Methods Mol Biol. 2022;2402:103-121. doi: 10.1007/978-1-0716-1843-1_9.
Drug Meets Monolayer: Understanding the Interactions of Sterol Drugs with Models of the Lung Surfactant Monolayer Using Molecular Dynamics Simulations.
Methods in molecular biology (Clifton, N.J.)
Sheikh I Hossain, Mohammad Z Islam, Suvash C Saha, Evelyne Deplazes
Affiliations
Affiliations
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW, Australia.
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh.
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia. [email protected].
PMID: 34854039
DOI: 10.1007/978-1-0716-1843-1_9
Abstract
The lung surfactant monolayer (LSM) is a thin layer of lipids and proteins that forms the air/water interface of the alveoli. The primary function of the LSM is to reduce the surface tension at the air/water interface during breathing. The LSM also forms the main biological barrier for any inhaled particles, including drugs, to treat lung diseases. Elucidating the mechanism by which these drugs bind to and absorb into the LSM requires a molecular-level understanding of any drug-induced changes to the morphology, structure, and phase changes of the LSM.Molecular dynamics simulations have been used extensively to study the structure and dynamics of the LSM. The monolayer is usually simulated in at least two states: the compressed state, mimicking exhalation, and the expanded state, mimicking inhalation. In this chapter, we provide detailed instructions on how to set up, run, and analyze coarse-grained MD simulations to study the concentration-dependent effect of a sterol drug on the LSM, both in the expanded and compressed state.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Keywords: Drug-lipid interactions; Lung surfactant monolayer; Molecular dynamics simulations; Molecular interactions; Pulmonary surfactants; Sterol drugs
References
- Zasadzinski JA, Ding J, Warriner HE, Bringezu F, Waring AJ (2001) The physics and physiology of lung surfactants. Curr Opin Colloid Interface Sci 6(5–6):506–513 - PubMed
- Alonso C, Alig T, Yoon J, Bringezu F, Warriner H, Zasadzinski JAJBJ (2004) More than a monolayer: relating lung surfactant structure and mechanics to composition. Biophys J 87(6):4188–4202 - PubMed
- Han S, Mallampalli RK (2015) The role of surfactant in lung disease and host defense against pulmonary infections. Ann Am Thorac Soc 12(5):765–774 - PubMed
- Hidalgo A, Cruz A, Perez-Gil J (2015) Barrier or carrier? Pulmonary surfactant and drug delivery. Eur J Pharm Biopharm 95(Pt a):117–127. https://doi.org/10.1016/j.ejpb.2015.02.014 - PubMed
- Ruge CA, Kirch J, Lehr C-M (2013) Pulmonary drug delivery: from generating aerosols to overcoming biological barriers—therapeutic possibilities and technological challenges. Lancet Respir Med 1(5):402–413. https://doi.org/10.1016/S2213-2600(13)70072-9 - PubMed
- Wang F, Liu J, Zeng HJ (2020) Interactions of particulate matter and pulmonary surfactant: implications for human health. Adv Colloid Interface Sci 284:102244 - PubMed
- Patton JS, Byron PR (2007) Inhaling medicines: delivering drugs to the body through the lungs. Nat Rev Drug Discov 6(1):67–74. https://doi.org/10.1038/nrd2153 - PubMed
- Parra E, Pérez-Gil J (2015) Composition, structure and mechanical properties define performance of pulmonary surfactant membranes and films. Chem Phys Lipids 185:153–175. https://doi.org/10.1016/j.chemphyslip.2014.09.002 - PubMed
