journal article·2024-11

Exploring the interaction of graphene-based nanomaterials with atherosclerosis-related protein targets: insights from molecular docking and dynamics simulations

Farizah Hanim Lat, Ahmad Naqib Shuid, Mohd Yusmaidie Aziz, Muhammad Mahyiddin Ramli, Rafeezul Mohamed

Journal of Nanoparticle Research· Volume 26· Issue 11
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Abstract

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OpenAlex topics: Graphene and Nanomaterials Applications · Nanoparticle-Based Drug Delivery · Nanoparticles: synthesis and applications

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References (65)

Show source-provided references
1. Libby P, Buring JE, Badimon L, Hansson GK, Deanfield J, Bittencourt MS, Tokgözoğlu L, Lewis EF (2019) Atherosclerosis. Nat Rev Dis Primers 5:5610.1038/s41572-019-0106-z ↗
2. Orekhov AN (2018) LDL and foam cell formation as the basis of atherogenesis. Curr Opin Lipidol 29:279–28410.1097/MOL.0000000000000525 ↗
3. Cochain C, Zernecke A (2017) Macrophages in vascular inflammation and atherosclerosis, Pflug. Arch Eur J Physiol 469:485–49910.1007/s00424-017-1941-y ↗
4. Xu Z, Wei Z, Zhou JJ, Ye F, Lo WS, Wang F, Lau CF, Wu J, Nangle LA, Chiang KP, Yang XL, Zhang M, Schimmel P (2012) Internally deleted human tRNA synthetase suggests evolutionary pressure for repurposing. Structure 20:1470–1477. https://doi.org/10.1016/j.str.2012.06.00210.1016/j.str.2012.06.002 ↗
5. Remmerie A, Scott CL (2018) Macrophages and lipid metabolism. Cell Immunol 330:27–4210.1016/j.cellimm.2018.01.020 ↗
6. Geim A, Novoselov K (2007) The rise of graphene (editorial). Nat Mat 6:18310.1038/nmat1849 ↗
7. Li X, Tao L, ChenH Z, Fang X, Li X, Wang JB, Xu HZhu (2017) Graphene and related two-dimensional materials: structure-property relationships for electronics and optoelectronics. Appl Phys Rev 4:02130610.1063/1.4983646 ↗
8. Narayan R, Kim SK (2015) Surfactant mediated liquid phase exfoliation of graphene. Nano Convergence 2:2010.1186/s40580-015-0050-x ↗
9. Trikkaliotis DG, Christoforidis AK, Mitropoulos AC, Kyzas GZ (2021) Graphene oxide synthesis, properties and characterization techniques: a comprehensive review. Chem Eng 5:64
10. Priyadarsini S, Mohanty S, Mukherjee S, Basu S, Mishra M (2018) Graphene and graphene oxide as nanomaterials for medicine and biology application. J Nanostruct Chem 8:123–13710.1007/s40097-018-0265-6 ↗
11. Krivak R, Hoksza D (2018) P2Rank: Machine learning-based tool for rapid and accurate prediction of ligand binding sites from protein structure. J Cheminform 10(1):3910.1186/s13321-018-0285-8 ↗
12. Cousins KR (2011) Computer review of ChemDraw ultra 12.0. J Am Chem Soc 133(33):8388–838810.1021/ja204075s ↗
13. Momohjimoh OI, Abechi SE, Shallangwa GA (2021) Computational evaluation of some compounds as potential anti-breast cancer agents. Future J Pharma Sci 7:16710.1186/s43094-021-00315-2 ↗
14. Jakubec D, Skoda P, Krivak R, Novotny M, Hoksza D (2022) PrankWeb 3: Accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res 50:593–59710.1093/nar/gkac389 ↗
15. Trott O, Olson AJ (2010) AutoDockVina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–46110.1002/jcc.21334 ↗
16. Durrant JD, McCammon JA (2011) BINANA: A novel algorithm for ligand-binding characterization. J Mol Graph Model 29(6):888–89310.1016/j.jmgm.2011.01.004 ↗
17. Kudin KN, Ozbas B, Schniepp HC, Prud’homme RK, Aksay IA, Car R (2008) Raman spectra of graphite oxide and functionalized graphene sheets. Nano Lett 8(1):36–4110.1021/nl071822y ↗
18. Hu Y, Gao H (2023) Chemical synthesis of reduced graphene oxide: a review. Miner Miner Mater 2:810.20517/mmm.2023.07 ↗
19. Biru EI, Necolau MI, Zainea A, Iovu H (2022) Graphene oxide-protein-based scaffolds for tissue engineering: recent advances and applications. Polymers 14:103210.3390/polym14051032 ↗
20. Stankovich S, Dikin DA, Piner RD, Kohlhaas KA, Kleinhammes A, Jia Y, Wu Y, Nguyen ST, Ruoff RS (2007) Synthesis of graphene-based nanosheets via chemical reduction of exfoliated graphite oxide. Carbon 45(7):1558–156510.1016/j.carbon.2007.02.034 ↗
21. Zhang CM (2016) Lieber, Nano-Bioelectronics. Chem Rev 116(1):49–9610.1021/acs.chemrev.5b00608 ↗
22. Rhainds D, Brissette L (2004) The role of scavenger receptor class B type I (SR-BI) in lipid trafficking: defining the rules for lipid traders. Int J Biochem Cell Biol 36(1):39–7710.1016/S1357-2725(03)00173-0 ↗
23. Park H, Adsit FG, Boyington JC (2005) The 1.4 Å Crystal structure of the human oxidized low density lipoprotein receptor LOX-1. J Biol Chem 280(14):13593–1359910.1074/jbc.M500768200 ↗
24. Bilinovich SM, Davis CM, Morris DL, Ray LA, Prokop JW, Buchan GJ, Leeper TC (2014) The C-terminal domain of SRA1p has a fold more similar to PRP18 than to an RRM and does not directly bind to the SRA1 RNA STR7 region. J Mol Biol 426(10):1753–176510.1016/j.jmb.2014.01.007 ↗
25. Zhou JJ, Wang F, Xu Z, Lo W-S, Lau C-F, Chiang KP, Nangle LA, Ashlock MA, Mendlein JD, Yang X-L, Zhang M, Schimmel P (2014) Secreted histidyl-tRNA synthetase splice variants elaborate major epitopes for autoantibodies in inflammatory myositis. J Biol Chem 289(28):19269–1927510.1074/jbc.C114.571026 ↗
26. Neculai N, Schwake M, Ravichandran M, Zunke F, Collins RF, Peters J, Neculai M, Plumb J, Loppnau P, Pizarro JC, Seitova A et al (2013) Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36. Nature 504(7478):172–17610.1038/nature12684 ↗
27. Novoselov KS, Geim AK, Morozov SV, Jiang D, Zhang Y, Dubonos SV, Grigorieva IV, Firsov AA (2004) Electric field effect in atomically thin carbon films. Science 306(5696):666–66910.1126/science.1102896 ↗
28. Jian JW, Elumalai P, Pitti T, Wu CY, Tsai KC, Chang JY, Peng HP, Yang AS (2016) Predicting ligand binding sites on protein surfaces by 3-dimensional probability density distributions of interacting atoms. PLoS One 11(8):01603110.1371/journal.pone.0160315 ↗
29. Wang Y, Li Z, Wang J, Li J, Lin Y (2011) Graphene and graphene oxide: biofunctionalization and applications in biotechnology. Trends Biotechnol 29(5):205–21210.1016/j.tibtech.2011.01.008 ↗
30. Hasan SA, Rigueur JL, Harl RR, Krejci AJ, Isabel GJ, Rogers BR (2010) Transferable graphene oxide films with tunable microstructures. ACS Nano 4(12):7367–737210.1021/nn102152x ↗
31. Paredes JI, Villar-Rodil S, Martínez-Alonso A, Tascón JMD (2008) Graphene oxide dispersions in organic solvents. Langmuir 24:10560–1056410.1021/la801744a ↗
32. Dreyer DR, Park S, Bielawski CW, Ruoff RS (2010) The chemistry of graphene oxide. Chem Soc Rev 39:228–24010.1039/B917103G ↗
33. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–279110.1002/jcc.21256 ↗
34. Aher A, Nickerson T, Jordan C, Thorpe F, Hatakeyama E, Ormsbee L, Majumder M, Bhattacharyya D (2020) Ion and organic transport in graphene oxide membranes: model development to difficult water remediation applications. J Membr Sci 604:11802410.1016/j.memsci.2020.118024 ↗
35. Ciric L, Sienkiewicz A, Gaal R, Jacimovic J, Vaju C, Magrez A, Forro L (2012) Defects and localization in chemically-derived graphene, Physical Review B: Condensed Matter and Materials. Physics 86:19
36. Liu J, Cui L, Losic D (2013) Graphene and graphene oxide as new nanocarriers for drug delivery applications. Acta Biomater 9:9243–925710.1016/j.actbio.2013.08.016 ↗
37. Trott O, Olson AJ (2010) AutoDockVina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455–46110.1002/jcc.21334 ↗
38. Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–15710.2174/157340911795677602 ↗
39. Bagri A, Mattevi C, Acik M, Chabal YJ, Chhowalla M, Shenoy VB (2010) Structural evolution during the reduction of chemically derived graphene oxide. Nat Chem 2(7):581–58710.1038/nchem.686 ↗
40. Cauet E, Rooman M, Wintjens R, Lievin J, Biot C (2005) Histidine-aromatic interactions in proteins and protein-ligand complexes: quantum chemical study of X-ray and model structures. J Chem Theory Comput 1:472–48310.1021/ct049875k ↗
41. Speight JG (2020) Water chemistry. Natural Water Remediation 127–12810.1016/B978-0-12-803810-9.00003-6 ↗
42. Brylinski M (2018) Aromatic interactions at the ligand-protein interface: implications for the development of docking scoring functions. ChemBiol Drug Des 91(2):380–39010.1111/cbdd.13084 ↗
