Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing

References

• Abdul Amin, Sk., Adhikari, N., Jha, T., & Ghosh, B. (2018). Designing potential HDAC3 inhibitors to improve memory and learning. Journal of Biomolecular Structure and Dynamics, 1–10. doi: 10.1080/07391102.2018.1477625
   Web of Science ®Google Scholar
• AbdulHameed, M. D. M., Hamza, A., Liu, J., & Zhan, C.-G. (2008). Combined 3D-QSAR modeling and molecular docking study on indolinone derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1. Journal of Chemical Information and Modeling, 48(9), 1760–1772. doi: 10.1021/ci800147v
   PubMed Web of Science ®Google Scholar
• Arora, R., Issar, U., & Kakkar, R. (2018). Identification of novel urease inhibitors: Pharmacophore modeling, virtual screening and molecular docking studies. Journal of Biomolecular Structure and Dynamics, 1–15. 46620 doi: 10.1080/07391102.2018
   PubMedGoogle Scholar
• Ashburn, T. T., & Thor, K. B. (2004). Drug repositioning: identifying and developing new uses for existing drugs. Nature Reviews Drug Discovery, 3(8), 673–683. doi: 10.1038/nrd1468
   PubMed Web of Science ®Google Scholar
• Bressi, J. C., Jennings, A. J., Skene, R., Wu, Y., Melkus, R., Jong, R. D., … Gangloff, A. R. (2010). Exploration of the HDAC2 foot pocket: Synthesis and SAR of substituted N-(2-aminophenyl)benzamides. Bioorganic and Medicinal Chemistry Letters, 20(10), 3142–3145. doi: 10.1016/j.bmcl.2010.03.091
   PubMed Web of Science ®Google Scholar
• Brown, B. A., Kantesaria, P. P., & McDevitt, L. M. (2007). Fingolimod: A novel immunosuppressant for multiple sclerosis. Annals of Pharmacotherapy, 41(10), 1660–1668. doi: 10.1345/aph.1G424
   PubMed Web of Science ®Google Scholar
• Case, D., Betz, R., Cerutti, D. S., Cheatham, T., Darden, T., Duke, R., … Kollman, P. A. (2016). Amber 2016. San Francisco: University of California.
   Google Scholar
• Cataldi, M., & Muscogiuri, G. (2018). Gender-related issues in the pharmacology of new anti-obesity drugs. Obesity Reviews, 20(3), 375–384. doi: 10.1111/obr.12805
   PubMed Web of Science ®Google Scholar
• Chai, T., & Draxler, R. R. (2014). Root mean square error (RMSE) or mean absolute error (MAE)? Geoscientific Model Development, 7(3), 1247–1250. doi: 10.5194/gmd-7-1247-2014
   Web of Science ®Google Scholar
• Chen, X., Gan, Q., Feng, C., Liu, X., & Zhang, Q. (2018). Virtual Screening of novel and selective inhibitors of protein tyrosine phosphatase 1b over t-cell protein tyrosine phosphatase using a bidentate inhibition strategy. Journal of Chemical Information and Modeling, 58(4), 837–847. doi: 10.1021/acs.jcim.8b00040
   PubMed Web of Science ®Google Scholar
• Clara, C. M. (2009). Romidepsin for the treatment of cutaneous T-cell lymphoma. Drugs Today, 45(11), 787–795. doi: 10.1358/dot.2009.45.11.1437052
   PubMed Web of Science ®Google Scholar
• De Simone, A., Russo, D., Ruda, G. F., Micoli, A., Ferraro, M., Di Martino, R. M. C., … Bottegoni, G. (2017). Design, synthesis, structure-activity relationship studies, and three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling of a series of o-biphenyl carbamates as dual modulators of dopamine d3 receptor and fatty acid amide hydrolase. Journal of Medicinal Chemistry, 60(6), 2287–2304. doi: 10.1021/acs.jmedchem.6b01578
   PubMed Web of Science ®Google Scholar
• Di Micco, S., Chini, M. G., Terracciano, S., Bruno, I., Riccio, R., & Bifulco, G. (2013). Structural basis for the design and synthesis of selective HDAC inhibitors. Bioorganic and Medicinal Chemistry, 21(13), 3795–3807. doi: 10.1016/j.bmc.2013.04.036
   PubMed Web of Science ®Google Scholar
