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Molecular Interaction Fields [[electronic resource] ] : Applications in Drug Discovery and ADME Prediction
| Molecular Interaction Fields [[electronic resource] ] : Applications in Drug Discovery and ADME Prediction |
| Autore | Cruciani Gabriele |
| Pubbl/distr/stampa | Hoboken, : Wiley, 2006 |
| Descrizione fisica | 1 online resource (323 p.) |
| Disciplina | 615.19 |
| Altri autori (Persone) |
MannholdRaimund
KubinyiHugo FolkersGerd |
| Collana | Methods and Principles in Medicinal Chemistry |
| Soggetto topico |
Biomolecules
Chemical reactions -- Computer simulation Chemicals -- Pharmacokinetics -- Forecasting Chemicals -- Physiological effect -- Forecasting Drug development Pharmaceutical chemistry Structure-activity relationships (Biochemistry) -- Computer simulation Pharmaceutical chemistry - Physiological effect - Forecasting Chemicals - Computer simulation Chemical reactions - Computer simulation Structure-activity relationships (Biochemistry) Computational Biology Models, Molecular Quantitative Structure-Activity Relationship Computer Simulation Drug Design Pharmaceutical Preparations Software Structure-Activity Relationship Biology Drug Discovery Computing Methodologies Chemicals and Drugs Models, Theoretical Biological Science Disciplines Chemistry, Pharmaceutical Biochemical Phenomena Information Science Pharmacological Phenomena Investigative Techniques Natural Science Disciplines Analytical, Diagnostic and Therapeutic Techniques and Equipment Pharmacology Physiological Phenomena Chemistry Chemical Phenomena Phenomena and Processes Disciplines and Occupations Pharmacy, Therapeutics, & Pharmacology History of Medicine Health & Biological Sciences Medicine |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-280-85421-9
9786610854219 3-527-60767-6 3-527-60713-7 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Molecular Interaction Fields; A Personal Foreword; Contents; Preface; List of Contributors; I Introduction; 1 The Basic Principles of GRID; 1.1 Introduction; 1.2 Philosophy and Objectives; 1.3 Priorities; 1.4 The GRID Method; 1.4.1 GRID Probes Are Anisometric; 1.4.2 The Target "Responds" to the Probe; 1.4.3 The Target is Immersed in Water; 1.5 The GRID Force Field; 1.5.1 The Lennard-Jones Term; 1.5.2 The Electrostatic Term; 1.5.3 The Hydrogen Bond Term; 1.5.4 The Other Terms; 1.6 Nomenclature; 1.6.1 "ATOM" Records; 1.6.2 "HETATM" Records; 1.7 Calibrating the GRID Force Field
1.7.1 Checking the Calibration1.7.2 Checking Datafile GRUB; 1.8 The Output from GRID; 1.8.1 GRID Maps from Macromolecules; 1.8.2 GRID Maps from a Small Molecule; 1.9 Conclusions; 2 Calculation and Application of Molecular Interaction Fields; 2.1 Introduction; 2.2 Calculation of MIFs; 2.2.1 The Target; 2.2.2 The Probe; 2.2.3 The Interaction Function; 2.2.3.1 Van der Waals Interactions; 2.2.3.2 Electrostatic Interactions; 2.2.3.3 Hydrogen Bonds; 2.2.3.4 Entropy; 2.3 Selected Applications of MIFs; 2.3.1 Mapping a Ligand Binding Site in a Protein; 2.3.2 Deriving 3D-QSARs 2.3.3 Similarity Analysis of a Set of Related Molecules2.4 Concluding Remarks and Outlook; II Pharmacodynamics; 3 Protein Selectivity Studies Using GRID-MIFs; 3.1 Introduction; 3.2 GRID Calculations and Chemometric Analysis; 3.2.1 Source and Selection of Target Structures; 3.2.2 Selection and Superimposition of Binding Sites; 3.2.3 Calculation of the