Molecular Conceptor - Table of Contents

Structural Bioinformatics Last updated on September 2012

A - DRUG DISCOVERY 1. Introduction to Drug Discovery 2. Principles of Rational Drug Design B - PROTEIN STRUCTURE AND MODELING 1. Structural Bioinformatics (in progress) 2. Protein Structure 3. Molecular Dynamics C - STRUCTURE-BASED DESIGN 1. Introduction to Protein-Ligand Binding 2. Principles of Structure-Based Design 3. Molecular Docking: Principles and Methods 4. Case Studies in Structure-Based Design 5. Case Studies of Docking in Drug Discovery 6. Analyses of Protein-Ligand Complexes D - MOLECULAR BASIS OF DRUGS 1. Molecular Geometry 2. Molecular Properties 3. Stereochemistry 4. Molecular Energies 5. Conformational Analysis 6. Molecular Graphics 7. Selected Examples in 3D Analysis E - GENERAL TOPICS 1. General Introduction to Drugs

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2. Drug Discovery 3. Drug Development

A. DRUG DISCOVERY
A1. INTRODUCTION TO DRUG DISCOVERY

A1.1 From the Origin of Medicines to Today

A1.1.1 Attempts to Cure Diseases in Antiquity A1.1.2 Medicines Used in Ancient Civilizations A1.1.3 5th-4th BC Centuries: The Greek Period A1.1.4 2nd Century: The Roman Period A1.1.5 13th Century: The Arab School A1.1.6 13th Century: First Apothecary Shops A1.1.7 16th Century: Pharmaceutical Science A1.1.8 16th Century: Maritime Routes to India and America A1.1.9 18th Century: First Vaccine A1.1.10 19th Century: Drug Administration A1.1.11 19th Century: Isolation of Compounds A1.1.12 19th Century: Relief of Pain in Surgical Operations A1.1.13 19th Century: New Classes of Drugs A1.1.14 20th Century: Pioneer Work of Paul Ehrlich A1.1.15 20th Century: Sulfonamide Antibacterial Dyes A1.1.16 20th Century: Recognition of Vitamins A1.1.17 20th Century: The Antibiotic Era A1.1.18 20th Century: Pfizer Management Decision A1.1.19 20th Century: Large Scale Production of Penicillin A1.1.20 20th Century: Antibacterial Agents Isolated from Plants A1.1.21 20th Century: Discovery of Adrenal Cortex Hormones A1.1.22 20th Century: NSAIDs A1.1.23 20th Century: Key Transition Discoveries A1.1.24 20th Century: Some Drug Discovery Projects A1.1.25 Example-1 of Project: Factor Xa A1.1.26 Example-2 of Project: Motilin Antagonists A1.1.27 Example-3 of Project: COX-2 Inhibitors A1.1.28 Example-4 of Project: Rotamase Inhibitors A1.1.29 20th Century: From Apothecaries to Factories

A1.2 Revolutions that Changed Drug Discovery

A1.2.1 Major Achievements

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A1.2.2 Understanding Drug-Receptor Recognition A1.2.3 Consolidation of Concept of Biological Targets A1.2.4 Recombinant Technologies and Cloning of Genes A1.2.5 Deciphering the Sequences of Genomes A1.2.6 Determination of Proteins 3D Architectures A1.2.7 Automated Methods in Synthetic Chemistry A1.2.8 HTS Screening A1.2.9 Automation in Drug Discovery A1.2.10 In-Silico Modeling becomes Mature

A1.3 In-Silico Technologies

A1.3.1 The Explosion of In-Silico Technologies A1.3.2 Encoding Molecules: 2D and 3D Databases A1.3.3 Development of Molecule Encoding A1.3.4 3D Searching is not Trivial A1.3.5 Encoding Molecular Properties A1.3.6 Development of Models for Data Analysis A1.3.7 Molecular Modeling A1.3.8 Development of Computer Graphics A1.3.9 Development of Models for Data Visualization A1.3.10 In-Silico Molecular Mechanics A1.3.11 In-Silico Molecular Dynamics A1.3.12 In-Silico Docking A1.3.13 In-Silico Virtual Screening A1.3.14 3D Searching and Bioisosterism A1.3.15 Pharmacophore Elucidation and Mapping A1.3.16 Structure-Activity Relationships - SAR A1.3.17 Chemometrics A1.3.18 Development of QSAR A1.3.19 3D-QSAR A1.3.20 In-Silico Library Design A1.3.21 In-Silico Homology Modeling A1.3.22 In-Silico Free Energy Simulations A1.3.23 Cheminformatics A1.3.24 Structural Bioinformatics A1.3.25 Reaction Searching A1.3.26 Computer-Assisted Structure Elucidation A1.3.27 In-Silico Prediction of ADME/Tox Properties A1.3.28 Quantum Chemical Calculations

A1.4 The Drug Discovery Process

A1.4.1 Outline of Drug Discovery A1.4.2 Starting Idea in a Project A1.4.3 Importance of Assay Validation A1.4.4 The Drug Discovery Process

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A1.4.5 Starting Molecule in a Project A1.4.6 Optimization of the Lead A1.4.7 Potency and Selectivity A1.4.8 Beyond Potency and Selectivity in Lead Optimization A1.4.9 Drugability A1.4.10 Resistance A1.4.11 Pharmacodynamics A1.4.12 Drug Delivery A1.4.13 Metabolism A1.4.14 Bioavailability A1.4.15 Toxicity A1.4.16 Patentability A1.4.17 Protection of Drug Discovery Achievements A1.4.18 Lifetime and Effective Lifetime of a Patent A1.4.19 Assessing Patentability: The Viagra-Levitra Example A1.4.20 Drug Discovery before and after 1980 A1.4.21 Intelligent Management Strategy

A1.5 Rational Drug Design Strategy

A1.5.1 Two Major Approaches A1.5.2 Underlying Principles A1.5.3 Contribution of Molecular Modeling A1.5.4 The Molecular Similarity Principle A1.5.5 The Molecular Complementarity A1.5.6 The Concept of 2D and 3D Pharmacophores A1.5.7 Structure-Based Drug Discovery: The Aliskiren Example A1.5.8 Therapeutic Risk in a Project

A1.6 The Major Players in Drug Research

A1.6.1 Role of Each Scientist A1.6.2 Organic Chemist A1.6.3 Prepare new Molecules A1.6.4 Analyze SAR Data A1.6.5 Order new Molecules and Libraries A1.6.6 Design of a Library of Molecules A1.6.7 Scale Up a Chemical Synthesis A1.6.8 Biologist A1.6.9 Develop Biological Assays A1.6.10 Develop in-vivo Models for Testing new Molecules A1.6.11 Test New Molecules A1.6.12 Compare Results Obtained by Other Groups A1.6.13 Develop Models for Early Assessment of Toxicity A1.6.14 Implement Platform for High Throughput Screening A1.6.15 Molecular Modeler A1.6.16 Provide Structural Models of Good Quality

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A1.6.17 Analyze and Suggest Candidate Molecules A1.6.18 Assess Molecules Submitted the Team A1.6.19 Explore Ways for 3D Alignment of Molecules A1.6.20 Biotechnologist A1.6.21 Cloning DNA Sequences A1.6.22 Isolation of Enzyme A1.6.23 Identify Disease-Relevant Target A1.6.24 Validate a New Assay A1.6.25 Computational Chemist A1.6.26 Search for a Predictive 3D-QSAR Model A1.6.27 Launch High Throughput Docking Simulations A1.6.28 Estimate the Binding Energies of New Molecules A1.6.29 Assess the Quality of QSAR Models A1.6.30 Structural Bioinformatician A1.6.31 Encoding and Visualizing Biomolecules A1.6.32 Understand Protein Flexibility A1.6.33 Create 3D Models of new Proteins A1.6.34 Decode the Function of a Protein from its 3D Structure A1.6.35 Reveal Key Residues in a Protein A1.6.36 Cheminformatician A1.6.37 Calculate Molecular Properties A1.6.38 Find Similar Molecules A1.6.39 Analyze HTS Results A1.6.40 Contribute to Virtual Screening and Library Design A1.6.41 Update and Maintain Databases A1.6.42 Biophysicist A1.6.43 X-Ray Crystallographer A1.6.44 Prepare Crystals of a Protein or a Complex A1.6.45 Diffraction Pattern and Density Map A1.6.46 Fit the Electron Density Map A1.6.47 Refine the 3D Atomic Model A1.6.48 NMR Spectroscopist

A1.7 Chemistry in Drug Discovery

A1.7.1 Chemistry in Drug Discovery A1.7.2 Synthesis of Complicated Molecules A1.7.3 Three Methods in Synthetic Chemistry A1.7.4 Classical Drug Discovery A1.7.5 Parallel Drug Discovery A1.7.6 Combinatorial Drug Discovery A1.7.7 Chemistry in Lead Discovery A1.7.8 Protein Kinase Example A1.7.9 Lead Optimization A1.7.10 Example: Optimization of the Gleevec Series A1.7.11 Chemistry in Drug Development

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A1.8 The Present and Future Face of Drug Discovery

A1.8.1 Outsourcing: an Important Cultural Shift A1.8.2 Why Outsourcing Develops so Well? A1.8.3 Management Response to Challenging Situations A1.8.4 Management Challenges A1.8.5 Mergers and Mega-Mergers A1.8.6 Drug Discovery and Mergers A1.8.7 Massive Cut of Jobs Following Mergers A1.8.8 Headcount are not always Reduced A1.8.9 Creation and Development of Startup Companies A1.8.10 Startup Example-1: Amgen A1.8.11 Startup Example-2: Actelion A1.8.12 Startup Example-3: Speedel A1.8.13 Increasing Importance of Generics A1.8.14 Economical Implications of Generics A1.8.15 Emergence of New Industrial Players A1.8.16 Pharmaceutical Industry in India and China A1.8.17 Personalized Medicines A1.8.18 Pharmacogenomics Example A1.8.19 Stem Cell Therapy A1.8.20 Some Facts and Figures A1.8.21 The Cost of Developing a New Drug A1.8.22 The R&D Process A1.8.23 Innovation of Drug Discovery (1997-2007) A1.8.24 Improvements in Life Expectancy A1.8.25 Drug Discovery in the Industry A1.8.26 Success of Drug Discovery (in 2008) A1.8.27 60 Years of Drug Discovery Achievements A1.8.28 Concluding Remarks

A2. PRINCIPLES OF RATIONAL DRUG DESIGN

A2.1 Rational Drug Design

A2.1.1 Drug Design Basis: Molecular Recognition A2.1.2 Lock-and-Key Model A2.1.3 Induced-Fit Model A2.1.4 Rational Drug Design A2.1.5 Rational Drug Design Process A2.1.6 Receptor-Based Drug Design A2.1.7 Pharmacophore-Based Drug Design

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A2.2 Pharmacophore-Based Design

A2.2.1 Pharmacophore-Based Drug Design Approach A2.2.2 Similarity Concepts and Molecular Mimicry A2.2.3 Examples of Molecular Mimicry A2.2.4 ATP A2.2.5 Dopamine A2.2.6 Histamine A2.2.7 Estradiol A2.2.8 Peptidomimetics A2.2.9 Strengths of Pharmacophore-Based Drug Design

A2.3 Receptor-Based Design

A2.3.1 Design by Direct Interaction with Receptor Sites A2.3.2 Exploiting the Receptor Recognition Concepts A2.3.3 Initial Data in Receptor-Based Drug Design A2.3.4 Strengths of Receptor Based Drug Design

A2.4 Integration in a Global Perspective

A2.4.1 Typical Projects A2.4.2 Exploit the Two Methods, Independently A2.4.3 Synergy Between the Two Approaches A2.4.4 Example of Synergy Between the Two Approaches A2.4.5 Good Binding Models, the Synergy Condition A2.4.6 Ideal Situation A2.4.7 Example 1 A2.4.8 Example 2 A2.4.9 Integration in a Global Perspective A2.4.10 Pharmacophore-Based Drug Design A2.4.11 Receptor-Based Drug Design A2.4.12 Integrated Global Approach

A2.5 Challenge of the Genomics Era

A2.5.1 The Genomic Era A2.5.2 A New Challenge in Drug Design

A2.6 Typical Projects

A2.6.1 Typical Pharmacophore-Based Project A2.6.2 Design Based on 3D Mimicry A2.6.3 Typical Receptor-Based Project A2.6.4 Design Based in Making Favorable 3D Interactions A2.6.5 Typical Genomic Project

A2.7 Perspectives

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A2.7.1 Drug Discovery of the 1970's A2.7.2 Drug Discovery of the 1980's A2.7.3 Drug Discovery of the 1990's A2.7.4 The Present Situation A2.7.5 Initial Skepticism Towards Rational Drug Design A2.7.6 Success Stories in Rational Drug Design A2.7.7 Future Perspectives

A2.8 CHAPTER QUIZZES (Available only in Academic License)

B. PROTEIN STRUCTURE AND MODELING

B1. STRUCTURAL BIOINFORMATICS

B1.1 Introduction to Structural Bioinformatics

B1.1.1 Challenges in the Post Genomic Era B1.1.2 The Informational Chaos B1.1.3 Integration through Computational Science B1.1.4 Structural Bioinformatics B1.1.5 Grouping Fields into One Discipline B1.1.6 3D Basis of Structural Bioinformatics B1.1.7 The Structural Genomics Effort B1.1.8 The Protein Structure Initiative B1.1.9 Strategy of the Protein Structure Initiative B1.1.10 The Structural Genomics Consortium B1.1.11 Global Planning of Structural Genomics B1.1.12 The Impact of Structural Genomics B1.1.13 The Relationship between Structure and Function B1.1.14 Example of a Structure-Function Relationship B1.1.15 Learning from Evolution B1.1.16 Learning from Structural Folds B1.1.17 Learning from Molecular Shape B1.1.18 Example of Knowledge Derived from 3D Structure B1.1.19 Is Structure Sufficient to Predict Function? B1.1.20 Exploiting Knowledge to Design New Drugs B1.1.21 Bridge between Genomics and Drug Discovery B1.1.22 Tools Developed by Structural Bioinformatics

B1.2 Architecture of Biomolecules

B1.2.1 Biomolecules in the Cell B1.2.2 DNA/RNA Structure

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B1.2.3 DNA is the Genetic Material B1.2.4 DNA Variability B1.2.5 Importance of the DNA 3D Structure B1.2.6 The Building Blocks B1.2.7 Base B1.2.8 Sugar B1.2.9 Phosphate B1.2.10 Putting the Building Blocks Together B1.2.11 Nomenclature of Nucleotides and Nucleosides B1.2.12 Nucleotides of Nucleic Acids B1.2.13 The Double Helix Structure B1.2.14 DNA Helices are Antiparallel B1.2.15 Hydrogen Bonding Pattern B1.2.16 Aromatic Base Stacking B1.2.17 Major and Minor Grooves B1.2.18 DNA forms B1.2.19 G-Quadruplex Conformation B1.2.20 DNA versus RNA B1.2.21 3D Folds of RNA B1.2.22 Protein Structure B1.2.23 Proteins are Fundamental to Life B1.2.24 Structural Diversity of Proteins B1.2.25 Importance of Protein 3D Structures B1.2.26 Chemical Nature of Proteins B1.2.27 Challenges in Understanding Protein Structure B1.2.28 Protein Structure Complexity B1.2.29 The Four Levels of Protein Architecture B1.2.30 Primary Structure B1.2.31 Secondary Structure B1.2.32 Tertiary Structure B1.2.33 Quaternary Structure

B1.3 Biomolecular Properties

B1.3.1 Protein Flexibility and Motion B1.3.2 Importance of Dynamic Motions in Biological Processes B1.3.3 Example of Function: ATP Synthase B1.3.4 Example of Function: DNA Biosynthesis B1.3.5 Example of Function: Molecular Switch B1.3.6 Example of Induced-Fit: RNA-Protein Recognition B1.3.7 Example of Induced-Fit: Ubiquitous Proteins B1.3.8 Types of Molecular Motions B1.3.9 Time Scale of Protein Motion B1.3.10 Methods to Study Protein Motions B1.3.11 Experimental Techniques to Study Protein Motions B1.3.12 Simulation Methods to Study Protein Motions B1.3.13 Normal Mode Analyses (NMA)

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B1.3.14 Molecular Dynamics vs Normal Mode Analyses B1.3.15 Database of Macromolecular Movements

B1.4 Assembly of Biomolecules

B1.4.1 Biological Molecule Association B1.4.2 Molecular Recognition B1.4.3 The Recognition Process B1.4.4 Complementary Features Upon Binding B1.4.5 Role of Native Protein Configuration B1.4.6 Tolerance Upon Binding B1.4.7 The "Induced-Fit" Theory B1.4.8 Example of Enzyme Adaptation to Inhibitor Binding B1.4.9 Example of Ligand Adaptation upon Binding B1.4.10 Maximizing Surface Contacts B1.4.11 Motions Associated to Induced-Fit B1.4.12 Experimental Evidence of the Induced-Fit Model B1.4.13 Large Rearrangements B1.4.14 Role of Large Rearrangements B1.4.15 The Domino Effect B1.4.16 Proteins Described as Ensemble of Conformations B1.4.17 Energy Landscape of a Protein B1.4.18 Conformational Selection Operated by a Ligand B1.4.19 Energetic Induction Upon Binding B1.4.20 Forces Involved in Molecular Recognition B1.4.21 Van der Waals Forces B1.4.22 Electrostatic Interactions B1.4.23 Hydrogen Bonds B1.4.24 Solvent Effect B1.4.25 The Role of the Solvent B1.4.26 The Hydrophobic Effect B1.4.27 The Entropic Effects B1.4.28 Enthalpy-Entropy Compensation B1.4.29 Assessing Binding Interactions B1.4.30 Free Energy of Binding B1.4.31 Importance of Free Energy of Binding B1.4.32 Experimental Measures of Binding Affinities B1.4.33 Titration Curve to Measure Kd B1.4.34 Scatchard-Rosenthal Plots B1.4.35 Conversion of Kd into Energies B1.4.36 Theoretical Prediction of Binding Energies B1.4.37 Solving the Schrodinger Equation B1.4.38 Molecular Mechanics B1.4.39 Force-Field B1.4.40 Example of Force-Fields B1.4.41 Other Methods B1.4.42 Incorporation of the Solvent

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B1.5 Obtaining Macromolecular 3D-Structures

B1.5.1 Experimental Methods B1.5.2 X-ray Crystallography B1.5.3 Protein Production and Purification B1.5.4 Growing of Single Crystal B1.5.5 The Single Crystal B1.5.6 Collecting the Diffraction Data B1.5.7 Recovering the Phase Angle B1.5.8 Structure Determination and Refinement B1.5.9 Atomic Coordinates B1.5.10 The Advantages of X-ray Crystallography B1.5.11 The Limitations of X-ray Crystallography B1.5.12 NMR Spectroscopy B1.5.13 NMR Concepts B1.5.14 Spin-Spin Coupling B1.5.15 Data Collection B1.5.16 Structure Determination B1.5.17 Analysis B1.5.18 The Advantages of NMR B1.5.19 The Limitations of NMR B1.5.20 Electron Microscopy B1.5.21 Basic Concept B1.5.22 The Advantages of Electron Microscopy B1.5.23 The Limitations of Electron Microscopy

B2. PROTEIN STRUCTURE

B2.1 Structural and Functional Diversity of Proteins

B2.1.1 Proteins are Fundamental to Life B2.1.2 Great Diversity of Protein Biological Functions B2.1.3 Chemical Nature of Proteins B2.1.4 Structural Diversity of Proteins

B2.2 Link between Protein Sequence, Folding and Function

B2.2.1 Importance of Protein 3D Structures B2.2.2 Protein Folding B2.2.3 Anfinsen's Dogma B2.2.4 Anfinsen's Dogma and Levinthal's Paradox B2.2.5 The Pathway Theory and Energy Funnels B2.2.6 Mechanisms of Protein Folding

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B2.2.7 The Protein Misfolding Problem B2.2.8 Challenge in Understanding Protein Structure

B2.3 Amino Acids: Building Blocks of Proteins

B2.3.1 Amino acids: Building Blocks of Proteins B2.3.2 -Amino Acids B2.3.3 -Amino Acid Stereoisomers B2.3.4 Diversity of the Properties of Amino Acids B2.3.5 Amino Acids Properties B2.3.6 Classification of Amino Acids Properties B2.3.7 Non-Standard Amino Acids

B2.4 From Amino Acids to Proteins

B2.4.1 Amino Acids are Linked by Peptide Bonds B2.4.2 Peptide Biosynthesis B2.4.3 Polymer Amino-Acids B2.4.4 Length of Proteins B2.4.5 More than One Polypeptide Chain B2.4.6 Conjugated Proteins B2.4.7 Examples of Conjugated Proteins B2.4.8 Cross-Linked Polypeptide Chains

B2.5 Geometry of Proteins and Peptides

B2.5.1 Peptide Bonds are Planar B2.5.2 Why the Peptide Bond is Planar? B2.5.3 Cis and Trans Isomers of the Peptide Bond B2.5.4 Trans Isomer Favored B2.5.5 Isomers of Proline B2.5.6 Peptide Torsion Angles B2.5.7 Conformational Freedom B2.5.8 Conformational Complexity of Polypeptide Chains B2.5.9 Not All / Torsion Angles are Possible B2.5.10 The Ramachandran Plot B2.5.11 and Distribution B2.5.12 Interactive Ramachandran Plot B2.5.13 Torsion Angles Observed in Proteins B2.5.14 Glycine Residue Torsion Angles B2.5.15 Side Chain Conformations B2.5.16 Side Chain Atomic and 3D Nomenclature B2.5.17 Side Chain Conformations B2.5.18 Non-Rotameric Side Chain Conformations

B2.6 Protein Structure Overview

B2.6.1 Protein Structure Complexity B2.6.2 The Four Levels of Protein Architecture

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B2.6.3 Primary Structure B2.6.4 Secondary Structure B2.6.5 Tertiary Structure B2.6.6 Quaternary Structure B2.6.7 Forces Involved in Protein Stability B2.6.8 Proteins are not Static B2.6.9 Representing Protein Structures B2.6.10 Wireframe Representation B2.6.11 Ball and Stick Representation B2.6.12 C Trace Representation B2.6.13 Ribbon Representation B2.6.14 Cartoon Representation B2.6.15 Space Filling - CPK Representation B2.6.16 Surface Representation

B2.7 Primary Structure

B2.7.1 Primary Structure B2.7.2 Unique Primary Structure for Each Protein B2.7.3 Primary Sequence and Protein Properties

B2.8 Secondary Structure

B2.8.1 Secondary Structure B2.8.2 Periodic and Non Periodic Secondary Structure Elements B2.8.3 Hydrogen Bonds in Secondary Structure Elements B2.8.4 The -Helix B2.8.5 Packing of the -Helix B2.8.6 and Torsion Angles of the -Helix B2.8.7 Two Enantiomeric -Helices B2.8.8 Geometry Described with Pitch and Rise B2.8.9 Helix Macro-Dipole B2.8.10 Amphipathic Character of the Helix B2.8.11 3(10)-Helix and -Helix B2.8.12 Helices Geometrical Parameters B2.8.13 Occurrence of Helices in Proteins B2.8.14 The -Sheet B2.8.15 The -Strand Unit B2.8.16 and Torsion Angles in -Sheets B2.8.17 Stability of the -Sheet B2.8.18 Parallel and Anti-Parallel -Sheets B2.8.19 Occurrence of -Sheets in Proteins B2.8.20 Twist of the -sheet B2.8.21 Turns B2.8.22 -Turns B2.8.23 and Torsion Angles of Turns B2.8.24 Non-Regular Coil and Loops

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B2.8.25 Coil B2.8.26 Loops

B2.9 Super-Secondary Structure (Motifs)

B2.9.1 Super-Secondary Structures and Motifs B2.9.2 Classification of Super-Secondary Structures B2.9.3 All super-secondary structures B2.9.4 -Hairpin B2.9.5 -Meander B2.9.6 Greek-Key B2.9.7 All Super-Secondary Structures B2.9.8 -Hairpin B2.9.9 -Corners B2.9.10 EF Hand B2.9.11 Helix-Turn-Helix B2.9.12 Four-Helix Bundle B2.9.13 Mixed & Super-Secondary Structures B2.9.14 -- Motif B2.9.15 Rossmann Fold

B2.10 Tertiary Structure

B2.10.1 Tertiary Structure B2.10.2 Domains in the Tertiary Structure B2.10.3 Domains and Sequence B2.10.4 Domains and Function B2.10.5 New Look on Proteins Levels of Architecture B2.10.6 Blurred Boundaries B2.10.7 Tertiary Structure Patterns: Folds B2.10.8 Fold Diversity B2.10.9 Protein Folds and Function B2.10.10 Classification of Protein Folds B2.10.11 Mainly Folds B2.10.12 Mainly Folds B2.10.13 Mixed - Folds B2.10.14 Databases of Folds

