Molecular Dynamics Simulations in Drug Discovery and Drug Delivery

Molecular dynamics (MD) simulation acts as an important supporting tool to experimental methods in the process of drug discovery. With the recent growth in computational power and development of efficient and fast computational techniques, the role of MD simulations has become even more prominent. In this chapter, we discuss the role played by MD simulations at different stages of the drug discovery process. We also discuss the contribution of MD simulations in developing drug-delivery strategies and highlight how the molecular resolution offered by the MD simulations aids in better understanding of the systems involved.

[1]  H. Dai,et al.  Carbon nanotubes as intracellular protein transporters: generality and biological functionality. , 2005, Journal of the American Chemical Society.

[2]  Fabian Kiessling,et al.  Tumor targeting via EPR: Strategies to enhance patient responses. , 2018, Advanced drug delivery reviews.

[3]  Zhiping Weng,et al.  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers , 2014, Bioinform..

[4]  William L. Jorgensen,et al.  Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water , 1983 .

[5]  Xavier Periole,et al.  The Martini coarse-grained force field. , 2013, Methods in molecular biology.

[6]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[7]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[8]  Mattaparthi Venkata Satish Kumar,et al.  PAMAM dendrimer-drug interactions: effect of pH on the binding and release pattern. , 2012, The journal of physical chemistry. B.

[9]  C. Dasgupta,et al.  Translocation of Bioactive Molecules through Carbon Nanotubes Embedded in the Lipid Membrane. , 2018, ACS applied materials & interfaces.

[10]  H. Dai,et al.  Nanotube molecular transporters: internalization of carbon nanotube-protein conjugates into Mammalian cells. , 2004, Journal of the American Chemical Society.

[11]  Huajian Gao,et al.  Molecular-dynamics studies of competitive replacement in peptide–nanotube assembly for control of drug release , 2009, Nanotechnology.

[12]  J. Mongan,et al.  Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.

[13]  Eric T. Kim,et al.  How does a drug molecule find its target binding site? , 2011, Journal of the American Chemical Society.

[14]  Bradley D Anderson,et al.  A computer simulation of functional group contributions to free energy in water and a DPPC lipid bilayer. , 2002, Biophysical journal.

[15]  R. Larson,et al.  The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.

[16]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[17]  A. Pohorille,et al.  Interactions of anesthetics with the membrane-water interface. , 1996, Chemical physics.

[18]  D. Bhatia,et al.  Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations. , 2017, Nanoscale.

[19]  Thierry Langer,et al.  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters , 2005, J. Chem. Inf. Model..

[20]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[21]  R. Larson,et al.  Membrane Pore Formation Induced by Acetylated and Polyethylene Glycol-Conjugated Polyamidoamine Dendrimers , 2011 .

[22]  Seungpyo Hong,et al.  Interaction of poly(amidoamine) dendrimers with supported lipid bilayers and cells: hole formation and the relation to transport. , 2004, Bioconjugate chemistry.

[23]  Using nonequilibrium measurements to determine macromolecule free-energy differences , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  B. Orr,et al.  Lipid bilayer disruption by polycationic polymers: the roles of size and chemical functional group. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[25]  K. Misura,et al.  PROTEINS: Structure, Function, and Bioinformatics 59:15–29 (2005) Progress and Challenges in High-Resolution Refinement of Protein Structure Models , 2022 .

[26]  K. Ayappa,et al.  Dendrimer Interactions with Lipid Bilayer: Comparison of Force Field and Effect of Implicit vs Explicit Solvation. , 2018, Journal of chemical theory and computation.

[27]  R. Larson,et al.  Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: the effect of molecular shape. , 2008, The journal of physical chemistry. B.

[28]  B. Jin,et al.  Characterization of Lipid Membrane Dynamics by Simulation: 3. Probing Molecular Transport Across the Phospholipid Bilayer , 1996, Pharmaceutical Research.

[29]  Terry R. Stouch,et al.  Mechanism of Solute Diffusion through Lipid Bilayer Membranes by Molecular Dynamics Simulation , 1995 .

[30]  A. Laio,et al.  Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .

[31]  J. Mihály,et al.  A mechanistic view of lipid membrane disrupting effect of PAMAM dendrimers. , 2014, Colloids and surfaces. B, Biointerfaces.

[32]  Youyong Li,et al.  Computational simulation of drug delivery at molecular level. , 2010, Current medicinal chemistry.

[33]  H. Sone,et al.  Effects of PAMAM dendrimers with various surface functional groups and multiple generations on cytotoxicity and neuronal differentiation using human neural progenitor cells. , 2016, The Journal of toxicological sciences.

[34]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[35]  Helgi I. Ingólfsson,et al.  Martini Coarse-Grained Force Field: Extension to RNA. , 2015, Biophysical journal.

[36]  Andrej Sali,et al.  Fold assessment for comparative protein structure modeling , 2007, Protein science : a publication of the Protein Society.

[37]  Julianna Kardos,et al.  Sodium selective ion channel formation in living cell membranes by polyamidoamine dendrimer. , 2013, Biochimica et biophysica acta.

[38]  M. Pickholz,et al.  Coarse grained simulations of local anesthetics encapsulated into a liposome. , 2010, The journal of physical chemistry. B.

[39]  Qi Wang,et al.  Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes. , 2009, The Journal of chemical physics.

