2,319
Views
6
CrossRef citations to date
0
Altmetric
Articles

In silico study of the interactions of Pilocarpus microphyllus imidazolic alkaloids with the main protease (Mpro) of SARS-CoV-2

, , , , &
Pages 74-87 | Received 16 Sep 2020, Accepted 03 Jan 2021, Published online: 12 Jan 2021

References

  • Huynh T, Wang H, Luan B. In silico exploration of the molecular mechanism of clinically oriented drugs for possibly inhibiting SARS-CoV-2’s main protease. J Phys Chem Lett. 2020;11:4413–4420. doi:10.1021/acs.jpclett.0c00994
  • Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. New Engl J Med. 2020;382:727–733. doi:10.1056/NEJMoa2001017
  • Lancet T. Global coalition to accelerate COVID-19 clinical research in resource-limited settings. J Lancet Healthy Longevity. 2020;395:1322–1325. doi:10.1016/S0140-6736(20)30798-4.
  • OPAS/OMS Brazil. (2020). Fact sheet - COVID-19 (disease caused by the new coronavirus). Brasilia, DF, Brazil. https://www.paho.org/bra/ (accessed 30.11.2020).
  • Zhang L, Lin D, Sun X, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Science. 2020;368:409–412. doi:10.1126/science.abb3405
  • Anand K, Palm GJ, Mesters JR, et al. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain. EMBO J. 2002;21:3213–3224. doi:10.1093/emboj/cdf327
  • Yang H, Yang M, Ding Y, et al. The crystal structures of severe acute respiratory syndrome vírus main protease and its complex with an inhibitor. Proc Nat Acad Sci. 2003;100:13190–13195.doi:10.1073/pnas.1835675100
  • Jin Z, Du X, Xu Y, et al. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582:289–293. doi:10.1038/s41586-020-2223-y
  • Yang H, Xie W, Xue X, et al. Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol. 2005;3:e324. doi:10.1371/journal.pbio.0030324
  • Wang F, Chen C, Tan W, et al. Structure of main protease from human coronavirus NL63: insights for amplo espectro anti-coronavirus drug design. Sci Rep. 2016;6:22677. doi:10.1038/srep22677
  • Aanouz I, Belhassan A, El-Khatabi K, et al. Moroccan medicinal plants as inhibitors against SARS-CoV-2 main protease: computational investigations. J Biomol Struct Dyn. 2020. doi:10.1080/07391102.2020.1758790.
  • Ferreira ET, Santos ES, Monteiro JS, et al. The use of medicinal and phytotherapy plants: An integrational review on the nurses performance. Braz J Health Rev. 2019;2:1511–1523. https://www.brazilianjournals.com/index.php/BJHR/article/view/1383 (accessed 20.04.2020).
  • Lima DF, Lima LI, Rocha JA, et al. Seasonal change in main alkaloids of jaborandi (Pilocarpus microphyllus Stapf ex Wardleworth), an economically important species from the Brazilian flora. PLoS ONE. 2017;12:e0170281. doi:10.1371/journal.pone.0170281.
  • Duke JA. Handbook of medicinal herbs. 2nd ed New York: CRC Press; 2002; 896 p.
  • Devi R, Singh V, Chaudhary AK. Antidiabetic activity of pilocarpus microphyllus extract on streptozotocin-induced diabetic mice. Int J Pharm Sci Rev Res. 2010;5:87–92. https://www.semanticscholar.org/paper/ANTIDIABETIC-ACTIVITY-OF-PILOCARPUS-MICROPHYLLUS-ON-Devi-Singh/9f0c6d63d0de9a46337316684b215293a7e8de7c#citing-papers (accessed 25.04.2020).
  • Agban Y, Lian J, Prabakar S, et al. Nanoparticle cross-linked collagen shields for sustained delivery of pilocarpine hydrochloride. Int J Pharm. 2016;501:96–101. doi:10.1016/j.ijpharm.2016.01.069
  • Gil-Montoya JA, Silvestre FJ, Barrios R, et al. Treatment of xerostomia and hyposalivation in the elderly: a systematic review. Oral Medicine Oral Pathology and Oral Surgery. 2016;21:e355–e366. doi:10.4317/medoral.20969.
