title: The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis.
abstract: DHCR24 encodes 3β-hydroxysterol-Δ(24)-reductase (DHCR24) catalyzing the cholesterol synthesis from desmosterol using the flavin adenine dinucleotide (FAD) as a co-factor. It is generally accepted that U18666a inhibits the reductase activity of DHCR24, but the detailed mechanism remains elusive. To explore the mechanism of the inhibitory effect of U18666a on DHCR24, we performed molecular dynamics (MD) simulations of two complexes including complexes of DHCR24-FAD-desmosterol enzymatic reactive components with and without the inhibitor U18666a. We found that the U18666a bound into the hydrophobic package near the FAD package of DHCR24. Furthermore, binding free energy of DHCR24 and desmosterol without U18666a is -54.86 kcal/mol, while the system with U18666a is -62.23 kcal/mol, suggesting that the affinity of the substrate desmosterol to DHCR24 was increased in response to the U18666a. In addition, U18666a interacts with FAD by newly forming three hydrogen bonds with Lys292, Lys367, and Gly438 of DHCR24. Finally, secondary structural analysis data obtained from the surrounding hot spots showed that U18666a induced dramatic secondary structural changes around the key residues in the interaction of DHCR24, FAD, and desmosterol. Taken together, these results for the first time demonstrate at the molecular structure level that U18666a blocks DHCR24 activity through an allosteric inhibiting mechanism, which may provide new insight into the development of a new type of cholesterol-lowering drug targeting to block the activity of DHCR24.
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Quan
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Xiuqiang
authors.initials: X
authors.lastname: Chen
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Deliang
authors.initials: D
authors.lastname: Sun
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Xu
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Zhao
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Shi
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China.
authors.forename: Hongsheng
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Cell Biology and Genetics, School of Basic Medical Science, Shenyang Medical College, Huang-he-bei-dajie, No. 146, Shenyang, 110034, China. gaobingdr@hotmail.com.
authors.forename: Bing
authors.initials: B
authors.lastname: Gao
authors.affiliation: The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China. luxiulidr@gmail.com.|Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, China. luxiulidr@gmail.com.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Lu
keywords: Allosteric modulator; DHCR24; Molecular dynamics simulation; U18666a
references.citation: J Clin Endocrinol Metab. 2001 Nov;86(11):5130-7
references.pmid: 11701665
references.citation: Epilepsia. 1982 Jun;23(3):257-68
references.pmid: 7084137
references.citation: Biochem Biophys Res Commun. 2004 Mar 5;315(2):408-17
references.pmid: 14766223
references.citation: Am J Med Genet. 1998 Jan 13;75(2):145-52
references.pmid: 9450875
references.citation: Neuroscience. 2002;113(2):301-10
references.pmid: 12127087
references.citation: BMC Bioinformatics. 2008 Jan 23;9:40
references.pmid: 18215316
references.citation: Genes Dev. 2004 Aug 15;18(16):1981-96
references.pmid: 15289463
references.citation: Proteins. 2005 Oct 1;61(1):79-93
references.pmid: 16080143
references.citation: Arch Biochem Biophys. 2011 Dec 1;516(1):29-34
references.pmid: 21951815
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D190-5
references.pmid: 18045787
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: Biochemistry. 1983 Dec 6;22(25):5687-92
references.pmid: 6661410
references.citation: Nat Methods. 2011 Sep 29;8(10):785-6
references.pmid: 21959131
references.citation: Biochim Biophys Acta. 1990 Jun 28;1045(1):40-8
references.pmid: 2369585
references.citation: J Neurosci. 2000 Oct 1;20(19):7345-52
references.pmid: 11007892
references.citation: Endocrinology. 2008 Jul;149(7):3267-73
references.pmid: 18339707
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: PLoS One. 2014 Feb 25;9(2):e87077
references.pmid: 24586263
references.citation: Drug Metab Rev. 2011 Feb;43(1):69-90
references.pmid: 21247357
references.citation: Lipids. 2009 Jun;44(6):477-87
references.pmid: 19440746
references.citation: J Biol Chem. 1989 Jul 15;264(20):11796-806
references.pmid: 2745416
references.citation: Biochem J. 1997 Sep 1;326 ( Pt 2):609-16
references.pmid: 9291139
references.citation: Nature. 2004 Dec 2;432(7017):640-5
references.pmid: 15577914
references.citation: Am J Med Genet A. 2011 Jul;155A(7):1597-604
references.pmid: 21671375
references.citation: J Mol Graph Model. 2010 Jun;28(8):766-74
references.pmid: 20227312
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Am J Hum Genet. 2001 Oct;69(4):685-94
references.pmid: 11519011
references.citation: Plant Cell. 1998 Oct;10(10):1677-90
references.pmid: 9761794
references.citation: Steroids. 2008 Aug;73(7):708-19
references.pmid: 18394665
references.citation: Cell Signal. 2006 Nov;18(11):1844-53
references.pmid: 16797161
references.citation: Protein Sci. 1995 Jun;4(6):1243-4
references.pmid: 7549889
references.citation: Bioinformatics. 2008 Aug 1;24(15):1662-8
references.pmid: 18474507
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W465-8
references.pmid: 19429891
references.citation: Am J Med Genet. 2002 Dec 15;113(4):315-9
references.pmid: 12457401
references.citation: Pharmacol Ther. 2010 Jul;127(1):19-40
references.pmid: 20420853