B2.11 Quaternary Structure

B2.11.1 Quaternary Structure B2.11.2 Dimers, Trimers, Tetramers etc... B2.11.3 Homo-Oligomers: Identical Polypeptide Chains B2.11.4 Hetero-Oligomers: Different Polypeptide Chains

B2.12 Structural Classification of Proteins

B2.12.1 Structural Classification of Proteins B2.12.2 Globular Proteins

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B2.12.3 Hydrophilic Surface and Hydrophobic Core B2.12.4 Hydrophobic Effect B2.12.5 Hydration Layer B2.12.6 Membrane Proteins B2.12.7 The Lipid Bilayer B2.12.8 Membrane Model B2.12.9 Membrane Proteins Types B2.12.10 Transmembrane Protein Surface B2.12.11 Transmembrane Protein Folds B2.12.12 Fibrous Proteins B2.12.13 Collagen B2.12.14 -Keratin B2.12.15 Silk Fibroin

B2.13 Perspectives
B2.13.1 The History B2.13.2 The Pharmaceutical Connection B2.13.3 A Fascinating Field

B2.14 CHAPTER QUIZZES (Available only in Academic License)

B3. MOLECULAR DYNAMICS

B3.1 Introduction
B3.1.1 What is Molecular Dynamics? B3.1.2 Ergodicity Assumption B3.1.3 Historical Note B3.1.4 Four Types of Applications of MD Simulation B3.1.5 Macroscopic Behavior B3.1.6 MD Between Experiment and Theory B3.1.7 Refinement and Validation of MD B3.1.8 Access to Unavailable Data B3.1.9 MD Applied to Living Systems B3.1.10 Example 1: Relation between Structure and Function B3.1.11 Example 2: Relation between Structure and Function B3.1.12 Example 3: Relation between Structure and Function B3.1.13 Proteins are not Static B3.1.14 Thermal Fluctuations B3.1.15 Conformational Changes B3.1.16 MD as a Way to Study Molecular Motions B3.1.17 Mimicking the Way a Molecule Moves B3.1.18 Average Properties Derived from MD Trajectories

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B3.1.19 Calculating Molecular Properties of a System B3.1.20 Studying Thermodynamic Properties B3.1.21 Studying Kinetic Properties B3.1.22 Studying Conformational Changes

B3.2 Energy Calculations

B3.2.1 Calculation of Forces & Energies B3.2.2 Two Families of MD Methods B3.2.3 The Quantum Mechanics Approach B3.2.4 Quantum Methods are Computationally Expensive B3.2.5 The Classical Mechanics Approach B3.2.6 Classical vs. Quantum Methods B3.2.7 Classical MD Simulates the Dynamics of the Nuclei B3.2.8 The Born-Oppenheimer Approximation B3.2.9 Force Field for Classical MD B3.2.10 General Force Field Equation B3.2.11 Stretching Term B3.2.12 Bending Term B3.2.13 Torsional Term B3.2.14 Van der Waals Term B3.2.15 Electrostatic Term B3.2.16 A Couple of Practical Remarks B3.2.17 The Link between Forces and Potential Energies

B3.3 MD Algorithm
B3.3.1 Newton's Equation of Motion B3.3.2 Prediction of Next Position B3.3.3 Integration Step B3.3.4 Molecular Dynamics Algorithm B3.3.5 Trajectories: List of Positions and Velocities B3.3.6 Atomic Positions at Time (t+t) B3.3.7 Solving Newton's Equations B3.3.8 Numerical Integration with the Verlet Formula B3.3.9 Summary of the MD Algorithm

B3.4 Fundamental Issues

B3.4.1 Time Step B3.4.2 Choice of Time Step B3.4.3 Time-Scale of Molecular Motions B3.4.4 Method for Increasing the Time Step: Constrained MD B3.4.5 Periodic Boundary Condition B3.4.6 Importance of Long Range Forces B3.4.7 The Distance Cutoff Concept B3.4.8 Problems with Cutoffs B3.4.9 Switching Functions

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B3.4.10 Choice of the Cutoff B3.4.11 Strategies to Incorporate the Solvent B3.4.12 Implicit Solvent Model B3.4.13 Explicit Solvent Molecules B3.4.14 The Ewald Summation Method

B3.5 MD Protocols
B3.5.1 Typical Steps for MD Simulation B3.5.2 Define and Prepare the Molecular System B3.5.3 Preparing the Coordinates B3.5.4 Manual Assembly of a Complex Molecular System B3.5.5 Solvating the System B3.5.6 Addition of Counterions B3.5.7 Choose the MD Package & Force-Field B3.5.8 Extending the Parameterization of the Force Field B3.5.9 Configuration Parameters of the MD Simulation B3.5.10 Time-step B3.5.11 Length of the Simulation B3.5.12 Distance Cutoffs B3.5.13 Reassigning the List of Non-Bonded Atom Pairs B3.5.14 Initial Velocities B3.5.15 SHAKE Parameters B3.5.16 Preliminary Treatments: Minimization & Equilibration B3.5.17 Minimization of Initial Coordinates B3.5.18 Thermal Equilibration of the System B3.5.19 Maxwell-Boltzmann Equation B3.5.20 Molecular Dynamics Run B3.5.21 Conservation of the Total Energy B3.5.22 Test Energy Fluctuation B3.5.23 Possible Crash of the Program

B3.6 Analysis of the Results of the MD Simulation

B3.6.1 Analysis of the Results B3.6.2 Thermodynamic Properties B3.6.3 Kinetic Properties B3.6.4 Visualization of Time Dependent Properties B3.6.5 Deriving Average Properties from the Trajectory B3.6.6 Average Energies B3.6.7 Specific Heat B3.6.8 Radius of Gyration B3.6.9 Local Motions B3.6.10 Interesting Motions B3.6.11 Movies

B3.7 Examples of MD Applications

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B3.7.1 First s MD Simulation of Protein Folding B3.7.2 Protein-Folding Dynamics using Folding@Home B3.7.3 MD of the Complete Satellite Tobacco Mosaic Virus B3.7.4 How Does RNA Moves Along DNA?

B3.8 Using MD for Conformational Sampling

B3.8.1 The Sampling Approach in Optimization Problems B3.8.2 MD as a Tool for Sampling the Space B3.8.3 Sampling to Find the Global Minimum B3.8.4 Conformational Analysis of a Small Molecule B3.8.5 Conformational Analysis of Biomolecules B3.8.6 Loop Conformation in Proteins B3.8.7 How Do Ligands and Receptors Bind Together? B3.8.8 Protein Folding Problem B3.8.9 Systematic and Random Sampling B3.8.10 Alternative Methods for Sampling B3.8.11 Monte Carlo Random Search B3.8.12 Monte Carlo Algorithm B3.8.13 Metropolis Monte Carlo Approach B3.8.14 Simulated Annealing B3.8.15 Diffusion Equation Methods B3.8.16 Replica Exchange MD Method

B3.9 MD for the Calculation of Binding Energies

B3.9.1 In Silico Drug Design B3.9.2 FEP Approach for Calculating Binding Energies B3.9.3 FEP Thermodynamic Cycle B3.9.4 Exploiting the Thermodynamic Cycle B3.9.5 FEP: Computational Alchemy B3.9.6 Limitation of FEP Method B3.9.7 FEP Study: Example 1 B3.9.8 FEP Study: Example 2

B3.10 MD Packages
B3.10.1 Examples of Popular MD Packages B3.10.2 NAMD B3.10.3 VMD B3.10.4 TINKER B3.10.5 AMBER B3.10.6 CHARMM B3.10.7 GROMACS B3.10.8 MOIL B3.10.9 GROMOS

B3.11 Limitations and Perspectives

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B3.11.1 Limitations of MD B3.11.2 Error Introduced by Empirical Potentials? B3.11.3 Trade Off Between Efficiency and Accuracy B3.11.4 Supramolecular Systems B3.11.5 Long Range Forces as a Computational Bottleneck B3.11.6 Time and Size Limitations B3.11.7 Alternative Techniques for Long Time Dynamics B3.11.8 From Impossible to Feasible B3.11.9 Classical MD is not for Bond Breaking Mechanisms B3.11.10 Present and Future

B3.12 CHAPTER QUIZZES (Available only in Academic License)

C. STRUCTURE-BASED DESIGN
C1. INTRODUCTION TO PROTEIN-LIGAND BINDING

C1.1 Introduction
C1.1.1 Receptor-Based Drug Design C1.1.2 Macromolecular Targets C1.1.3 Mechanism of Action of Drugs C1.1.4 Drug Targets C1.1.5 Contribution of Recombinant Technologies C1.1.6 Operational Strategy: Docking

C1.2 Analytical Process

C1.2.1 The Analytical Process C1.2.2 Data Collection: X-Ray Crystallography C1.2.3 Data Collection: NMR Spectroscopy C1.2.4 Data Collection: Homology Models C1.2.5 Analysis C1.2.6 Design Phase

C1.3 Principles of Analysis

C1.3.1 Analysis of the Morphology of the Active Site C1.3.2 Morphology of the Active Site of a Protein Kinase C1.3.3 Complexes with Ligands C1.3.4 Forces That Contribute to the Binding C1.3.5 The Molecular Recognition Process C1.3.6 Electrostatic C1.3.7 Hydrogen Bonding

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C1.3.8 Hydrophobic C1.3.9 Hydrophobic Interactions C1.3.10 Consider Hydrophobic Interactions C1.3.11 Elementary Hydrophobic Interactions C1.3.12 Example of Hydrophobic Binding C1.3.13 Strengthening Hydrophobic Interactions C1.3.14 Hydrogen Bond Features C1.3.15 Proteins Capabilities in Hydrogen Bonding C1.3.16 Consider Hydrogen Bond Formations C1.3.17 Elementary Hydrogen Bond Interactions C1.3.18 Example of the Hydrogen Bond Binding C1.3.19 Electrostatic Interactions C1.3.20 Elementary Electrostatic Interactions C1.3.21 Strength of Electrostatic Interactions C1.3.22 Example of Electrostatic Interactions C1.3.23 Increase of Potency by the Formation of a Salt Bridge C1.3.24 OH Analog Much Less Potent

C1.4 Example of Tight Interactions

C1.4.1 An Example of a Tight Ligand-Receptor Interaction C1.4.2 The X-ray Structure of the Biotin/Streptavidin C1.4.3 The Binding Mode of Biotin with Streptavidin (1/4) C1.4.4 The Binding Mode of Biotin with Streptavidin (2/4) C1.4.5 The Binding Mode of Biotin with Streptavidin (3/4) C1.4.6 The Binding Mode of Biotin with Streptavidin (4/4)

C1.5 Receptor & Ligand Flexibility

C1.5.1 Flexibility of the Receptor C1.5.2 Flexibility of The Ligand C1.5.3 Entropic Effects

C1.6 Role of the Solvent

C1.6.1 Solvation and Desolvation C1.6.2 The Role of the Solvent C1.6.3 Relay with Water Molecules C1.6.4 Relay with Several Water Molecules C1.6.5 Relay with Water Molecule Having Four H-Bonds

C1.7 Prediction of Binding Modes

C1.7.1 Binding Modes Predicted by Analogy C1.7.2 Inversion of Binding Modes C1.7.3 Inverted Binding Mode of Olomoucine C1.7.4 X-Ray Structure of ATP Bound to a Protein Kinase C1.7.5 Intuitive 2D Alignment for Olomoucine C1.7.6 Experimental Binding Mode of Olomoucine

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C1.7.7 Origin of the Inverted Binding Mode of Olomoucine C1.7.8 Inverted Binding Mode of Methotrexate C1.7.9 Intuitive 2D Alignment for Methotrexate C1.7.10 Experimental Binding Mode of Methotrexate C1.7.11 Origin of the Inverted Binding Mode of Methotrexate C1.7.12 Binding Mode Predicted from SAR

C1.8 Methods for Analyzing Binding

C1.8.1 Analyzing Ligand-Receptor Binding C1.8.2 Ligand-Binding Predictions C1.8.3 Visual Analyses C1.8.4 Docking Analyses C1.8.5 Manual Docking with Computer Graphics C1.8.6 Automated Methods for Docking C1.8.7 Calculation of Binding Energies C1.8.8 Free Energy Perturbation Techniques C1.8.9 Energies from Force Field Calculations C1.8.10 Correlation with Biological Activities C1.8.11 Energies from Scoring Functions C1.8.12 Limitations of Scoring Functions C1.8.13 Calculating Desolvation Energies

C1.9 Conclusion
C1.9.1 Conclusion

C1.10 CHAPTER QUIZZES (Available only in Academic License)

