342
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Virtual screening and molecular dynamics study of natural products against Rab10 for the treatment of Alzheimer’s disease

ORCID Icon, ORCID Icon & ORCID Icon
Pages 6728-6748 | Received 03 Mar 2022, Accepted 03 Aug 2022, Published online: 22 Aug 2022

References

  • Andersen, C. A. F., Palmer, A. G., Brunak, S., & Rost, B. (2002). Continuum secondary structure captures protein flexibility. Structure (London, England : 1993), 10(2), 175–184. https://doi.org/10.1016/S0969-2126(02)00700-1
  • Andrade, S., Ramalho, M. J., Loureiro, J. A., & Pereira, M. C. (2019). Natural compounds for Alzheimer’s disease therapy: A systematic review of preclinical and clinical studies. International Journal of Molecular Sciences, 20(9), 2313. https://doi.org/10.3390/ijms20092313
  • Araya, J. A., Ramírez, A. E., Figueroa-Aroca, D., Sotes, G. J., Pérez, C., Becerra, J., Saez-Orellana, F., Guzmán, L., Aguayo, L. G., & Fuentealba, J. (2014). Modulation of neuronal nicotinic receptor by quinolizidine alkaloids causes neuroprotection on a cellular Alzheimer model. Journal of Alzheimer's Disease, 42(1), 143–155. https://doi.org/10.3233/JAD-132045
  • Athar, T., Balushi, K. A., & Khan, S. A. (2021). Recent advances on drug development and emerging therapeutic agents for Alzheimer’s disease. Molecular Biology Reports, 48(7), 5629–5645. https://doi.org/10.1007/s11033-021-06512-9
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Boyd, B. J., Bergström, C. A. S., Vinarov, Z., Kuentz, M., Brouwers, J., Augustijns, P., Brandl, M., Bernkop-Schnürch, A., Shrestha, N., Préat, V., Müllertz, A., Bauer-Brandl, A., & Jannin, V. (2019). Successful oral delivery of poorly water-soluble drugs both depends on the intraluminal behavior of drugs and of appropriate advanced drug delivery systems. European Journal of Pharmaceutical Sciences, 137(107), 104967–102502. https://doi.org/10.1016/j.ejps.2019.104967
  • Cherfils, J., & Zeghouf, M. (2013). Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiological Reviews, 93(1), 269–309. https://doi.org/10.1152/physrev.00003.2012
  • Choy, R. W., Cheng, Z., & Schekman, R. (2012). Amyloid precursor protein (APP) traffics from the cell surface via endosomes for amyloid β (Aβ) production in the trans-Golgi network. Proceedings of the National Academy of Sciences of the United States of America, 109(30), E2077–E2082. https://doi.org/10.1073/pnas.1208635109
  • Daina, A., & Zoete, V. (2016). A BOILED‐Egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem, 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, druglikeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
  • English, A. R., & Voeltz, G. K. (2013). Rab10 GTPase regulates ER dynamics and morphology. Nature Cell Biology, 15(2), 169–178. https://doi.org/10.1038/ncb2647
  • Gauthier, S., Rosa-Neto, P., Morais, J. A., & Webster, C. (2021). World Alzheimer Report 2021. Journey through the diagnosis of dementia (pp. 1–314). Alzheimer’s Disease International (ADI). https://www.alzint.org/u/World-Alzheimer-Report-2021.pdf
  • Goody, R. S., Müller, M. P., & Wu, Y. (2017). Mechanisms of action of Rab proteins, key regulators of intracellular vesicular transport. Biological Chemistry, 398(5–6), 565–575. https://doi.org/10.1515/hsz-2016-0274
  • Hamulakova, S., Janovec, L., Soukup, O., Jun, D., & Kuca, K. (2017). Synthesis, in vitro acetylcholinesterase inhibitory activity and molecular docking of new acridine-coumarin hybrids. International Journal of Biological Macromolecules, 104(Pt A), 333–338. https://doi.org/10.1016/j.ijbiomac.2017.06.006
  • Hardy, J., & Selkoe, D. J. (2002). The amyloid hypothesis of Alzheimer's disease: Progress and problems on the road to therapeutics. Science (New York, N.Y.), 297(5580), 353–356. 10.1126/science.1072994