Molecular Interaction Field; 3.2.4 Matrix Generation and Pretreatments; 3.2.4.1 Region Cut-outs; 3.2.5 GRID/PCA; 3.2.5.1 Score Plots; 3.2.5.2 Two-Dimensional Loading Plots; 3.2.5.3 Loading Contour Maps; 3.2.5.4 Problems of GRID/PCA 3.2.6 GRID/CPCA3.2.6.1 Block Unscaled Weights; 3.2.6.2 CPCA; 3.2.6.3 Identification of Important Variable Blocks for Selectivity; 3.2.6.4 Contour Plots; 3.3 Applications; 3.3.1 DNA Minor Groove Binding - Compare AAA and GGG Double Helix; 3.3.2 Dihydrofolate Reductase; 3.3.3 Cyclooxygenase; 3.3.4 Penicillin Acylase; 3.3.5 Serine Proteases; 3.3.5.1 S1 Pocket; 3.3.5.2 P Pocket; 3.3.5.3 D Pocket; 3.3.6 CYP450; 3.3.7 Target Family Landscapes of Protein Kinases; 3.3.8 Matrix Metalloproteinases (MMPs); 3.3.9 Nitric Oxide Synthases; 3.3.10 PPARs; 3.3.11 Bile Acid Transportation System 3.3.12 Ephrin Ligands and Eph Kinases3.4 Discussion and Conclusion; 4 FLAP: 4-Point Pharmacophore Fingerprints from GRID; 4.1 Introduction; 4.1.1 Pharmacophores and Pharmacophore Fingerprints; 4.1.2 FLAP; 4.2 FLAP Theory; 4.3 Docking; 4.3.1 GLUE: A New Docking Program Based on Pharmacophores; 4.3.2 Case Study; 4.4 Structure Based Virtual Screening (SBVS); 4.5 Ligand Based Virtual Screening (LBVS); 4.6 Protein Similarity; 4.7 TOPP (Triplets of Pharmacophoric Points); 4.8 Conclusions; 5 The Complexity of Molecular Interaction: Molecular Shape Fingerprints by the PathFinder Approach 5.1 Introduction |
| Record Nr. | UNINA-9910144275303321 |
Cruciani Gabriele
|
||
| Hoboken, : Wiley, 2006 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Molecular Interaction Fields [[electronic resource] ] : Applications in Drug Discovery and ADME Prediction
| Molecular Interaction Fields [[electronic resource] ] : Applications in Drug Discovery and ADME Prediction |
| Autore | Cruciani Gabriele |
| Pubbl/distr/stampa | Hoboken, : Wiley, 2006 |
| Descrizione fisica | 1 online resource (323 p.) |
| Disciplina | 615.19 |
| Altri autori (Persone) |
MannholdRaimund
KubinyiHugo FolkersGerd |
| Collana | Methods and Principles in Medicinal Chemistry |
| Soggetto topico |
Biomolecules
Chemical reactions -- Computer simulation Chemicals -- Pharmacokinetics -- Forecasting Chemicals -- Physiological effect -- Forecasting Drug development Pharmaceutical chemistry Structure-activity relationships (Biochemistry) -- Computer simulation Pharmaceutical chemistry - Physiological effect - Forecasting Chemicals - Computer simulation Chemical reactions - Computer simulation Structure-activity relationships (Biochemistry) Computational Biology Models, Molecular Quantitative Structure-Activity Relationship Computer Simulation Drug Design Pharmaceutical Preparations Software Structure-Activity Relationship Biology Drug Discovery Computing Methodologies Chemicals and Drugs Models, Theoretical Biological Science Disciplines Chemistry, Pharmaceutical Biochemical Phenomena Information Science Pharmacological Phenomena Investigative Techniques Natural Science Disciplines Analytical, Diagnostic and Therapeutic Techniques and Equipment Pharmacology Physiological Phenomena Chemistry Chemical Phenomena Phenomena and Processes Disciplines and Occupations Pharmacy, Therapeutics, & Pharmacology History of Medicine Health & Biological Sciences Medicine |
| ISBN |
1-280-85421-9
