α-Helical Antimicrobial Peptide Encapsulation and Release from Boron Nitride Nanotubes: A Computational Study

References

• Bodanszky M. Peptide Chemistry. Berlin, Germany: Springer-Verlag; 1993.
   Google Scholar
• Mondal S, Das S, Nandi AK. A review on recent advances in polymer and peptide hydrogels. Soft Matter. 2020;16:1404–1454.
   PubMed Web of Science ®Google Scholar
• Powers J-PS, Hancock RE. The relationship between peptide structure and antibacterial activity. Peptides. 2003;24(11):1681–1691. doi:10.1016/j.peptides.2003.08.023
   PubMed Web of Science ®Google Scholar
• Tamerler C, Sarikaya M. Genetically designed peptide-based molecular materials. Acs Nano. 2009;3(7):1606–1615. doi:10.1021/nn900720g
   PubMedGoogle Scholar
• Knorr R, Trzeciak A, Bannwarth W, Gillessen D. New coupling reagents in peptide chemistry. Tetrahedron Lett. 1989;30(15):1927–1930. doi:10.1016/S0040-4039(00)99616-3
   Google Scholar
• Kuzmicheva G, Belyavskaya V. Peptide phage display in biotechnology and biomedicine. Biochem (Mosc) Suppl Ser B Biomed Chem. 2017;11(1):1–15. doi:10.1134/S1990750817010061
   Google Scholar
• De La Rica R, Matsui H. Applications of peptide and protein-based materials in bionanotechnology. Chem Soc Rev. 2010;39(9):3499–3509. doi:10.1039/b917574c
   PubMed Web of Science ®Google Scholar
• Kuzmicheva G, Belyavskaya V. Peptide phage display in biotechnology and biomedicine. Biomed Khim. 2016;62(5):481–495. doi:10.18097/PBMC20166205481
   PubMedGoogle Scholar
• Fosgerau K, Hoffmann T. Peptide therapeutics: current status and future directions. Drug Discov Today. 2015;20(1):122–128. doi:10.1016/j.drudis.2014.10.003
   PubMed Web of Science ®Google Scholar
• Honigberg MC, Chang L-S, McGuire DK, Plutzky J, Aroda VR, Vaduganathan M. Use of glucagon-like peptide-1 receptor agonists in patients with type 2 diabetes and cardiovascular disease: a review. JAMA Cardiol. 2020;5(10):1182–1190. doi:10.1001/jamacardio.2020.1966
   PubMed Web of Science ®Google Scholar
• Shahidi F, Zhong Y. Bioactive peptides. J AOAC Int. 2008;91(4):914–931. doi:10.1093/jaoac/91.4.914
   PubMed Web of Science ®Google Scholar
• Daliri EB-M, Oh DH, Lee BH. Bioactive peptides. Foods. 2017;6(5):32. doi:10.3390/foods6050032
   PubMed Web of Science ®Google Scholar
• Wang P, Cui Q, Zhang Y, et al. A review of pedal peptide/orcokinin-type neuropeptides. Curr Protein Pept Sci. 2021;22(1):41–49. doi:10.2174/1389203721666201109112758
   PubMedGoogle Scholar
• Liu W-P, Chen Y-H, Ming X, Kong Y. Design and synthesis of a novel cationic peptide with potent and broad-spectrum antimicrobial activity. Biomed Res Int. 2015;2015:578764. doi:10.1155/2015/578764
   PubMed Web of Science ®Google Scholar
• Yeaman MR, Yount NY. Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev. 2003;55(1):27–55. doi:10.1124/pr.55.1.2
   PubMed Web of Science ®Google Scholar
• Mukhopadhyay S, Prasad AB, Mehta CH, Nayak UY. Antimicrobial peptide polymers: no escape to ESKAPE pathogens—a review. World J Microbiol Biotechnol. 2020;36(9):1–14. doi:10.1007/s11274-020-02907-1
   Web of Science ®Google Scholar
• Hitchner MA, Santiago-Ortiz LE, Necelis MR, et al. Activity and characterization of a pH-sensitive antimicrobial peptide. Biochim Biophys Acta. 2019;1861(10):182984. doi:10.1016/j.bbamem.2019.05.006
   Google Scholar
• Jenssen H, Hamill P, Hancock RE. Peptide antimicrobial agents. Clin Microbiol Rev. 2006;19(3):491–511. doi:10.1128/CMR.00056-05
   PubMed Web of Science ®Google Scholar
• Gough M, Hancock R, Kelly NM. Antiendotoxin activity of cationic peptide antimicrobial agents. Infect Immun. 1996;64(12):4922–4927. doi:10.1128/IAI.64.12.4922-4927.1996
   PubMed Web of Science ®Google Scholar
• Lei J, Sun L, Huang S, et al. The antimicrobial peptides and their potential clinical applications. Am J Transl Res. 2019;11(7):3919.