- Goerke J (1998) Pulmonary surfactant: functions and molecular composition. Biochim Biophys Acta (BBA) Mol Basis Dis 1408(2–3):79–89. https://doi.org/10.1016/S0925-4439(98)00060-X - PubMed
- Sethi G, Singhal KK (2008) Pulmonary diseases and corticosteroids. Indian J Pediatrics 75(10):1045–1056 - PubMed
- Polin RA, Carlo WAJP (2014) Surfactant replacement therapy for preterm and term neonates with respiratory distress. Pediatrics 133(1):156–163 - PubMed
- Baoukina S, Tieleman DP (2016) Computer simulations of lung surfactant. Biochim Biophys Acta Biomembr 1858(10):2431–2440. https://doi.org/10.1016/j.bbamem.2016.02.030 - PubMed
- Baoukina S, Tieleman DP (2013) Simulations of lipid monolayers. In: Biomolecular simulations, vol 924, pp 431–444. https://doi.org/10.1007/978-1-62703-017-5_16 - PubMed
- Rose D, Rendell J, Lee D, Nag K, Booth V (2008) Molecular dynamics simulations of lung surfactant lipid monolayers. Biophys Chem 138(3):67–77. https://doi.org/10.1016/j.bpc.2008.08.006 - PubMed
- Rekvig L, Hafskjold B, Smit BJ (2004) Chain length dependencies of the bending modulus of surfactant monolayers. Phys Rev Lett 92(11):116101 - PubMed
- Baoukina S, Tieleman DP (2011) Lung surfactant protein SP-B promotes formation of bilayer reservoirs from monolayer and lipid transfer between the interface and subphase. Biophys J 100(7):1678–1687. https://doi.org/10.1016/j.bpj.2011.02.019 - PubMed
- Laing C, Baoukina S, Peter Tieleman D (2009) Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions. Phys Chem Chem Phys 11(12):1916–1922. https://doi.org/10.1039/B819767A - PubMed
- Duncan SL, Larson RG (2010) Folding of lipid monolayers containing lung surfactant proteins SP-B1–25 and SP-C studied via coarse-grained molecular dynamics simulations. Biochim Biophys Acta Biomembr 1798(9):1632–1650. https://doi.org/10.1016/j.bbamem.2010.04.006 - PubMed
- Mohammad-Aghaie D, Mace E, Sennoga CA, Seddon JM, Bresme F (2010) Molecular dynamics simulations of liquid condensed to liquid expanded transitions in DPPC monolayers. J Phys Chem B 114(3):1325–1335. https://doi.org/10.1021/jp9061303 - PubMed
- Duncan SL, Dalal IS, Larson RG (2011) Molecular dynamics simulation of phase transitions in model lung surfactant monolayers. Biochim Biophys Acta Biomembr 1808(10):2450–2465. https://doi.org/10.1016/j.bbamem.2011.06.026 - PubMed
- Baoukina S, Monticelli L, Risselada HJ, Marrink SJ, Tieleman DP (2008) The molecular mechanism of lipid monolayer collapse. Proc Natl Acad Sci U S A 105(31):10803–10808. https://doi.org/10.1073/pnas.0711563105 - PubMed
- Baoukina S, Monticelli L, Amrein M, Tieleman DP (2007) The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations. Biophys J 93(11):3775–3782. https://doi.org/10.1529/biophysj.107.113399 - PubMed
- Baoukina S, Mendez-Villuendas E, Tieleman DP (2012) Molecular view of phase coexistence in lipid monolayers. J Am Chem Soc 134(42):17543–17553. https://doi.org/10.1021/ja304792p - PubMed
- Hossain SI, Gandhi NS, Hughes ZE, Saha S (2020) The role of SP-B1-25 peptides in lung surfactant monolayers exposed to gold nanoparticles. Phys Chem Chem Phys 22(27):15231–15241. https://doi.org/10.1039/D0CP00268B - PubMed
- Hossain SI, Gandhi NS, Hughes ZE, Gu YT, Saha SC (2019) Molecular insights on the interference of simplified lung surfactant models by gold nanoparticle pollutants. Biochim Biophys Acta Biomembr 1861(8):1458–1467. https://doi.org/10.1016/j.bbamem.2019.06.001 - PubMed
- Hossain SI, Gandhi NS, Hughes ZE, Saha SC (2019) Computational modelling of the interaction of gold nanoparticle with lung surfactant monolayer. MRS Adv 4(20):1177–1185. https://doi.org/10.1557/adv.2019.93 - PubMed
