Chapter
In Silico Approaches for Drug Discovery and Development
2. COMPUTER AIDED DRUG DESIGN STRATEGIES
2.1. Ligand Based Drug Discovery
2.2. Structure Based Drug Discovery
3.1.1. Small Molecule Databases
3.1.2. Preparation of Ligand Libraries
3.1.3. Virtual Combinatorial libraries
3.1.4. Representation of Small Molecules
3.1.5. Molecular Descriptors/Features
3.2. Target Databases for Computer-Aided Drug Design
3.4. Quantitative Structure-Activity Relationship (QSAR)
3.4.1. Classical QSAR (1D/2D)
3.4.3. Multidimensional QSAR
3.6. Comparative Modeling
3.7. Binding Site Detection and Characterization
3.8. Protein – Ligand Docking
3.8.1. Molecular Docking Methods
3.8.2. Protein Flexibility in Docking
4. MOLECULAR DYNAMICS SIMULATIONS IN DRUG DISCOVERY AND DESIGN
4.2. Refinement of Homology Models
4.3. Combining Docking and MD Simulations
4.3.1. Receptor Conformation (Preparation of Receptor Structure)
4.3.2. Ensemble Generation
4.3.3. Refinement of Docked Complexes
4.4. Free Energy Calculations
5. ASSESSMENT OF ABSORPTION DISTRIBUTION METABOLISM EXCRETION AND TOXICITY PROPERTIES
5.1. Drug Attrition in the Drug Development Phase
5.2. Compound Library Filters
5.3. Drug Metabolism: Cytochrome P450
5.4. Prediction of Human Ether-A-Go-Go Related Gene Binding
6. PROTEIN – PROTEIN INTERACTIONS AS DRUG TRAGETS
6.1. Peptide and Peptidomimetics as ppi Inhibitors
Computational Chemistry Assisted Design and Screening of Ligand-Solvent Systems for Metal Ion Separation
2. COMPUTATIONAL METHODOLOGY
2.1. Moller-Plesset Perturbation Theory
2.2. Couple Cluster Method
2.3. Density Functional Theory (DFT)
2.4. Local Density Approximation
2.5. Generalized Gradient Approximation
2.6. Conductor Like Screening Model (COSMO)
2.7. Basis Set Superposition Error (BSSE)
2.8. Present Approach of Design and Evaluation
2.8.1. Evaluation of Structural Parameters
2.8.2. Evaluation of Interaction Parameters
2.8.3. Evaluation of Thermodynamic Parameters
2.8.4. Calculation of Separation Parameters
3. STRUCTURES AND STRCTURAL PARAMETERS
3.1. Microsolvation of Metal Ions
3.2. Coordination Number and Radial Distribution Function
3.3. Macrocyclic Crown Ethers
3.4. Cavity Size of the Host Crown Ethers
3.5. Tuned Extended Crown Ethers
3.9. Organophosphorus Ligands
3.10. Diglycolamide Ligands
3.11. Carbon Nanotube Functionalized Diglycolamic Acids
4. INTERACTION PARAMETERS -BINDING ENEGY
4.2. Conformer Dependence
4.3. Donor Atom Dependence
4.4. Binding Interaction towards Calix-Crown Ethers
4.5. Binding Interaction with Organophosphorous Ligands
4.6. Binding Interaction with Diglycolamide Ligands
4.7. Binding Interaction with CNT-DGA
5. THEMODYNAMIC PARAMETERS - ENTHALPY, ENTROPYAND FREE ENERGY
5.1. Free Energy of Extraction using Thermodynamical Cycle for Cs+
5.2. Free Energy of Extraction with TMDGA
5.3. Free Energy of Extraction using Thermodynamical Cycle with TMDGA
5.4. Free Energy of Extraction with CNT-DGA
5.5. Free Energy of Extraction using Thermodynamical Cycle
6. SEPARATION PARAMETERS -PARTITION COEFFICIENTS
6.1. Dual Mode of Extraction for Cs+ and Na+ Ions in Ionic Liquids
7. STRUCTURAL AND DYNAMICAL PROPERTIES AT LIQUID-LIQUID INTERFACE
7.1. Simulation Methodology
7.2. Hydration Structure of DB18C6/Li+ Complex in Water
7.3. Dynamic Behaviour of DB18C6/Li+ Complex in Water
7.4. Effect of Solvents on the Cation Shielding from Solvent and Relative Stabilities
7.5. Dynamics of Li+ and DB18C6 at Interface
Molecular Mechanisms of Cellular Transport, Resistance and Cytotoxic Side Effects of Platinum and Adjuvant Anti-cancer Drugs – A Molecular Orbital Study
1.1. Cytotoxic Side Effects
1.1.1. Factors that Determine Cytotoxic Side Effects
1.2. Resistance to Pt Drugs
1.3. Reversal of Resistance to Pt Drugs
1.4. Changes to Cell Membranes as a Basis for Reduced Accumulation of Pt in Resistant Cells
1.5. Combinatorial Chemotherapeutic Regimes
2. RESULTS AND DISCUSSION
2.1. Cytotoxic Side Effects
2.2. Resistance to Pt Drugs
2.3. Reversal of Resistance to Pt Drugs
2.4. Combinatorial Regimes and Adjuvant Drugs used with Pt Drugs
3. COMPUTATIONAL MOLECULAR ORBITAL METHODS
Elucidating Allosteric Communications in Proteins via Computational Methods
2. INDUCED FIT VS POPULATION SHIFT PARADIGMS
3. WHAT IS ALLOSTERICITY?
4. ELUCIDATING ALLOSTERICITY: COLLECTIVE MOTIONS VS. ENERGY TRANSPORT CHANNELS
4.2. Elastic Network Models
4.3. Equilibrium and Non-equilibrium Simulations
4.4. MC/MD Perturbation Methods
4.5. Integration of Graph Theory Techniques with Simulation Based Methods
4.6. Statistical Coupling Analysis
Information-Theoretic Representation of the Chemical Space of Many Electron Systems
2. INFORMATION-THEORETICAL MEASURES
3. INFORMATION-THEORETIC CHEMICAL SPACE FOR MANY ELECTRON SYSTEMS
4. CHEMICAL SPACE OF SELECTED BACTERIOSTATIC SULFONAMIDES
5. PREDOMINANT INFORMATION QUALITY SCHEME FOR THE ESSENTIAL AMINO ACIDS
Frontiers in Computational Chemistry, Volume 3
( Frontiers in Computational Chemistry )
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