Identification of a novel drug molecule for neurodegenerative disease from marine algae through in-silico analysis

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Carmo Bastos, M. L., Silva-Silva, J. V., Neves Cruz, J., Palheta da Silva, A. R., Bentaberry-Rosa, A. A., da Costa Ramos, G., de Sousa Siqueira, J. E., Coelho-Ferreira, M. R., Percário, S., Santana Barbosa Marinho, P., Marinho, A. M., do, R., de Oliveira Bahia, M., & Dolabela, M. F. (2023). Alkaloid from Geissospermum sericeum Benth. & Hook.f. ex Miers (Apocynaceae) induce apoptosis by caspase pathway in human gastric cancer cells. Pharmaceuticals, 16(5), 765. https://doi.org/10.3390/ph16050765
   Web of Science ®Google Scholar
• Cavdar, H., Senturk, M., Guney, M., Durdagi, S., Kayik, G., Supuran, C. T., & Ekinci, D. (2019). Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: Kinetic and computational studies. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 429–437. https://doi.org/10.1080/14756366.2018.1543288
   PubMed Web of Science ®Google Scholar
• Chaudhari, S. M., Patel, K. Y., & Badole, S. L. (2014). Punica granatum (Pomegranate Fruit). In Polyphenols in Human Health and Disease (pp. 1393–1400). Elsevier. https://doi.org/10.1016/B978-0-12-398456-2.00106-7
   Google Scholar
• Cheung, J., Gary, E. N., Shiomi, K., & Rosenberry, T. L. (2013). Structures of human acetylcholinesterase bound to dihydrotanshinone I and territrem B show peripheral site flexibility. ACS Medicinal Chemistry Letters, 4(11), 1091–1096. https://doi.org/10.1021/ml400304w
   PubMed Web of Science ®Google Scholar
• Da Silva, D. F., de Souza, J. L., da Costa, D. M., Costa, D. B., Moreira, P. O. L., Fonseca, A. L. D., Varotti, F. D P., Cruz, J. N., dos Santos, C. B. R., Alves, C. Q., Leite, F. H. A., & Brandão, H. N. (2023). Antiplasmodial activity of coumarins isolated from Polygala boliviensis : In vitro and in silico studies. Journal of Biomolecular Structure & Dynamics, 41(22), 13383–13403. https://doi.org/10.1080/07391102.2023.2173295
   PubMed Web of Science ®Google Scholar
• De Almeida, R. B. M., Barbosa, D. B., do Bomfim, M. R., Amparo, J. A. O., Andrade, B. S., Costa, S. L., Campos, J. M., Cruz, J. N., Santos, C. B. R., Leite, F. H. A., & Botura, M. B. (2023). Identification of a novel dual inhibitor of acetylcholinesterase and butyrylcholinesterase: In vitro and in silico studies. Pharmaceuticals (Basel, Switzerland), 16(1), 95. https://doi.org/10.3390/ph16010095
   PubMedGoogle Scholar
• DeLano, W. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 700.
   Google Scholar
• Farid, R., Day, T., Friesner, R. A., & Pearlstein, R. A. (2006). New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorganic & Medicinal Chemistry, 14(9), 3160–3173. https://doi.org/10.1016/j.bmc.2005.12.032
   PubMed Web of Science ®Google Scholar
• Federation, T. W., & Neurological, N. (2020). World Brain Day 2020 – Challenges and Opportunities in India, 2020–2021. https://doi.org/10.4103/AOMD.AOMD
   Google Scholar
• García-Ayllón, M.-S., Cauli, O., Silveyra, M.-X., Rodrigo, R., Candela, A., Compañ, A., Jover, R., Pérez-Mateo, M., Martínez, S., Felipo, V., & Sáez-Valero, J. (2008). Brain cholinergic impairment in liver failure. Brain: A Journal of Neurology, 131(Pt 11), 2946–2956. https://doi.org/10.1093/brain/awn209
   PubMedGoogle Scholar
• Halgren, T. (2007). New method for fast and accurate binding-site identification and analysis. Chemical Biology & Drug Design, 69(2), 146–148. https://doi.org/10.1111/j.1747-0285.2007.00483.x
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472.
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2023). PubChem 2023 update. Nucleic Acids Research, 51(D1), D1373–D1380. https://doi.org/10.1093/nar/gkac956
   PubMed Web of Science ®Google Scholar
• Lemkul, J. (2019). From proteins to perturbed hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package [Article v1.0]. Living Journal of Computational Molecular Science, 1(1), 1–53. https://doi.org/10.33011/livecoms.1.1.5068
   Google Scholar
• McGleenon, B. M., Dynan, K. B., & Passmore, A. P. (1999). Acetylcholinesterase inhibitors in Alzheimer’s disease. British Journal of Clinical Pharmacology, 48(4), 471–480. https://doi.org/10.1046/j.1365-2125.1999.00026.x
   PubMed Web of Science ®Google Scholar
• McHardy, S. F., Wang, H.-Y L., McCowen, S. V., & Valdez, M. C. (2017). Recent advances in acetylcholinesterase inhibitors and reactivators: An update on the patent literature (2012-2015). Expert Opinion on Therapeutic Patents, 27(4), 455–476. https://doi.org/10.1080/13543776.2017.1272571
   PubMed Web of Science ®Google Scholar
• Pereira, L., & Valado, A. (2021). The seaweed diet in prevention and treatment of the neurodegenerative diseases. Marine Drugs, 19(3), 128. https://doi.org/10.3390/md19030128
   PubMed Web of Science ®Google Scholar
• Petersen, H. G. (1995). Accuracy and efficiency of the particle mesh Ewald method. Journal of Chemical Physics, 103(9), 3668–3679. https://doi.org/10.1063/1.470043
   Web of Science ®Google Scholar
• Przedborski, S., Vila, M., Jackson-Lewis, V., Przedborski, S., Vila, M., & Jackson-Lewis, V. (2003). Series introduction: Neurodegeneration: What is it and where are we ? Journal of Clinical Investigation, 111(1), 3–10. https://doi.org/10.1172/JCI200317522
   PubMed Web of Science ®Google Scholar
• Riyadh Ahmed, A. A., Abd El-Mageed, H. R., Ahmed, S., Mohamed, H. S., Hamza, Z. S., Rafi, M. O., Ahmad, I., & Patel, H. (2023). In silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: Computer-aided drug design perspective. Journal of Biomolecular Structure & Dynamics, 41(23), 14484–14496. https://doi.org/10.1080/07391102.2023.2212778
   PubMed Web of Science ®Google Scholar
• Sadigh-Eteghad, S., Sabermarouf, B., Majdi, A., Talebi, M., Farhoudi, M., & Mahmoudi, J. (2015). Amyloid-beta: A crucial factor in Alzheimer’s disease. Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre, 24(1), 1–10. https://doi.org/10.1159/000369101
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2014-2. (2014). LigPrep. Schrödinger.
   Google Scholar
• Sherman, W., Beard, H. S., & Farid, R. (2006). Use of an induced fit receptor structure in virtual screening. Chemical Biology & Drug Design, 67(1), 83–84. https://doi.org/10.1111/j.1747-0285.2005.00327.x
   PubMed Web of Science ®Google Scholar
• Silva, L. B., Ferreira, E. F. B., Espejo-Román, J. M., Costa, G. V., Cruz, J. V., Kimani, N. M., Costa, J. S., Bittencourt, J. A. H. M., Cruz, J. N., Campos, J. M., Santos, C. B. R., & Maryam. (2023). Galantamine based novel acetylcholinesterase enzyme inhibitors: A molecular modeling design approach. Molecules (Basel, Switzerland), 28(3), 1035. https://doi.org/10.3390/molecules28031035
   PubMed Web of Science ®Google Scholar
• Skovronsky, D. M., Lee, V. M.-Y., & Trojanowski, J. Q. (2006). Neurodegenerative diseases: New concepts of pathogenesis and their therapeutic implications. Annual Review of Pathology, 1(1), 151–170. https://doi.org/10.1146/annurev.pathol.1.110304.100113
   PubMed Web of Science ®Google Scholar
• Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & MacKerell, A. D. Jr., (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.CHARMM
   PubMed Web of Science ®Google Scholar
• Varvara, S., Popa, M., Rustoiu, G., Bostan, R., & Mureşan, L. (2009). Evaluation of some amino acids as bronze corrosion inhibitors in aqueous solution. Studia Universitatis Babes-Bolyai Chemia, 2(18), 73–85.
   Google Scholar
• Wang, P. H., Nguyen, K., Pham, D., Huynh, T.-B N., Le, H., Wang, P., & Ren, R. L. (2019). Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. Physiology & Behavior, 176(3), 139–148. https://doi.org/10.1002/jcc.24467.Calculating
   Google Scholar
• Wimo, A., & Prince, M. (2010). Design, dignity, dementia: dementia-related design and the built environment. Dementia, I, 96. http://www.alz.co.uk/research/files/WorldAlzheimerReport.pdf
   Google Scholar