In silico Methods for Evaluating the Mode of Interaction of Nanoparticles with Molecular Target


In silico Methods for Evaluating the Mode of Interaction of Nanoparticles with Molecular Target

Suraj N. Mali, Jorddy Neves Cruz, Akshay R. Yadav

An essential tool for structure-based drug design is molecular docking. As mentioned at the outset, docking aims to anticipate the most advantageous ligand-target spatial arrangement and quantify the associated complex free energy. However, precise scoring systems are still difficult to come across. This chapter overviews current molecular docking techniques and their uses in nanostructures.

Nanoparticle, Docking, in silico, Drug Design, Methodologies

Published online , 14 pages

Citation: Suraj N. Mali, Jorddy Neves Cruz, Akshay R. Yadav, In silico Methods for Evaluating the Mode of Interaction of Nanoparticles with Molecular Target, Materials Research Proceedings, Vol. 145, pp 236-249, 2023


Part of the book on Nanobiomaterials

[1] J. Adams, M. Wright, H. Wagner, J. Valiente, D. Britt, A. Anderson, Cu from dissolution of CuO nanoparticles signals changes in root morphology, Plant Physiol. Biochem. 110 (2017) 108–117.
[2] A. Ambrosone, C. Tortiglione, Methodological approaches for nanotoxicology using cnidarian models, Toxicol. Mech. Methods. 23 (2013) 207–216.
[3] A.C. Anselmo, S. Mitragotri, Nanoparticles in the clinic: An update, Bioeng. Transl. Med. 4 (2019).
[4] S. Ates, E. Zor, I. Akin, H. Bingol, S. Alpaydin, E.G. Akgemci, Discriminative sensing of DOPA enantiomers by cyclodextrin anchored graphene nanohybrids, Anal. Chim. Acta. 970 (2017) 30–37.
[5] M. Sotelo-Boyás, Z. Correa-Pacheco, S. Bautista-Baños, Y. Gómez y Gómez, Release study and inhibitory activity of thyme essential oil-loaded chitosan nanoparticles and nanocapsules against foodborne bacteria, Int. J. Biol. Macromol. 103 (2017) 409–414.
[6] E. Baranowska-Wójcik, D. Szwajgier, P. Oleszczuk, A. Winiarska-Mieczan, Effects of Titanium Dioxide Nanoparticles Exposure on Human Health—a Review, Biol. Trace Elem. Res. 193 (2020) 118–129.
[7] F. Barbero, L. Russo, M. Vitali, J. Piella, I. Salvo, M.L. Borrajo, M. Busquets-Fité, R. Grandori, N.G. Bastús, E. Casals, V. Puntes, Formation of the Protein Corona: The Interface between Nanoparticles and the Immune System, Semin. Immunol. 34 (2017) 52–60.
[8] H. Bayraktar, C.C. You, V.M. Rotello, M.J. Knapp, Facial control of nanoparticle binding to cytochrome c, J. Am. Chem. Soc. 129 (2007) 2732–2733.
[9] S.F. Bellah, H. Akbar, S.M.S. Billah, D.M. Sedzro, The Role of CCL18 protein in Breast Cancer Development and Progression, Cell Biol. Res. Ther. 07 (2018).
[10] L. Bertilsson, M.L. Dahl, P. Dalén, A. Al-Shurbaji, Molecular genetics of CYP2D6: Clinical relevance with focus on psychotropic drugs, Br. J. Clin. Pharmacol. 53 (2002) 111–122.
[11] F. Bertoli, D. Garry, M.P. Monopoli, A. Salvati, K.A. Dawson, The Intracellular Destiny of the Protein Corona: A Study on its Cellular Internalization and Evolution, ACS Nano. 10 (2016) 10471–10479.
[12] G. Brancolini, D.B. Kokh, L. Calzolai, R.C. Wade, S. Corni, Docking of ubiquitin to gold nanoparticles, ACS Nano. 6 (2012) 9863–9878.