• Dowling, D. P., Gantt, S. L., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2008). Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry, 47(51), 13554–13563. doi: 10.1021/bi801610c
   PubMed Web of Science ®Google Scholar
• Frampton, J. E., & Keating, G. M. (2007). Celecoxib: A review of its use in the management of arthritis and acute pain. Drugs, 67(16), 2433–2472. doi: 10.2165/00003495-200767160-00008
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. doi: 10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Fuster, V., & Sweeny, J. M. (2011). Aspirin: A historical and contemporary therapeutic overview. Circulation, 123(7), 768–778. doi: 10.1161/CIRCULATIONAHA.110.963843
   PubMed Web of Science ®Google Scholar
• Garnock-Jones, K. P. (2015). Panobinostat: First global approval. Drugs, 75(6), 695–704. doi: 10.1007/s40265-015-0388-8
   PubMed Web of Science ®Google Scholar
• Ghofrani, H. A., Osterloh, I. H., & Grimminger, F. (2006). Sildenafil: From angina to erectile dysfunction to pulmonary hypertension and beyond. Nature Reviews Drug Discovery, 5(8), 689–702. doi: 10.1038/nrd2030
   PubMed Web of Science ®Google Scholar
• Gregoretti, I. V., Lee, Y. M., & Goodson, H. V. (2004). Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. Journal of Molecular Biology, 338(1), 17–31. doi: 10.1016/j.jmb.2004.02.006
   Google Scholar
• Ha, H., Debnath, B., Odde, S., Bensman, T., Ho, H., Beringer, P. M., & Neamati, N. (2015). Discovery of Novel CXCR2 Inhibitors Using Ligand-Based Pharmacophore Models. Journal of Chemical Information and Modeling, 55(8), 1720–1738. doi: 10.1021/acs.jcim.5b00181
   Google Scholar
• Haberland, M., Johnson, A., Mokalled, M. H., Montgomery, R. L., & Olson, E. N. (2009). Genetic dissection of histone deacetylase requirement in tumor cells. Proceedings of the National Academy of Sciences of the United States of America, 106(19), 7751–7755. doi: 10.1073/pnas.0903139106
   Google Scholar
• Hauschild, A., Trefzer, U., Garbe, C., Kaehler, K. C., Ugurel, S., Kiecker, F., … Schadendorf, D. (2008). Multicenter phase II trial of the histone deacetylase inhibitor pyridylmethyl-N-{4-[(2-aminophenyl)-carbamoyl]-benzyl}-carbamate in pretreated metastatic melanoma. Melanoma Research, 18(4), 274–278. doi: 10.1097/CMR.0b013e328307c248
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2010). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. doi: 10.1002/prot.21123
   Google Scholar
• Hornig, E., Heppt, M. V., Graf, S. A., Ruzicka, T., & Berking, C. (2016). Inhibition of histone deacetylases in melanoma-a perspective from bench to bedside. Experimental Dermatology, 25(11), 831–838. doi: 10.1111/exd.13089
   PubMed Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. Journal of Computational Chemistry, 32(5), 866–877. doi: 10.1002/jcc.21666
   PubMed Web of Science ®Google Scholar
• Kang, D., Pang, X., Lian, W., Xu, L., Wang, J., Jia, H., … Du, G.-H. (2018). Discovery of VEGFR2 inhibitors by integrating naïve Bayesian classification, molecular docking and drug screening approaches. RSC Advances, 8(10), 5286–5297. doi: 10.1039/C7RA12259D
   Web of Science ®Google Scholar
• Kashyap, K., & Kakkar, R. (2019). An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies, . Journal of Biomolecular Structure and Dynamics, 1–18. doi: 10.1080/07391102.2019.1567388
   PubMed Web of Science ®Google Scholar
• Kuzmanic, A., & Zagrovic, B. (2010). Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal, 98(5), 861–871. doi: 10.1016/j.bpj.2009.11.011
   PubMed Web of Science ®Google Scholar
• Lauffer, B. E. L., Mintzer, R., Fong, R., Mukund, S., Tam, C., Zilberleyb, I., … Steiner, P. (2013). Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability. Journal of Biological Chemistry, 288(37), 26926–26943. doi: 10.1074/jbc.M113.490706
   PubMed Web of Science ®Google Scholar
• Lee, J. H., Choy, M. L., & Marks, P. A. (2012). Mechanisms of resistance to histone deacetylase inhibitors. Advances in Cancer Research, 116, 39–86. doi: 10.1016/b978-0-12-394387-3.00002-1
   Google Scholar
• Li, X., Hou, J., Li, X., Jiang, Y., Liu, X., Mu, W., … Xu, W. (2015). Development of 3-hydroxycinnamamide-based HDAC inhibitors with potent in vitro and in vivo anti-tumor activity. European Journal of Medicinal Chemistry, 89, 628–637. doi: 10.1016/j.ejmech.2014.10.077
   PubMed Web of Science ®Google Scholar
• Liu, J., Feng, K., & Ren, Y. (2018). In silico studies on potential TNKS inhibitors: a combination of pharmacophore and 3D-QSAR modelling, virtual screening, molecular docking and molecular dynamics. Journal of Biomolecular Structure and Dynamics, 1. doi: 10.1080/07391102.2018.1528887
   Web of Science ®Google Scholar
• Li, X., Wu, J., Li, X., Mu, W., Liu, X., Jin, Y., … Zhang, Y. (2015). Development of N-hydroxybenzamide derivatives with indole-containing cap group as histone deacetylases inhibitors. Bioorganic Medicinal Chemistry, 23(19), 6258–6270. doi: 10.1016/j.bmc.2015.08.040
   PubMed Web of Science ®Google Scholar
• Mahalakshmi, R., Husayn Ahmed, P., & Mahadevan, V., (2018). HDAC inhibitors show differential epigenetic regulation and cell survival strategies on p53 mutant colon cancer cells. Journal of Biomolecular Structure and Dynamics, 3(4), 938–955. doi: 10.1080/07391102.2017.1302820
   Google Scholar
• Manal, M., Selvaraj, A., Chandrasekar, M. J. N., Manish, K., Devadasan, V., & Sanal, D. (2017). Novel HDAC8 inhibitors: A multi-computational approach. SAR and Qsar in Environmental Research, 28(9), 707–733. doi: 10.1080/1062936X.2017.1375978
   PubMed Web of Science ®Google Scholar
• Marek, M., Kannan, S., Hauser, A.-T., Moraes Mourão, M., Caby, S., Cura, V., … Romier, C. (2013). Structural basis for the inhibition of histone deacetylase 8 (HDAC8), a key epigenetic player in the blood fluke Schistosoma mansoni. PLoS Pathogens, 9(9), e1003645. doi: 10.1371/journal.ppat.1003645
   PubMed Web of Science ®Google Scholar
• Marks, P. A., & Breslow, R. (2007). Dimethyl sulfoxide to vorinostat: Development of this histone deacetylase inhibitor as an anticancer drug. Nature Biotechnology, 25(1), 84–90. doi: 10.1038/nbt1272
   PubMed Web of Science ®Google Scholar
• Miller, L. C., O’Loughlin, C. T., Zhang, Z., Siryaporn, A., Silpe, J. E., Bassler, B. L., & Semmelhack, M. F. (2015). Development of potent inhibitors of pyocyanin production in Pseudomonas aeruginosa. Journal of Medicinal Chemistry, 58(3), 1298–1306. doi: 10.1021/jm5015082
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. doi: 10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Mottamal, M., Zheng, S., Huang, T. L., & Wang, G. (2015). Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules, 20(3), 3898–3941. doi: 10.3390/molecules20033898
   PubMed Web of Science ®Google Scholar
• Nair, S. B., Teli, M. K., Pradeep, H., & Rajanikant, G. K. (2012). Computational identification of novel histone deacetylase inhibitors by docking based QSAR. Computers in Biology and Medicine, 42(6), 697–705. doi: 10.1016/j.compbiomed.2012.04.001
   Google Scholar
• Nakagawa, M., Oda, Y., Eguchi, T., Aishima, S., Yao, T., Hosoi, F., … Tanaka, M. (2007). Expression profile of class I histone deacetylases in human cancer tissues. Oncology Reports, 18(4), 769–774.