C2. PRINCIPLES OF STRUCTURE-BASED DESIGN

C2.1 Introduction
C2.1.1 Design of Drug Candidates: An Iterative Process C2.1.2 Steps in Structure-Based Drug Design C2.1.3 Small Changes Can Produce Huge Effects C2.1.4 p38 Wild C2.1.5 p38 Mutant C2.1.6 ERK-2 Wild C2.1.7 ERK-2 Mutant C2.1.8 Increasing Biological Activity C2.1.9 Beginning the Design Phase C2.1.10 A Simple Example of Design C2.1.11 Extension of the Molecule to Form another H-Bond

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C2.1.12 Checking the Validity of the Design C2.1.13 Definition of Docking C2.1.14 Docking Treatments

C2.2 Eight Golden Rules

C2.2.1 Eight Golden Rules in Receptor-Based Ligand Design C2.2.2 Rule 1: Coordinate to Key Anchoring Sites C2.2.3 Desolvation Upon Binding C2.2.4 Rule 2: Exploit Hydrophobic Interactions C2.2.5 Many Small Contributions C2.2.6 Rule 3: Exploit Hydrogen Bonding Capabilities C2.2.7 Hydrogen Bonds with Backbone Atoms C2.2.8 Geometry of a Hydrogen Bond and Solvation Issues C2.2.9 Hydrogen Bonds with Residue Atoms C2.2.10 Rule 4: Exploit Electrostatic Interactions C2.2.11 Rule 5: Favor Bioactive Form & Avoid Energy Strain C2.2.12 Advantage and Limitation of a Rigid Ligands C2.2.13 Rule 6: Optimize VDW Contacts and Avoid Bumps C2.2.14 The Frontier between an Excellent Fit and a Bump C2.2.15 Rule 7: Structural Water Molecules and Solvation C2.2.16 Desolvation Energies C2.2.17 Leave Some Room to Solvate Charged Centers C2.2.18 Rule 8: Consider Entropic Effect C2.2.19 Gaining Binding by Reduction of Entropy C2.2.20 Example of Ligand Rigidification C2.2.21 Making a Flexible Molecule More Rigid

C2.3 The Four Design Methods

C2.3.1 The Four Design Methods

C2.4 Analog Design

C2.4.1 Principles of Analog Design C2.4.2 Example of Analog Design C2.4.3 Additional Binding with Arginine Residue

C2.5 Database Searching

C2.5.1 3D Database Searching C2.5.2 Scoring the Hits C2.5.3 Advantages of Database Searching C2.5.4 Problems of Conformational Complexity C2.5.5 Assessing the Validity of the 3D Structures C2.5.6 Example of Database Searching C2.5.7 Limitations in Database Approaches C2.5.8 Unexpected Binding Mode of Haloperidol C2.5.9 Databases of Molecules in 3D

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C2.5.10 The Main Purpose of a 3D-Database Search

C2.6 De-Novo Design

C2.6.1 Automated Construction Approaches C2.6.2 Molecule Generated by an Automated Method

C2.7 Manual Design

C2.7.1 Manual Design C2.7.2 Importance of Visualization C2.7.3 Tools in Manual Design C2.7.4 Fully Exploiting the Fruits of the Analyses C2.7.5 Design of a Hybrid Molecule

C2.8 Another Iteration

C2.8.1 Another Round of Analysis & Design

C2.9 A Success Story

C2.9.1 Example of Successful Structure-Based Design C2.9.2 Mechanism of Action of the HIV-1 Protease C2.9.3 The Crystallographic Structure of the HIV-1 Protease C2.9.4 Hydrophobic Cavity of the HIV-1 Protease C2.9.5 Flap of the HIV-1 Protease C2.9.6 Transition State Concept for the Design of Inhibitors C2.9.7 Topography of the Active Site of the Enzyme C2.9.8 The MVT-101 Inhibitor C2.9.9 Crystallographic Resolution of the HIV-1 Protease C2.9.10 X-ray of the Complex of MVT-101 with the Enzyme (1/3) C2.9.11 X-ray of the Complex of MVT-101 with the Enzyme (2/3) C2.9.12 X-ray of the Complex of MVT-101 with the Enzyme (3/3) C2.9.13 Design of Peptide-Like Structures C2.9.14 Optimization to Fit the hydrophobic pockets C2.9.15 Example of Optimized Structure C2.9.16 X-ray Structure of the A-77003 Complex (1/4) C2.9.17 X-ray Structure of the A-77003 Complex (2/4) C2.9.18 X-ray Structure of the A-77003 Complex (3/4) C2.9.19 X-ray Structure of the A-77003 Complex (4/4) C2.9.20 A Drug Design Solution Using Database Searching C2.9.21 The Terphenyl Hit C2.9.22 In Depth Analysis of the Hit C2.9.23 Incorporating Binding Features of the Water Molecule C2.9.24 Rigidification of the Linear Inhibitor C2.9.25 Considerations for Specificity C2.9.26 Design of Cyclohexanone Scaffold C2.9.27 The Design of Cyclic Ureas C2.9.28 Limitation of the 6-Membered Ring Scaffold

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C2.9.29 The 7-Membered cyclic Urea Scaffold C2.9.30 Design of the Cyclic Urea XK-263 C2.9.31 The Crystallographic Structure of XK-263 Complex (1/3) C2.9.32 The Crystallographic Structure of XK-263 Complex (2/3) C2.9.33 The Crystallographic Structure of XK-263 Complex (3/3) C2.9.34 Lessons From HIV-1 Protease Inhibition

C2.10 Conclusion
C2.10.1 Conclusion

C2.11 CHAPTER QUIZZES (Available only in Academic License)

C3. MOLECULAR DOCKING: PRINCIPLES AND METHODS

C3.1 Introduction to Computational Docking

C3.1.1 Molecular Recognition C3.1.2 Molecular Recognition Process: Molecular Docking C3.1.3 Understanding Molecular Recognition C3.1.4 Molecular Docking Models C3.1.5 The Lock and Key Theory C3.1.6 The Induced-Fit Theory C3.1.7 The Conformation Ensemble Model C3.1.8 From the Lock and Key to the Ensemble Model C3.1.9 Experimental Methods to Study Molecular Docking C3.1.10 Limitations of Experimental Techniques C3.1.11 A Bottleneck in Drug Discovery C3.1.12 Triggering the Computational Docking Discipline C3.1.13 Definition of Computational Docking C3.1.14 Applications of Computational Docking

C3.2 The Docking Problem

C3.2.1 The Docking Problem C3.2.2 Great Diversity of Molecular Interactions C3.2.3 Atomic Basis of Molecular Recognition C3.2.4 Definition of the "Pose" C3.2.5 Docking Viewed as a Black Box C3.2.6 Current Computational Docking Programs C3.2.7 Simulation and non-Simulation Approaches C3.2.8 Simulation Approaches C3.2.9 Non-Simulation Approaches C3.2.10 Molecular Complementarity in Computational Docking

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C3.2.11 Shape Complementarity C3.2.12 Chemical Complementarity C3.2.13 Energy Dictates Molecular Associations C3.2.14 Find a Complex that Minimizes the Energy C3.2.15 Accounting for Molecular Flexibility in Docking C3.2.16 Flexible Docking: Increasing Levels of Complexity C3.2.17 Initial Data and Nature of the Docking Difficulty C3.2.18 Bound Docking C3.2.19 Unbound Docking C3.2.20 Modeled Docking C3.2.21 The Three Generations in Computational Docking C3.2.22 Three Components of Docking Software

C3.3 System Representation

C3.3.1 Molecular Representation C3.3.2 Atomic Representation C3.3.3 Complexity of the Atomic Repesentation C3.3.4 Internal Coordinates C3.3.5 Protein Preparation C3.3.6 Small Molecule Preparation C3.3.7 Surface Representation C3.3.8 Molecular Surface Matching C3.3.9 Surface-Based Representation C3.3.10 Accessible Surface Area C3.3.11 Solvent Contact & Reentrant Surfaces C3.3.12 Example of Contact & Reentrant Surface C3.3.13 Describing the Molecular Shape C3.3.14 Connolly's Contact and Reentrant Surfaces C3.3.15 Sparse Surface C3.3.16 Delaunay Triangulation C3.3.17 "Knob" and "Hole" Descriptors C3.3.18 Using Knobs and Holes for Complementarity C3.3.19 Other Examples of Shape Descriptors C3.3.20 Grid Representation C3.3.21 Use of GRID Potentials to Simplify the Docking C3.3.22 Assessing Shape Complementarity Using Grid

C3.4 Scoring Methods

C3.4.1 Need to Assess the Quality of Docked Complexes C3.4.2 A Good Understanding of the Binding C3.4.3 Important Questions C3.4.4 Molecular Determinants for Binding C3.4.5 Interaction Forces and Binding Energies C3.4.6 Favorable Forces C3.4.7 Unfavorable Forces

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C3.4.8 Desolvation Energies C3.4.9 Entropic Effects C3.4.10 Calculation of the Binding Energies C3.4.11 Free Energy Equations C3.4.12 Conversion of K to Energies C3.4.13 Difficulty of Calculating Free Energies of Binding G C3.4.14 Approximating G by Molecular Mechanics C3.4.15 Force-Field Calculations C3.4.16 CHARMM Force Field to Score the Docking C3.4.17 Approximating G by Quantum Mechanics C3.4.18 Development of Scoring Functions for Docking C3.4.19 Scoring Functions C3.4.20 Empirical Scoring Functions C3.4.21 Example of Empirical Scoring Function C3.4.22 Knowledge-Based Scoring Functions C3.4.23 The Statistical Analyses C3.4.24 Knowledge-Based Potentials C3.4.25 The DrugScore Program C3.4.26 DrugScore: The Thrombin Example C3.4.27 Refinement of Scoring Functions C3.4.28 Other Scoring Methods C3.4.29 Shape and Property Complementarity Scoring C3.4.30 Method to Measure Shape Complementarity C3.4.31 Free Energy Perturbation

C3.5 Rigid Docking Methods

C3.5.1 Docking Algorithms C3.5.2 The Mathematical Problem C3.5.3 Two Docking Philosophies C3.5.4 The Feature-Based Matching Approach C3.5.5 Docking Using Feature-Based Methods C3.5.6 Match Complementarity or Similarity Features C3.5.7 Components of Feature-Based Matching Methods C3.5.8 Step 1: Feature Extraction C3.5.9 Step 2: Feature Matching C3.5.10 Step 3: Transformation (Assembly) C3.5.11 Step 4: Filtering and Scoring C3.5.12 Virtual Screening and De Novo Design C3.5.13 Programs with Feature-Based Matching Methods C3.5.14 Algorithms of Matching C3.5.15 Clique-Search Based Approaches C3.5.16 Goal of the Docking Algorithm C3.5.17 Distance Compatibility Graph C3.5.18 Clique Detection Methods C3.5.19 Pose-Clustering C3.5.20 Searching for Compatible Triangles

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C3.5.21 Transformation that Align a Maximum of Triangles C3.5.22 Complementarity and Similarity Matching C3.5.23 Speed up of Pose-Clustering C3.5.24 The Bottleneck of Pose-Clustering C3.5.25 Geometric Hashing C3.5.26 Fast Retrieval of Matching Features C3.5.27 Invariant Representation of Features C3.5.28 Improvement of Pose-Clustering C3.5.29 PatchDock Example C3.5.30 The Stepwise Search Approach C3.5.31 Components of a Stepwise Docking Program C3.5.32 Exhaustive and Stochastic Search C3.5.33 Exhaustive vs. Stochastic Search C3.5.34 Exhaustive Search C3.5.35 Mapped-Grid Method C3.5.36 Physico-Chemical Properties of the Receptor C3.5.37 Assessing Shape Complementarity C3.5.38 Fast-Fourier Transform (FFT) Method C3.5.39 FFT vs. Exhaustive Method C3.5.40 FFT - Geometric Shape Complementarity C3.5.41 FFT - Different Scores C3.5.42 Docking of Plastocyanin and Cytochrome C C3.5.43 Spherical Polar Fourier Correlations - Fast FFT C3.5.44 Stochastic Algorithms C3.5.45 A Typical Computational Docking Program C3.5.46 Optimization Methods to Find the Best Solution C3.5.47 Monte Carlo Methods C3.5.48 Simulated Annealing C3.5.49 Genetic Algorithms (GA) C3.5.50 General Principle of GA C3.5.51 Creating a New Generation C3.5.52 Simulating the Reproduction Process C3.5.53 Steps in Genetic Algorithms C3.5.54 Lamarckian Genetic Algorithm C3.5.55 Tabu Search C3.5.56 Tabu Algorithm C3.5.57 Avoiding Being Trapped in a Local Minimum C3.5.58 Better Exploration of the Space C3.5.59 The Hybrid Docking Method

