Structure based design, synthesis, pharmacophore modeling, virtual screening, and molecular docking studies for identification of novel cyclophilin D inhibitors

Journal of Chemical Information and Modeling

Volumn 54, Issue 3, 2014, Pages 902-912

  Valasani, Koteswara Rao ^a   Vangavaragu, Jhansi Rani ^a   Day, Victor W ^b   Yan, Shirley Shidu ^a  

^a UNIVERSITY OF KANSAS   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D MODELING; CELL DEATH; COMPUTATIONAL CHEMISTRY; DIAGNOSIS; MITOCHONDRIA; MOLECULAR DYNAMICS; MOLECULAR MODELING; MOLECULES; NEURODEGENERATIVE DISEASES; PHARMACODYNAMICS; SULFUR COMPOUNDS;

INNER MITOCHONDRIAL MEMBRANES; MITOCHONDRIAL MEMBRANES; MOLECULAR DYNAMICS SIMULATIONS; PEPTIDYL-PROLYL ISOMERASE; PRINCIPLE COMPONENT ANALYSIS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP METHODS; SMALL ORGANIC MOLECULES; STRUCTURE-BASED DESIGNS;

LEAD COMPOUNDS;

CYCLOPHILIN; CYCLOPHILIN D; ENZYME INHIBITOR; MOLECULAR LIBRARY;

ALZHEIMER DISEASE; ANTAGONISTS AND INHIBITORS; CHEMISTRY; DRUG DESIGN; ENZYMOLOGY; HUMAN; METABOLISM; MOLECULAR DOCKING; MOLECULAR LIBRARY; PHARMACOLOGY; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ALZHEIMER DISEASE; CYCLOPHILINS; DRUG DESIGN; ENZYME INHIBITORS; HUMANS; MOLECULAR DOCKING SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SMALL MOLECULE LIBRARIES;

EID: 84896928887     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci5000196     Document Type: Article

References (44)