   PubMed Web of Science ®Google Scholar
• Moravej H, Moravej Z, Yazdanparast M, et al. Antimicrobial peptides: features, action, and their resistance mechanisms in bacteria. Microb Drug Resist. 2018;24(6):747–767. doi:10.1089/mdr.2017.0392
   PubMed Web of Science ®Google Scholar
• Pardridge WM. Recent developments in peptide drug delivery to the brain. Pharmacol Toxicol. 1992;71(1):3–10. doi:10.1111/j.1600-0773.1992.tb00512.x
   PubMedGoogle Scholar
• Pizzolato-Cezar LR, Okuda-Shinagawa NM, Machini MT. Combinatory therapy antimicrobial peptide-antibiotic to minimize the ongoing rise of resistance. Front Microbiol. 2019;10:1703. doi:10.3389/fmicb.2019.01703
   PubMedGoogle Scholar
• Subbalakshmi C, Bikshapathy E, Sitaram N, Nagaraj R. Antibacterial and hemolytic activities of single tryptophan analogs of indolicidin. Biochem Biophys Res Commun. 2000;274(3):714–716. doi:10.1006/bbrc.2000.3214
   PubMedGoogle Scholar
• Band VI, Weiss DS. Mechanisms of antimicrobial peptide resistance in gram-negative bacteria. Antibiotics. 2015;4(1):18–41. doi:10.3390/antibiotics4010018
   Google Scholar
• Smith AW. Biofilms and antibiotic therapy: is there a role for combating bacterial resistance by the use of novel drug delivery systems? Adv Drug Deliv Rev. 2005;57(10):1539–1550. doi:10.1016/j.addr.2005.04.007
   PubMed Web of Science ®Google Scholar
• Zarrintaj P, Ramsey JD, Samadi A, et al. Poloxamer: a versatile tri-block copolymer for biomedical applications. Acta Biomater. 2020.
   PubMed Web of Science ®Google Scholar
• Yoosefian M, Etminan N. Density functional theory (DFT) study of a new novel bionanosensor hybrid; tryptophan/Pd doped single walled carbon nanotube. Physica E Low Dimens Syst Nanostruct. 2016;81:116–121. doi:10.1016/j.physe.2016.03.009
   Web of Science ®Google Scholar
• Skandani AA, Al-Haik M. Reciprocal effects of the chirality and the surface functionalization on the drug delivery permissibility of carbon nanotubes. Soft Matter. 2013;9(48):11645–11649. doi:10.1039/C3SM52126E
   PubMed Web of Science ®Google Scholar
• Ramos MADS, Da Silva PB, Spósito L, et al. Nanotechnology-based drug delivery systems for control of microbial biofilms: a review. Int J Nanomedicine. 2018;13:1179. doi:10.2147/IJN.S146195
   PubMed Web of Science ®Google Scholar
• Bernkop-Schnürch A, Bratengeyer I, Valenta C. Development and in vitro evaluation of a drug delivery system protecting from trypsinic degradation. Int J Pharm. 1997;157(1):17–25. doi:10.1016/S0378-5173(97)00198-1
   Web of Science ®Google Scholar
• Arsawang U, Saengsawang O, Rungrotmongkol T, et al. How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system? J Mol Graph Model. 2011;29(5):591–596. doi:10.1016/j.jmgm.2010.11.002
   PubMed Web of Science ®Google Scholar
• Zarghami MD, Bagheri B, Nasiriasayesh A, et al. Insight into the self-insertion of a protein inside the boron nitride nanotube. ACS Omega. 2020;5(49):32051. doi:10.1021/acsomega.0c05080
   PubMedGoogle Scholar
• Chen X, Wu P, Rousseas M, et al. Boron nitride nanotubes are noncytotoxic and can be functionalized for interaction with proteins and cells. J Am Chem Soc. 2009;131(3):890–891. doi:10.1021/ja807334b
   PubMed Web of Science ®Google Scholar
• Cohen ML, Zettl A. The physics of boron nitride nanotubes. Phys Today. 2010;63(11):34–38. doi:10.1063/1.3518210
   Web of Science ®Google Scholar
• Mirhaji E, Afshar M, Rezvani S, Yoosefian M. Boron nitride nanotubes as a nanotransporter for anticancer docetaxel drug in water/ethanol solution. J Mol Liq. 2018;271:151–156. doi:10.1016/j.molliq.2018.08.142
