Volume 19, Issue 10 (October 2019)                   Modares Mechanical Engineering 2019, 19(10): 2481-2489 | Back to browse issues page

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Mollaei F, Aliparast P, Naghash A. Vancomycin Adsorption on Microcantilever Based on Molecular Dynamics Simulation. Modares Mechanical Engineering 2019; 19 (10) :2481-2489
URL: http://mme.modares.ac.ir/article-15-22300-en.html
1- Aerospace Research Institute, Tehran, Iran
2- Aerospace Research Institute, Tehran, Iran , aliparast@ari.ac.ir
3- Aerospace Department, Amirkabir University of Technology, Tehran, Iran
Abstract:   (3438 Views)

Adsorption simulation of vancomycin antibiotic is done using molecular dynamics. The simulation results show the adsorption behavior of vancomycin on a functionalized biosensor. Regarding the importance of vancomycin, its molecular function is simulated using multiscale discipline. Adsorption to a single assembly monolayer is considered according to vancomycin’s in-vivo function. A selected biosensor is a non-symmetrically functionalized microcantilever which undergoes deformation as a result of changes in surface tension regarding functionalized surface. Multiscale simulations implemented to calculate microcantilever deformation. Molecular models in a vacuum and aquatic media are taken into account. Energy parameters related to surface tension is studied versus the distance of target molecules to the surface of the biosensor. To calculate the distance between receptor molecules in single assembly monolayer, an algorithm is proposed based on experimental results.

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Article Type: Original Research | Subject: Micro & Nano Systems
Received: 2018/06/21 | Accepted: 2019/02/23 | Published: 2019/10/22

1. Nelson DL, Cox MM. Principles of biochemistry. New York: W.H. Freeman; 2012. pp. 84-252. [Link]
2. Schäfer M, Schneider TR, Sheldrick GM. Crystal structure of vancomycin. Structure. 1996;4(12):1509-1515. [Link] [DOI:10.1016/S0969-2126(96)00156-6]
3. Leclercq R, Derlot E, Weber M, Duval J, Courvalin P. Transferable vancomycin and teicoplanin resistance in Enterococcus faecium. Antimicrobial Agents and Chemotherapy. 1989;33(1):10-15. [Link] [DOI:10.1128/AAC.33.1.10]
4. Neu HC. The crisis in antibiotic resistance. Science. 1992;257(5073):1064-1073. [Link] [DOI:10.1126/science.257.5073.1064]
5. Bai X, Lu B, Chen X, Zhang B, Tang J. Reversible detection of vancomycin using peptide-functionalized cantilever array sensor. Biosensors and Bioelectronics. 2014;62:145-150. [Link] [DOI:10.1016/j.bios.2014.06.024]
6. Lang HP, Hegner M, Gerber C. Cantilever array sensors. Materials Today. 2005;8(4):30-36. [Link] [DOI:10.1016/S1369-7021(05)00792-3]
7. Shnayerson M, Plotkin M. The killers within: The deadly rise of drug-resistant bacteria. New York: B Demco Media; 2003. [Link]
8. Liu C, Bayer A, Cosgrove SE, Daum RS, Fridkin SK, Gorwitz RJ, et al. Clinical practice guidelines by the infectious diseases society of America for the treatment of methicillin-resistant Staphylococcus aureus infections in adults and children: Executive summary. Clinical Infectious Diseases. 2011;52(3):285-292. [Link] [DOI:10.1093/cid/cir034]
9. Watanakunakorn C. Mode of action and in-vitro activity of vancomycin. Journal of Antimicrobial Chemotherapy. 1984;14(Suppl D):7-18. [Link] [DOI:10.1093/jac/14.suppl_D.7]
10. Hoshyarmanesh S, Bahrami M, Kalantarinejad R. A multiscale approach in the computational modeling of bio-physical environment of micro-mechanical biosensor towards the prostate specific antigen diagnosis. Journal of Computational and Theoretical Nanoscience. 2014;11(5):1374-1384. [Link] [DOI:10.1166/jctn.2014.3507]
11. Alder BJ, Wainwright TE. Studies in molecular dynamics. I. general method. The Journal of Chemical Physics. 1959;31(2):459. [Link] [DOI:10.1063/1.1730376]
12. Small PM, Chambers HF. Vancomycin for Staphylococcus aureus endocarditis in intravenous drug users. Antimicrobial Agents and Chemotherapy. 1990;34(6):1227-1231. [Link] [DOI:10.1128/AAC.34.6.1227]
13. Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, et al. Improving the representation of peptide-like inhibitor and antibiotic molecules in the protein data bank. Biopolymers. 2014;101(6):659-668. [Link] [DOI:10.1002/bip.22434]
14. Nitanai Y, Kikuchi T, Kakoi K, Hanamaki Sh, Fujisawa I, Aoki K. Crystal structures of the complexes between vancomycin and cell-wall precursor analogs. Journal of Molecular Biology. 2009;385(5):1422-1432. [Link] [DOI:10.1016/j.jmb.2008.10.026]
15. Loll PJ, Bevivino AE, Korty BD, Axelsen PH. Simultaneous recognition of a carboxylate-containing ligand and an intramolecular surrogate ligand in the crystal structure of an asymmetric vancomycin dimer. Journal of the American Chemical Society. 1997;119(7):1516-1522. [Link] [DOI:10.1021/ja963566p]
16. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Research. 2000;28(1):235-242. [Link] [DOI:10.1093/nar/28.1.235]
17. Pedretti A, Villa L, Vistoli G. Atom-type description language: A universal language to recognize atom types implemented in the VEGA program. Theoretical Chemistry Accounts. 2003;109(4):229-232. [Link] [DOI:10.1007/s00214-002-0402-6]
18. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 2005;26(16):1781-1802. [Link] [DOI:10.1002/jcc.20289]
19. Arlett JL, Myers EB, Roukes ML. Comparative advantages of mechanical biosensors. Nature Nanotechnology. 2011;6(4):203-215. [Link] [DOI:10.1038/nnano.2011.44]
20. Khaled ARA, Vafai K, Yang M, Zhang X, Ozkan CS. Analysis, control and augmentation of microcantilever deflections in bio-sensing systems. Sensors and Actuators B Chemical. 2003;94(1):103-115. [Link] [DOI:10.1016/S0925-4005(03)00231-4]
21. Mohammadi P, Liu LP, Sharma P, Kukta RV. Surface energy, elasticity and the homogenization of rough surfaces. Journal of the Mechanics and Physics of Solids. 2013;61(2):325-340. [Link] [DOI:10.1016/j.jmps.2012.10.010]
22. Matsunaga M, Nakanishi T, Asahi T, Osaka T. Effect of surface coverage of gold (111) electrode with cysteine on the chiral discrimination of DOPA. Chirality. 2007;19(4):295-299. [Link] [DOI:10.1002/chir.20376]
23. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, et al. 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. 2010;31(4):671-690. [Link] [DOI:10.1002/jcc.21367]
24. Gfeller D, Michielin O, Zoete V. SwissSidechain: A molecular and structural database of non-natural sidechains. Nucleic Acids Research. 2013;41(D1):D327-D332. [Link] [DOI:10.1093/nar/gks991]

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