Molecular Dynamics and Docking Investigations of Several Zoanthamine-Type Marine Alkaloids As Matrix Metaloproteinase-1 Inhibitors

Overview

Journal Iran J Pharm Res

Publisher Brieflands

Specialty Pharmacology

Date 2017 May 13

PMID 28496473

Citations 5

Authors

Maryam Farrokhnia

Karim Mahnam

Affiliations

Soon will be listed here.

Abstract

Zoanthamine-type alkaloids display a wide spectrum of biological effects. This study aimed to examine the inhibitory effects of norzoanthamine and its ten homologues of zoanthamine class on human fibroblast collagenase by modeling a three-dimensional structure of the ligands at collagenase using energy minimization, docking, molecular dynamics simulation and MM-PB/GBSA binding free energy calculations. The results showed that zoanthamide, zooxathellamine and enol-iminium form of norzoanthamine, with lower binding free energies than other compounds, are potent inhibitors of collagenase. However, the enol-iminium form of norzoanthamine showed a more inhibitory activity against collagenase than its keto form. This suggests that it can be used for treatment of many diseases such as osteoporosis, autoimmune diseases, and cancer. Zinc-binding residues such as His 118, His 122 and His 128 for hydrogen bonds and Leu 81, Tyr 110, Val 115, Leu 126, Pro 138, Ser 139 for hydrophobic interactions should be considered for designing an inhibitor for collagenase. Our theoretical results and MM/GBSA binding free energy calculations are consistent with experimental studies.

Citing Articles

Synthesis of some novel coumarin isoxazol sulfonamide hybrid compounds, 3D-QSAR studies, and antibacterial evaluation.

Esfahani S, Damavandi M, Sadeghi P, Nazifi Z, Salari-Jazi A, Massah A Sci Rep. 2021; 11(1):20088.

PMID: 34635732 PMC: 8505453. DOI: 10.1038/s41598-021-99618-w.

Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide.

Mahnam K, Lotfi M, Shapoorabadi F J Mol Graph Model. 2021; 107:107952.

PMID: 34119951 PMC: 8174010. DOI: 10.1016/j.jmgm.2021.107952.

Bioactive Salen-type Schiff Base Transition Metal Complexes as Possible Anticancer Agents.

Damercheli M, Mahdi M, Mehravi B, Shafiee Ardestani M Iran J Pharm Res. 2020; 18(4):2055-2066.

PMID: 32184869 PMC: 7059031. DOI: 10.22037/ijpr.2019.12792.11151.

Identification of Novel PI3Kδ Selective Inhibitors by SVM-Based Multistage Virtual Screening and Molecular Dynamics Simulations.

Liang J, Wang S, Wang M, Li S, Li W, Meng F Int J Mol Sci. 2019; 20(23).

PMID: 31795217 PMC: 6928688. DOI: 10.3390/ijms20236000.

A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs.

Wang M, Liang J, Olounfeh K, Sun Q, Zhao N, Meng F Molecules. 2018; 23(9).

PMID: 30231506 PMC: 6225272. DOI: 10.3390/molecules23092385.

References

Krane S, Inada M . Matrix metalloproteinases and bone. Bone. 2008; 43(1):7-18. DOI: 10.1016/j.bone.2008.03.020. View

Yang Y, Qin J, Liu H, Yao X . Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors. J Chem Inf Model. 2011; 51(3):680-92. DOI: 10.1021/ci100427j. View

Ling B, Dong L, Zhang R, Wang Z, Liu Y, Liu C . Theoretical studies on the interactions of XIAP-BIR3 domain with bicyclic and tricyclic core monovalent Smac mimetics. J Mol Graph Model. 2010; 29(3):354-62. DOI: 10.1016/j.jmgm.2010.09.011. View

Wang J, Wolf R, Caldwell J, Kollman P, Case D . Development and testing of a general amber force field. J Comput Chem. 2004; 25(9):1157-74. DOI: 10.1002/jcc.20035. View

Wang J, Morin P, Wang W, Kollman P . Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc. 2001; 123(22):5221-30. DOI: 10.1021/ja003834q. View

Bikadi Z, Hazai E, Zsila F, Lockwood S . Molecular modeling of non-covalent binding of homochiral (3S,3'S)-astaxanthin to matrix metalloproteinase-13 (MMP-13). Bioorg Med Chem. 2006; 14(16):5451-8. DOI: 10.1016/j.bmc.2006.04.047. View

Sanner M . Python: a programming language for software integration and development. J Mol Graph Model. 2000; 17(1):57-61. View

Murphy G, Lee M . What are the roles of metalloproteinases in cartilage and bone damage?. Ann Rheum Dis. 2005; 64 Suppl 4:iv44-7. PMC: 1766921. DOI: 10.1136/ard.2005.042465. View

Lee , Yang , PARR . Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter. 1988; 37(2):785-789. DOI: 10.1103/physrevb.37.785. View

10.

Lovejoy B, Hassell A, Luther M, Weigl D, Jordan S . Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself. Biochemistry. 1994; 33(27):8207-17. DOI: 10.1021/bi00193a006. View

11.

Fields G . Interstitial collagen catabolism. J Biol Chem. 2013; 288(13):8785-93. PMC: 3610953. DOI: 10.1074/jbc.R113.451211. View

12.

Rao B . Recent developments in the design of specific Matrix Metalloproteinase inhibitors aided by structural and computational studies. Curr Pharm Des. 2005; 11(3):295-322. DOI: 10.2174/1381612053382115. View

13.

Micaelo N, Macedo A, Goodfellow B, Felix V . Tetrapyrrole binding affinity of the murine and human p22HBP heme-binding proteins. J Mol Graph Model. 2010; 29(3):396-405. DOI: 10.1016/j.jmgm.2010.07.008. View

14.

Genji T, Fukuzawa S, Tachibana K . Distribution and possible function of the marine alkaloid, norzoanthamine, in the zoanthid Zoanthus sp. using MALDI imaging mass spectrometry. Mar Biotechnol (NY). 2009; 12(1):81-7. DOI: 10.1007/s10126-009-9202-5. View

15.

Vincenti M, White L, Schroen D, Benbow U, Brinckerhoff C . Regulating expression of the gene for matrix metalloproteinase-1 (collagenase): mechanisms that control enzyme activity, transcription, and mRNA stability. Crit Rev Eukaryot Gene Expr. 1996; 6(4):391-411. DOI: 10.1615/critreveukargeneexpr.v6.i4.40. View

16.

Nagase H, Visse R, Murphy G . Structure and function of matrix metalloproteinases and TIMPs. Cardiovasc Res. 2006; 69(3):562-73. DOI: 10.1016/j.cardiores.2005.12.002. View

17.

Browner M, Smith W, Castelhano A . Matrilysin-inhibitor complexes: common themes among metalloproteases. Biochemistry. 1995; 34(20):6602-10. DOI: 10.1021/bi00020a004. View

18.

Kinugawa M, Fukuzawa S, Tachibana K . Skeletal protein protection: the mode of action of an anti-osteoporotic marine alkaloid, norzoanthamine. J Bone Miner Metab. 2009; 27(3):303-14. DOI: 10.1007/s00774-009-0049-7. View

19.

Chambers A, Matrisian L . Changing views of the role of matrix metalloproteinases in metastasis. J Natl Cancer Inst. 1997; 89(17):1260-70. DOI: 10.1093/jnci/89.17.1260. View

20.

Stote R, Karplus M . Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins. 1995; 23(1):12-31. DOI: 10.1002/prot.340230104. View