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E-grāmata: Computational Pharmaceutics: Application of Molecular Modeling in Drug Delivery

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Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques  are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems.

The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems.

Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field.

This book is included in the Advances in Pharmaceutical Technology book series.
List of Contributors xi
Series Preface xiii
Preface xv
Editors' Biographies xvii
1 Introduction to Computational Pharmaceutics 1(6)
Defang Ouyang
Sean C. Smith
1.1 What Is Computational Pharmaceutics?
1(2)
1.2 Application of Computational Pharmaceutics
3(1)
1.3 Future Prospects
4(1)
References
4(3)
2 Crystal Energy Landscapes for Aiding Crystal Form Selection 7(24)
Sarah L. Price
2.1 Introduction
7(3)
2.2 CSP Methods for Generating Crystal Energy Landscapes
10(8)
2.2.1 Assessment of Flexibility Required in Molecular Model
11(2)
2.2.2 Search Method for Generating Putative Structures
13(1)
2.2.3 Methods for Computing Relative Crystal Energies
14(2)
2.2.4 Comparing Crystal Structures, and Idealised Types of Crystal Energy Landscapes
16(1)
2.2.5 Multicomponent Systems
17(1)
2.3 Examples of the Use of Crystal Energy Landscapes as a Complement to Solid Form Screening
18(6)
2.3.1 Is the Thermodynamically Stable Form Known?
18(2)
2.3.2 Supporting and Developing the Interpretation of Experiments
20(4)
2.4 Outlook
24(1)
Acknowledgements
25(1)
References
25(6)
3 Solubilization of Poorly Soluble Drugs: Cyclodextrin-Based Formulations 31(22)
Sachin S. Thakur
Harendra S. Parekh
Carl H. Schwable
Yong Gan
Defang Ouyang
3.1 Cyclodextrins in Pharmaceutical Formulations-Overview
31(4)
3.2 Drug-CD Complexes-Preparation Methods
35(1)
3.3 Physicochemical Principles Underlying Drug-CD Complexes
36(2)
3.3.1 Inclusion Drug-CD Complexes
36(1)
3.3.2 Non-inclusion Drug-CD Complexes
37(1)
3.4 Characterization of Drug-CD Complexes
38(3)
3.4.1 Thermo-Analytical Methods
38(1)
3.4.2 Microscopic Methods
39(1)
3.4.3 Wettability/Solubility Studies
39(1)
3.4.4 Chromatographic Methods
39(1)
3.4.5 Spectroscopic Methods
40(1)
3.4.6 X-Ray Techniques
40(1)
3.4.7 Other Techniques
41(1)
3.5 Theoretical Progress of CD Studies
41(3)
3.5.1 Quantum Mechanics
41(1)
3.5.2 Molecular Dynamics Simulation
42(1)
3.5.3 Monte Carlo Simulation
43(1)
3.5.4 Docking Studies
43(1)
3.5.5 Quantitative Structure-Activity Relationship
44(1)
3.6 Future Prospects of Cyclodextrin Formulation
44(1)
References
44(9)
4 Molecular Modeling of Block Copolymer Self-Assembly and Micellar Drug Delivery 53(28)
Myungshim Kang
Dennis Lam
Dennis E. Discher
Sharon M. Loverde
4.1 Introduction
53(5)
4.2 Simulation Methods
58(5)
4.2.1 All-Atom Models
58(1)
4.2.2 Coarse-Grained Models
58(2)
4.2.3 Mesoscale Methods: BD and DPD
60(1)
4.2.4 Free Energy Methods
61(2)
4.3 Simulations of Micellar Drug Delivery
63(5)
4.3.1 Characterization of PCL Micelles with Simulation
63(2)
4.3.2 Advantages of Worm-Like Micelles, Breakup of Micelles
65(3)
4.4 Taxol
68(6)
4.4.1 Taxol Behavior in Membranes
71(1)
4.4.2 Ligand-Protein Binding
72(1)
4.4.3 Taxol-Tubulin Binding
72(2)
4.5 Summary and Conclusions
74(1)
References
74(7)
5 Solid Dispersion-a Pragmatic Method to Improve the Bioavailability of Poorly Soluble Drugs 81(20)
Peng Ke
Sheng Qi
Gabriele Sadowski
Defang Ouyang
5.1 Introduction of Solid Dispersion
81(2)
5.2 Preparation Methods for Solid Dispersions
83(2)
5.2.1 Melting Method
83(1)
5.2.2 Solvent Method
84(1)
5.2.3 Ball Milling
85(1)
5.3 Thermodynamics of Solid Dispersions
85(4)
5.4 Molecular Structure of Amorphous Solid Dispersions
89(2)
5.5 Physical Stability of Solid Dispersions
91(6)
5.5.1 Detection of Physical Instability of Amorphous Solid Dispersions
91(1)
5.5.2 Glass Transition Temperature
92(1)
5.5.3 Molecular Mobility and Structural Relaxation of Amorphous Drugs