   Web of Science ®Google Scholar
• Khatti Z, Hashemianzadeh SM. Boron nitride nanotube as a delivery system for platinum drugs: drug encapsulation and diffusion coefficient prediction. Eur J Pharm Sci. 2016;88:291–297. doi:10.1016/j.ejps.2016.04.011
   PubMed Web of Science ®Google Scholar
• Roosta S, Nikkhah SJ, Sabzali M, Hashemianzadeh SM. Molecular dynamics simulation study of boron-nitride nanotubes as a drug carrier: from encapsulation to releasing. RSC Adv. 2016;6(11):9344–9351. doi:10.1039/C5RA22945F
   Web of Science ®Google Scholar
• Mortazavifar A, Raissi H, Shahabi M. Comparative prediction of binding affinity of hydroxyurea anti-cancer to boron nitride and carbon nanotubes as smart targeted drug delivery vehicles. J Biomol Struct Dyn. 2019;37(18):4852–4862. doi:10.1080/07391102.2019.1567385
   PubMed Web of Science ®Google Scholar
• Roosta S, Hashemianzadeh SM, Ketabi S. Encapsulation of cisplatin as an anticancer drug into boron-nitride and carbon nanotubes: molecular simulation and free energy calculation. Mater Sci Eng C. 2016;67:98–103. doi:10.1016/j.msec.2016.04.100
   PubMedGoogle Scholar
• Hasanzade Z, Raissi H. Carbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach. J Biomol Struct Dyn. 2020;38(3):697–707. doi:10.1080/07391102.2019.1585951
   PubMed Web of Science ®Google Scholar
• Zarghami MD, Bagheri B, Yousefi F, et al. Boron nitride nanotube as an antimicrobial peptide carrier: a theoretical insight. Int J Nanomedicine. 2021;16:1837. doi:10.2147/IJN.S298699
   PubMedGoogle Scholar
• Iranmanesh‐Zarandy Z, Dehestani M. Molecular dynamics simulation of paracetamol drug adsorption on boron nitride nanotube: effects of temperature, nanotube length, diameter, and chirality. ChemistrySelect. 2019;4(27):7866–7873. doi:10.1002/slct.201900644
   Google Scholar
• Sedghamiz E, Jamalizadeh E, Hosseini SMA, Sedghamiz T, Zahedi E. Molecular dynamics simulation of boron nitride nanotube as a drug carrier. Arab J Sci Eng. 2014;39(9):6737–6742. doi:10.1007/s13369-014-1228-y
   Google Scholar
• El Khalifi M, Bentin J, Duverger E, Gharbi T, Boulahdour H, Picaud F. Encapsulation capacity and natural payload delivery of an anticancer drug from boron nitride nanotube. Phys Chem Chem Phys. 2016;18(36):24994–25001. doi:10.1039/C6CP01387B
   PubMed Web of Science ®Google Scholar
• Mehrjouei E, Akbarzadeh H, Shamkhali AN, Abbaspour M, Salemi S, Abdi P. Delivery of cisplatin anticancer drug from carbon, boron nitride, and silicon carbide nanotubes forced by Ag-nanowire: a comprehensive molecular dynamics study. Mol Pharm. 2017;14(7):2273–2284. doi:10.1021/acs.molpharmaceut.7b00106
   PubMedGoogle Scholar
• Saikia N, Jha AN, Deka RC. Interaction of pyrazinamide drug functionalized carbon and boron nitride nanotubes with pncA protein: a molecular dynamics and density functional approach. RSC Adv. 2013;3(35):15102–15107. doi:10.1039/c3ra42534g
   Google Scholar
• Katiyar RS, Jha PK. Molecular simulations in drug delivery: opportunities and challenges. Wiley Interdiscip Rev Comput Mol Sci. 2018;8:e1358.
   Web of Science ®Google Scholar
• Singh A, Vanga SK, Orsat V, Raghavan V. Application of molecular dynamic simulation to study food proteins: a review. Crit Rev Food Sci Nutr. 2018;58(16):2779–2789. doi:10.1080/10408398.2017.1341864
   PubMed Web of Science ®Google Scholar
• Bagheri B, Dehaghani MZ, Karami Z, et al. Correlation between surface topological defects and fracture mechanism of γ-graphyne-like boron nitride nanosheets. Comput Mater Sci. 2020;110152.