1. Caspersen, C.; Wang, N.; Yao, J.; Sosunov, A.; Chen, X.; Lustbader, J. W.; Xu, H. W.; Stern, D.; McKhann, G.; Yan, S. D. Mitochondrial Abeta: a potential focal point for neuronal metabolic dysfunction in Alzheimers disease FASEB J. 2005, 19, 2040-1
2. Reddy, P. H.; Beal, M. F. Amyloid beta, mitochondrial dysfunction and synaptic damage: implications for cognitive decline in aging and Alzheimers disease Trends in Mol. Med. 2008, 14, 45-53
3. Du, H.; Guo, L.; Yan, S.; Sosunov, A. A.; McKhann, G. M.; Yan, S. S. Early deficits in synaptic mitochondria in an Alzheimers disease mouse model Proc. Natl. Acad. Sci. USA 2010, 107, 18670-5
4. Lunnon, K.; Ibrahim, Z.; Proitsi, P.; Lourdusamy, A.; Newhouse, S.; Sattlecker, M.; Furney, S.; Saleem, M.; Soininen, H.; Kloszewska, I.; Mecocci, P.; Tsolaki, M.; Vellas, B.; Coppola, G.; Geschwind, D.; Simmons, A.; Lovestone, S.; Dobson, R.; Hodges, A.; AddNeuroMed, C. Mitochondrial dysfunction and immune activation are detectable in early Alzheimers disease blood J. Alzheimers Disease: JAD 2012, 30, 685-710
5. Valasani, K. R.; Sun, Q.; Hu, G.; Li, J.; Du, F.; Guo, Y.; Carlson, E. A.; Gan, X.; Yan, S. S. Identification of Human ABAD Inhibitors for Rescuing Abeta-Mediated Mitochondrial Dysfunction Curr. Alzheimer Res. 2014, 10.2174/1567205011666140130150108
6. Du, H.; Guo, L.; Fang, F.; Chen, D.; Sosunov, A. A.; McKhann, G. M.; Yan, Y.; Wang, C.; Zhang, H.; Molkentin, J. D.; Gunn-Moore, F. J.; Vonsattel, J. P.; Arancio, O.; Chen, J. X.; Yan, S. D. Cyclophilin D deficiency attenuates mitochondrial and neuronal perturbation and ameliorates learning and memory in Alzheimers disease Nature Med. 2008, 14, 1097-105
7. Manczak, M.; Anekonda, T. S.; Henson, E.; Park, B. S.; Quinn, J.; Reddy, P. H. Mitochondria are a direct site of A beta accumulation in Alzheimers disease neurons: implications for free radical generation and oxidative damage in disease progression Human Mol. Genetics 2006, 15, 1437-49
8. Lustbader, J. W.; Cirilli, M.; Lin, C.; Xu, H. W.; Takuma, K.; Wang, N.; Caspersen, C.; Chen, X.; Pollak, S.; Chaney, M.; Trinchese, F.; Liu, S.; Gunn-Moore, F.; Lue, L. F.; Walker, D. G.; Kuppusamy, P.; Zewier, Z. L.; Arancio, O.; Stern, D.; Yan, S. S.; Wu, H. ABAD directly links Abeta to mitochondrial toxicity in Alzheimers disease Science 2004, 304, 448-52
9. Hauptmann, S.; Scherping, I.; Drose, S.; Brandt, U.; Schulz, K. L.; Jendrach, M.; Leuner, K.; Eckert, A.; Muller, W. E. Mitochondrial dysfunction: an early event in Alzheimer pathology accumulates with age in AD transgenic mice Neurobiol. Aging 2009, 30, 1574-86
10. Yao, J.; Irwin, R. W.; Zhao, L.; Nilsen, J.; Hamilton, R. T.; Brinton, R. D. Mitochondrial bioenergetic deficit precedes Alzheimers pathology in female mouse model of Alzheimers disease Proc. Natl. Acad. Sci. USA 2009, 106, 14670-5
11. Yan, S. D.; Fu, J.; Soto, C.; Chen, X.; Zhu, H.; Al-Mohanna, F.; Collison, K.; Zhu, A.; Stern, E.; Saido, T.; Tohyama, M.; Ogawa, S.; Roher, A.; Stern, D. An intracellular protein that binds amyloid-beta peptide and mediates neurotoxicity in Alzheimers disease Nature 1997, 389, 689-95
12. Valasani, K. R.; Hu, G.; Chaney, M. O.; Yan, S. S. Structure-Based Design and Synthesis of Benzothiazole Phosphonate Analogues with Inhibitors of Human ABAD-A beta for Treatment of Alzheimers Disease Chem. Biol. Drug Des. 2013, 81, 238-249
13. Stains, C. I.; Mondal, K.; Ghosh, I. Molecules that target beta-amyloid ChemMedChem 2007, 2, 1674-92
14. Ghosh, A. K.; Venkateswara Rao, K.; Yadav, N. D.; Anderson, D. D.; Gavande, N.; Huang, X.; Terzyan, S.; Tang, J. Structure-Based Design of Highly Selective beta-Secretase Inhibitors: Synthesis, Biological Evaluation, and Protein-Ligand X-ray Crystal Structure J. Med. Chem. 2012, 55, 9195-207