  • He, Q., Liu, J., Lan, J. S., Ding, J., Sun, Y., Fang, Y., Jiang, N., Yang, Z., Sun, L., Jin, Y., & Xie, S. S. (2018). Coumarin-dithiocarbamate hybrids as novel multitarget AChE and MAO-B inhibitors against Alzheimer’s disease: Design, synthesis and biological evaluation. Bioorganic Chemistry, 81, 512–528. https://doi.org/10.1016/j.bioorg.2018.09.010
  • Hevener, K. E., Zhao, W., Ball, D. M., Babaoglu, K., Qi, J., White, S. W., & Lee, R. E. (2009). Validation of molecular docking programs for virtual screening against dihydropteroate synthase. Journal of Chemical Information and Modeling, 49(2), 444–460. https://doi.org/10.1021/ci800293n
  • Homma, Y., Hiragi, S., & Fukuda, M. (2021). Rab family of small GTPases: An updated view on their regulation and functions. The FEBS Journal, 288(1), 36–55. https://doi.org/10.1111/febs.15453
  • Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D., Jr. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
  • Jaghoori, M. M., Bleijlevens, B., & Olabarriaga, S. D. (2016). 1001 ways to run AutoDock Vina for virtual screening. Journal of Computer-Aided Molecular Design, 30(3), 237–249. https://doi.org/10.1007/s10822-016-9900-9
  • Junaid, M., Muhseen, Z. T., Ullah, A., Wadood, A., Liu, J., & Zhang, H. (2014). Molecular modeling and molecular dynamics simulation study of the human Rab9 and RhoBTB3 C-terminus complex. Bioinformation, 10(12), 757–763. 10.6026/97320630010757
  • Kametani, F., & Hasegawa, M. (2018). Reconsideration of amyloid hypothesis and tau hypothesis in Alzheimer’s disease. Frontiers Neuroscience, 12, 25. https://doi.org/10.3389/fnins.2018.00025
  • Kamiya, Y., Lai, N. M. S., & Schmid, K. (2021). World Population Ageing 2020 highlights. Living arrangements of older persons (pp. 1–47). United Nations. https://www.un.org/development/desa/pd/sites/www.un.org.development.desa.pd/files/undesa_pd-2020_world_population_ageing_highlights.pdf
  • Lanoiselée, H. M., Nicolas, G., Wallon, D., Rovelet-Lecrux, A., Lacour, M., Rousseau, S., Richard, A. C., Pasquier, F., Rollin-Sillaire, A., Martinaud, O., Quillard-Muraine, M., de la Sayette, V., Boutoleau-Bretonniere, C., Etcharry-Bouyx, F., Chauviré, V., Sarazin, M., le Ber, I., Epelbaum, S., Jonveaux, T., … Campion, D.; Collaborators of the CNR-MAJ Project. (2017). APP, PSEN1, and PSEN2 mutations in early-onset Alzheimer disease: A genetic screening study of familial and sporadic cases. PLoS Medicine, 14(3), e1002270. https://doi.org/10.1371/journal.pmed.1002270
  • Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249. https://doi.org/10.1016/S1056-8719(00)00107-6
  • Makhatadze, G. I. (2005). Thermodynamics Of α‐helix formation. Advances in Protein Chemistry, 72, 199–226. https://doi.org/10.1016/s0065-3233(05)72008-8
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33. https://doi.org/10.1186/1758-2946-3-33
  • Paul, M., Panda, M. K., & Thatoi, E. H. (2019). Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. J. Biomolecular Struct. and Dynamics, 37(15), 3947–3967. https://doi.org/10.1080/07391102.2018.1532321
  • Pylypenko, O., Hammich, H., Yu, I., & Houdusse, A. (2018). RAB GTPases and their interacting protein partners: Structural insights into RAB functional diversity. Small GTPases, 9(1-2), 22–48. https://doi.org/10.1080/21541248.2017.1336191
  • Ridge, P. G., Karch, C. M., Hsu, S., Arano, I., Teerlink, C. C., Ebbert, M. T. W., Murcia, J. D. G., Farnham, J. M., Damato, A. R., Allen, M., Wang, X., Harari, O., Fernandez, V. M., Guerreiro, R., Bras, J., Hardy, J., Munger, R., Norton, M., Sassi, C., … Kauwe, J. S. K. (2017). Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience. Genome Medicine, 9(1), 100–114. https://doi.org/10.1186/s13073-017-0486-1
  • Sahni, T., Sharma, S., Verma, D., & Kaur, P. (2021). Overview of coumarins and its derivatives: Synthesis and biological activity. Letters in Organic Chemistry, 18(11), 880–823. http://dx.doi.org/10.2174/1570178617999201006195742
  • Schrödinger. (2021). Schrödinger release 2021–2: Maestro. Schrödinger, LLC.