[13] C. Buzea, I.I. Pacheco, K. Robbie, Nanomaterials and nanoparticles: sources and toxicity., Biointerphases. 2 (2007) MR17-71.
[14] J. Cao, Y. Pan, Y. Jiang, R. Qi, B. Yuan, Z. Jia, J. Jiang, Q. Wang, Computer-aided nanotoxicology: risk assessment of metal oxide nanoparticlesvianano-QSAR, Green Chem. 22 (2020) 3512–3521.
[15] F. Carnal, A. Clavier, S. Stoll, Polypeptide-nanoparticle interactions and corona formation investigated by monte carlo simulations, Polymers (Basel). 8 (2016).
[16] F.S. Alves, J. de A. Rodrigues Do Rego, M.L. Da Costa, L.F. Lobato Da Silva, R.A. Da Costa, J.N. Cruz, D.D.S.B. Brasil, Spectroscopic methods and in silico analyses using density functional theory to characterize and identify piperine alkaloid crystals isolated from pepper (Piper Nigrum L.), J. Biomol. Struct. Dyn. 38 (2020) 2792–2799.
[17] T. Cedervall, I. Lynch, S. Lindman, T. Berggård, E. Thulin, H. Nilsson, K.A. Dawson, S. Linse, Understanding the nanoparticle-protein corona using methods to quntify exchange rates and affinities of proteins for nanoparticles, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 2050–2055.
[18] J.N. Cruz, S.N. Mali, Antimalarial Hemozoin Inhibitors (β-Hematin Formation Inhibition): Latest Updates, Comb. Chem. High Throughput Screen. 25 (2022) 1987–1990.
[19] C.I. Chang, W.J. Lee, T.F. Young, S.P. Ju, C.W. Chang, H.L. Chen, J.G. Chang, Adsorption mechanism of water molecules surrounding Au nanoparticles of different sizes, J. Chem. Phys. 128 (2008).
[20] Y.C. Chen, Beware of docking!, Trends Pharmacol. Sci. 36 (2015) 78–95.
[21] R.S. Kalash, V.K. Lakshmanan, C.S. Cho, I.K. Park, Theranostics, Biomater. Nanoarchitectonics. (2016) 197–215.
[22] A.R.J.A. de M. Lima, A.S. Siqueira, M.L.S. Möller, R.C. de Souza, J.N. Cruz, A.R.J.A. de M. Lima, R.C. da Silva, D.C.F. Aguiar, J.L. da S.G.V. Junior, E.C. Gonçalves, In silico improvement of the cyanobacterial lectin microvirin and mannose interaction, J. Biomol. Struct. Dyn. (2020).
[23] N. Chowdhury, A. Bagchi, Molecular insight into the activity of LasR protein from Pseudomonas aeruginosa in the regulation of virulence gene expression by this organism, Gene. 580 (2016) 80–87.
[24] A.J. Clark, P. Tiwary, K. Borrelli, S. Feng, E.B. Miller, R. Abel, R.A. Friesner, B.J. Berne, Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations, J. Chem. Theory Comput. 12 (2016) 2990–2998.
[25] R. Concu, V. V. Kleandrova, A. Speck-Planche, M.N.D.S. Cordeiro, Probing the toxicity of nanoparticles: a unified in silico machine learning model based on perturbation theory, Nanotoxicology. 11 (2017) 891–906.
[26] V.M. Almeida, Ê.R. Dias, B.C. Souza, J.N. Cruz, C.B.R. Santos, F.H.A. Leite, R.F. Queiroz, A. Branco, Methoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays, J. Biomol. Struct. Dyn. 40 (2022) 7574–7583.
[27] M.M. D’Elios, F. Vallese, N. Capitani, M. Benagiano, M.L. Bernardini, M. Rossi, G.P. Rossi, M. Ferrari, C.T. Baldari, G. Zanotti, M. De Bernard, G. Codolo, The Helicobacter cinaedi antigen CAIP participates in atherosclerotic inflammation by promoting the differentiation of macrophages in foam cells, Sci. Rep. 7 (2017).