[40]  N. Dixit,et al.  Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer. , 2013, Journal of Chemical Physics.

[41]  R. Larson,et al.  Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer. , 2008, The journal of physical chemistry. B.

[42]  Michael W. Mahoney,et al.  A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions , 2000 .

[43]  F. Ritort,et al.  Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  K. Schulten,et al.  Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality , 2003 .

[45]  Lorenz C. Blum,et al.  970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. , 2009, Journal of the American Chemical Society.

[46]  P Mark,et al.  298KでのTIP3P,SPC及びSPC/E水モデルの構造及び動力学 , 2001 .

[47]  K. Dawson,et al.  The dendrimer impact on vesicles can be tuned based on the bilayer charge and the presence of albumin. , 2013, Soft matter.

[48]  J. A. Laszlo,et al.  Carboxyl-terminated PAMAM dendrimer interaction with 1-palmitoyl-2-oleoyl phosphocholine bilayers. , 2014, Biochimica et biophysica acta.

[49]  Jiahai Zhang,et al.  High-throughput screening of dendrimer-binding drugs. , 2010, Journal of the American Chemical Society.

[50]  Yi-Ping Phoebe Chen,et al.  Structure-based drug design to augment hit discovery. , 2011, Drug discovery today.

[51]  Stefano Piana,et al.  Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations , 2012, Proteins.

[52]  W. Goddard,et al.  PAMAM dendrimers undergo pH responsive conformational changes without swelling. , 2009, Journal of the American Chemical Society.

[53]  L. Nilsson,et al.  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .

[54]  Mai Mai,et al.  Steered Molecular Dynamics-A Promising Tool for Drug Design , 2012 .

[55]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[56]  R. Zhou Replica exchange molecular dynamics method for protein folding simulation. , 2007, Methods in molecular biology.

[57]  V. Vyas,et al.  Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives , 2012, Indian journal of pharmaceutical sciences.

[58]  T R Stouch,et al.  Solute diffusion in lipid bilayer membranes: an atomic level study by molecular dynamics simulation. , 1993, Biochemistry.

[59]  R. Larson,et al.  Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model. , 2006, The journal of physical chemistry. B.

[60]  Hwangseo Park,et al.  Discovery and biological evaluation of novel alpha-glucosidase inhibitors with in vivo antidiabetic effect. , 2008, Bioorganic & medicinal chemistry letters.

[61]  M. Prato,et al.  How do functionalized carbon nanotubes land on, bind to and pierce through model and plasma membranes. , 2013, Nanoscale.

[62]  D. Barreca,et al.  Effect of anionic and cationic polyamidoamine (PAMAM) dendrimers on a model lipid membrane. , 2016, Biochimica et biophysica acta.

[63]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[64]  F. Zerbetto,et al.  Molecular dynamics of a dendrimer-dye guest-host system. , 2003, Journal of the American Chemical Society.

[65]  D. Hazuda,et al.  Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase inhibitor for the treatment of HIV-AIDS infection. , 2008, Journal of medicinal chemistry.

[66]  M. Prato,et al.  Cellular uptake of functionalized carbon nanotubes is independent of functional group and cell type. , 2007, Nature nanotechnology.

[67]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[68]  N. Dixit,et al.  The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex. , 2015, Nanoscale.

[69]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[70]  Himanshu Joshi,et al.  Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes , 2017, Nucleic acids research.

[71]  Paul Robustelli,et al.  Water dispersion interactions strongly influence simulated structural properties of disordered protein states. , 2015, The journal of physical chemistry. B.

[72]  Jean-Louis Reymond,et al.  Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery , 2007, J. Chem. Inf. Model..

[73]  Subhash C Basak,et al.  Chemobioinformatics: the advancing frontier of computer-aided drug design in the post-genomic era. , 2012, Current computer-aided drug design.

[74]  Christopher R Williams,et al.  Surface interaction and behavior of poly(amidoamine) dendrimers: deformability and lipid bilayer disruption. , 2009, Journal of computational and theoretical nanoscience.

[75]  Rakwoo Chang,et al.  Free energy of PAMAM dendrimer adsorption onto model biological membranes. , 2014, The journal of physical chemistry. B.

[76]  J. Šponer,et al.  Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .

[77]  S. Pogodin,et al.  Surface patterning of carbon nanotubes can enhance their penetration through a phospholipid bilayer. , 2011, ACS nano.

[78]  Aatto Laaksonen,et al.  Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model. , 2014, Journal of chemical theory and computation.

[79]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[80]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[81]  Jing Chen,et al.  Pocket v.2: Further Developments on Receptor-Based Pharmacophore Modeling , 2006, J. Chem. Inf. Model..

[82]  Burkhard Rost,et al.  Evaluation of template‐based models in CASP8 with standard measures , 2009, Proteins.

[83]  C. Prestidge,et al.  PAMAM dendrimer interactions with supported lipid bilayers: a kinetic and mechanistic investigation. , 2008, Langmuir : the ACS journal of surfaces and colloids.

[84]  Richard J Gillams,et al.  On the ability of PAMAM dendrimers and dendrimer/DNA aggregates to penetrate POPC model biomembranes. , 2010, The journal of physical chemistry. B.

[85]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[86]  H. Urbassek,et al.  Accelerating Steered Molecular Dynamics: Toward Smaller Velocities in Forced Unfolding Simulations. , 2016, Journal of chemical theory and computation.

[87]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .