OpenLB
Open Library of Bioscience
Advanced Search
International journal of molecular sciences
Jul 15, 2019;20 (14):

Molecular Docking and Molecular Dynamics Studies on Selective Synthesis of α-Amyrin and β-Amyrin by Oxidosqualene Cyclases from .

Zhixue Wu, Hui Xu, Meiling Wang, Ruoting Zhan, Weiwen Chen, Ren Zhang, Zaoyuan Kuang, Fengxue Zhang, Kui Wang, Jiangyong Gu
Author Information
  1. Zhixue Wu: Research Centre for Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
  2. Hui Xu: Research Centre of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Centre for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China.
  3. Meiling Wang: Research Centre of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Centre for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China.
  4. Ruoting Zhan: Research Centre of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Centre for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China.
  5. Weiwen Chen: Research Centre of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Centre for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China.
  6. Ren Zhang: Department of Medical Biotechnology, College of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
  7. Zaoyuan Kuang: Research Centre for Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
  8. Fengxue Zhang: Research Centre for Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
  9. Kui Wang: Research Centre of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Centre for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China. uk0829@126.com. ORCID
  10. Jiangyong Gu: The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China. gujy@gzucm.edu.cn.
PMID: 31311103 DOI: 10.3390/ijms20143469

Abstract

Amyrins are the immediate precursors of many pharmaceutically important pentacyclic triterpenoids. Although various amyrin synthases have been identified, little is known about the relationship between protein structures and the constituent and content of the products. IaAS1 and IaAS2 identified from in our previous work belong to multifunctional oxidosqualene cyclases and can produce α-amyrin and β-amyrin at different ratios. More than 80% of total production of IaAS1 is α-amyrin; while IaAS2 mainly produces β-amyrin with a yield of 95%. Here, we present a molecular modeling approach to explore the underlying mechanism for selective synthesis. The structures of IaAS1 and IaAS2 were constructed by homology modeling, and were evaluated by Ramachandran Plot and Verify 3D program. The enzyme-product conformations generated by molecular docking indicated that ASP484 residue plays an important role in the catalytic process; and TRP611 residue of IaAS2 had interaction with β-amyrin through π-σ interaction. MM/GBSA binding free energy calculations and free energy decomposition after 50 ns molecular dynamics simulations were performed. The binding affinity between the main product and corresponding enzyme was higher than that of the by-product. Conserved amino acid residues such as TRP257; TYR259; PHE47; TRP534; TRP612; and TYR728 for IaAS1 (TRP257; TYR259; PHE473; TRP533; TRP611; and TYR727 for IaAS2) had strong interactions with both products. GLN450 and LYS372 had negative contribution to binding affinity between α-amyrin or β-amyrin and IaAS1. LYS372 and ARG261 had strong repulsive effects for the binding of α-amyrin with IaAS2. The importance of Lys372 and TRP612 of IaAS1, and Lys372 and TRP611 of IaAS2, for synthesizing amyrins were confirmed by site-directed mutagenesis. The different patterns of residue-product interactions is the cause for the difference in the yields of two products.

Keywords

amyrin molecular modeling oxidosqualene cyclase residue-product interaction selective synthesis