  • Guimarães MA, Campelo YD, Véras LM, et al. Nanopharmaceutical approach of epiisopiloturine alkaloid carried in liposome system: preparation and in vitro schistosomicidal activity. J Nanosci Nanotechnol. 2014;14:4519–4528. doi:10.1166/jnn.2014.8248
  • Guimarães MA, de Oliveira RN, Véras LMC, et al. Anthelmintic activity in vivo of epiisopiloturine against juvenile and adult worms of Schistosoma mansoni. PLoS Negl Trop Dis. 2015;9:e0003656. doi:10.1371/journal.pntd.0003656
  • Rocha JA, Rego NCS, Carvalho BTS, et al. Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties. PLoS ONE. 2018;13:e0198476. doi:10.1371/journal.pone.0198476.
  • Silva VG, Silva RO, Damasceno SRB, et al. Anti-inflammatory and antinociceptive activity of epiisopiloturine, an imidazole alkaloid isolated from Pilocarpus microphyllus. J Nat Prod. 2013;76:1071–1077. doi:10.1021/np400099m
  • Nicolau LAD, Carvalho NS, Pacífico DM, et al. Epiisopiloturine hydrochloride, an imidazole alkaloid isolated from Pilocarpus microphyllus leaves, protects against naproxen-induced gastrointestinal damage in rats. Biomed Pharmacother. 2017;87:188–195. doi:10.1016/j.biopha.2016.12.101
  • Rocha JA, Andrade IM, Véras LMC, et al. Anthelmintic, antibacterial and cytotoxicity activity of imidazole alkaloids from Pilocarpus microphyllus leaves. Phytother Res. 2017;31:624–630. doi:10.1002/ptr.5771
  • Lima Neto JX. (2019). Estudo em complexos fármaco-receptor utilizando bioquímica quântica [Quantum biochemistry study in drug-receptor complexes]. 140f. Thesis (Doctorate in Biochemistry). Federal University of Rio Grande do Norte, Natal, Brazil. Portuguese. https://repositorio.ufrn.br/jspui/handle/123456789/26645 (accessed 02.05.2020).
  • Das S, Sarmah S, Lyndem S, et al. An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. J Biomol Struct Dyn. 2020; doi:10.1080/07391102.2020.1763201.
  • Kadan, R. U., Roy, N. Recent Trends in drug likeness prediction: a comprehensive review of In silico methods. Indian J Pharm Sci. 2007;69: 609–615. doi:10.4103/0250-474X.38464
  • Berman HM, Westbrook J, Feng Z, et al. The protein data Bank. Nucleic Acids Res. 2000;28:235–242. doi:10.1093/nar/28.1.235
  • Santos AP, Moreno PRH. Pilocarpus spp.: a survey of its chemical constituents and biological activities. Braz J Pharm Sci. 2004;40:115–137. doi:10.1590/S1516-93322004000200002.
  • Abreu IN, Mazzafera P, Eberlin MN, et al. Characterization of the variation in the imidazole alkaloid profile of Pilocarpus microphyllus in different seasons and parts of the plant by electrospray ionization mass spectrometry fingerprinting and identification of novel alkaloids by tandem mass spectrometry. Rapid Commun Mass Spectrom. 2007;21:1205–1213. doi:10.1002/rcm.2942
  • Véras LMC, Cunha VRR, Lima FCDA, et al. Industrial scale Isolation, structural and spectroscopic characterization of epiisopiloturine from pilocarpus microphyllus Stapf leaves: a promising alkaloid against schistosomiasis. PLoS ONE. 2013;8:e66702. doi:10.1371/journal.pone.0066702
  • Dennington R, Keith TA, Millam JM. (2016). GaussView, version 6, Semichem Inc., Shawnee Mission, KS. https://gaussian.com/gaussview6/ (accessed 03.05.2020).