   Google Scholar
• Dehaghani MZ, Mashhadzadeh AH, Salmankhani A, et al. Fracture toughness and crack propagation behavior of nanoscale beryllium oxide graphene-like structures: a molecular dynamics simulation analysis. Eng Fract Mech. 2020;235:107194. doi:10.1016/j.engfracmech.2020.107194
   Web of Science ®Google Scholar
• Zarghami dehaghani M, Salmankhani A, Hamed mashhadzadeh A, Habibzadeh S, Abida O, Reza Saeb M. Fracture mechanics of polycrystalline beryllium oxide nanosheets: a theoretical basis. Eng Fract Mech. 2021;244:107552. doi:10.1016/j.engfracmech.2021.107552
   Google Scholar
• Bagheri B, Dehaghani MZ, Safa ME, et al. Fracture fingerprint of polycrystalline C3N nanosheets: theoretical basis. J Mol Graph Model. 2021;106:107899. doi:10.1016/j.jmgm.2021.107899
   PubMed Web of Science ®Google Scholar
• Salmankhani A, Karami Z, Mashhadzadeh AH, et al. A theoretical scenario for the mechanical failure of boron carbide nanotubes. Comput Mater Sci. 2021;186:110022. doi:10.1016/j.commatsci.2020.110022
   Web of Science ®Google Scholar
• Albooyeh A, Dadrasi A, Mashhadzadeh AH. Effect of point defects and low-density carbon-doped on mechanical properties of BNNTs: a molecular dynamics study. Mater Chem Phys. 2020;239:122107. doi:10.1016/j.matchemphys.2019.122107
   Google Scholar
• Zhu S, Aumelas A, Gao B. Convergent evolution-guided design of antimicrobial peptides derived from influenza A virus hemagglutinin. J Med Chem. 2011;54(4):1091–1095. doi:10.1021/jm1010463
   PubMed Web of Science ®Google Scholar
• Plimpton S. Fast parallel algorithms for short-range molecular dynamics. J Comput Phys. 1995;117(1):1–19. doi:10.1006/jcph.1995.1039
   Web of Science ®Google Scholar
• Park S, Schulten K. Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys. 2004;120(13):5946–5961. doi:10.1063/1.1651473
   PubMed Web of Science ®Google Scholar
• Los J, Kroes J, Albe K, Gordillo R, Katsnelson M, Fasolino A. Extended tersoff potential for boron nitride: energetics and elastic properties of pristine and defective h-BN. Phys Rev B. 2017;96(18):184108. doi:10.1103/PhysRevB.96.184108
   Web of Science ®Google Scholar
• Hirschfelder JO, Curtiss CF, Bird RB, Mayer MG. Molecular Theory of Gases and Liquids. New York: Wiley; 1964.
   Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–38. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Sargsyan K, Grauffel C, Lim C. How molecular size impacts RMSD applications in molecular dynamics simulations. J Chem Theory Comput. 2017;13:1518–1524.
   PubMed Web of Science ®Google Scholar
• Kang Y, Liu Y-C, Wang Q, Shen J-W, Wu T, Guan W-J. On the spontaneous encapsulation of proteins in carbon nanotubes. Biomaterials. 2009;30(14):2807–2815. doi:10.1016/j.biomaterials.2009.01.024
   PubMed Web of Science ®Google Scholar
• Veclani D, Melchior A. Adsorption of ciprofloxacin on carbon nanotubes: insights from molecular dynamics simulations. J Mol Liq. 2020;298:111977. doi:10.1016/j.molliq.2019.111977
   Web of Science ®Google Scholar
• Zhang D, Gullingsrud J, McCammon JA. Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc. 2006;128(9):3019–3026. doi:10.1021/ja057292u
   PubMed Web of Science ®Google Scholar
• Zhang L, Peng G, Li J, et al. Molecular dynamics study on the configuration and arrangement of doxorubicin in carbon nanotubes. J Mol Liq. 2018;262:295–301. doi:10.1016/j.molliq.2018.04.097
   Web of Science ®Google Scholar
• Shen J-W, Tang T, Wei X-H, et al. On the loading mechanism of ssDNA into carbon nanotubes. RSC Adv. 2015;5(70):56896–56903. doi:10.1039/C5RA01941A
   Web of Science ®Google Scholar
• Shen J-W, Wu T, Wang Q, Kang Y. Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces. Biomaterials. 2008;29(28):3847–3855. doi:10.1016/j.biomaterials.2008.06.013
   PubMed Web of Science ®Google Scholar
• Raffaini G, Ganazzoli F. Surface topography effects in protein adsorption on nanostructured carbon allotropes. Langmuir. 2013;29(15):4883–4893. doi:10.1021/la3050779
   PubMedGoogle Scholar
• Raffaini G, Ganazzoli F. Separation of chiral nanotubes with an opposite handedness by chiral oligopeptide adsorption: a molecular dynamics study. J Chromatogr A. 2015;1425:221–230. doi:10.1016/j.chroma.2015.11.045
   PubMed Web of Science ®Google Scholar