinc chelation with hydroxamate in histone deacetylases modulated. Journal of the American Chemical Society, 133(16), 6110–6113. https://doi.org/10.1021/ja111104p
  • Yahaya, M. A. F., Bakar, A. R. A., Stanslas, J., Nordin, N., Zainol, M., & Mehat, M. Z. (2021). Insights from molecular docking and molecular dynamics on the potential of vitexin as an antagonist candidate against lipopolysaccharide (LP S) for microglial activation in neuroinflammation. BMC Biotechnology, 21(1), 1–10. https://doi.org/10.1186/s12896-021-00697-4
  • Yang, F., Zhao, N., Ge, D., & Chen, Y. (2019). Next-generation of selective histone deacetylase inhibitors. RSC Advances, 9(34), 19571–19583. https://doi.org/10.1039/c9ra02985k
  • Yuan, S., Chan, H. C. S., & Hu, Z. (2017). Using PyMOL as a platform for computational drug design. Wiley Interdisciplinary Reviews: Computational Molecular Science, 7(2), e1298. https://doi.org/10.1002/wcms.1298
  • Zhao, Y., & Truhlar, D. G. (2008). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other function. Theoretical Chemistry Accounts, 120(1–3), 215–241. https://doi.org/10.1007/s00214-007-0310-x
  • Zheng, S., Tang, Q., He, J., Du, S., Xu, S., Wang, C., Xu, Y., & Lin, F. (2016). VFFDT: A new software for preparing AMBER force field parameters for metal-containing molecular systems. Journal of Chemical Information and Modeling, 56(4), 811–818. https://doi.org/10.1021/acs.jcim.5b00687

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