  • Costa RA, Junior ESA, Lopes GBP, et al. Structural, vibrational, UV–vis, quantum-chemical properties, molecular docking and anti-cancer activity study of annomontine and N-hydroxyannomontine β-carboline alkaloids: a combined experimental and DFT approach. J Mol Struct. 2018;1171:682–695. doi:10.1016/j.molstruc.2018.06.054
  • Costa RA, Oliveira KMT, Nunomura RCS, et al. Quantum chemical properties investigation and molecular docking analysis with DNA topoisomerase II of β-carboline indole alkaloids from Simaba guianensis: a combined experimental and theoretical DFT study. Struct Chem. 2018;29:299–314. doi:10.1007/s11224-017-1029-5
  • Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian09, Revision C.01. Wallingford (CT): Gaussian, Inc.; 2010; https://gaussian.com (accessed 05.05.2020).
  • Lee C, Yang W, Parr RG. Development of the colle-salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B. 1988;37:785–789. doi:10.1103/PhysRevB.37.785
  • Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys. 1993;98:5648–5652. doi:10.1063/1.464913
  • Mclean AD, Chandler GS. Contracted Gaussian-basis sets for molecular calculations. 1. second row atoms, Z = 11–18. J Chem Phys. 1980;72:5639–5648. doi:10.1063/1.438980
  • Krishnan R, Binkey JS, Seeger R, et al. Self-consistent molecular orbital methods. XX. Basis set for correlated wave-functions. J Chem Phys. 1980;72:650–654. doi:10.1063/1.438955
  • Janak JF. Proof that in density-functional Theory. Phys Rev B. 1978;18:7165–7168. doi:10.1103/PhysRevB.18.7165
  • Perdew JP, Parr RG, Levy M, et al. Density-functional theory for fractional particle number: derivative discontinuities of the energy. Phys Rev Lett. 1982;49:1691–1694. doi:10.1103/PhysRevLett.49.1691
  • Parr RG, Chattaraj PK. Principle of maximum hardness. J Am Chem Soc. 1991;113:1854–1855. doi:10.1021/ja00005a072
  • Parr RG, Szentpály LV, Liu S. Electrophilicity index. J Am Chem Soc. 1999;121:1922–1924. doi:10.1021/ja983494x
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–1612. doi:10.1002/jcc.20084
  • Goodsell DS, Morris G, Olson AJ. Automated docking of flexible ligands: applications of AutoDock. J Mol Recogn. 1996;9:1–5. doi:10.1002/(SICI)1099-1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6
  • Huey R, Morris GM, Forli S. (2012). Using AutoDock4 and AutoDock Vina with AutoDockTools: A tutorial. The Scripps Research Institute. https://www.yumpu.com/en/document/view/52169976/using-autodock-4-and-autodock-vina-with-autodocktools-a-tutorial (accessed 08.05.2020).
  • Trott O, Olson AJ. Autodock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31:455–461. doi:10.1002/jcc.21334.
  • Ravindranath PA, Forli S, Goodsell DS, et al. AutoDockFR: advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS Comput Biol. 2015;11:e1004586. doi:10.1371/journal.pcbi.1004586
  • Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem. 1998;19:1639–1662. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
  • Barros RO, Junior FLCC, Pereira JWS, et al. Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19. J Proteome Res. 2020; doi:10.1021/acs.jproteome.0c00327.
  • Biovia DS. (2020). Discovery studio visualizer, San Diego: Dassault Systèmes. https://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization.html (accessed 15.05.2020).
  • Breneman CM, Wiberg KB. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J Comput Chem. 1990;11:361–373. doi:10.1002/jcc.540110311
  • Chirlian LE, Francl MM. Atomic charges derived from electrostatic potentials: a detailed study. J Comput Chem. 1987;8:894–905. doi:10.1002/jcc.540080616
  • Mei Y, Simmonett AC, Pickard FC, et al. Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. J Phys Chem A. 2015;119:5865–5882. doi:10.1021/acs.jpca.5b03159
  • Gordon JC, Myers JB, Folta T, et al. Hþþ: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res. 2005;33:w368–w371. doi:10.1093/nar/gki464
  • Abraham MJ, Van Der Spoel D, Lindahl E, et al. (2018). The GROMACS development team. GROMACS user manual version 2018.1. www.gromacs.org (accessed 20.05.2020).