9786610854219 3-527-60767-6 3-527-60713-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Molecular Interaction Fields; A Personal Foreword; Contents; Preface; List of Contributors; I Introduction; 1 The Basic Principles of GRID; 1.1 Introduction; 1.2 Philosophy and Objectives; 1.3 Priorities; 1.4 The GRID Method; 1.4.1 GRID Probes Are Anisometric; 1.4.2 The Target "Responds" to the Probe; 1.4.3 The Target is Immersed in Water; 1.5 The GRID Force Field; 1.5.1 The Lennard-Jones Term; 1.5.2 The Electrostatic Term; 1.5.3 The Hydrogen Bond Term; 1.5.4 The Other Terms; 1.6 Nomenclature; 1.6.1 "ATOM" Records; 1.6.2 "HETATM" Records; 1.7 Calibrating the GRID Force Field
1.7.1 Checking the Calibration1.7.2 Checking Datafile GRUB; 1.8 The Output from GRID; 1.8.1 GRID Maps from Macromolecules; 1.8.2 GRID Maps from a Small Molecule; 1.9 Conclusions; 2 Calculation and Application of Molecular Interaction Fields; 2.1 Introduction; 2.2 Calculation of MIFs; 2.2.1 The Target; 2.2.2 The Probe; 2.2.3 The Interaction Function; 2.2.3.1 Van der Waals Interactions; 2.2.3.2 Electrostatic Interactions; 2.2.3.3 Hydrogen Bonds; 2.2.3.4 Entropy; 2.3 Selected Applications of MIFs; 2.3.1 Mapping a Ligand Binding Site in a Protein; 2.3.2 Deriving 3D-QSARs 2.3.3 Similarity Analysis of a Set of Related Molecules2.4 Concluding Remarks and Outlook; II Pharmacodynamics; 3 Protein Selectivity Studies Using GRID-MIFs; 3.1 Introduction; 3.2 GRID Calculations and Chemometric Analysis; 3.2.1 Source and Selection of Target Structures; 3.2.2 Selection and Superimposition of Binding Sites; 3.2.3 Calculation of the Molecular Interaction Field; 3.2.4 Matrix Generation and Pretreatments; 3.2.4.1 Region Cut-outs; 3.2.5 GRID/PCA; 3.2.5.1 Score Plots; 3.2.5.2 Two-Dimensional Loading Plots; 3.2.5.3 Loading Contour Maps; 3.2.5.4 Problems of GRID/PCA 3.2.6 GRID/CPCA3.2.6.1 Block Unscaled Weights; 3.2.6.2 CPCA; 3.2.6.3 Identification of Important Variable Blocks for Selectivity; 3.2.6.4 Contour Plots; 3.3 Applications; 3.3.1 DNA Minor Groove Binding - Compare AAA and GGG Double Helix; 3.3.2 Dihydrofolate Reductase; 3.3.3 Cyclooxygenase; 3.3.4 Penicillin Acylase; 3.3.5 Serine Proteases; 3.3.5.1 S1 Pocket; 3.3.5.2 P Pocket; 3.3.5.3 D Pocket; 3.3.6 CYP450; 3.3.7 Target Family Landscapes of Protein Kinases; 3.3.8 Matrix Metalloproteinases (MMPs); 3.3.9 Nitric Oxide Synthases; 3.3.10 PPARs; 3.3.11 Bile Acid Transportation System 3.3.12 Ephrin Ligands and Eph Kinases3.4 Discussion and Conclusion; 4 FLAP: 4-Point Pharmacophore Fingerprints from GRID; 4.1 Introduction; 4.1.1 Pharmacophores and Pharmacophore Fingerprints; 4.1.2 FLAP; 4.2 FLAP Theory; 4.3 Docking; 4.3.1 GLUE: A New Docking Program Based on Pharmacophores; 4.3.2 Case Study; 4.4 Structure Based Virtual Screening (SBVS); 4.5 Ligand Based Virtual Screening (LBVS); 4.6 Protein Similarity; 4.7 TOPP (Triplets of Pharmacophoric Points); 4.8 Conclusions; 5 The Complexity of Molecular Interaction: Molecular Shape Fingerprints by the PathFinder Approach 5.1 Introduction |
| Record Nr. | UNINA-9910829869103321 |
|
Cruciani Gabriele
|
||
| Hoboken, : Wiley, 2006 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Thermodynamics and kinetics of drug binding / / edited by György M. Keserü and David C. Swinney
| Thermodynamics and kinetics of drug binding / / edited by György M. Keserü and David C. Swinney |
| Pubbl/distr/stampa | Weinheim, Germany : , : Wiley-VCH Verlag, , 2015 |
| Descrizione fisica | 1 online resource (765 p.) |
| Disciplina | 615.7 |
| Collana | Methods and Principles in Medicinal Chemistry |