C3.6 Methods for Incorporating Flexibility

C3.6.1 Implementation of Flexibility into Docking Software C3.6.2 Degrees of Freedom in Flexible Docking C3.6.3 Possible Classification of Methods for Flexibility C3.6.4 Classification of Methods C3.6.5 Incorporating Small Molecule Flexibility

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C3.6.6 Modeling Small Molecules as Flexible Entities C3.6.7 Small Molecule Flexibility C3.6.8 Integration of Ligand Flexibility and Protein Structure C3.6.9 Methods for Handling Ligand Flexibility Explicitly C3.6.10 The Ensemble Docking Method C3.6.11 Advantage of the Ensemble Docking Method C3.6.12 The FLOG Software C3.6.13 Problem of the Ensemble Docking Approach C3.6.14 The Improved Ensemble Docking Method C3.6.15 Remove Redundancy in the Rigid Fragment C3.6.16 Remove Redundancy in the Flexible Fragment C3.6.17 Score: Sum of Atom Interactions C3.6.18 Step-1: Conformational Analysis C3.6.19 Step-2: Superimposition and Positioning C3.6.20 Step-3: Conformational Analysis C3.6.21 Dramatic Improvement in Computing Time C3.6.22 Efficient Treatment of Clashes C3.6.23 Validation of the Lorber-Shoichet Method C3.6.24 Extension to Analog Compounds C3.6.25 The Fragmentation Docking Method C3.6.26 Place-and-Join Algorithm C3.6.27 Principle of the Place-and-Join Method C3.6.28 Difficulty of the Place and Join Method C3.6.29 Incremental-Based Methods C3.6.30 Incremental Algorithm C3.6.31 Stochastic Search Methods C3.6.32 GOLD Program C3.6.33 Incorporating Protein Flexibility C3.6.34 Importance of Modeling Protein Flexibility C3.6.35 Historical Note C3.6.36 Flexibility Through Soft Scoring Functions C3.6.37 Reduce the Importance of Steric Clashes C3.6.38 Soft Van der Waals Repulsion Functions C3.6.39 Decreasing Van der Waals Radii C3.6.40 Soft Electrostatic Repulsion Potentials C3.6.41 Soft Scoring Functions in Protein-Protein Docking C3.6.42 Implicit Flexibility in Protein-Protein Docking C3.6.43 Problems with Soft Scoring C3.6.44 Soft Scoring as a First Filtering Method C3.6.45 Protein Side-Chains Flexibility C3.6.46 Importance of Modeling Side-Chain Mobility C3.6.47 Determine the Optimum Combination of Side-Chains C3.6.48 Combinatorial Explosion C3.6.49 Side Chain Rotamer Libraries C3.6.50 From Folding to Docking C3.6.51 The Leach Algorithm

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C3.6.52 Generation and Minimization of Complexes C3.6.53 Other Optimization Methods C3.6.54 Restricting Searches and Minimizations C3.6.55 Identify Key Residues for the Interaction C3.6.56 Restrict the Search to Exposed Side Chains C3.6.57 Backbone and Side Chain Flexibility C3.6.58 Conventional Methods not Adapted C3.6.59 The Multiple Protein Structure (MPS) Approach C3.6.60 Principle of the MPS Approach C3.6.61 Sources of Multiple Protein Structures C3.6.62 MPS: a Good Model for the Recognition Process C3.6.63 How the MPS are Exploited? C3.6.64 Successive and Independent Docking Treatments C3.6.65 Acetylcholinesterase Example C3.6.66 The United Protein Approach C3.6.67 Key Concept of FlexE C3.6.68 Remove Redundant Information C3.6.69 FlexE: Incompatibility Graph C3.6.70 FlexE: Search & Scoring C3.6.71 The Average Grid Approach C3.6.72 Single Grid Combining MPS Information C3.6.73 Scoring Tolerance with MPS-based Grids C3.6.74 Average Grid Approach vs. Soft Scoring C3.6.75 Dynamic Pharmacophore-Based Approach C3.6.76 Dynamic Pharmacophore Model for HIV-1 Integrase C3.6.77 Hybrid Pharmacophore Models using LigandScout C3.6.78 Domain Movements C3.6.79 Example of Calmodulin Domain Movements C3.6.80 Conventional Modeling Methods are not Suited C3.6.81 Intrinsic Flexibility C3.6.82 Hinge-Bent Movements C3.6.83 Automated Methods for Hinge Detection C3.6.84 Incorporating Hinge-Bent Movements in Docking C3.6.85 Docking with Hinge-Bent Movements C3.6.86 Ball-and-Socket Motions

C3.7 Uses of Docking in Research

C3.7.1 Computational Docking in Drug Discovery C3.7.2 Virtual Screening C3.7.3 Lead Hopping C3.7.4 Increasing HTS Hit Rates C3.7.5 Confirm Choice of Prototype Structure C3.7.6 Manual Design of a New Scaffold C3.7.7 New Cores from a Database of Scaffolds C3.7.8 De Novo Design of Spacers C3.7.9 Modulating Protein-Protein Interactions

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C3.7.10 Query for 3D Database Searching C3.7.11 Creative Molecular Design Conditions C3.7.12 Design of Combinatorial Libraries C3.7.13 Understanding SAR C3.7.14 Reducing Multiple Hypotheses to a Single One C3.7.15 Series Optimization C3.7.16 Explaining Incomprehensible Observations C3.7.17 Identifying Incorrect Working Hypotheses C3.7.18 Align Chemically Unrelated Molecules in 3D C3.7.19 Improving the Solubility of a Ligand C3.7.20 Understand the Intrinsic Limitations of a Scaffold C3.7.21 Assessing the Potential of a Hit C3.7.22 Elucidating Exact Mode of Action C3.7.23 Assessing Multiple Alignment Hypotheses C3.7.24 Molecular Mimicry C3.7.25 Computational Validation of Hypotheses

C3.8 Docking Softwares

C3.8.1 Docking Programs C3.8.2 Dock C3.8.3 Autodock C3.8.4 DockVision C3.8.5 DockIt C3.8.6 FlexX C3.8.7 Ligin C3.8.8 FT-Dock C3.8.9 GOLD C3.8.10 GRAMM C3.8.11 Hex C3.8.12 eHiTS C3.8.13 LigandFit C3.8.14 FRED C3.8.15 Glide C3.8.16 Which Software is Better?

C3.9 Future and Perspectives

C3.9.1 Limitations in Computational Docking C3.9.2 Trade Off Between Efficiency and Accuracy C3.9.3 Screening Large Chemical Libraries C3.9.4 A Two Step Strategy C3.9.5 High-throughput Docking Using Grid-Computing C3.9.6 How Does it Work? C3.9.7 Wide In Silico Docking On Malaria (WISDOM) C3.9.8 Enrichment Factor C3.9.9 Current Status of the Docking Problem

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C3.9.10 The Docking Bottlenecks C3.9.11 More Effective Scoring Functions C3.9.12 Modeling the Solvent C3.9.13 Validation of Scoring Functions C3.9.14 Target Trainable Scoring Functions C3.9.15 Database of Decoys C3.9.16 Consensus Scoring C3.9.17 The Molecular Flexibility Challenge C3.9.18 Developing Better Models of Flexibility C3.9.19 Importance of Visual Docking C3.9.20 Requirement for Manual Docking C3.9.21 Illustration of Manual Docking C3.9.22 Manual Docking with Solid Models C3.9.23 Virtual Reality Docking System C3.9.24 Example of Docking using CAVE C3.9.25 Synergy Between Interactive & Automated Docking C3.9.26 Interactive Computer-Guided Docking C3.9.27 Protein-Protein Docking Benchmarks C3.9.28 The CAPRI Competition C3.9.29 Six Weeks for Submitting Predicted Complexes C3.9.30 Assessment of the Predictions C3.9.31 A New CAPRI Scoring Category C3.9.32 CAPRI History and Experience C3.9.33 Perspectives

C3.10 CHAPTER QUIZZES (Available only in Academic License)

C4. CASE STUDIES IN STRUCTURE-BASED DESIGN

C4.1 Case Study-1 : Phenyl Imidazoles

C4.1.1 Phenyl-Imidazoles Inhibit Cytochrome P450 C4.1.2 Simple Consideration: Shape Similarity C4.1.3 Perhaps Binding Elements are more Complex ? C4.1.4 The Structure-Based Answer C4.1.5 Phenyl-Imidazole Browser C4.1.6 Limitations of Chemical Intuition

C4.2 Case Study-2 : BACE-1 Inhibitors

C4.2.1 BACE-1 Inhibitors C4.2.2 Screening the J&J Corporate Compound Collection C4.2.3 Structural Determinants of the Biological Activity of 1 C4.2.4 X-ray Structure of the Complex of 1 with BACE-1

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C4.2.5 Flap Flexibility in Aspartyl Proteases C4.2.6 Compound with Increased Folding Capability C4.2.7 How to Gain Additional Binding C4.2.8 Design of a More Potent Inhibitor C4.2.9 X-Ray Structure of the Complex with 3a C4.2.10 Pharmacological Action of Compound 3a C4.2.11 Important Structural Determinants for Binding C4.2.12 Summary

C4.3 Case Study-3 : Factor Xa Inhibitors

C4.3.1 Therapeutic Utility of Factor Xa Inhibitors C4.3.2 DX-9065a : a Factor Xa Inhibitor C4.3.3 Complex Between Factor Xa and DX-9065a C4.3.4 Analysis of the Factor Xa and DX-9065a Complex (1/4) C4.3.5 Analysis of the Factor Xa and DX-9065a Complex (2/4) C4.3.6 Analysis of the Factor Xa and DX-9065a Complex (3/4) C4.3.7 Analysis of the Factor Xa and DX-9065a Complex (4/4) C4.3.8 Role of the Carboxylic Acid in Selectivity (1/3) C4.3.9 Role of the Carboxylic Acid in Selectivity (2/3) C4.3.10 Role of the Carboxylic Acid in Selectivity (3/3) C4.3.11 Initial Inhibitor Design C4.3.12 Design (step 1): Structural Moiety for Pocket S1 C4.3.13 Phenyl-Amidine Entered into the S1 Pocket C4.3.14 Phenyl-Amidine Oriented in Lowest Energy Orientation C4.3.15 Design (step 2): Structural Moiety for Pocket S4 C4.3.16 Phenyl Ring Introduced in Pocket S4 C4.3.17 Phenyl Substituted with an Amidine C4.3.18 Stacking Interaction of Phenyl-Amidine with Trp-215 C4.3.19 Phenyl-Amidine Orientation C4.3.20 Design (step 3): Design of the Spacer C4.3.21 Phenyl-Amidine Groups in their Preferred Orientations C4.3.22 Spacer with three Atoms C4.3.23 Candidate Prototype in the Catalytic Site C4.3.24 Design (step 4): Positioning of the Carboxylate C4.3.25 Discovery of a Lead Compound C4.3.26 Optimization of the Designed Series C4.3.27 Interaction of Compound 21 with Factor Xa C4.3.28 Finding an Optimal Spacer

C4.4 Case Study-4 : Kinase Inhibitors

C4.4.1 Pyrrolo-Pyrimidine & Quinazoline EGF-R Inhibitors C4.4.2 Novartis and Parke-Davis Opposite Binding Models C4.4.3 Controversy: Novartis & Parke-Davis Binding Modes C4.4.4 Parke-Davis Analyses C4.4.5 Novartis Analyses

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C4.4.6 X-ray Structure of ATP Bound to a Kinase C4.4.7 Binding Mode of ATP C4.4.8 Binding Mode of Staurosporine C4.4.9 Homology Model of EGF-R Catalytic Site C4.4.10 From Staurosporine to Pyrrolo-pyrimidine C4.4.11 The Novartis Binding Mode of Pyrrolo-pyrimidine C4.4.12 The Pyrrole Ring in the Large Pocket C4.4.13 The Pyrrole Ring Pointing Towards the Sugar Pocket C4.4.14 Parke-Davis Analyses the Quinazoline Scaffold C4.4.15 Additional SAR Analyses made by Parke-Davis C4.4.16 Parke-Davis Model of the Quinazoline Analogs C4.4.17 Specificity Observed in EGF-R Kinase Inhibition C4.4.18 Anilino Towards the Sugar Pocket not Reasonable C4.4.19 Parke-Davis Model Consistent with Observed SAR C4.4.20 Binding Mode of the Pyrrolo-Pyrimidine Series C4.4.21 Binding Mode of the Quinazoline Series C4.4.22 What is the Correct Solution? C4.4.23 Ligand Observed with a Novartis Binding Mode C4.4.24 Alignment with the Novartis Model C4.4.25 Ligand Observed with a Parke-Davis Binding Mode C4.4.26 Alignment with the Parke-Davis Model C4.4.27 X-Ray Resolution of Tarceva Bound to EGF-R Kinase C4.4.28 Conclusion