  • Oostenbrink C, Villa A, Mark AE, et al. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004;25:1656–1676. doi:10.1002/jcc.20090
  • Arcanjo DDR, Vasconcelos AG, Nascimento LA, et al. Structure-function studies of BPP-BrachyNH 2 and synthetic analogues thereof with Angiotensin I-converting enzyme. Eur J Med Chem. 2017;139:401–411. doi:10.1016/j.ejmech.2017.08.019
  • Van der Spoel D, Van Maaren PJ, Berendsen HJC. A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field. J Chem Phys. 1998;108:10220–10230. doi:10.1063/1.476482
  • Ramos RM, Perez JM, Baptista LA, et al. Interaction of wild type, G68R and L125M isoforms of the arylamineN-acetyltransferase from mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance. J Mol Model. 2012;18:4013–4024. doi:10.1007/s00894-012-1383-6
  • Nosé S, Klein ML. Constant pressure molecular dynamics for molecular systems. Mol Phys. 1983;50:1055–1076. doi:10.1080/00268978300102851
  • Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys. 1981;52:7182–7190. doi:10.1063/1.328693
  • Hess B, Bekker H, Berendsen HJC, et al. LINCS: a linear constraint solver for molecular simulations. J Comput Chem. 1997;18:1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: an N, log(N) method for Ewald sums in large systems. J Appl Phys. 1993;98:10089–10092. doi:10.1063/1.464397.
  • Lemkul J. From proteins to perturbed hamiltonians: a suite of tutorials for the GROMACS-2018 molecular simulation package [Article v1.0]. Living J Comput Mol Sci. 2019;1:1–53. doi:10.33011/livecoms.1.1.5068
  • Verli H. Bioinformática da biologia à flexibilidade molecular [Bioinformatics from biology to molecular flexibility]. 1st ed São Paulo: SBBq; 2014; 282 p. Portuguese. https://www.ufrgs.br/bioinfo/ebook/ (accessed 23.12.2020).
  • Lagorce D, Bouslama L, Becot J, et al. FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics. 2017;33:3658–3660. doi:10.1093/bioinformatics/btx491
  • Lee SK, Chang GS, Lee IH, et al. The PreADME: pc-based program for batch prediction of adme properties. EuroQSAR. 2004;9:5–10. https://scholar.google.com/scholar?cluster=9485303528805910143&hl=pt-BR&as_sdt=2005&sciodt=0,5 (accessed 10.06.2020).
  • Daiana A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:1–13. doi:10.1038/srep42717
  • Filimonov DA, Lagunin AA, Gloriozova TA, et al. Prediction of the biological activity spectra of organic compounds using the PASS online web resource. Chem Heterocycl Compd (NY). 2014;50:444–457. doi:10.1007/s10593-014-1496-1
  • Kramer C, Ting A, Zheng H, et al. Learning medicinal chemistry absorption, distribution, metabolism, excretion, and toxicity (ADMET) rules from cross-company matched molecular Pairs analysis (MMPA). J Med Chem. 2018;61:3277–3292. doi:10.1021/acs.jmedchem.7b00935
  • Sá ERA, Nascimento LA, Lima FCA. Termodinâmica: Uma Proposta de Ensino a partir da Química Computacional [Thermodynamics: a teaching proposal based on computational chemistry]. Virtual J Chem. 2020;12:795–808. Portuguese. doi:10.21577/1984-6835.20200062.
