IN SILICO INVESTIGATION OF ECHINODERMATA SECONDARY METABOLITES AS HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) REVERSE TRANSCRIPTASE INHIBITORS

  • NURRAHMA NAZWIR Department of Pharmaceutical Chemistry, Biomedical Computation Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, Indonesia.
  • ARRY YANUAR Department of Pharmaceutical Chemistry, Biomedical Computation Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, Indonesia.
  • REZI RIADHI SYAHDI Department of Pharmaceutical Chemistry, Biomedical Computation Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, Indonesia

Abstract

Objective: Human immunodeficiency virus (HIV) targets the immune system and weakens immune surveillance and defenses against infections,
leading to acute immunodeficiency syndrome. Recent trends in drug discovery from natural sources emphasize investigations of compounds from
marine ecosystems.
Methods: In this study, we compiled a database of chemical compounds from echinoderms and virtually screened for those that inhibit HIV-1 reverse
transcriptase (RT). The database was generated from literature searches. Virtual screening analyses for inhibitors of HIV-1 RT were then performed
using AutoDock software.
Results: Based on screening results, the top thirteen ranked compounds were nobilisidenol B, Ech_005, 17-deoxyholothurinogenin,
22,25-oxidoholothurinogenin, Ech_022, Ech_026, Ech_021, nobilisidenol A, Ech_025, 5α-cholest-8(14)-ene-3ß,7α-diol, astropecten A, Ech_004, and
phrygiasterol.
Conclusion: The present in silico screening analyses of compounds from marine ecosystems can be used to identify candidate compounds with high
potential as drugs for the treatment of refractory HIV infections.

Keywords: Echinoderms, Human immunodeficiency virus, Reverse transcriptase inhibitor