| Soggetto topico |
Binding sites (Biochemistry) - Thermodynamics
Pharmacokinetics |
| ISBN |
3-527-67302-4
3-527-67304-0 3-527-67305-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Series; Title Page; Copyright; List of Contributors; Preface; A Personal Foreword; Section I; Chapter 1: The Binding Thermodynamics of Drug Candidates; 1.1 Affinity Optimization; 1.2 The Binding Affinity; 1.3 The Enthalpy Change; 1.4 The Entropy Change; 1.5 Engineering Binding Contributions; 1.6 Lipophilic Efficiency and Binding Enthalpy; Acknowledgments; References; Chapter 2: van't Hoff Based Thermodynamics; 2.1 Relevance of Thermodynamics to Pharmacology; 2.2 Affinity Constant Determination; 2.3 The Origin of van't Hoff Equation
2.4 From van't Hoff toward Thermodynamic Discrimination2.5 Representation of ΔG°, ΔH°, and ΔS° Data; 2.6 The Adenosine Receptors Binding Thermodynamics Story; 2.7 Binding Thermodynamics of G-Protein Coupled Receptors; 2.8 Binding Thermodynamics of Ligand-Gated Ion Channel Receptors; 2.9 Discussion; Abbreviations; References; Chapter 3: Computation of Drug-Binding Thermodynamics; 3.1 Introduction; 3.2 Potential of Mean Force Calculations; 3.3 Alchemical Transformations; 3.4 Nonequilibrium Methods; 3.5 MM-PBSA; 3.6 Linear Interaction Energy; 3.7 Scoring Functions; 3.8 Free-energy Components 3.9 SummaryReferences; Chapter 4: Thermodynamics-Guided Optimizations in Medicinal Chemistry; 4.1 Introduction; 4.2 The Thermodynamics of Medicinal Chemistry Optimizations; 4.3 Selection of Suitable Starting Points; 4.4 Thermodynamics Based Optimization Strategies; References; Chapter 5: From Molecular Understanding to Structure-Thermodynamic Relationships, the Case of Acetylcholine Binding Proteins; 5.1 Introduction; 5.2 Acetylcholine Binding Proteins (AChBPs); 5.3 Thermodynamics of Small Molecule Binding at AChBPs; 5.4 Concluding Remarks and Outlook; References Chapter 6: Thermodynamics in Lead Optimization6.1 Introduction to Lead Optimization in Drug Discovery; 6.2 Measurement of Thermodynamic Parameters in Lead Optimization; 6.3 Advantages during Lead Optimization for Thermodynamic Measurements; 6.4 Exploitation of Measured Thermodynamics in Lead Optimization; 6.5 Lead Optimization beyond Affinity; 6.6 Exemplary Case Studies; 6.7 Potential Complicating Factors in Exploiting Thermodynamics in Lead Optimization; 6.8 Summary; References; Chapter 7: Thermodynamic Profiling of Carbonic Anhydrase Inhibitors; 7.1 Introduction 7.2 Thermodynamic Profiles of Fragment Inhibitors7.3 Thermodynamics of Fragment Growing; 7.4 Conclusions; Acknowledgments; References; Section II; Chapter 8: Drug-Target Residence Time; 8.1 Introduction; 8.2 Open and Closed Systems in Biology; 8.3 Mechanisms of Drug-Target Interactions; 8.4 Impact of Residence Time on Cellular Activity; 8.5 Impact on Efficacy and Duration In vivo; 8.6 Limitations of Drug-Target Residence Time; 8.7 Summary; References; Chapter 9: Experimental Methods to Determine Binding Kinetics; 9.1 Introduction; 9.2 Definitions; 9.3 Experimental Strategy 9.4 Experimental Methodologies |
| Record Nr. | UNINA-9910131450303321 |
| Weinheim, Germany : , : Wiley-VCH Verlag, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Thermodynamics and kinetics of drug binding / / edited by György M. Keserü and David C. Swinney
| Thermodynamics and kinetics of drug binding / / edited by György M. Keserü and David C. Swinney |