  • Honório KM, da Silva ABF. An AM1 study on the electron-donating and electron-accepting character of biomolecules. Int J Quantum Chem. 2003;95:126–132. doi:10.1002/qua.10661
  • Da Silva RR, Ramalho TC, Santos JM, et al. On the limits of highest-occupied molecular orbital driven reactions: the frontier effective-for-reaction molecular orbital concept. J Phys Chem. 2006;110:1031–1040. doi:10.1021/jp054434y
  • Maltarollo VG, Silva DC, Honório KM. Advanced QSAR studies on PPARδ ligands related to metabolic diseases. J Braz Chem Soc. 2012;23:85–95. doi:10.1590/S0103-50532012000100013
  • Pang X, Zhou L, Zhang M, et al. Two rules on the protein-ligand interaction. Open Conf Proc J. 2012;3:70–80. doi:10.2174/2210289201203010070
  • Costa AN, Sá ERA, Bezerra RDS, et al. Constituents of buriti oil (Mauritia flexuosa L.) like inhibitors of the SARS-coronavirus main peptidase: an investigation by docking and molecular dynamics. J Biomol Struct Dyn. 2020. doi:10.1080/07391102.2020.1778538.
  • Arnott JA, Planey SL. The influence of lipophilicity in drug discovery and design. Expert Opin Drug Discov. 2012;7:863–875. doi:10.1517/17460441.2012.714363
  • Storpirtis S, Gai MN, Campos DR, et al. Farmacocinética básica e aplicada [Basic and applied pharmacokinetics]. Rio de Janeiro: Guanabara Koogan; 2011; 240 p. Portuguese.
  • Gurunga AB, Bhattacharjeea A, Ali MA. Exploring the physicochemical profile and the binding patterns of selected novel anticancer himalayan plant derived active compounds with macromolecular targets. Inf Med Unlocked. 2016;5:1–14. doi:10.1016/j.imu.2016.09.004
  • Ertl P, Rohde B, Selzer P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug Transport properties. J Med Chem. 2000;43:3714–3717. doi:10.1021/jm000942e
  • Lipinski CA, Lombardo F, Dominy BW, et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001;46:3–26. doi:10.1016/S0169-409X(00)00129-0
  • Lagorce D, Douguet D, Miteva MA, et al. Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. Sci Rep. 2017;7:46277. doi:10.1038/srep46277
  • Bickerton GR, Paolini GV, Besnard J, et al. Quantifying the chemical beauty of drugs. Nat Chem. 2012;4:90–98. doi:10.1038/nchem.1243
  • Brown RD, Hassan M, Waldman M. Combinatorial library design for diversity, cost efficiency, and drug-like character. J Mol Graphics Model. 2000;18:427–437. doi:10.1016/S1093-3263(00)00072-3
  • Kobayashi M, Sada N, Sugawara M, et al. Development of a new system for prediction of drug absorption that takes into account drug dissolution and pH change in the gastro-intestinal tract. Int J Pharm. 2001;221:87–94. doi:10.1016/S0378-5173(01)00663-9
  • Irvine JD, Takahashi L, Lockhart K, et al. MDCK (Madin-Darby Canine Kidney) cells: a tool for membrane permeability screening. J Pharm Sci. 1999;88:28–33. doi:10.1021/js9803205
  • Souza J, Freitas ZMF, Storpirtis S. In vitro models for the determination of drug absorption and a prediction of dissolution/absorption relationships. Braz J Pharm Sci. 2007;43:515–527. doi:10.1590/S1516-93322007000400004.
  • Sripriya N, Ranjith Kumar M, Ashwin Karthick N, et al. In silico evaluation of multispecies toxicity of natural compounds. Drug Chem Toxicol. 2019;21:1–7. doi:10.1080/01480545.2019.1614023.
  • Costa LF. (2012). Rinovírus humano em infecções respiratórias agudas em crianças menores de cinco anos de idade: fatores envolvidos no agravamento da doença [Human rhinovirus in acute respiratory infections in children under five years of age: factors involved in the worsening of the disease]. 71f. Thesis (Doctorate in Biological Sciences) - Federal University of Uberlândia, Uberlândia, Brazil. Portuguese. https://repositorio.ufu.br/handle/123456789/16573 (accessed 08.08.2020).
  • Kuskoski EM, Asuero AG, Troncoso AM, et al. Application of several chemical methods to determine antioxidant activity in fruit pulp. Food Sci Tech. 2005;25:726–732. doi:10.1590/S0101-20612005000400016.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.