Binding profiles of cholesterol ester transfer protein with current inhibitors: a look at mechanism and drawback

References

• Accelrys. (2011). Discovery studio (3.1). Retrieved from https://accelrys.com/
   Google Scholar
• Aijanen, T., Koivuniemi, A., Javanainen, M., Rissanen, S., Rog, T., & Vattulainen, I. (2014). How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations. PLoS Computational Biology, 10, e1003987.10.1371/journal.pcbi.1003987
   PubMed Web of Science ®Google Scholar
• Barter, P. J., Brewer, H. B., Jr, Chapman, M. J., Hennekens, C. H., Rader, D. J., & Tall, A. R. (2003). Cholesteryl ester transfer protein: A novel target for raising HDL and inhibiting atherosclerosis. Arteriosclerosis, Thrombosis, and Vascular Biology, 23, 160–167.10.1161/01.ATV.0000054658.91146.64
   PubMed Web of Science ®Google Scholar
• Barter, P. J., & Jones, M. E. (1980). Kinetic-studies of the transfer of esterified cholesterol between human-plasma low and high-density lipoproteins. Journal of Lipid Research, 21, 238–249.
   PubMed Web of Science ®Google Scholar
• Barter, P. J., & Rye, K.-A. (2016). Cholesteryl ester transfer protein inhibition is not yet dead-pro. Arteriosclerosis, Thrombosis, and Vascular Biology, 36, 439–441.10.1161/ATVBAHA.115.306879
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690.10.1063/1.448118
   Web of Science ®Google Scholar
• Brooijmans, N., & Kuntz, I. D. (2003). Molecular recognition and docking algorithms. Annual Review of Biophysics and Biomolecular Structure, 32, 335–373.10.1146/annurev.biophys.32.110601.142532
   PubMed Web of Science ®Google Scholar
• Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr, Nilsson, L., Petrella, R. J., Roux, B., & Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30, 1545–1614.10.1002/jcc.v30:10
   PubMed Web of Science ®Google Scholar
• Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4, 187–217.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Brown, M. L., Inazu, A., Hesler, C. B., Agellon, L. B., Mann, C., Whitlock, M. E., … Takeda, R (1989). Molecular basis of lipid transfer protein deficiency in a family with increased high-density lipoproteins. Nature, 342, 448–451.10.1038/342448a0
   PubMed Web of Science ®Google Scholar
• Cao, G., Beyer, T. P., Zhang, Y., Schmidt, R. J., Chen, Y. Q., Cockerham, S. L., & Mantlo, N. B. (2011). Evacetrapib is a novel, potent, and selective inhibitor of cholesteryl ester transfer protein that elevates HDL cholesterol without inducing aldosterone or increasing blood pressure. Journal of Lipid Research, 52, 2169–2176.10.1194/jlr.M018069
   PubMed Web of Science ®Google Scholar
• Chirasani, V. R., Sankar, R., & Senapati, S. (2016). Mechanism of inhibition of cholesteryl ester transfer protein by small molecule inhibitors. The Journal of Physical Chemistry B, 120, 8254–8263.10.1021/acs.jpcb.6b01928
   PubMed Web of Science ®Google Scholar
• Cilpa-Karhu, G., Jauhiainen, M., & Riekkola, M. L. (2015). Atomistic MD simulation reveals the mechanism by which CETP penetrates into HDL enabling lipid transfer from HDL to CETP. Journal of Lipid Research, 56, 98–108.10.1194/jlr.M054288
   PubMed Web of Science ®Google Scholar
• Clark, R. W., Ruggeri, R. B., Cunningham, D., & Bamberger, M. J. (2006). Description of the torcetrapib series of cholesteryl ester transfer protein inhibitors, including mechanism of action. Journal of Lipid Research, 47, 537–552.10.1194/jlr.M500349-JLR200
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N [center-dot] log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
   Web of Science ®Google Scholar
• Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W. F., & Mark, A. E. (1999). Peptide folding: When simulation meets experiment. Angewandte Chemie-International Edition, 38, 236–240.10.1002/(ISSN)1521-3773
   Web of Science ®Google Scholar
• Deedwania, P., Barter, P., Carmena, R., Fruchart, J. C., Grundy, S. M., Haffner, S., … Waters, D. D. (2006). Reduction of low-density lipoprotein cholesterol in patients with coronary heart disease and metabolic syndrome: Analysis of the treating to new targets study. The Lancet, 368, 919–928.10.1016/S0140-6736(06)69292-1
   PubMed Web of Science ®Google Scholar
• Dergunov, A. D., Shabrova, E. V., & Dobretsov, G. E. (2014). Cholesteryl ester diffusion, location and self-association constraints determine CETP activity with discoidal HDL: Excimer probe study. Archives of Biochemistry and Biophysics, 564, 211–218.10.1016/j.abb.2014.09.019
   PubMed Web of Science ®Google Scholar
• Dong, B. L., Liao, Q. H., & Wei, J. (2011). Docking and molecular dynamics study on the inhibitory activity of N, N-disubstituted-trifluoro-3-amino-2-propanols-based inhibitors of cholesteryl ester transfer protein. Journal of Molecular Modeling, 17, 1727–1734.10.1007/s00894-010-0881-7
   PubMed Web of Science ®Google Scholar
• Drayna, D., Jarnagin, A. S., McLean, J., Henzel, W., Kohr, W., Fielding, C., & Lawn, R. (1987). Cloning and sequencing of human cholesteryl ester transfer protein cDNA. Nature, 327, 632–634.10.1038/327632a0
   PubMed Web of Science ®Google Scholar
• Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., & Scharf, M. (1995). The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. Journal of Computational Chemistry, 16, 273–284.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Funder, J. W. (2009). The off-target effects of torcetrapib. Endocrinology, 150, 2024–2026.