References

1. Newman DJ, Cragg GM. Marine natural products and related
compounds in clinical and advanced preclinical trials. J Nat Prod
2004;67:1216-38.
2. Fenical W. Marine pharmaceuticals: Past, present, and future.
Oceanography 2006;19:110-9.
3. World Health Organization. HIV/AIDS Fact Sheet; 2016. Available
from: http://www.who.int/mediacentre/factsheets/fs360/en.
4. Prothero DR. Bringing Fossils to Life: An Introduction to Paleobiology.
USA: Columbia University Press; 2013.
5. Jha RK, Zi-Rong X. Biomedical compounds from marine organisms.
Mar Drugs 2004;2:123-46.
6. Carte BK. Biomedical potential of marine natural products. Bioscience
1996;46:271-86.
7. Malyarenko TV, Malyarenko Vishchuk OS, Ivanchina NV,
Kalinovsky AI, Popov RS, Kicha AA. Four new sulfated polar steroids
from the far eastern starfish Leptasterias ochotensis: Structures and
activities. Mar Drugs 2015;13:4418-35.
8. Kita M, Watanabe M, Takada N, Suenaga K, Yamada K, Uemura D.
Hedathiosulfonic acids A and B, novel thiosulfonic acids from the deepsea
urchin Echinocardium cordatum. Tetrahedron 2002;58:6405-12.
9. Levina EV, Andriyashchenko PV, Kalinovsky AI, Dmitrenok PS,
Stonik VA, Prokof NG. Steroid compounds from the starfish
Lysastrosoma anthosticta collected in the sea of Japan. Russ Chem Bull
2002;51:535-9.
10. Wang W, Li F, Alam N, Liu Y, Hong J, Lee CK, et al. New saponins from
the starfish Certonardoa semiregularis. J Nat Prod 2002;65:1649-56.
11. Maithri G, Manasa B, Vani SS, Narendra A, Harshita T. Computational
drug design and molecular dynamic studies a review. Int J Biomed Data
Min 2016;6:1-7.
12. Yanuar A, Chavarina KK, Syahdi RR. Molecular dynamic simulation
analysis on marine fungi compounds against EGFR and VEGFR-2
inhibitory activity in non-small cell lung cancer. J Young Pharm
2018;10:S25.
13. Yanuar A, Pratiwi I, Syahdi RR. In silico activity analysis of saponins
and 2, 5-piperazinedione from marine organism against murine
double minute-2 inhibitor and procaspase-3 activator. J Young Pharm
2018;20:S16.
14. Watty M, Syahdi RR, Yanuar A. Database compilation and virtual
Int J App Pharm, Vol 12, Special Issue 1, 2020
Nazwir et al.
The 4th International Conference on Global Health 2019 55
screening of secondary metabolites derived from marine fungi as
epidermal growth factor receptor tyrosine abstract kinase inhibitors.
Asian J Pharm Clin Res 2017;10:142-7.
15. MarvinSketch (version 6.2.2), Calculation Module Developed by Chem
Axon 2014. Available from: http://www.chemaxon.com/products/
marvin/marvinsketch.
16. Su HP, Yan Y, Prasad GS, Smith RF, Daniels CL, Abeywickrema PD,
et al. Structural basis for the inhibition of RNase H activity of HIV-1
reverse transcriptase by RNase H active site-directed inhibitors. J Virol
2010;84:7625-33.
17. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS,
et al. Auto dock4 and auto dock tools4: Automated docking with
selective receptor flexibility. J Comput Chem 2009;30:2785.
18. Wolf LK. PyRx. Chem Eng New 2009;87:31.
19. DeLano WL. The PyMOL Molecular Graphics System, Version 0.99.
New York: Schrödinger, LLC; 2002.
20. Wolber G, Langer T. Ligand scout: 3-D pharmacophores derived from
protein-bound ligands and their use as virtual screening filters. J Chem
Inf Model 2005;45:160-9.
21. De Clercq E. Anti-HIV drugs: 25 compounds approved within 25 years
after the discovery of HIV. Int J Antimicrob Agents 2009;33:307-20.
22. Blunt JW, Copp BR, Hu WP, Munro MH, Northcote PT, Prinsep MR.
Marine natural products. Nat Prod Rep 2007;24:31-86.
23. Blunt JW, Copp BR, Munro MH, Northcote PT, Prinsep MR. Marine
natural products. Nat Prod Rep 2003;20:1-48.
24. Bhakuni DS, Rawat DS. Bioactive Marine Natural Products. India:
Springer and Anamaya Publisher; 2005.
25. Thao NP, No JH, Luyen BT, Yang G, Byun SY, Goo J, et al. Secondary
metabolites from Vietnamese marine invertebrates with activity against
Trypanosoma brucei and T. cruzi. Molecules 2014;19:7869-80.
26. Im S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, et al.
PubChem substance and compound databases. Nucleic Acids Res
2016;44: D1202-13.
27. Yanuar A, Mun’im A, Lagho AB, Syahdi RR, Rahmat M, Suhartanto H.
Medicinal plants database and three dimensional structure of the
chemical compounds from medicinal plants in Indonesia. Int J Comput
Sci Issues 2011;8:180-3.
28. Syahdi RR, Mun’im A, Suhartanto H, Yanuar A. Virtual screening of
Indonesian herbal database as HIV-1 reverse transcriptase inhibitor.
Bioinformation 2012;8:1206-10.
29. Pence HE, Williams A. Chemspider: An online chemical information
resource. J Chem Educ 2010;87:1123-4.
30. Hubbard RE, Haider MK. Hydrogen Bonds in Proteins: Role and
Strength. UK: ELS; 2010.
31. Kusuma SA, Manan WS, Budiman F. Inhibitory effect of red piper
betel leaf ethanol extract (Piper crocatum Ruiz and Pav.) against
Trichomonas vaginalis trophozoites in vitro. Asian J Pharm Clin Res
2017;10:311-4.
32. Adiga R. Molecular docking of Hyrtimomine A-K from marine sponge
Hyrtios spp. as anticancer target of phospoinositide-dependent kinase 1.
Asian J Pharm Clin Res 2019;12:130-5.
33. Kwan EE. An Introduction to Hydrogen Bonding. Presented at an
Evans Group Afternoon Seminar; 2009.
34. Skowron G, Ogden R. Transcriptase Inhibitors in HIV/AIDS Therapy.
New Jersey: Humana Press Inc.; 2006.
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NAZWIR, N., YANUAR, A., & SYAHDI, R. R. (2020). IN SILICO INVESTIGATION OF ECHINODERMATA SECONDARY METABOLITES AS HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) REVERSE TRANSCRIPTASE INHIBITORS. International Journal of Applied Pharmaceutics, 12(1), 51-55. https://doi.org/10.22159/ijap.2020.v12s1.FF006
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