   PubMed Web of Science ®Google Scholar
• Nicola, C., & Paola, G. (2011). Real external predictivity of QSAR models: How to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. Journal of Chemical Information and Modeling, 51(9), 2320–2335. doi: 10.1021/ci200211n
   PubMed Web of Science ®Google Scholar
• Ojha, P. K., & Roy, K. (2011). Comparative QSARs for antimalarial endochins: Importance of descriptor-thinning and noise reduction prior to feature selection. Chemometrics and Intelligent Laboratory Systems, 109(2), 146–161. doi: 10.1016/j.chemolab.2011.08.007
   Web of Science ®Google Scholar
• Onufriev, A., Bashford, D., & Case, D. A. (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Structure, Function, and Bioinformatics, 55(2), 383–394. doi: 10.1002/prot.20033
   PubMed Web of Science ®Google Scholar
• Pantziarka, P., Bouche, G., Meheus, L., Sukhatme, V., Sukhatme, V. P., & Vikas, P. (2014). The Repurposing Drugs in Oncology (ReDO) Project. Ecancermedicalscience, 8(1), 442. doi: 10.3332/ecancer.2014.442
   PubMedGoogle Scholar
• Partha, P. R., Somnath, P., Indrani, M., & Kunal, R. (2009). On two novel parameters for validation of predictive QSAR models. Molecules, 14(5), 1660–1701.
   PubMed Web of Science ®Google Scholar
• Patil, V., Sodji, Q. H., Kornacki, J. R., Mrksich, M., & Oyelere, A. K. (2013). 3-Hydroxypyridin-2-thione as novel zinc binding group for selective histone deacetylase inhibition. Journal of Medicinal Chemistry, 56(9), 3492–3506. doi: 10.1021/jm301769u
   PubMed Web of Science ®Google Scholar
• Poole, R. M. (2014). Belinostat: First global approval. Drugs, 74(13), 1543–1554. doi: 10.1007/s40265-014-0275-8
   PubMed Web of Science ®Google Scholar
• Pourbasheer, E., Aalizadeh, R., Shokouhi Tabar, S., Ganjali, M. R., Norouzi, P., & Shadmanesh, J. (2014). 2D and 3D quantitative structure-activity relationship study of hepatitis C virus NS5B polymerase inhibitors by comparative molecular field analysis and comparative molecular similarity indices analysis methods. Journal of Chemical Information and Modeling, 54(10), 2902–2914. doi: 10.1021/ci500216c
   PubMed Web of Science ®Google Scholar
• Pulla, V. K., Sriram, D. S., Viswanadha, S., Sriram, D., & Yogeeswari, P. (2016). Energy-based pharmacophore and three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling combined with virtual screening to identify novel small-molecule inhibitors of silent mating-type information regulation 2 Homologue 1 (SIRT1). Journal of Chemical Information and Modeling, 56(1), 173–187. doi: 10.1021/acs.jcim.5b00220
   PubMed Web of Science ®Google Scholar
• Rajak, H., Kumar, P., Parmar, P., Thakur, B. S., Veerasamy, R., Sharma, P. C., … Dangi, J. S. (2012). Appraisal of GABA and PABA as linker: design and synthesis of novel benzamide based histone deacetylase inhibitors. European Journal of Medicinal Chemisty, 53, 390–397. doi: 10.1016/j.ejmech.2012.03.058
   PubMed Web of Science ®Google Scholar
• Robbins, T. W. (2017). Cross-species studies of cognition relevant to drug discovery: A translational approach. British Journal of Pharmacology, 174(19), 3191–3199. doi: 10.1111/bph.13826
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Rd, C. T. (2013). PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. Journal of Chemical Theory and Computation, 9(7), 3084. doi: 10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Roy, K., Das, R. N., Ambure, P., & Aher, R. B. (2016). Be aware of error measures. Further studies on validation of predictive QSAR models. Chemometrics and Intelligent Laboratory Systems, 152, 18–33. doi: 10.1016/j.chemolab.2016.01.008
   Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n -alkanes. Journal of Computational Physics, 23(3), 327–341. doi: 10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sabatini, S., Gosetto, F., Iraci, N., Barreca, M. L., Massari, S., Sancineto, L., … Cecchetti, V. (2013). Re-evolution of the 2-phenylquinolines: ligand-based design, synthesis, and biological evaluation of a potent new class of Staphylococcus aureus NorA efflux pump inhibitors to combat antimicrobial resistance. Journal of Medicinal Chemistry, 56(12), 4975–4989. doi: 10.1021/jm400262a
   PubMed Web of Science ®Google Scholar
• Singhal, S., Mehta, J., Desikan, R., Ayers, D., Roberson, P., Eddlemon, P., … Barlogie, B. (1999). Antitumor activity of thalidomide in refractory multiple myeloma. New England Journal of Medicine, 341(21), 1565–1571. doi: 10.1056/NEJM199911183412102
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2018b). Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6. Journal of Biomolecular Structure and Dynamics, 1–56. doi: 10.1080/07391102.2018.1557560
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2018a). Insights into structural features of HDAC1 and its selectivity inhibition elucidated by molecular dynamic simulation and molecular docking. Journal of Biomolecular Structure and Dynamics, 1–27. doi: 10.1080/07391102.2018.1441072
   PubMed Web of Science ®Google Scholar
• Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., … Tari, L. W. (2004). Structural snapshots of human HDAC8 provide insights into the Class I histone deacetylases. Structure, 12(7), 1325–1334. doi: 10.1016/j.str.2004.04.012
   PubMed Web of Science ®Google Scholar
• Sprague, P. W. (1995). Automated chemical hypothesis generation and database searching with Catalyst®. Perspectives in Drug Discovery and Design, 3(1), 1–20. doi: 10.1007/BF02174464
   Google Scholar
• Suresh, P. S., Devaraj, V. C., Srinivas, N. R., & Mullangi, R. (2016). Review of bioanalytical assays for the quantitation of various HDAC inhibitors such as vorinostat, belinostat, panobinostat, romidepsin and chidamine. Biomedical Chromatography, 31(1), e3807. doi: 10.1002/bmc.3807
   Web of Science ®Google Scholar
• Suzuki, T., Ota, Y., Ri, M., Bando, M., Gotoh, A., Itoh, Y., … Miyata, N. (2012). Rapid discovery of highly potent and selective inhibitors of histone deacetylase 8 using click chemistry to generate candidate libraries. Journal of Medicinal Chemistry, 55(22), 9562–9575. doi: 10.1021/jm300837y
   PubMed Web of Science ®Google Scholar
• Tabackman, A. A., Frankson, R., Marsan, E. S., Perry, K., & Cole, K. E. (2016). Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket. Journal of Structural Biology, 195(3), 373–378. doi: 10.1016/j.jsb.2016.06.023
   PubMed Web of Science ®Google Scholar
• Tang, J., Yan, H., & Zhuang, S. (2013). Histone deacetylases as targets for treatment of multiple diseases. Clinical Science, 124(11), 651–662. doi: 10.1042/CS20120504
   PubMed Web of Science ®Google Scholar
• Terasaka, T., Kinoshita, T., Kuno, M., Seki, N., Tanaka, K., & Nakanishi, I. (2004). Structure-based design, synthesis, and structure-activity relationship studies of novel non-nucleoside adenosine deaminase inhibitors. Journal of Medicinal Chemistry, 47(15), 3730–3743. doi: 10.1021/jm0306374