C4.5 ADDITIONAL CASE STUDIES

C4.5.1 Additional Case Studies

C5. CASE STUDIES OF DOCKING IN DRUG DISCOVERY

C5.1 Case Study 1 : Pyrimidin-4-yl-ureas for Kinase Inhibition

C5.1.1 Inhibitor Active on Several Protein Kinases C5.1.2 Structural Determinants for the Activity C5.1.3 Correlation with the Volume of Gate Keeper Residue C5.1.4 Outcome of this Study

C5.2 Case Study 2 : Inhibition of CHK1

C5.2.1 The CHK1 Kinase C5.2.2 The Indazole Series C5.2.3 Binding Mode of the Indazole Core C5.2.4 Binding Modes of the Potent Indazole Analog C5.2.5 Pocket may Help for Selectivity

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C5.2.6 Overlay with Other Chk1 Inhibitors C5.2.7 Structure-Based Screening of Chk1 Inhibitors C5.2.8 Hits Identified by Virtual Screening C5.2.9 X-Ray Structures of Four Virtual Screening Hits C5.2.10 Binding Modes Predicted for Other Five Hits C5.2.11 Outcome of this Study

C5.3 Case Study 3 : Thrombin Inhibitors

C5.3.1 Two Methods of Virtual Screening C5.3.2 Combining Structure-Based and Ligand-Based VS C5.3.3 Screening Protocol C5.3.4 Steps of the Docking Treatment C5.3.5 Specificity Pockets in Thrombin C5.3.6 Development of the Hybrid Approach C5.3.7 Inhibition Assays of Top-Scoring Compounds C5.3.8 Analysis of the Binding Mode of Compound 1 C5.3.9 Binding Mode Compared with Known Inhibitors C5.3.10 What was Learned in this Test Study ? C5.3.11 Analyzing Top Ranked Compounds C5.3.12 Limitations of Scoring Functions

C5.4 Case Study 4 : Salicylamide Renin Inhibitor

C5.4.1 Search for New Scaffold in Renin Inhibition C5.4.2 3D Analyses C5.4.3 Preferred Location of Phenyl Ring in Pocket P3 C5.4.4 Docking Experiment C5.4.5 Results of the Docking C5.4.6 Search for an Optimal Spacer C5.4.7 The Salicylamide Lead C5.4.8 Predictions Confirmed by X-Ray Study C5.4.9 Browser of Salicylamide Inhibitor C5.4.10 Optimization of the Salicylamide Series C5.4.11 Summary C5.4.12 Lead Hopping

C5.5 Case Study 5 : Inhibition of Human Neutrophil Elastase

C5.5.1 Inhibition of Human Neutrophil Elastase C5.5.2 Sesquiterpene Lactones C5.5.3 Studies on 17 Sesquiterpene Lactones C5.5.4 Docking Studies C5.5.5 Docking Protocol C5.5.6 Results of the Docking Studies C5.5.7 Elucidation of the Mode of Action C5.5.8 Docking Results of Melampolides 2 and 4 C5.5.9 Docking Results of Podachaenin 14

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C5.5.10 Docking Results of Germacranolide 8 C5.5.11 Structural Determinants for Binding to HNE C5.5.12 Summary

C5.6 ADDITIONAL CASE STUDIES

C5.6.1 Additional Case Studies

C6. ANALYSES OF PROTEIN-LIGAND COMPLEXES

C6.1 Elastase Inhibitors

C6.1.1 Therapeutic Utility of Elastase Inhibitors C6.1.2 Analysis of the HLE Active Site (1/3) C6.1.3 Analysis of the HLE Active Site (2/3) C6.1.4 Analysis of the HLE Active Site (3/3) C6.1.5 Complex of MSACK with HLE C6.1.6 Analysis of the Binding of MSACK (1/3) C6.1.7 Analysis of the Binding of MSACK (2/3) C6.1.8 Analysis of the Binding of MSACK (3/3) C6.1.9 The Design of a New Elastase Inhibitor C6.1.10 Complex of Inhibitor with PPE Elastase C6.1.11 Binding of Aminopyrimidone Candidate (1/4) C6.1.12 Binding of Aminopyrimidone Candidate (2/4) C6.1.13 Binding of Aminopyrimidone Candidate (3/4) C6.1.14 Binding of Aminopyrimidone Candidate (4/4)

C6.2 Thymidylate Synthase Inhibitors

C6.2.1 The Thymidylate Synthase Enzyme C6.2.2 The Thymidylate Synthase Active Site C6.2.3 The Thymidylate Synthase Catalytic Mechanism C6.2.4 Two Possible Strategies for Inhibiting TS C6.2.5 Inhibition by Binding to the TS Substrate Site C6.2.6 X-Ray of TS with 5-FdUMP and Cofactor C6.2.7 Inhibition by Binding to Cofactor Site C6.2.8 Complex of CB3717 with Thymidylate Synthase C6.2.9 Analysis of the Binding of CB3717 (1/4) C6.2.10 Analysis of the Binding of CB3717 (2/4) C6.2.11 Analysis of the Binding of CB3717 (3/4) C6.2.12 Analysis of the Binding of CB3717 (4/4) C6.2.13 Design of a New TS Inhibitor C6.2.14 The Quinazolinone Scaffold C6.2.15 One Atom Spacer

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C6.2.16 The Glutamic Acid Component C6.2.17 Designed and Reference Molecules in 3D

C6.3 Inhibitors of Phospholipase A-2

C6.3.1 Phospholipase A2 C6.3.2 PLA2 Transition State Analogues C6.3.3 Complex of an Inhibitor with PLA2 C6.3.4 Analysis of the Binding of the Inhibitor (1/4) C6.3.5 Analysis of the Binding of the Inhibitor (2/4) C6.3.6 Analysis of the Binding of the Inhibitor (3/4) C6.3.7 Analysis of the Binding of the Inhibitor (4/4) C6.3.8 Design of a New Class of PLA2 Inhibitors C6.3.9 Binding of Acenaphthene with PLA2

C6.4 Thrombin Inhibitors

C6.4.1 Therapeutic Utility of Thrombin Inhibitors C6.4.2 Examples of Thrombin Inhibitors C6.4.3 The Catalytic Mechanism of Thrombin C6.4.4 The "Ser-His-Asp" Catalytic Triad C6.4.5 First Step: Transfer of H from the Ser to the His C6.4.6 Second Step: Tetrahedral Intermediate C6.4.7 Third Step: Binding to the Oxyanion Hole C6.4.8 Final Step: The Peptide Bond is Cleaved C6.4.9 The Product of the Reaction C6.4.10 Reaction-Intermediate-Based Inhibitors C6.4.11 Another Class of Potent Thrombin Inhibitors C6.4.12 The Complex of Thrombin with NAPAP C6.4.13 Analysis of the NAPAP-Thrombin Complex (1/5) C6.4.14 Analysis of the NAPAP-Thrombin Complex (2/5) C6.4.15 Analysis of the NAPAP-Thrombin Complex (3/5) C6.4.16 Analysis of the NAPAP-Thrombin Complex (4/5) C6.4.17 Analysis of the NAPAP-Thrombin Complex (5/5) C6.4.18 The Design of a New Thrombin Inhibitor

C6.5 Human Rhinovirus Inhibitors

C6.5.1 Inhibition of Human Rhinovirus Protein C6.5.2 The Mechanism of Action of WIN54954 C6.5.3 Complex of WIN54954 with Rhinovirus HRV14 C6.5.4 Binding of WIN54954 with Rhinovirus HRV14 (1/6) C6.5.5 Binding of WIN54954 with Rhinovirus HRV14 (2/6) C6.5.6 Binding of WIN54954 with Rhinovirus HRV14 (3/6) C6.5.7 Binding of WIN54954 with Rhinovirus HRV14 (4/6) C6.5.8 Binding of WIN54954 with Rhinovirus HRV14 (5/6) C6.5.9 Binding of WIN54954 with Rhinovirus HRV14 (6/6) C6.5.10 Optimization of WIN54954

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C6.6 Rotamase Inhibitors

C6.6.1 Utility of Rotamase Inhibitors C6.6.2 Complex of FK506 with FKBP C6.6.3 Analysis of the Binding of FK506 (1/4) C6.6.4 Analysis of the Binding of FK506 (2/4) C6.6.5 Analysis of the Binding of FK506 (3/4) C6.6.6 Analysis of the Binding of FK506 (4/4) C6.6.7 Design of a New Rotamase Inhibitor C6.6.8 The Pipecolyl Inhibitor Mimics FK506 C6.6.9 Binding of the Pipecolyl Inhibitor (1/3) C6.6.10 Binding of the Pipecolyl Inhibitor (2/3) C6.6.11 Binding of the Pipecolyl Inhibitor (3/3)

C6.7 Renin Inhibitors

C6.7.1 Therapeutic Utility of Renin Inhibitors C6.7.2 The Design of Renin Inhibitors C6.7.3 Complex of Statine with Rhizopuspepsin C6.7.4 Analysis of the Binding of Statine (1/3) C6.7.5 Analysis of the Binding of Statine (2/3) C6.7.6 Analysis of the Binding of Statine (3/3) C6.7.7 Design of a Macrocyclic Renin Inhibitor C6.7.8 Inaccuracies in Homology Models

C6.8 Inhibitors of PNP

C6.8.1 The Purine Nucleoside Phosphorylase Protease C6.8.2 Therapeutic Utility of PNP Inhibitors C6.8.3 The Complex of Guanine with PNP C6.8.4 Analysis of the Active Site of PNP (1/2) C6.8.5 Analysis of the Active Site of PNP (2/2) C6.8.6 Strategy for the Design of PNP Inhibitors C6.8.7 Design of 9-Deazaguanine Derivatives C6.8.8 Binding of 9-Deaza-Guanine Candidate (1/3) C6.8.9 Binding of 9-Deaza-Guanine Candidate (2/3) C6.8.10 Binding of 9-Deaza-Guanine Candidate (3/3) C6.8.11 Browser of PNP Inhibitors

C6.9 Intercalating Antibiotics

C6.9.1 Therapeutic Utility of Intercalating Agents C6.9.2 Daunorubicin a Potent Anthracycline Antibiotic C6.9.3 Prerequisite for Antibiotic Activity C6.9.4 Complex of Daunorubicin with a Hexanucleotide C6.9.5 Analysis of the Binding of Daunorubicin (1/5) C6.9.6 Analysis of the Binding of Daunorubicin (2/5) C6.9.7 Analysis of the Binding of Daunorubicin (3/5)

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C6.9.8 Analysis of the Binding of Daunorubicin (4/5) C6.9.9 Analysis of the Binding of Daunorubicin (5/5) C6.9.10 Design of Novel Intercalating Agents

C6.10 Dihydrofolate Reductase Inhibitors

C6.10.1 Utility of Dihydrofolate Reductase Inhibitors C6.10.2 Complex of Methotrexate with DHFR C6.10.3 Binding Mode of Methotrexate with DHFR (1/5) C6.10.4 Binding Mode of Methotrexate with DHFR (2/5) C6.10.5 Binding Mode of Methotrexate with DHFR (3/5) C6.10.6 Binding Mode of Methotrexate with DHFR (4/5) C6.10.7 Binding Mode of Methotrexate with DHFR (5/5) C6.10.8 Trimethoprim: a DHFR Inhibitor C6.10.9 The Design of a Novel DHFR-Inhibitor C6.10.10 Complex of Brodimoprim with DHFR C6.10.11 Binding of Brodimoprim with DHFR (1/2) C6.10.12 Binding of Brodimoprim with DHFR (2/2)

C6.11 Sialidase Inhibitors

C6.11.1 The Sialidase Enzyme C6.11.2 Therapeutic Utility of Sialidase Inhibitors C6.11.3 Complex of Sialic Acid with Sialidase C6.11.4 Analysis of Sialic Acid Binding (1/4) C6.11.5 Analysis of Sialic Acid Binding (2/4) C6.11.6 Analysis of Sialic Acid Binding (3/4) C6.11.7 Analysis of Sialic Acid Binding (4/4) C6.11.8 The Design of a Potent Sialidase Inhibitor

C6.12 ADDITIONAL CASE STUDIES

C6.12.1 Additional Case Studies

C6.13 CHAPTER QUIZZES (Available only in Academic License)