93(1)
5.5.4 Interactions between Drug and Polymer in Solid Dispersions
94(1)
5.5.5 Characterization Phase Separation in Amorphous Solid Dispersion
95(2)
5.6 Future Prospects
97(1)
References
97(4)
6 Computer Simulations of Lipid Membranes and Liposomes for Drug Delivery 101(22)
David William O'Neill
Sang Young Noh
Rebecca Notman
6.1 Introduction
101(1)
6.2 Methodological Considerations
102(3)
6.2.1 Representations of Model Lipids
102(1)
6.2.2 Measurable Properties
103(2)
6.3 Model Membranes
105(3)
6.3.1 Phospholipid Bilayers
105(1)
6.3.2 Liposomes
105(1)
6.3.3 Skin-Lipid Membranes for Transdermal Drug Delivery
106(2)
6.4 Small Molecule Uptake and Permeation across Membranes
108(3)
6.5 Nanoparticle-Membrane Interactions
111(3)
6.6 Mechanisms of Action of Chemical Penetration Enhancers
114(2)
6.7 Future Challenges
116(1)
Acknowledgements
116(1)
References
116(7)
7 Molecular Modeling for Protein Aggregation and Formulation 123(26)
Dorota Roberts
Jim Warwicker
Robin Curtis
7.1 Introduction
123(4)
7.2 Protein Aggregation Pathways in Liquid Formulations
127(2)
7.2.1 Multiple Pathways Can Lead to Protein Aggregation
127(1)
7.2.2 Overview of Cosolvent Effects on Protein-Protein Interactions
128(1)
7.3 Protein-Cosolvent Interactions
129(4)
7.3.1 Lyotropic Series and Hofmeister Series Classifications of Ions
129(1)
7.3.2 Modeling and Simulation of Ion-Interface Interactions
129(1)
7.3.3 Ion Interactions with Protein Charged Groups
130(2)
7.3.4 Protein Interactions with Other Excipients
132(1)
7.4 Protein-Protein Interactions
133(3)
7.4.1 The Osmotic Second Virial Coefficient and DLVO Theory
133(1)
7.4.2 Incorporating Specific Salt and Ion Effects
134(1)
7.4.3 Inclusion of Nonionic Excipients
135(1)
7.4.4 Models Accounting for Anisotropic Protein-Protein Electrostatic Interactions
135(1)
7.5 Informatics Studies of Protein Aggregation
136(4)
7.5.1 Comparison with Modeling Used for Small Molecule Pharmaceutics
136(1)
7.5.2 Prediction Schemes Deriving from Amyloid Deposition
137(1)
7.5.3 Solubility Prediction Based on Sequence, Structural, and Surface Properties
137(3)
7.6 Future Prospects
140(1)
References
141(8)
8 Computational Simulation of Inorganic Nanoparticle Drug Delivery Systems at the Molecular Level 149(20)
Xiaotian Sun
Zhiwei Feng
Tingjun Hou
Youyong Li
8.1 Introduction
149(3)
8.2 Materials and Methods
152(12)
8.2.1 Prepared Structures
152(1)
8.2.2 MD Simulations
152(1)
8.2.3 Computational Simulation of Drug Delivery Strategies with CNTs
153(2)
8.2.4 Computational Simulation of Drug Delivery Strategies with Graphene/GO
155(3)
8.2.5 Computational Simulation of Drug Delivery Strategies with Silicon Nanomaterials
158(4)
8.2.6 Computational Simulation of Drug Delivery Strategies with Au Nanomaterials
162(2)
8.3 Summary
164(1)
Acknowledgements
165(1)
References
165(4)
9 Molecular and Analytical Modeling of Nanodiamond for Drug Delivery Applications 169(28)
Lin Lai
Amanda S. Barnard
9.1 Introduction
169(1)
9.2 Structure of Individual NDs
170(2)
9.3 Surface Chemistry and Interactions
172(15)
9.3.1 Surface Passivation and Environmental Stability
173(5)
9.3.2 Surface Functionalization
178(2)
9.3.3 Consequences for Interactions and Self-Assembly
180(7)
9.4 NDs as a Therapeutic Platform
187(2)
9.4.1 Simulations with Doxorubicin
187(1)
9.4.2 Experimental Progress
187(2)
9.5 Outlook
189(2)
References
191(6)
10 Molecular Modeling of Layered Double Hydroxide Nanoparticles for Drug Delivery 197(20)
Vinuthaa Murthy
Zhi Ping Xu
Sean C. Smith
10.1 Introduction
197(1)
10.2 Basic Structure of LDH
198(1)
10.3 Synthesis of LDH
199(1)
10.4 Molecular Modeling Methodology
200(14)
10.4.1 Intercalation of Oxymetal Anions into LDH
200(7)
10.4.2 Intercalation of Organic Anions into LDH
207(2)
10.4.3 Intercalation of siRNA into LDH
209(3)
10.4.4 Intercalation of DNA into Layered Double Hydroxides
212(2)
10.5 Conclusions
214(1)
References
214(3)