| Pubbl/distr/stampa | Weinheim, Germany : , : Wiley-VCH Verlag, , 2015 |
| Descrizione fisica | 1 online resource (765 p.) |
| Disciplina | 615.7 |
| Collana | Methods and Principles in Medicinal Chemistry |
| Soggetto topico |
Binding sites (Biochemistry) - Thermodynamics
Pharmacokinetics |
| ISBN |
3-527-67302-4
3-527-67304-0 3-527-67305-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover; Series; Title Page; Copyright; List of Contributors; Preface; A Personal Foreword; Section I; Chapter 1: The Binding Thermodynamics of Drug Candidates; 1.1 Affinity Optimization; 1.2 The Binding Affinity; 1.3 The Enthalpy Change; 1.4 The Entropy Change; 1.5 Engineering Binding Contributions; 1.6 Lipophilic Efficiency and Binding Enthalpy; Acknowledgments; References; Chapter 2: van't Hoff Based Thermodynamics; 2.1 Relevance of Thermodynamics to Pharmacology; 2.2 Affinity Constant Determination; 2.3 The Origin of van't Hoff Equation
2.4 From van't Hoff toward Thermodynamic Discrimination2.5 Representation of ΔG°, ΔH°, and ΔS° Data; 2.6 The Adenosine Receptors Binding Thermodynamics Story; 2.7 Binding Thermodynamics of G-Protein Coupled Receptors; 2.8 Binding Thermodynamics of Ligand-Gated Ion Channel Receptors; 2.9 Discussion; Abbreviations; References; Chapter 3: Computation of Drug-Binding Thermodynamics; 3.1 Introduction; 3.2 Potential of Mean Force Calculations; 3.3 Alchemical Transformations; 3.4 Nonequilibrium Methods; 3.5 MM-PBSA; 3.6 Linear Interaction Energy; 3.7 Scoring Functions; 3.8 Free-energy Components 3.9 SummaryReferences; Chapter 4: Thermodynamics-Guided Optimizations in Medicinal Chemistry; 4.1 Introduction; 4.2 The Thermodynamics of Medicinal Chemistry Optimizations; 4.3 Selection of Suitable Starting Points; 4.4 Thermodynamics Based Optimization Strategies; References; Chapter 5: From Molecular Understanding to Structure-Thermodynamic Relationships, the Case of Acetylcholine Binding Proteins; 5.1 Introduction; 5.2 Acetylcholine Binding Proteins (AChBPs); 5.3 Thermodynamics of Small Molecule Binding at AChBPs; 5.4 Concluding Remarks and Outlook; References Chapter 6: Thermodynamics in Lead Optimization6.1 Introduction to Lead Optimization in Drug Discovery; 6.2 Measurement of Thermodynamic Parameters in Lead Optimization; 6.3 Advantages during Lead Optimization for Thermodynamic Measurements; 6.4 Exploitation of Measured Thermodynamics in Lead Optimization; 6.5 Lead Optimization beyond Affinity; 6.6 Exemplary Case Studies; 6.7 Potential Complicating Factors in Exploiting Thermodynamics in Lead Optimization; 6.8 Summary; References; Chapter 7: Thermodynamic Profiling of Carbonic Anhydrase Inhibitors; 7.1 Introduction 7.2 Thermodynamic Profiles of Fragment Inhibitors7.3 Thermodynamics of Fragment Growing; 7.4 Conclusions; Acknowledgments; References; Section II; Chapter 8: Drug-Target Residence Time; 8.1 Introduction; 8.2 Open and Closed Systems in Biology; 8.3 Mechanisms of Drug-Target Interactions; 8.4 Impact of Residence Time on Cellular Activity; 8.5 Impact on Efficacy and Duration In vivo; 8.6 Limitations of Drug-Target Residence Time; 8.7 Summary; References; Chapter 9: Experimental Methods to Determine Binding Kinetics; 9.1 Introduction; 9.2 Definitions; 9.3 Experimental Strategy 9.4 Experimental Methodologies |
| Record Nr. | UNINA-9910830179403321 |
| Weinheim, Germany : , : Wiley-VCH Verlag, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||