   PubMed Web of Science ®Google Scholar
• Gautier, T., Masson, D., & Lagrost, L. (2016). The potential of cholesteryl ester transfer protein as a therapeutic target. Expert Opinion on Therapeutic Targets, 20, 47–59.10.1517/14728222.2015.1073713
   PubMed Web of Science ®Google Scholar
• Ge, H., Wang, Y., Li, C., Chen, N., Xie, Y., Xu, M., & Xu, J. (2013). Molecular dynamics-based virtual screening: Accelerating the drug discovery process by high-performance computing. Journal of Chemical Information and Modeling, 53, 2757–2764.10.1021/ci400391s
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10, 449–461.10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gerstein, M., Lesk, A. M., & Chothia, C. (1994). Structural mechanisms for domain movements in proteins. Biochemistry, 33, 6739–6749.10.1021/bi00188a001
   PubMed Web of Science ®Google Scholar
• Grossfield, A., & Zuckerman, D. M. (2009). Quantifying uncertainty and sampling quality in biomolecular simulations. Annual Reports in Computational Chemistry, 5, 23–48.10.1016/S1574-1400(09)00502-7
   PubMedGoogle Scholar
• 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, 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51, 69–82.10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Inazu, A., Brown, M. L., Hesler, C. B., Agellon, L. B., Koizumi, J., Takata, K., & Tall, A. R. (1990). Increased high-density lipoprotein levels caused by a common cholesteryl-ester transfer protein gene mutation. New England Journal of Medicine, 323, 1234–1238.10.1056/NEJM199011013231803
   PubMed Web of Science ®Google Scholar
• Jamalan, M., Zeinali, M., & Ghaffari, M. A. (2016). A molecular dynamics investigation on the inhibition mechanism of cholesteryl ester transfer protein by anacetrapib. Medicinal Chemistry Research, 25, 62–69.10.1007/s00044-015-1471-0
   Web of Science ®Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637.10.1002/(ISSN)1097-0282
   PubMed Web of Science ®Google Scholar
• Kato, A., & Nakai, S. (1980). Hydrophobicity determined by a fluorescence probe method and its correlation with surface properties of proteins. Biochimica et Biophysica Acta (BBA) – Protein Structure, 624, 13–20.10.1016/0005-2795(80)90220-2
   PubMed Web of Science ®Google Scholar
• Kingwell, B. A., Chapman, M. J., Kontush, A., & Miller, N. E. (2014). HDL-targeted therapies: Progress, failures and future. Nature Reviews Drug Discovery, 13, 445–464.10.1038/nrd4279
   PubMed Web of Science ®Google Scholar
• Koivuniemi, A., Vuorela, T., Kovanen, P. T., Vattulainen, I., & Hyvonen, M. T. (2012). Lipid exchange mechanism of the cholesteryl ester transfer protein clarified by atomistic and coarse-grained simulations. PLoS Computational Biology, 8, e1002299.10.1371/journal.pcbi.1002299
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Lynn, A., & Consort, O. S. D. D. (2014). g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54, 1951–1962.10.1021/ci500020 m
   PubMed Web of Science ®Google Scholar
• Lei, D., Zhang, X., Jiang, S., Cai, Z., Rames, M. J., Zhang, L., & Zhang, S. (2013). Structural features of cholesteryl ester transfer protein: A molecular dynamics simulation study. Proteins: Structure, Function, and Bioinformatics, 81, 415–425.10.1002/prot.24200
   PubMed Web of Science ®Google Scholar
• Liu, S. P., Mistry, A., Reynolds, J. M., Lloyd, D. B., Griffor, M. C., Perry, D. A., & Qiu, X. Y. (2012). Crystal structures of cholesteryl ester transfer protein in complex with inhibitors. Journal of Biological Chemistry, 287, 37321–37329.10.1074/jbc.M112.380063
   PubMed Web of Science ®Google Scholar
• Luzar, A. (2000). Resolving the hydrogen bond dynamics conundrum. The Journal of Chemical Physics, 113, 10663–10675.10.1063/1.1320826
   Web of Science ®Google Scholar