43. Panigrahi SK, Desiraju GR (2007) Strong and weak hydrogen bonds in the protein-ligand interface. Proteins. 67(1):128–141. https://doi.org/10.1002/prot.2125310.1002/prot.21253 ↗
44. Boehr DD, Farley AR, Wright GD, Cox JR (2002) Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3′)-IIIa and its nucleotide ligands. Chem Biol 9:1209–121710.1016/S1074-5521(02)00245-4 ↗
45. Pyrkov TV, Pyrkova DV, Balitskaya ED, Efremov RG (2009) The role of stacking interactions in complexes of proteins with adenine and Guanine fragments of ligands. Acta Naturae 1:124–12710.32607/20758251-2009-1-1-124-127 ↗
46. Wu R, McMahon TB (2008) Investigation of cation-pi interactions in biological systems. J Am Chem Soc 130:12554–1255510.1021/ja802117s ↗
47. Efremov RG, Chugunov AO, Pyrkov TV, Priestle JP, Arseniev AS, Jacoby E (2007) Molecular lipophilicity in protein modeling and drug design. Curr Med Chem 14:393–41510.2174/092986707779941050 ↗
48. Gallina AM, Bork P, Bordo D (2014) Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs. J MolRecognit 27:65–7210.1002/jmr.2332 ↗
49. Lu Y, Wang Y, Zhu W (2010) Nonbonding interactions of organic halogens in biological systems: implications for drug discovery and biomolecular design. PhysChemChem Phys 12:4543–4551
50. Zhou P, Tian F, Zou J, Shang Z (2010) Rediscovery of halogen bonds in protein-ligand complexes. Mini Rev Med Chem 10:309–31410.2174/138955710791331016 ↗
51. Kukic P, Nielsen JE (2010) Electrostatics in proteins and protein-ligand complexes, Future. Med Chem 2:647–666
52. Zhou P, Huang J, Tian F (2012) Specific noncovalent interactions at protein-ligand interface: implications for rational drug design. Curr Med Chem 19:226–23810.2174/092986712803414150 ↗
53. Chen K, Kurgan L (2009) Investigation of atomic level patterns in protein–small ligand interactions. PLoS One 4:447310.1371/journal.pone.0004473 ↗
54. Shahriari S, Sastry M, Panjikar S, Singh Raman RK (2021) Graphene and graphene oxide as a support for biomolecules in the development of biosensors. Mater Sci Eng C 118:111546
55. Chen SH, Bell DR, Luan B (2022) Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes. Adv Drug Deliv Rev 186:11433610.1016/j.addr.2022.114336 ↗
56. Kumar SR, Hsu Y-H, Vi TTT, Pang J-HS, Lee Y-C, Hsieh C-H, Lue SJ (2021) Graphene oxide-induced protein conformational change in nasopharyngeal carcinoma cells: a joint research on cytotoxicity and photon therapy. Materials (Basel) 14(6):139610.3390/ma14061396 ↗
57. Park BS, Song DH, Kim HM, Choi B-S, Lee H, Lee J-O (2009) The structural basis of lipopolysaccharide recognition by the TLR4–MD-2 complex. Nature 458:1191–119510.1038/nature07830 ↗
58. Dasari TP, McShan S, Dasmahapatra AK, Tchounwou PB (2018) A review on graphene-based nanomaterials in biomedical applications and risks in environment and health. Nano-Micro Lett 10(3):5310.1007/s40820-018-0206-4 ↗
59. Casalini T, Limongelli V, Schmutz M, Som C, Jordan O, Wick P, Borchard G, Perale G (2019) Molecular modeling for nanomaterial–biology interactions: opportunities, challenges, and perspectives. Front Bioeng Biotechnol 7:26810.3389/fbioe.2019.00268 ↗
60. Tuffery P, Derreumaux P (2012) Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface 9(66):20–3310.1098/rsif.2011.0584 ↗
61. Chaudhary K, Kumar K, Venkatesu P, Masram DT (2021) Protein immobilization on graphene oxide or reduced graphene oxide surface and their applications: influence over activity, structural and thermal stability of protein. Adv Colloid Interface Sci 289:10236710.1016/j.cis.2021.102367 ↗
62. Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789–79610.1038/nchembio.232 ↗
63. Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275(1):1–2110.1111/j.1742-4658.2007.06178.x ↗
64. Chen GY, Pang DW, Hwang SM, Tuan HY, Hu YC (2012) A graphene-based platform for induced pluripotent stem cells culture and differentiation. Biomaterials 33(2):418–42710.1016/j.biomaterials.2011.09.071 ↗
65. Gough PJ, Gordon S (2000) The role of scavenger receptors in the innate immune system. Microbes Infect 2(3):305–31110.1016/S1286-4579(00)00297-5 ↗