D. MOLECULAR BASIS OF DRUGS

D1. MOLECULAR GEOMETRY

D1.1 2D/3D
D1.1.1 Molecules Considered as 2D Structures D1.1.2 The Three-Dimensional Shape of a Molecule

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D1.1.3 2D and 3D Representations D1.1.4 A Molecule: An Assembly of Atoms in 3D D1.1.5 Molecular Lego D1.1.6 Molecular Fragments for Constructing Molecules

D1.2 Conformers
D1.2.1 A Molecule is a Flexible Entity D1.2.2 Conformation Definition D1.2.3 Example of Conformations of a Molecule D1.2.4 Bioactive Conformation

D1.3 Torsion Angles

D1.3.1 Interconversion Between Conformers D1.3.2 How Do Interconversions Occur? D1.3.3 Definition of the Conformers of a Molecule D1.3.4 The Torsion Angle Concept D1.3.5 Definition of Torsion Angles D1.3.6 Monitoring Torsion Angles D1.3.7 Newman Projections and Torsion Angles D1.3.8 Convention for the Sign of Torsion Angles D1.3.9 Ring Conformations

D1.4 Conformational Complexity

D1.4.1 Rigid and Flexible Molecules D1.4.2 Codeine and Fenoxedil D1.4.3 Monitoring Torsion Angle Combinations D1.4.4 Conformational Explosion

D1.5 Ratio of Conformers

D1.5.1 Mixtures of Conformers D1.5.2 Ratio of Conformers and Population

D1.6 CHAPTER QUIZZES (Available only in Academic License)

D2. MOLECULAR PROPERTIES

D2.1 Introduction
D2.1.1 Properties of a Molecule D2.1.2 Average of a Conformational-Dependent Property D2.1.3 Importance of the 3D Molecular Geometries

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D2.2 Biological Properties

D2.2.1 Biological Properties of Proteins D2.2.2 Biological Properties of Chiral Analgesics

D2.3 Physical Properties

D2.3.1 Physical Properties D2.3.2 Calculation of Other Physical Properties

D2.4 Chemical Properties

D2.4.1 Chemical Properties D2.4.2 Enolization of Keto-3 Steroids D2.4.3 Relative Stability of Isomers D2.4.4 Relative Stability of the two Isomers of Trans-Octalin D2.4.5 Geometrical Preference Explains Enolization D2.4.6 Reactivity of Alkyl Halides D2.4.7 SN2 Mechanism D2.4.8 E2 Elimination Mechanism D2.4.9 Molecular Geometries and Chemical Properties

D2.5 Many Properties

D2.5.1 Many Properties of a Molecule

D2.6 CHAPTER QUIZZES (Available only in Academic License)

D3. STEREOCHEMISTRY

D3.1 Introduction
D3.1.1 Introduction on Stereochemistry D3.1.2 Bond Lengths D3.1.3 Bond Multiplicity D3.1.4 Atom Size D3.1.5 Electronegativity D3.1.6 Hybridization D3.1.7 Bond Angles D3.1.8 Thorpe-Ingold Effect D3.1.9 Torsion Angles D3.1.10 Torsion Angle Sign Convention D3.1.11 Examples of Torsion Angles D3.1.12 Torsion Angle Descriptor (sp3-sp3) D3.1.13 Torsion Angle Descriptor (sp2-sp3)

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D3.2 Chirality
D3.2.1 Chirality D3.2.2 Example 1 D3.2.3 Example 2 D3.2.4 Chirality Descriptor: Optical Rotation D3.2.5 Chirality Nomenclature D3.2.6 The Order of Priority (1/5) D3.2.7 The Order of Priority (2/5) D3.2.8 The Order of Priority (3/5) D3.2.9 The Order of Priority (4/5) D3.2.10 The Order of Priority (5/5) D3.2.11 Examples of R/S Assignments (1/4) D3.2.12 Examples of R/S Assignments (2/4) D3.2.13 Examples of R/S Assignments (3/4) D3.2.14 Examples of R/S Assignments (4/4) D3.2.15 The Newman Projection D3.2.16 The Fischer Projection (1/3) D3.2.17 The Fischer Projection (2/3) D3.2.18 The Fischer Projection (3/3) D3.2.19 Chirality: D/L D3.2.20 D-alanine D3.2.21 L-alanine D3.2.22 Chirality: Erythro/Threo D3.2.23 Threo D3.2.24 Erythro D3.2.25 Other Examples of Chiral Molecules: Example 1 D3.2.26 Example 2 of Chiral Molecule D3.2.27 Example 3 of Chiral Molecule D3.2.28 Example 4 of Chiral Molecule D3.2.29 Example 5 of Chiral Molecule D3.2.30 Example 6 of Chiral Molecule

D3.3 Double Bonds

D3.3.1 Cis-Trans Stereochemistry of Double Bonds D3.3.2 E/Z Stereochemistry of Double Bonds D3.3.3 s-cis/s-trans Conformations D3.3.4 Re/Si Nomenclature of the Faces of Double Bonds

D3.4 Rings
D3.4.1 Rings D3.4.2 Chair D3.4.3 Boat D3.4.4 Twist Boat D3.4.5 Crown

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D3.4.6 Rings: Axial and Equatorial Orientations

D3.5 Symmetry
D3.5.1 Introduction on Symmetry Operations D3.5.2 Symmetry C2 D3.5.3 Symmetry C3 D3.5.4 Symmetry Sigma D3.5.5 Inversion (i) D3.5.6 Example of Inversion D3.5.7 Rotatory Reflection (Sn)

D3.6 CHAPTER QUIZZES (Available only in Academic License)

D4. MOLECULAR ENERGIES

D4.1 Introduction
D4.1.1 Internal Energy of a Molecule D4.1.2 Internal Energy Associated to a Conformation D4.1.3 Transition State D4.1.4 Potential Surface D4.1.5 Thermodynamics & Kinetics

D4.2 Thermodynamics
D4.2.1 Thermodynamics: Conformer Populations D4.2.2 Thermodynamics: Boltzmann Equation D4.2.3 Boltzmann Population Analysis for Two Conformers D4.2.4 Boltzmann Population Analysis for 3 Conformers D4.2.5 Thermodynamics: Cyclohexane Example D4.2.6 Populations of Twisted-Boat and Chair Conformers D4.2.7 Thermodynamics: Methylcyclohexane Example

D4.3 Kinetics
D4.3.1 Kinetics D4.3.2 Kinetics: Arrhenius Equation D4.3.3 Kinetics: Arrhenius Graph D4.3.4 Kinetics Ethane Example D4.3.5 Torsional Barrier in Ethane D4.3.6 Kinetics Cyclohexane Example D4.3.7 Interconversion Barrier in Cyclohexane D4.3.8 Kinetics Amide Bond Example D4.3.9 Amide Barrier Crossed Every 10 Seconds

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D4.4 Molecular Modeling

D4.4.1 Molecular Modeling D4.4.2 Example of Kinetic or Thermodynamic Control D4.4.3 Interconversion Between the Two Forms D4.4.4 Lowering the Energy of the Transition State D4.4.5 Interconversion Between the Two Forms D4.4.6 Raising the Energy of the Transition State D4.4.7 Interconversion Between the Two Forms D4.4.8 Modifying Conformers Populations D4.4.9 Repulsions More Important in the Boat Form D4.4.10 Tropane is Found Only in a Chair Conformation D4.4.11 Example of Atropisomerism D4.4.12 Molecular Energies: The Key of Molecular Modeling

D4.5 Modeling in Drug Design

D4.5.1 Molecular Modeling in Drug Design D4.5.2 Importance of Energies: the Morphinan Example D4.5.3 Morphinan and D-nor Morphinan Alignment D4.5.4 Conformational Analysis of Morphinan D4.5.5 Conformational Analysis of D-nor Morphinan D4.5.6 A Rationale for Explaining the Activities Observed D4.5.7 Morphinan: Validation and Design D4.5.8 Preferred Conformer of Active Enantiomer D4.5.9 Preferred Conformer of Inactive Enantiomer D4.5.10 Restoring Activities to the Inactive Analog? D4.5.11 Morphinan Browser D4.5.12 What We Can Learn From The Morphinan Example

D4.6 How to Calculate Energies

D4.6.1 The Need of Tools for Calculating Energies D4.6.2 Two Methods for Calculating Energies

D4.7 Quantum Mechanics

D4.7.1 Calculation of Energies by the Schrodinger Equation D4.7.2 Ab-Initio and Semi-empirical Calculations D4.7.3 Calculation of Energies D4.7.4 The Density Function Theory D4.7.5 The Choice of a Method

D4.8 Molecular Mechanics

D4.8.1 Molecular Mechanics D4.8.2 Force-Field D4.8.3 Force Field Components D4.8.4 Bond Lengths: Stretching Contributions

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D4.8.5 Function D4.8.6 Examples of Elementary Stretching Contributions D4.8.7 Bond Angles: Bending Contributions D4.8.8 Function D4.8.9 Examples of Elementary Bending Contributions D4.8.10 Torsion Angles: Torsional Contributions D4.8.11 Function D4.8.12 Examples of Elementary Torsional Contributions D4.8.13 Van der Waals Interactions D4.8.14 Function D4.8.15 Examples of Elementary Van der Waals D4.8.16 Electrostatic Dipolar Contributions D4.8.17 Function D4.8.18 Examples of Elementary Electrostatic Contributions D4.8.19 Hydrogen Bond Energy Contributions D4.8.20 Function D4.8.21 Examples of Elementary Hydrogen Bond Contributions D4.8.22 Total Energy in a Force Field Calculation D4.8.23 Main Force Fields D4.8.24 What One Should Remember D4.8.25 Relative Energies

D4.9 CHAPTER QUIZZES (Available only in Academic License)

D5. CONFORMATIONAL ANALYSIS

D5.1 Introduction
D5.1.1 Geometries, Energies and Conformational Analysis D5.1.2 Energy Profile: a Global Information D5.1.3 Definition of Conformational Analysis

D5.2 Potential Surface

D5.2.1 Conformational Potential Surface: One Rotation D5.2.2 Conformational Potential Surface: Two Rotations D5.2.3 Energy Profile Viewed from the Top D5.2.4 Energy Profile Viewed as Contour Lines D5.2.5 Conformational Potential Surface D5.2.6 Special Forms D5.2.7 Interconversion Between Conformers D5.2.8 Energy Barriers D5.2.9 Interconversion Pathway

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D5.3 Conformational Analysis

D5.3.1 Conformational Analysis Principles D5.3.2 Systematic Scanning of All Potential Surfaces D5.3.3 Systematic Scanning is Time Consuming D5.3.4 How to Reduce Conformational Search? D5.3.5 One Conformer Represents a Whole Family D5.3.6 Working with a Set of Representative Conformers D5.3.7 Sildenafil Example D5.3.8 Family Representatives: Small Rings D5.3.9 Family Representatives: Acyclic Bonds D5.3.10 Consequence: Minimization Treatments D5.3.11 Example: Analysis of Elementary Fragments D5.3.12 Example: Generation of Representative Conformers D5.3.13 Example: Results of Conformational Analysis D5.3.14 Conformational Analysis Principles: Summary

D5.4 Minimizations
D5.4.1 Definition of the Minimization of a Conformer D5.4.2 Improved Geometries and Good Energies D5.4.3 The Minimization Treatment D5.4.4 How Does Minimization Works? D5.4.5 Minimization Methods D5.4.6 Many Variables Are Minimized D5.4.7 Minimization is a Time-Consuming Treatment

D5.5 Examples of Minimization

D5.5.1 Minimization with Stretching Strain D5.5.2 Minimization with Bending Strain D5.5.3 Minimization with Torsional Strain D5.5.4 Minimization with Van der Waals Strain D5.5.5 Minimization with Electrostatic Component D5.5.6 Minimization with Hydrogen Bond Component D5.5.7 Typical Minimization Example D5.5.8 Distribution of Energy Strain

D5.6 Conformational Analysis in Drug Design

D5.6.1 Conformational Analysis in Drug Design D5.6.2 Energy of the Bioactive Form D5.6.3 Low Energy of the Bioactive Conformation D5.6.4 Geometry of the Bioactive Conformation D5.6.5 The Experienced Molecular Modeler D5.6.6 Common Errors Made with Minimization D5.6.7 Example 1 D5.6.8 Example 2

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D5.7 Molecular Dynamics

D5.7.1 Molecular Dynamics D5.7.2 Theoretical Basis of Molecular Dynamic Calculations D5.7.3 Local Minima and Global Minimum D5.7.4 Simulated Annealing, a Special Type of Dynamics D5.7.5 Coherency of Molecular Motions D5.7.6 A Typical Molecular Dynamics Run