• Nicholls, S. J., Lincoff, A. M., Barter, P. J., Brewer, H. B., Fox, K. A. A., Gibson, C. M., & Nissen, S. E. (2015). Assessment of the clinical effects of cholesteryl ester transfer protein inhibition with evacetrapib in patients at high-risk for vascular outcomes: Rationale and design of the accelerate trial. American Heart Journal, 170, 1061–1069.10.1016/j.ahj.2015.09.007
   PubMed Web of Science ®Google Scholar
• Okamoto, H., Yonemori, F., Wakitani, K., Minowa, T., Maeda, K., & Shinkai, H. (2000). A cholesteryl ester transfer protein inhibitor attenuates atherosclerosis in rabbits. Nature, 406, 203–207.10.1038/35018119
   PubMed Web of Science ®Google Scholar
• Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845–854.10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Qiu, X., Mistry, A., Ammirati, M. J., Chrunyk, B. A., Clark, R. W., Cong, Y., & Seddon, A. P. (2007). Crystal structure of cholesteryl ester transfer protein reveals a long tunnel and four bound lipid molecules. Nature Structural & Molecular Biology, 14, 106–113.10.1038/nsmb1197
   PubMed Web of Science ®Google Scholar
• Rader, D. J., & Degoma, E. M. (2014). Future of cholesteryl ester transfer protein inhibitors. Annual Review of Medicine, 65, 385–403.10.1146/annurev-med-050311-163305
   PubMed Web of Science ®Google Scholar
• Ranalletta, M., Bierilo, K. K., Chen, Y., Milot, D., Chen, Q., Tung, E., & Fisher, T. S. (2010). Biochemical characterization of cholesteryl ester transfer protein inhibitors. Journal of Lipid Research, 51, 2739–2752.10.1194/jlr.M007468
   PubMed Web of Science ®Google Scholar
• Segrest, J. P., Jones, M. K., Catte, A., Manchekar, M., Datta, G., Zhang, L., & Ren, G. (2015). Surface density-induced pleating of a lipid monolayer drives nascent high-density lipoprotein assembly. Structure, 23, 1214–1226.10.1016/j.str.2015.05.010
   PubMed Web of Science ®Google Scholar
• Stein, E. A., Stroes, E. S., Steiner, G., Buckley, B. M., Capponi, A. M., Burgess, T., … Kastelein, J. J. (2009). Safety and tolerability of dalcetrapib. The American Journal of Cardiology, 104, 82–91.10.1016/j.amjcard.2009.02.061
   PubMed Web of Science ®Google Scholar
• Wu, G., Robertson, D. H., Brooks, C. L., & Vieth, M. (2003). Detailed analysis of grid-based molecular docking: A case study of CDOCKER—A CHARMM-based MD docking algorithm. Journal of Computational Chemistry, 24, 1549–1562.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Wu, F., Yang, Z., Yin, S., Song, C., & Yuan, X. (2014). Interaction mechanisms of novel antiviral peptides against N1 subtype neuraminidase: A computational exploration. Digest Journal of Nanomaterials and Biostructures, 9, 975–985.
   Web of Science ®Google Scholar
• Yang, Z., Wu, F., Yuan, X., Zhang, L., & Zhang, S. (2016). Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies. Journal of Molecular Graphics and Modelling, 65, 27–34.10.1016/j.jmgm.2016.02.006
   PubMed Web of Science ®Google Scholar
• Yang, Z., Yang, G., & Zhou, L. (2013). Mutation effects of neuraminidases and their docking with ligands: A molecular dynamics and free energy calculation study. Journal of Computer-Aided Molecular Design, 27, 935–950.10.1007/s10822-013-9691-1
   PubMed Web of Science ®Google Scholar
• Zhang, L., Yan, F., Zhang, S. L., Lei, D. S., Charles, M. A., Cavigiolio, G., & Ren, G. (2012). Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein. Nature Chemical Biology, 8, 342–349.10.1038/nchembio.796
   PubMed Web of Science ®Google Scholar
• Zhang, M., Charles, R., Tong, H., Zhang, L., Patel, M., Wang, F., … Ren, G. (2015). HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation. Scientific Reports, 5, 8741.10.1038/srep08741
   PubMed Web of Science ®Google Scholar
• Zhong, S., Sharp, D. S., Grove, J. S., Bruce, C., Yano, K., Curb, J. D., & Tall, A. R. (1996). Increased coronary heart disease in Japanese-American men with mutation in the cholesteryl ester transfer protein gene despite increased HDL levels. Journal of Clinical Investigation, 97, 2917–2923.10.1172/JCI118751
   PubMed Web of Science ®Google Scholar