- Schneemilch M, Quirke N (2010) Molecular dynamics of nanoparticle translocation at lipid interfaces. Mol Simul 36(11):831–835. https://doi.org/10.1080/08927021003775433 - PubMed
- Choe S, Chang R, Jeon J, Violi A (2008) Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle. Biophys J 95(9):4102–4114. https://doi.org/10.1529/biophysj.107.123976 - PubMed
- Estrada-Lopez ED, Murce E, Franca MPP, Pimentel AS (2017) Prednisolone adsorption on lung surfactant models: insights on the formation of nanoaggregates, monolayer collapse and prednisolone spreading. RSC Adv 7(9):5272–5281. https://doi.org/10.1039/C6RA28422A - PubMed
- Hu J, Liu H, Xu P, Shang Y, Liu HJL (2019) Investigation of drug for pulmonary administration–model pulmonary surfactant monolayer interactions using Langmuir–Blodgett monolayer and molecular dynamics simulation: a case study of Ketoprofen. Langmuir 35(41):13452–13460 - PubMed
- Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19–25 - PubMed
- Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, De Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111(27):7812–7824 - PubMed
- Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38. https://doi.org/10.1016/0263-7855(96)00018-5 - PubMed
- Martini coarse grain forcefield for biomolecules. http://cgmartini.nl/index.php/force-field-parameters . Accessed Jan 2021 - PubMed
- Wassenaar TA, Ingolfsson HI, Bockmann RA, Tieleman DP, Marrink SJ (2015) Computational Lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. J Chem Theory Comput 11(5):2144–2155. https://doi.org/10.1021/acs.jctc.5b00209 - PubMed
- Romo TD, Grossfield AJ (2011) Block covariance overlap method and convergence in molecular dynamics simulation. J Chem Theory Comput 7(8):2464–2472 - PubMed
- Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O (2011) MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem 32(10):2319–2327 - PubMed
- Buchoux SJB (2017) FATSLiM: a fast and robust software to analyze MD simulations of membranes. Bioinformatics 33(1):133–134 - PubMed
- Gapsys V, de Groot BL, Briones RJ (2013) Computational analysis of local membrane properties. J Comput Aided Mol Des 27(10):845–858 - PubMed
- Lukat G, Krüger J, Sommer B (2013) APL@ Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories. J Chem Inf Model 53(11):2908–2925 - PubMed
- Seelig J (1977) Deuterium magnetic resonance: theory and application to lipid membranes. Q Rev Biophys 10(3):353–418 - PubMed
- Vermeer LS, de Groot BL, Réat V, Milon A, Czaplicki J (2007) Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur Biophys J 36(8):919–931. https://doi.org/10.1007/s00249-007-0192-9 - PubMed
- Piggot TJ, Allison JR, Sessions RB, Essex JW (2017) On the calculation of acyl chain order parameters from lipid simulations. J Chem Theory Comput 13(11):5683–5696. https://doi.org/10.1021/acs.jctc.7b00643 - PubMed
- Petrache HI, Tu K, Nagle JF (1999) Analysis of simulated NMR order parameters for lipid bilayer structure determination. Biophys J 76(5):2479–2487 - PubMed
- Martini coarse grain forcefield for biomolecules. http://www.cgmartini.nl/index.php/downloads/tools/229-do-order . Accessed Jan 2019 - PubMed
- Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11):1859–1865 - PubMed
- memgen. http://memgen.uni-goettingen.de/ . Accessed Apr 2017 - PubMed
- MemBuilder-II. http://bioinf.modares.ac.ir/software/mb2/ . Accessed Jan 2021 - PubMed
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