15. Gravenfors, Y.; Viklund, J.; Blid, J.; Ginman, T.; Karlstrom, S.; Kihlstrom, J.; Kolmodin, K.; Lindstrom, J.; von Berg, S.; von Kieseritzky, F.; Bogar, K.; Slivo, C.; Swahn, B. M.; Olsson, L. L.; Johansson, P.; Eketjall, S.; Falting, J.; Jeppsson, F.; Stromberg, K.; Janson, J.; Rahm, F. Correction to New Aminoimidazoles as beta-Secretase (BACE-1) Inhibitors Showing Amyloid-beta (Abeta) Lowering in Brain J. Med. Chem. 2012, 55, 9297-9311
16. Ogura, A.; Morizane, A.; Nakajima, Y.; Miyamoto, S.; Takahashi, J. gamma-Secretase Inhibitors Prevent Overgrowth of Transplanted Neural Progenitors Derived from Human-Induced Pluripotent Stem Cells Stem Cells Dev. 2013, 22, 374-382
17. Parker, M. F.; Barten, D. M.; Bergstrom, C. P.; Bronson, J. J.; Corsa, J. A.; Dee, M. F.; Gai, Y.; Guss, V. L.; Higgins, M. A.; Keavy, D. J.; Loo, A.; Mate, R. A.; Marcin, L. R.; McElhone, K. E.; Polson, C. T.; Roberts, S. B.; Macor, J. E. 2-(N-Benzyl-N-phenylsulfonamido)alkyl amide derivatives as gamma-secretase inhibitors Bioorg. Med. Chem. Lett. 2012, 22, 6828-6831
18. Ozudogru, S. N.; Lippa, C. F. Disease modifying drugs targeting beta-amyloid Am. J. Alzheimers Disease Other Dementias 2012, 27, 296-300
19. Panza, F.; Solfrizzi, V.; Frisardi, V.; Imbimbo, B. P.; Capurso, C.; DIntrono, A.; Colacicco, A. M.; Seripa, D.; Vendemiale, G.; Capurso, A.; Pilotto, A. Beyond the neurotransmitter-focused approach in treating Alzheimers disease: drugs targeting beta-amyloid and tau protein Aging Clin. Exp. Res. 2009, 21, 386-406
20. Frisardi, V.; Solfrizzi, V.; Imbimbo, P. B.; Capurso, C.; DIntrono, A.; Colacicco, A. M.; Vendemiale, G.; Seripa, D.; Pilotto, A.; Capurso, A.; Panza, F. Towards disease-modifying treatment of Alzheimers disease: drugs targeting beta-amyloid Curr. Alzheimer Res. 2010, 7, 40-55
21. Orlando, R. A.; Gonzales, A. M.; Royer, R. E.; Deck, L. M.; Vander Jagt, D. L. A chemical analog of curcumin as an improved inhibitor of amyloid Abeta oligomerization PloS One 2012, 7, e31869
22. Park, S. K.; Pegan, S. D.; Mesecar, A. D.; Jungbauer, L. M.; LaDu, M. J.; Liebman, S. W. Development and validation of a yeast high-throughput screen for inhibitors of Abeta(4)(2) oligomerization Disease Models Mech. 2011, 4, 822-831
23. Walsh, D. M.; Townsend, M.; Podlisny, M. B.; Shankar, G. M.; Fadeeva, J. V.; El Agnaf, O.; Hartley, D. M.; Selkoe, D. J. Certain inhibitors of synthetic amyloid beta-peptide (Abeta) fibrillogenesis block oligomerization of natural Abeta and thereby rescue long-term potentiation J. Neurosci. 2005, 25, 2455-2462
24. Du, H.; Guo, L.; Zhang, W.; Rydzewska, M.; Yan, S. Cyclophilin D deficiency improves mitochondrial function and learning/memory in aging Alzheimer disease mouse model Neurobiol. Aging 2011, 32, 398-406
25. Takuma, K.; Yao, J.; Huang, J.; Xu, H.; Chen, X.; Luddy, J.; Trillat, A. C.; Stern, D. M.; Arancio, O.; Yan, S. S. ABAD enhances Abeta-induced cell stress via mitochondrial dysfunction FASEB J. 2005, 19, 597-598
26. Tanveer, A.; Virji, S.; Andreeva, L.; Totty, N. F.; Hsuan, J. J.; Ward, J. M.; Crompton, M. Involvement of cyclophilin D in the activation of a mitochondrial pore by Ca2+ and oxidant stress Eur. J. Biochem./FEBS 1996, 238, 166-172
27. Griffiths, E. J.; Halestrap, A. P. Further evidence that cyclosporin A protects mitochondria from calcium overload by inhibiting a matrix peptidyl-prolyl cis-trans isomerase. Implications for the immunosuppressive and toxic effects of cyclosporin Biochem. J. 1991, 274 (Pt 2) 611-614
28. Galat, A.; Metcalfe, S. M. Peptidylproline cis/trans isomerases Progress Biophys. Molec. Biol. 1995, 63, 67-118
29. Khaspekov, L.; Friberg, H.; Halestrap, A.; Viktorov, I.; Wieloch, T. Cyclosporin A and its nonimmunosuppressive analogue N-Me-Val-4-cyclosporin A mitigate glucose/oxygen deprivation-induced damage to rat cultured hippocampal neurons Eur. J. Neurosci. 1999, 11, 3194-3198