11 Molecular Modeling as a Tool to Understand the Role of Poly(Ethylene) Glycol in Drug Delivery 217(18)
Alex Bunker
11.1 PEGylation in Drug Delivery
217(3)
11.2 A Brief History of the Computational Modeling of PEG
220(1)
11.3 Molecular Modeling Applied to the Role PEG Plays in Drug Delivery
221(3)
11.4 Future Directions
224(1)
References
225(10)
12 3D Structural Investigation of Solid Dosage Forms 235(28)
Xianzhen Yin
Li Wu
You He
Zhen Guo
Xiaohong Ren
Qun Shao
Jingkai Gu
Tiqiao Xiao
Peter York
Jiwen Zhang
12.1 Structural Architectures of Solid Dosage Forms and Methods of Investigation-an Overview
235(4)
12.2 Synchrotron Radiation X-Ray Computed Microtomography
239(1)
12.3 Principles and Procedures for SR-IICT Studies
239(6)
12.3.1 Preparation of Samples
239(3)
12.3.2 Image Acquisition and 3D Reconstruction
242(2)
12.3.3 Model Construction and Analysis
244(1)
12.4 3D Visualization and Quantitative Characterization
245(13)
12.4.1 Internal Structure of Particles
246(1)
12.4.2 Dynamic Structure of Granular Systems
246(1)
12.4.3 Microstructure of Monolith Osmotic Pump Tablets
247(4)
12.4.4 Fractal Structure of Monolith Osmotic Pump Tablets
251(1)
12.4.5 Dynamic Structure of HPMC Matrix
252(3)
12.4.6 Release Behavior of Single Pellets
255(3)
12.5 Future Prospects
258(1)
References
259(4)
13 Physiologically Based Pharmacokinetic Modelling in Drug Delivery 263(30)
Raj K. Singh Badhan
13.1 Introduction
263(1)
13.2 Modelling and Simulation Process
264(1)
13.3 Pharmacokinetic Principles
264(3)
13.3.1 Drug Absorption
264(2)
13.3.2 Drug Distribution
266(1)
13.3.3 Drug Metabolism and Elimination
266(1)
13.4 Pharmacokinetic Modelling Approaches
267(3)
13.4.1 Empirical (Classical Compartmental) Modelling
267(1)
13.4.2 Noncompartmental Analysis
268(1)
13.4.3 Mechanistic (Physiological) Modelling
268(2)
13.5 Pharmacokinetic Software for Modelling
270(1)
13.6 Developing a PBPK Model for an Orally Dosed Compound
270(10)
13.6.1 Conceptualisation of a PBPK Model Structure
270(1)
13.6.2 Parameterising the Model with Model Descriptors: Systems Data
271(1)
13.6.3 Parameterising the Model with Model Descriptors: Compound-Specific Data
272(1)
13.6.4 Orally Dosed Formulations
273(1)
13.6.5 Modelling Drug Dissolution
273(2)
13.6.6 Modelling Drug Permeability
275(2)
13.6.7 Modelling Drug Metabolism
277(1)
13.6.8 Modelling Renal Clearance
278(1)
13.6.9 Modelling Drug-Tissue Partitioning
278(2)
13.7 Developing the Model
280(6)
13.7.1 Physiological Considerations
281(2)
13.7.2 Constructing the Small Intestine PBPK Model
283(3)
13.8 Summary
286(1)
References
286(7)
Index 293
Dr Defang Ouyang is at the Institute of Medical Sciences, University of Macau in China as well as Aston University, UK. He has a multi-disciplinary and unique background and expertise in both drug delivery and molecular modeling. He completed his PhD at The University of Queensland, Australia in 2010. Since joining Aston, he has pioneered the application of molecular modeling techniques in the field of drug delivery - "computational pharmaceutics", including cyclodextrin-drug complexes, solid dispersions, non-viral gene delivery systems and liposome formulations. So far, he has authored over 20 refereed publications, consisting of an invited book, a book chapter, invited reviews, journal articles, conference papers and patents.

Professor Sean C. Smith is at the School of Chemical Engineering, University of New South Wales, Australia. He was previously Director of the Center for Nanophase Materials Sciences at Oak Ridge National Laboratory, USA. He is firmly established internationally as a significant figure in the field of theoretical and computational chemistry. His contributions include theoretical studies of chemical reactions, material sciences, nano science and biological sciences. His publications include one book, three invited chapters, three invited reviews, and 203 refereed journal articles.
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