[28] C.M.A. Rego, A.F. Francisco, C.N. Boeno, M. V. Paloschi, J.A. Lopes, M.D.S. Silva, H.M. Santana, S.N. Serrath, J.E. Rodrigues, C.T.L. Lemos, R.S.S. Dutra, J.N. da Cruz, C.B.R. dos Santos, S. da S. Setúbal, M.R.M. Fontes, A.M. Soares, W.L. Pires, J.P. Zuliani, Inflammasome NLRP3 activation induced by Convulxin, a C-type lectin-like isolated from Crotalus durissus terrificus snake venom, Sci. Rep. 12 (2022) 1–17.
[29] K.M. Darwish, I. Salama, S. Mostafa, M.S. Gomaa, E.S. Khafagy, M.A. Helal, Synthesis, biological evaluation, and molecular docking investigation of benzhydrol- and indole-based dual PPAR-γ/FFAR1 agonists, Bioorganic Med. Chem. Lett. 28 (2018) 1595–1602.
[30] T.R. De Kievit, R. Gillis, S. Marx, C. Brown, B.H. Iglewski, Quorum-Sensing Genes in Pseudomonas aeruginosa Biofilms: Their Role and Expression Patterns, Appl. Environ. Microbiol. 67 (2001) 1865–1873.
[31] L.B. de O. Freitas, L. de M. Corgosinho, J.A.Q.A. Faria, V.M. dos Santos, J.M. Resende, A.S. Leal, D.A. Gomes, E.M.B. de Sousa, Multifunctional mesoporous silica nanoparticles for cancer-targeted, controlled drug delivery and imaging, Microporous Mesoporous Mater. 242 (2017) 271–283.
[32] A.R. DeBofsky, R.H. Klingler, F.X. Mora-Zamorano, M. Walz, B. Shepherd, J.K. Larson, D. Anderson, L. Yang, F. Goetz, N. Basu, J. Head, P. Tonellato, B.M. Armstrong, C. Murphy, M.J. Carvan, Female reproductive impacts of dietary methylmercury in yellow perch (Perca flavescens) and zebrafish (Danio rerio), Chemosphere. 195 (2018) 301–311.
[33] R.J. Deeth, N. Fey, B. Williams-Hubbard, DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment, J. Comput. Chem. 26 (2005) 123–130.
[34] C.A. Dinarello, Overview of the IL-1 family in innate inflammation and acquired immunity., Immunol. Rev. 281 (2018) 8–27.
[35] C.P. Profaci, R.N. Munji, R.S. Pulido, R. Daneman, The blood-brain barrier in health and disease: Important unanswered questions., J. Exp. Med. 217 (2020).
[36] A. Elkashif, M.N. Seleem, Investigation of auranofin and gold-containing analogues antibacterial activity against multidrug-resistant Neisseria gonorrhoeae, Sci. Rep. 10 (2020).
[37] H. Mirzaei, S. Emami, Recent advances of cytotoxic chalconoids targeting tubulin polymerization: Synthesis and biological activity, Eur. J. Med. Chem. 121 (2016) 610–639.
[38] V.E. Fako, D.Y. Furgeson, Zebrafish as a correlative and predictive model for assessing biomaterial nanotoxicity, Adv. Drug Deliv. Rev. 61 (2009) 478–486.
[39] Z. Fei Yin, L. Wu, H. Gui Yang, Y. Hua Su, Recent progress in biomedical applications of titanium dioxide, Phys. Chem. Chem. Phys. 15 (2013) 4844–4858.
[40] K.R. Feingold, Introduction to Lipids and Lipoproteins., in: K.R. Feingold, B. Anawalt, A. Boyce, G. Chrousos, W.W. de Herder, K. Dhatariya, K. Dungan, J.M. Hershman, J. Hofland, S. Kalra, G. Kaltsas, C. Koch, P. Kopp, M. Korbonits, C.S. Kovacs, W. Kuohung, B. Laferrère, M. Levy, E.A. McGee, R. McLachlan, J.E. Morley, M. New, J. Purnell, R. Sahay, F. Singer, M.A. Sperling, C.A. Stratakis, D.L. Trence, D.P. Wilson (Eds.), South Dartmouth (MA), 2000
[41] C.C. Fleischer, C.K. Payne, Nanoparticle-cell interactions: Molecular structure of the protein corona and cellular outcomes, Acc. Chem. Res. 47 (2014) 2651–2659.
[42] F. Föger, W. Noonpakdee, B. Loretz, S. Joojuntr, W. Salvenmoser, M. Thaler, A. Bernkop-Schnürch, Inhibition of malarial topoisomerase II in Plasmodium falciparum by antisense nanoparticles., Int. J. Pharm. 319 (2006) 139–146.
[43] A. Strini, G. Roviello, L. Ricciotti, C. Ferone, F. Messina, L. Schiavi, D. Corsaro, R. Cioffi, TiO2-based photocatalytic geopolymers for nitric oxide degradation, Materials (Basel). 9 (2016).
[44] S. Fraga, A. Brandão, M.E. Soares, T. Morais, J.A. Duarte, L. Pereira, L. Soares, C. Neves, E. Pereira, M. de L. Bastos, H. Carmo, Short- and long-term distribution and toxicity of gold nanoparticles in the rat after a single-dose intravenous administration, Nanomedicine Nanotechnology, Biol. Med. 10 (2014) 1757–1766.
[45] E.L. Fuchs, E.D. Brutinel, A.K. Jones, N.B. Fulcher, M.L. Urbanowski, T.L. Yahr, M.C. Wolfgang, The Pseudomonas aeruginosa Vfr regulator controls global virulence factor expression through cyclic AMP-dependent and -independent mechanisms, J. Bacteriol. 192 (2010) 3553–3564.
[46] M. Dhayalan, L. Anitha Jegadeeshwari, N. Nagendra Gandhi, Biological activity sources from traditionally usedtribe and herbal plants material, Asian J. Pharm. Clin. Res. 8 (2015) 11–23
[47] S. Gandhi, I. Roy, Synthesis and characterization of manganese ferrite nanoparticles, and its interaction with bovine serum albumin: A spectroscopic and molecular docking approach, J. Mol. Liq. 296 (2019).
[48] M. Geetha, A.K. Singh, R. Asokamani, A.K. Gogia, Ti based biomaterials, the ultimate choice for orthopaedic implants – A review, Prog. Mater. Sci. 54 (2009) 397–425.
[49] R. Ghadari, A study on the interactions of amino acids with nitrogen doped graphene; Docking, MD simulation, and QM/MM studies, Phys. Chem. Chem. Phys. 18 (2016) 4352–4361.
[50] Z.N. Gheshlaghi, G.H. Riazi, S. Ahmadian, M. Ghafari, R. Mahinpour, Toxicity and interaction of titanium dioxide nanoparticles with microtubule protein, Acta Biochim. Biophys. Sin. (Shanghai). 40 (2008) 777–782.
[51] E. GIACOBINI, Histochemical Demonstration of AChE Activity in Isolated Nerve Cells, Acta Physiol. Scand. 36 (1956) 276–290.
[52] K. Giannousi, G. Geromichalos, D. Kakolyri, S. Mourdikoudis, C. Dendrinou-Samara, Interaction of ZnO Nanostructures with Proteins: In Vitro Fibrillation/Antifibrillation Studies and in Silico Molecular Docking Simulations, ACS Chem. Neurosci. 11 (2020) 436–444.
[53] M. González-Durruthy, A.K. Giri, I. Moreira, R. Concu, A. Melo, J.M. Ruso, M.N.D.S. Cordeiro, Computational modeling on mitochondrial channel nanotoxicity, Nano Today. 34 (2020) 100913.