30. Nicolli, A.; Basso, E.; Petronilli, V.; Wenger, R. M.; Bernardi, P. Interactions of cyclophilin with the mitochondrial inner membrane and regulation of the permeability transition pore, and cyclosporin A-sensitive channel J. Biol. Chem. 1996, 271, 2185-2192
31. Clarke, S. J.; McStay, G. P.; Halestrap, A. P. Sanglifehrin A acts as a potent inhibitor of the mitochondrial permeability transition and reperfusion injury of the heart by binding to cyclophilin-D at a different site from cyclosporin A J. Biol. Chem. 2002, 277, 34793-34799
32. Azzolin, L.; Antolini, N.; Calderan, A.; Ruzza, P.; Sciacovelli, M.; Marin, O.; Mammi, S.; Bernardi, P.; Rasola, A. Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore PloS One 2011, 6, e16280
33. Guo, H. X.; Wang, F.; Yu, K. Q.; Chen, J.; Bai, D. L.; Chen, K. X.; Shen, X.; Jiang, H. L. Novel cyclophilin D inhibitors derived from quinoxaline exhibit highly inhibitory activity against rat mitochondrial swelling and Ca2+ uptake/ release Acta Pharma. Sin. 2005, 26, 1201-1211
34. Wang, F.; Chen, J.; Liu, X. J.; Shen, X.; He, X. C.; Jiang, H. L.; Bai, D. L. Synthesis and peptidyl-prolyl isomerase inhibitory activity of quinoxalines as ligands of cyclophilin A Chem. Pharm. Bull. 2006, 54, 372-376
35. Guo, H. X.; Wang, F.; Yu, K. Q.; Chen, Y.; Bai, D. L.; Chen, K. X.; Shen, X.; Jiang, H. L. Novel cyclophilin D inhibitors derived from quinoxaline exhibit highly inhibitory activity against rat mitochondrial swelling and Ca2+ uptake/release Acta Pharma. Sin. 2005, 26, 1201-1211
36. Li, J.; Chen, J.; Zhang, L.; Wang, F.; Gui, C. S.; Zhang, L.; Qin, Y.; Xu, Q.; Liu, H.; Nan, F. J.; Shen, J. K.; Bai, D. L.; Chen, K. X.; Shen, X.; Jiang, H. L. One novel quinoxaline derivative as a potent human cyclophilin A inhibitor shows highly inhibitory activity against mouse spleen cell proliferation Bioorg. Med. Chem. 2006, 14, 5527-5534
37. Vilar, S.; Cozza, G.; Moro, S. Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery Curr. Top Med. Chem. 2008, 8, 1555-1572
38. Vilar, S.; Gonzalez-Diaz, H.; Santana, L.; Uriarte, E. QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks J. Comput. Chem. 2008, 29, 2613-2622
39. Kajitani, K.; Fujihashi, M.; Kobayashi, Y.; Shimizu, S.; Tsujimoto, Y.; Miki, K. Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution Proteins 2008, 70, 1635-1639
40. Valasani, K. R.; Chaney, M. O.; Day, V. W.; Yan, S. S. Acetylcholinesterase Inhibitors: Structure Based Design, Synthesis, Pharmacophore Modeling, and Virtual Screening J. Chem. Inf. Model. 2013, 53, 2033-2046
41. Zhi, H.; Chen, L. M.; Zhang, L. L.; Liu, S. J.; Wan, D. C. C.; Lin, H. Q.; Hu, C. Design, synthesis, and biological evaluation of 5H-thiazolo[3,2-a] pyrimidine derivatives as a new type of acetylcholinesterase inhibitors Arkivoc 2008, 266-277
42. Rivkin, A.; Ahearn, S. P.; Chichetti, S. M.; Kim, Y. R.; Li, C. M.; Rosenau, A.; Kattar, S. D.; Jung, J.; Shah, S.; Hughes, B. L.; Crispino, J. L.; Middleton, R. E.; Szewczak, A. A.; Munoz, B.; Shearman, M. S. Piperazinyl pyrimidine derivatives as potent gamma-secretase modulators Bioorg. Med. Chem. Lett. 2010, 20, 1269-1271
43. Messer, W. S., Jr.; Rajeswaran, W. G.; Cao, Y.; Zhang, H. J.; el-Assadi, A. A.; Dockery, C.; Liske, J.; OBrien, J.; Williams, F. E.; Huang, X. P.; Wroblewski, M. E.; Nagy, P. I.; Peseckis, S. M. Design and development of selective muscarinic agonists for the treatment of Alzheimers disease: characterization of tetrahydropyrimidine derivatives and development of new approaches for improved affinity and selectivity for M1 receptors Pharma. Acta Helvetiae 2000, 74, 135-40
44. Kypta, R. M. GSK-3 inhibitors and their potential in the treatment of Alzheimers disease Expert Opin. Ther. Pat. 2005, 15, 1315-1331