   PubMed Web of Science ®Google Scholar
• Thaler, F., Colombo, A., Mai, A., Amici, R., Bigogno, C., Boggio, R., … Varasi, M. (2010). Synthesis and biological evaluation of N-hydroxyphenylacrylamides and N-hydroxypyridin-2-ylacrylamides as novel histone deacetylase inhibitors. Journal of Medicinal Chemistry, 53(2), 822–839. doi: 10.1021/jm901502p
   PubMed Web of Science ®Google Scholar
• Thangapandian, S., John, S., Sakkiah, S., & Lee, K. W. (2010). Ligand and structure based pharmacophore modeling to facilitate novel histone deacetylase 8 inhibitor design. European Journal of Medicinal Chemistry, 45(10), 4409–4417. doi: 10.1016/j.ejmech.2010.06.024
   PubMed Web of Science ®Google Scholar
• Uba, A. I., & Yelekçi, K. (2018a). Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors. Journal of Biomolecular Structure and Dynamics, 1–10. doi: 10.1080/07391102.2018.1521747
   PubMedGoogle Scholar
• Uba, A. I., & Yelekçi, K. (2018b). Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: A combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay. Journal of Biomolecular Structure and Dynamics, 36(12), 3231–3245. doi: 10.1080/07391102.2017.1384402
   PubMed Web of Science ®Google Scholar
• Valassi, E., Crespo, I., Gich, I., Rodriguez, J., & Webb, S. M. (2012). A reappraisal of the medical therapy with steroidogenesis inhibitors in Cushing's syndrome. Clinical Endocrinology, 77(5), 735–742. doi: 10.1111/j.1365-2265.2012.04424.x
   PubMed Web of Science ®Google Scholar
• Van Veggel, M., Westerman, E., & Hamberg, P. (2018). Clinical pharmacokinetics and pharmacodynamics of panobinostat. Clinical Pharmacokinetics, 57(1), 21–29. doi: 10.1007/s40262-017-0565-x
   PubMed Web of Science ®Google Scholar
• Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., … Di Marco, S. (2004). Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy of Science of the United States of America, 101(42), 15064–15069. doi: 10.1073/pnas.0404603101
   PubMed Web of Science ®Google Scholar
• Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., … Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Reports, 8(9), 879–884. doi: 10.1038/sj.embor.7401047
   PubMed Web of Science ®Google Scholar
• Wagner, F. F., Weiwer, M., Steinbacher, S., Schomburg, A., Reinemer, P., Gale, J. P., … Holson, E. B. (2016). Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors. Bioorganic and Medicinal Chemistry, 24(18), 4008–4015. doi: 10.1016/j.bmc.2016.06.040
   PubMed Web of Science ®Google Scholar
• Wang, Y., Yang, L., Hou, J., Zou, Q., Gao, Q., Yao, W., Yao, Q., … Zhang, J. (2018). Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. Journal of Biomolecular Structure and Dynamics, 1–22. doi: 10.1080/07391102.2018.1434833
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157. doi: 10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, F., Yang, W., Shi, Y., & Le, G. (2015). 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors. Journal of Biomolecular Structure and Dynamics, 33(9), 1929–1940. doi: 10.1080/07391102.2014.980321
   PubMed Web of Science ®Google Scholar
• Wang, G., & Zhu, W. (2016). Molecular docking for drug discovery and development: a widely used approach but far from perfect. Future Med Chem, 8(14), 1707–1710.