[54] L. Gonzalez-Moragas, A. Roig, A. Laromaine, C. elegans as a tool for in vivo nanoparticle assessment, Adv. Colloid Interface Sci. 219 (2015) 10–26.
[55] M.M. Mihai, M.B. Dima, B. Dima, A.M. Holban, Nanomaterials for wound healing and infection control, Materials (Basel). 12 (2019) 2176.
[56] A. Kushwaha, L. Goswami, B.S. Kim, Nanomaterial-Based Therapy for Wound Healing, Nanomaterials. 12 (2022).
[57] S. Smulders, K. Luyts, G. Brabants, K. Van Landuyt, C. Kirschhock, E. Smolders, L. Golanski, J. Vanoirbeek, P.H.M. Hoet, Toxicity of nanoparticles embedded in paints compared with pristine nanoparticles in mice, Toxicol. Sci. 141 (2014) 132–140.
[58] A. Gupta, A.T. Müller, B.J.H. Huisman, J.A. Fuchs, P. Schneider, G. Schneider, Generative Recurrent Networks for De Novo Drug Design, Mol. Inform. 37 (2018) 1700111.
[59] T.I. Adelusi, A.-Q.K. Oyedele, I.D. Boyenle, A.T. Ogunlana, R.O. Adeyemi, C.D. Ukachi, M.O. Idris, O.T. Olaoba, I.O. Adedotun, O.E. Kolawole, Y. Xiaoxing, M. Abdul-Hammed, Molecular modeling in drug discovery, Informatics Med. Unlocked. 29 (2022) 100880.
[60] S. Dallakyan, A.J. Olson, Small-molecule library screening by docking with PyRx, Methods Mol. Biol. 1263 (2015) 243–250.
[61] D. Nath, F. Singh, R. Das, X-ray diffraction analysis by Williamson-Hall, Halder-Wagner and size-strain plot methods of CdSe nanoparticles- a comparative study, Mater. Chem. Phys. 239 (2020) 122021.
[62] E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, UCSF Chimera – A visualization system for exploratory research and analysis, J. Comput. Chem. 25 (2004) 1605–1612.
[63] H. Li, P. Xia, S. Pan, Z. Qi, C. Fu, Z. Yu, W. Kong, Y. Chang, K. Wang, D. Wu, X. Yang, The advances of ceria nanoparticles for biomedical applications in orthopaedics, Int. J. Nanomedicine. 15 (2020) 7199–7214.
[64] H.J. Wiggers, J.R. Rocha, J. Cheleski, C.A. Montanari, Integration of ligand- and target-based virtual screening for the discovery of cruzain inhibitors, Mol. Inform. 30 (2011) 565–578.
[65] N.C. da R. Galucio, D. de A. Moysés, J.R.S. Pina, P.S.B. Marinho, P.C. Gomes Júnior, J.N. Cruz, V.V. Vale, A.S. Khayat, A.M. do R. Marinho, Antiproliferative, genotoxic activities and quantification of extracts and cucurbitacin B obtained from Luffa operculata (L.) Cogn, Arab. J. Chem. 15 (2022) 103589.
[66] J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, D.A. Case, Development and testing of a general Amber force field, J. Comput. Chem. 25 (2004) 1157–1174.
[67] A.K. Malde, L. Zuo, M. Breeze, M. Stroet, D. Poger, P.C. Nair, C. Oostenbrink, A.E. Mark, An Automated force field Topology Builder (ATB) and repository: Version 1.0, J. Chem. Theory Comput. 7 (2011) 4026–4037.
[68] M. González-Durruthy, S. Manske Nunes, J. Ventura-Lima, M.A. Gelesky, H. González-Díaz, J.M. Monserrat, R. Concu, M.N.D.S. Cordeiro, MitoTarget Modeling Using ANN-Classification Models Based on Fractal SEM Nano-Descriptors: Carbon Nanotubes as Mitochondrial F0F1-ATPase Inhibitors, J. Chem. Inf. Model. 59 (2019) 86–97.