References

Eur J Biochem. 2000 Jun;267(12):3453-60 [PMID: 10848960]
Chem Biol. 2000 Aug;7(8):643-9 [PMID: 11048954]
Angew Chem Int Ed Engl. 2000 Nov 17;39(22):4090-4092 [PMID: 11093215]
Biochim Biophys Acta. 2001 Dec 3;1522(2):67-73 [PMID: 11750056]
Chem Biol. 2002 May;9(5):639-45 [PMID: 12031670]
Biochemistry. 2002 Jul 2;41(26):8238-44 [PMID: 12081472]
Plant J. 2002 Dec;32(6):1033-48 [PMID: 12492844]
J Med Chem. 2003 May 22;46(11):2083-92 [PMID: 12747780]
Phytochemistry. 2004 Feb;65(3):261-91 [PMID: 14751299]
Chem Biol. 2004 Jan;11(1):121-6 [PMID: 15113001]
Chembiochem. 2004 Dec 3;5(12):1712-5 [PMID: 15508118]
Nature. 2004 Nov 4;432(7013):118-22 [PMID: 15525992]
J Proteome Res. 2006 Jan;5(1):32-43 [PMID: 16396493]
Curr Opin Plant Biol. 2006 Jun;9(3):305-14 [PMID: 16581287]
J Am Chem Soc. 2006 May 17;128(19):6414-9 [PMID: 16683806]
Protein Sci. 2006 Nov;15(11):2507-24 [PMID: 17075131]
Phytochemistry. 2006 Dec;67(23):2517-24 [PMID: 17078982]
Nat Protoc. 2007;2(1):31-4 [PMID: 17401334]
FEBS J. 2007 Oct;274(19):5028-42 [PMID: 17803686]
Nat Prod Rep. 2007 Dec;24(6):1311-31 [PMID: 18033581]
Org Lett. 2008 Jun 19;10(12):2529-32 [PMID: 18494476]
Science. 1991 Jul 12;253(5016):164-70 [PMID: 1853201]
Phytochemistry. 2008 Oct;69(14):2559-64 [PMID: 18790509]
Plant Physiol Biochem. 2009 Jan;47(1):26-30 [PMID: 18977664]
J Comput Chem. 2009 Dec;30(16):2785-91 [PMID: 19399780]
Biol Pharm Bull. 2009 May;32(5):818-24 [PMID: 19420748]
J Chem Inf Model. 2011 Jan 24;51(1):69-82 [PMID: 21117705]
Org Biomol Chem. 2011 Feb 21;9(4):1092-7 [PMID: 21157613]
Curr Comput Aided Drug Des. 2011 Jun;7(2):146-57 [PMID: 21534921]
J Proteome Res. 2012 May 4;11(5):2982-95 [PMID: 22468754]
Biochimie. 2012 Nov;94(11):2376-81 [PMID: 22732192]
Planta. 2012 Nov;236(5):1571-81 [PMID: 22837051]
Org Lett. 2012 Oct 19;14(20):5222-5 [PMID: 23043506]
FEBS J. 2013 Mar;280(5):1267-80 [PMID: 23294602]
Org Biomol Chem. 2013 Jul 7;11(25):4214-9 [PMID: 23680980]
Biochem J. 2014 Apr 15;459(2):289-99 [PMID: 24483781]
Org Biomol Chem. 2014 Jun 21;12(23):3836-46 [PMID: 24695673]
Int J Mol Sci. 2015 Feb 05;16(2):3564-78 [PMID: 25664861]
Methods Mol Biol. 2015;1311:349-62 [PMID: 25981485]
Org Biomol Chem. 2015 Jul 14;13(26):7331-6 [PMID: 26058429]
Bioorg Med Chem Lett. 2015 Oct 1;25(19):4342-6 [PMID: 26259803]
J Chem Theory Comput. 2015 Aug 11;11(8):3696-713 [PMID: 26574453]
J Chem Theory Comput. 2012 Sep 11;8(9):3314-21 [PMID: 26605738]
Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4407-14 [PMID: 27412861]
Phys Chem Chem Phys. 2016 Aug 10;18(32):22129-39 [PMID: 27444142]
Org Biomol Chem. 2016 Dec 20;15(1):177-188 [PMID: 27942657]
J Mol Graph Model. 2017 Jun;74:273-287 [PMID: 28458006]
Chembiochem. 2017 Nov 2;18(21):2145-2155 [PMID: 28875584]
Chembiochem. 2018 Mar 2;19(5):486-495 [PMID: 29214725]
Phytochem Anal. 2018 Sep;29(5):516-527 [PMID: 29637651]
Phys Chem Chem Phys. 2018 May 30;20(21):14450-14460 [PMID: 29785435]
Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9274-8 [PMID: 7568116]
Trends Biochem Sci. 1994 Apr;19(4):157-8 [PMID: 8016864]
Protein Sci. 1993 Sep;2(9):1511-9 [PMID: 8401235]

Grants

  1. A1-AFD018161Z04/start-up support for scientific research of Xinglin Young Scholar in Guangzhou University of Chinese Medicine
  2. J1310017/Fostering Talents in Basic Science of the National Natural Science Foundation of China
  3. 31802099 and 81804111/National Natural Science Foundation of China
  4. 2018A030310497/Natural Science Foundation of Guangdong Province, China
  5. 2017KQNCX037/Young Innovative Talents in Higher Education Institutions of Guangdong Province
  6. A1-AFD018161Z0105, A1-AFD018171Z11016 & A1-AFD01817111013/Projects of Guangzhou University of Chinese Medicine
  7. 2016KYTD02/Guangdong Innovative Research Team Program
  8. 2016KCXTD015/Innovation team project of the Education Bureau of Guangdong Province-Research team on innovation of traditional Chinese medicine resources

MeSH Term

Binding Sites
Ilex
Intramolecular Transferases
Molecular Docking Simulation
Oleanolic Acid
Pentacyclic Triterpenes
Plant Proteins
Protein Binding

Chemicals

Pentacyclic Triterpenes
Plant Proteins
alpha-amyrin
Oleanolic Acid
Intramolecular Transferases
lanosterol synthase
beta-amyrin
Journal Article

Word Cloud

Similar Articles

Cited By