D5.8 CHAPTER QUIZZES (Available only in Academic License)

D6. MOLECULAR GRAPHICS

D6.1 Introduction
D6.1.1 Importance of Molecular Graphics D6.1.2 Almost Science Fiction D6.1.3 History of Molecular Visualizations D6.1.4 1975-1978 D6.1.5 1978-1980 D6.1.6 1980-1995 D6.1.7 1995-now D6.1.8 Commercially Available Molecular Kits D6.1.9 Progress in Graphical Hardware and Algorithms D6.1.10 Algorithm 1 D6.1.11 Algorithm 2 D6.1.12 Molecular Graphics Functions

D6.2 3D Perception
D6.2.1 The Perception of the Third Dimension D6.2.2 From 3D Coordinates to Screen Coordinates D6.2.3 2D Projection is Not Sufficient D6.2.4 Real Time Manipulation D6.2.5 Depth Cueing D6.2.6 Perspective D6.2.7 Stereo D6.2.8 Hardware Stereo

D6.3 Visualization
D6.3.1 3D Representation of Small Molecules D6.3.2 Line D6.3.3 Stick

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D6.3.4 Ball & Stick D6.3.5 CPK D6.3.6 Quality of Rendering D6.3.7 Atomic Color-Code Convention D6.3.8 Coloring Molecules or Sets of Atoms D6.3.9 By Atom-type D6.3.10 By Molecule D6.3.11 By Color D6.3.12 By Properties D6.3.13 Labeling Functionalities D6.3.14 Atom Labels D6.3.15 Atom Numbering D6.3.16 Proteins Representation D6.3.17 Carbon Alpha D6.3.18 Ribbon Representation D6.3.19 Ribbon Types D6.3.20 Visualization of Protein Properties

D6.4 Editing & Manipulation

D6.4.1 Structure Manipulation & Editing D6.4.2 Add Atoms Function D6.4.3 Delete Atoms Function D6.4.4 Fuse Atoms Function D6.4.5 Connect atoms Function D6.4.6 3D Molecular Constructions D6.4.7 Real-Time Rotations, Translations and Zoom D6.4.8 Translations D6.4.9 Rotations D6.4.10 Zoom D6.4.11 Control of Torsion Angles D6.4.12 Slab and Clip

D6.5 Surfaces & Volumes

D6.5.1 Concept and Definition of Molecular Surfaces D6.5.2 Van der Waals D6.5.3 Solvent D6.5.4 Connolly D6.5.5 Surface Types D6.5.6 Normal D6.5.7 Transparent D6.5.8 Dots D6.5.9 Visualization of Properties on Molecular Surfaces D6.5.10 Color Coded D6.5.11 Visualization of Properties on Molecular Surfaces D6.5.12 The Visualization of Volumes

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D6.5.13 Mathematical Boolean Operations with Volumes

D6.6 Visualizing Interactions

D6.6.1 Visualization of Hydrogen Bonds D6.6.2 Visualization of Molecular Bumps D6.6.3 Surface Representations for Bump Analyses D6.6.4 Complementary Surface Properties D6.6.5 Electrostatic Potentials D6.6.6 Lipophilicity Potentials D6.6.7 Visualization of Intramolecular Interaction D6.6.8 Schematic Complex Interaction D6.6.9 Visualization of a Complex Cavity D6.6.10 Overview of the Entire Complex D6.6.11 Results of Quantum Mechanical Calculations

D6.7 CHAPTER QUIZZES (Available only in Academic License)

D7. SELECTED EXAMPLES IN 3D ANALYSIS

D7.1 Conformational Analysis

D7.1.1 Ethane D7.1.2 n-Butane D7.1.3 1-Butene D7.1.4 Butadiene D7.1.5 Amide D7.1.6 Cyclohexane

D7.2 Conjugated Systems

D7.2.1 Butadiene D7.2.2 Pentenone D7.2.3 Dipyrrole D7.2.4 Biphenyl D7.2.5 Atropisomerism of Biphenyls D7.2.6 Binaphthyl

D7.3 Aromatic Systems

D7.3.1 Planarity of Polyaromatic Systems D7.3.2 Distorted Naphthalene D7.3.3 Annelated Polyaromatic Benzenes D7.3.4 Fusing Another Ring D7.3.5 Fusing Again Another Ring

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D7.3.6 Continue to Fuse Additional Rings

D7.4 Cyclic Systems

D7.4.1 Why Substituents Prefer to be Equatorial? D7.4.2 Mono-Substituted Cyclohexanes D7.4.3 t-Bu D7.4.4 Phenyl D7.4.5 Methyl D7.4.6 Hydroxy D7.4.7 Example of Preferred Axial Conformer D7.4.8 Di-Methyl-1,2-Cyclohexane D7.4.9 Trans D7.4.10 Cis D7.4.11 Di-Methyl-1,3-Cyclohexane D7.4.12 Trans D7.4.13 Cis D7.4.14 Di-Methyl-1,4-Cyclohexane D7.4.15 Trans D7.4.16 Cis D7.4.17 Trans 1,3-Di-t-Butyl-Cyclohexane D7.4.18 Chloro-2 Cyclohexanone

D7.5 Other Systems

D7.5.1 Decalins D7.5.2 Cis-decalin D7.5.3 Methyl-Cis-decalin D7.5.4 Trans-decalin D7.5.5 Interactions of Aromatic Rings D7.5.6 Interactions Revealed by X-Ray Crystallography D7.5.7 Two Major Types of Aromatic Interactions D7.5.8 Overview of Possible Interactions D7.5.9 Geometry of Ester Groups D7.5.10 Cyclic Ester D7.5.11 Geometry of Amide Groups D7.5.12 Substituted Amide D7.5.13 Cyclic Amide

E. GENERAL TOPICS
E1. GENERAL INTRODUCTION TO DRUGS

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E1.1 What is a Drug

E1.1.1 What is a Drug? E1.1.2 Improvement of Life Expectancy E1.1.3 Origin of Active Principles E1.1.4 Drug Formulation E1.1.5 Multiple Names of Drugs E1.1.6 Example of Multiple Names of a Drug E1.1.7 Requirements for the Ideal Drug E1.1.8 Safety E1.1.9 Properties E1.1.10 Compliance E1.1.11 Pharmacology E1.1.12 Metabolism and ADME E1.1.13 Side Effects and Toxicity

E1.2 The Pharmaceutical Industry

E1.2.1 Drug Discovery and Development, a Long Process E1.2.2 Drug Discovery and Drug Development E1.2.3 One Million Studied for One to Reach the Market E1.2.4 Pharmaceutical R&D, a High-Risk Undertaking E1.2.5 The Time of Developing a New Drug E1.2.6 The Cost of Developing a New Drug E1.2.7 Reasons for Termination of Development

E1.3 Industry Focus Area

E1.3.1 Industry Focus Areas and Examples of Useful Drugs E1.3.2 Cardiovascular System (CVS) E1.3.3 Antiarrhytmics E1.3.4 Antihypertensive E1.3.5 Vasodilatation E1.3.6 Anticoagulants E1.3.7 Antihyperlipidemic E1.3.8 Anti-infective Agents E1.3.9 Antibiotics E1.3.10 Antiviral E1.3.11 Antifungals E1.3.12 Antimalarias E1.3.13 Antituberculosis E1.3.14 Central Nervous System (CNS) Agents E1.3.15 Antipsychotics E1.3.16 Cholinergic E1.3.17 Parkinsonians E1.3.18 Anticonvulsants E1.3.19 Antidepressants

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E1.3.20 Tranquilizers E1.3.21 Adrenergic E1.3.22 Gastro-Intestinal Drugs E1.3.23 Antidiarrhea E1.3.24 Laxatives E1.3.25 Anti-emetics E1.3.26 Anti-Ulcers E1.3.27 Anti-Neoplastic (Anti Cancer) Agents E1.3.28 Alkylating E1.3.29 Antimetabolites E1.3.30 Anti-neoplastic E1.3.31 Immunosuppressants E1.3.32 Taxoids E1.3.33 Respiratory Agents E1.3.34 Bronchodilators E1.3.35 Antihistamines E1.3.36 Antitussives E1.3.37 Anti-Rheumatism and Pain Agents E1.3.38 Anti-inflammatory E1.3.39 Anti-rheumatism E1.3.40 Analgesics E1.3.41 Anesthetics E1.3.42 Agents Against Metabolic Disorders E1.3.43 Antidiabetic E1.3.44 Antiosteoporotic E1.3.45 Thyroid Hormone E1.3.46 Steroids E1.3.47 Diagnostic Agents

E1.4 CHAPTER QUIZZES (Available only in Academic License)

E2. DRUG DISCOVERY

E2.1 Introduction
E2.1.1 Drug Discovery E2.1.2 Target Identification E2.1.3 Lead Discovery E2.1.4 Lead Optimization E2.1.5 Disciplines Involved in Drug Discovery

E2.2 Discovery Methods

E2.2.1 How Are Leads Discovered?

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E2.3 Serendipity
E2.3.1 The Serendipitous Pathway E2.3.2 Penicillin E2.3.3 Aspirin E2.3.4 Glafenine E2.3.5 Furosemide E2.3.6 Chlorpromazine E2.3.7 Cyclosporin A E2.3.8 Viagra

E2.4 Screening
E2.4.1 The Screening Pathway E2.4.2 Example of Molecules Discovered by Screening

E2.5 Chemical Modification

E2.5.1 The Chemical Modification Pathway E2.5.2 Tagamet E2.5.3 Beta-Blockers E2.5.4 Limitation of the Chemical Modification Approach

E2.6 Rational Drug Design

E2.6.1 The Rational Pathway E2.6.2 Captopril Story E2.6.3 Cimetidine Story E2.6.4 The Histamine Action E2.6.5 Screening Molecules Related to Histamine E2.6.6 The Guanidine Analog E2.6.7 The Burimamide Lead E2.6.8 The Metiamide Molecule E2.6.9 The Cimetidine Drug E2.6.10 The Ranitidine Drug E2.6.11 Advantages of Rational Drug Design

E2.7 Chemistry in Drug Discovery

E2.7.1 Chemistry in Drug Discovery E2.7.2 Synthesis of Complicated Molecules E2.7.3 Penicillin E2.7.4 Taxol E2.7.5 Steroid E2.7.6 Three Methods in Synthetic Chemistry E2.7.7 Classical E2.7.8 Parallel E2.7.9 Combinatorial E2.7.10 Chemistry in Lead Discovery

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E2.7.11 Protein Kinase Example E2.7.12 Chemistry in Lead Optimization E2.7.13 Optimization of the Gleevec Series E2.7.14 CCK-A Receptor Antagonist Example E2.7.15 Chemistry in Drug Development

E2.8 Patents
E2.8.1 Intellectual Property and Patents E2.8.2 What Can be Patented? E2.8.3 Requirements for Patentability E2.8.4 Lifetime of a Patent E2.8.5 Effective Patent Lifetime E2.8.6 Patent Protection

E2.9 CHAPTER QUIZZES (Available only in Academic License)

E3. DRUG DEVELOPMENT

E3.1 Introduction
E3.1.1 Drug Development E3.1.2 Pipe-Line of Development E3.1.3 Pre-Clinical Development E3.1.4 Clinical Development E3.1.5 Post-marketing Surveillance E3.1.6 Disciplines Involved in Drug Development E3.1.7 Effective Teams: Interactivity and Cooperativity

E3.2 The Pre-Clinical Studies

E3.2.1 Pre-Clinical Studies E3.2.2 Chemical Development E3.2.3 Pharmacological Studies E3.2.4 Drug Metabolism and Pharmacokinetics E3.2.5 Toxicology Studies E3.2.6 Acute Toxicity E3.2.7 Safety Studies E3.2.8 Carcinogenicity E3.2.9 Mutagenicity E3.2.10 Reproduction Studies E3.2.11 Formulation Development E3.2.12 Stability Tests E3.2.13 Disciplines Involved in Pre-Clinical Development

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E3.3 Clinical Development

E3.3.1 Introduction on Clinical Trials E3.3.2 Clinical Trials Phase 1 E3.3.3 Clinical Trials Phase 2 E3.3.4 Clinical Trials Phase 3 E3.3.5 Clinical Trials Phase 4 E3.3.6 Disciplines Involved in Drug Development

E3.4 Regulatory Affairs

E3.4.1 The Role of the Food and Drug Administration (FDA) E3.4.2 The Investigational New Drug Application (IND) E3.4.3 The New Drug Application (NDA) E3.4.4 The Regulatory Approval Process

E3.5 CHAPTER QUIZZES (Available only in Academic License)

Molecular Conceptor 2.16 Synergix ltd. 1996-2012

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