   Google Scholar
• Weichert, W., Röske, A., Gekeler, V., Beckers, T., Stephan, C., Jung, K., … Kristiansen, G. (2008). Histone deacetylases 1, 2 and 3 are highly expressed in prostate cancer and HDAC2 expression is associated with shorter PSA relapse time after radical prostatectomy. British Journal of Cancer, 98(3), 604–610. doi: 10.1038/sj.bjc.6604199
   PubMed Web of Science ®Google Scholar
• Wishart, D. S., Knox, C., Guo, A. C., Shrivastava, S., Hassanali, M., Stothard, P., … Woolsey, J. (2006). DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res, 34(90001), D668–D672. Database, doi: 10.1093/nar/gkj067
   PubMedGoogle Scholar
• Xie, H., Chen, L., Zhang, J., Xie, X., Qiu, K., & Fu, J. (2015). A combined pharmacophore modeling, 3D QSAR and virtual screening studies on imidazopyridines as B-Raf inhibitors. International Journal of Molecular Sciences, 16(6), 12307–12323. doi: 10.3390/ijms160612307
   PubMed Web of Science ®Google Scholar
• Yang, K., Nong, K., Gu, Q., Dong, J., & Wang, J. (2018). Discovery of N-hydroxy-3-alkoxybenzamides as direct acid sphingomyelinase inhibitors using a ligand-based pharmacophore model. European Journal of Medicinal Chemistry, 151, 389–400. doi: 10.1016/j.ejmech.2018.03.065
   PubMed Web of Science ®Google Scholar
• Yang, K. W., Sobieski, D. N., Carenbauer, A. L., Crawford, P. A., Makaroff, C. A., & Crowder, M. W. (2003). Explaining the inhibition of glyoxalase II by 9-fluorenylmethoxycarbonyl-protected glutathione derivatives. Archives of Biochemistry and Biophysics, 414(2), 271–278. doi: 10.1016/S0003-9861(03)00193-0
   PubMed Web of Science ®Google Scholar
• Yuan, Y., Hu, Z., Bao, M., Sun, R., Long, X., Long, L., Li, J., … Bao, J. (2018). Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach. Journal of Biomolecular Structure and Dynamics, 1–12. doi: 10.1080/07391102.2018.1541141
   PubMed Web of Science ®Google Scholar
• Zang, J., Shi, B., Liang, X., Gao, Q., Xu, W., & Zhang, Y. (2017). Development of N-hydroxycinnamamide-based HDAC inhibitors with improved HDAC inhibitory activity and in vitro antitumor activity. Bioorganic and Medicinal Chemistry, 25(9), 2666–2675. doi: 10.1016/j.bmc.2016.12.001
   PubMed Web of Science ®Google Scholar
• Zhang, C., Feng, L.-J., Huang, Y., Wu, D., Li, Z., Zhou, Q., … Luo, H.-B. (2017). Discovery of novel phosphodiesterase-2a inhibitors by structure-based virtual screening, structural optimization, and bioassay. Journal of Chemical Information and Modeling, 57(2), 355–364. doi: 10.1021/acs.jcim.6b00551
   PubMed Web of Science ®Google Scholar
• Zhou, H., Wang, C., Deng, T., Tao, R., & Li, W. (2018). Novel urushiol derivatives as HDAC8 inhibitors: rational design, virtual screening, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure and Dynamics, 36(8), 1966–1978. doi: 10.1080/07391102.2017.1344568
   PubMed Web of Science ®Google Scholar
• Zhou, H., Gao, M., & Skolnick, J. (2015). Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Scientific Reports, 5, 11090. doi: 10.1038/srep11090
   PubMed Web of Science ®Google Scholar