  • Shukla, R., & Singh, T. R. (2020). Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer's disease. Journal of Biomolecular Structure and Dynamics, 38(1), 248–262. https://doi.org/10.1080/07391102.2019.1571947
  • Shukla, R., Shukla, H., Kalita, P., Sonkar, A., Pandey, T., Singh, D. B., Kumar, A., & Tripathi, T. (2018). Identification of potential inhibitors of Fasciola gigantica thioredoxin1: Computational screening, molecular dynamics simulation, and binding free energy studies. Journal of Biomolecular Structure & Dynamics, 36(8), 2147–2162. https://doi.org/10.1080/07391102.2017.1344141[PMC][28627969]
  • Small, S. A., Simoes-Spassov, S., Mayeux, R., & Petsko, G. A. (2017). Endosomal traffic jams represent a pathogenic hub and therapeutic target in Alzheimer’s disease. Trends in Neurosciences, 40(10), 592–602. https://doi.org/10.1016/j.tins.2017.08.003[PMC][28962801]
  • Spoel, D. V. D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Sterling, T., & Irwin, J. J. (2015). ZINC 15 – Ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
  • Stewart, K. D., Johnston, J. A., Matza, L. S., Curtis, S. E., Havel, H. A., Sweetana, S. A., & Gelhorn, H. L. (2016). Preference for pharmaceutical formulation and treatment process attributes. Patient Preference and Adherence, 10, 1385–1399. https://doi.org/10.2147/PPA.S101821
  • Stillhart, C., Vučićević, K., Augustijns, P., Basit, A. W., Batchelor, H., Flanagan, T. R., Gesquiere, I., Greupink, R., Keszthelyi, D., Koskinen, M., Madla, C. M., Matthys, C., Miljuš, G., Mooij, M. G., Parrott, N., Ungell, A. L., de Wildt, S. N., Orlu, M., Klein, S., & Müllertz, A. (2020). Impact of gastrointestinal physiology on drug absorption in special populations – An UNGAP review. European Journal of Pharmaceutical Sciences, 147, 105280. https://doi.org/10.1016/j.ejps.2020.105280
  • Tavana, J. P., Rosene, M., Jensen, N. O., Ridge, P. G., Kauwe, J. S. K., & Karch, C. M. (2019). Rab10: An alzheimer’s disease resilience locus and potential drug target. Clinical Interventions in Aging, 14, 73–79. https://doi.org/10.2147/CIA.S159148
  • Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multi-threading. Journal of Computacional Chemistry, 31, 455–461. https://doi.org/10.1002/jcc.21334
  • Udayar, V., Buggia-Prévot, V., Guerreiro, R. L., Siegel, G., Rambabu, N., Soohoo, A. L., Ponnusamy, M., Siegenthaler, B., Bali, J., Simons, M., Ries, J., Puthenveedu, M. A., Hardy, J., Thinakaran, G., Rajendran, L., Guerreiro, R., Brás, J., Sassi, C., Gibbs, J. R., … Hardy, J. (2013). A paired RNAi and RabGAP overexpression screen identifies Rab11 as a regulator of b-amyloid production. Cell Reports, 5(6), 1536–1551. https://doi.org/10.1016/j.celrep.2013.12.005
  • Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2010). CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
  • Williams, H. D., Trevaskis, N. L., Charman, S. A., Shanker, R. M., Charman, W. N., Pouton, C. W., & Porter, C. J. H. (2013). Strategies to address low drug solubility in discovery and development. Pharmacological Reviews, 65(1), 315–499. https://doi.org/10.1124/pr.112.005660
  • Yamazaki, Y., Painter, M. M., Bu, G., & Kanekiyo, T. (2016). Apolipoprotein E as a therapeutic target in Alzheimer's disease: A review of basic research and clinical evidence. CNS Drugs, 30(9), 773–779. https://doi.org/10.1007/s40263-016-0361-4
  • Yan, T., Wang, L., Gao, J., Siedlak, S. L., Huntley, M. L., Termsarasab, P., Perry, G., Chen, S. G., & Wang, X. (2018). Rab10 phosphorylation is a prominent pathological feature in Alzheimer’s disease. Journal of Alzheimer's Disease, 63(1), 157–165. https://doi.org/10.3233/JAD-180023
  • Zhao, Z., Tan, W., Sheng, W., & Li, X. (2016). Identification of biomarkers associated with Alzheimer’s disease by bioinformatics analysis. American Journal of Alzheimer's Disease & Other Dementiasr, 31(2), 163–168. https://doi.org/10.1177/1533317515588181
  • Zou, W., Yadav, S., DeVault, L., Jan, Y. N., & Sherwood, D. R. (2015). Rab10-dependent membrane transport is required for dendrite arborization. PLOS Genetics, 11(9), e1005484. https://doi.org/10.1371/journal.pgen.1005484

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.