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Protein-ligand interactions from molecular recognition to drug design / / edited by H.-J. Bohm and G. Schneider
| Protein-ligand interactions from molecular recognition to drug design / / edited by H.-J. Bohm and G. Schneider |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | Weinheim, : Cambridge, : Wiley-VCH, 2003 |
| Descrizione fisica | 1 online resource (264 p.) |
| Disciplina |
572.33
615.19 615/.19 |
| Altri autori (Persone) |
BohmHans-Joachim
SchneiderGisbert <1965-> |
| Collana | Methods and Principles in Medicinal Chemistry |
| Soggetto topico |
Ligand binding (Biochemistry)
Biochemistry |
| ISBN |
1-280-52057-4
9786610520572 3-527-60551-7 3-527-60181-3 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Protein-Ligand Interactions From Molecular Recognition to Drug Design; Contents; Preface; A Personal Foreword; List of Contributors; List of Abbreviations; Prologue; 1 Prediction of Non-bonded Interactions in Drug Design; 1.1 Introduction; 1.2 Major Contributions to Protein-Ligand Interactions; 1.3 Description of Scoring Functions for Receptor-Ligand Interactions; 1.3.1 Force Field-based Methods; 1.3.2 Empirical Scoring Functions; 1.3.3 Knowledge-based Methods; 1.4 Some Limitations of Current Scoring Functions; 1.4.1 Influence of the Training Data; 1.4.2 Molecular Size
1.4.3 Water Structure and Protonation State1.5 Application of Scoring Functions in Virtual Screening and De Novo Design; 1.5.1 Successful Identification of Novel Leads Through Virtual Screening; 1.5.2 De novo Ligand Design with LUDI; 1.6 Outlook; 1.7 Acknowledgments; 1.8 References; 2 Introduction to Molecular Recognition Models; 2.1 Introduction and Scope; 2.2 Additivity of Pairwise Interactions - The Chelate Effect; 2.3 Geometric Fitting: The Hole-size Concept; 2.4 Di- and Polytopic Interactions: Change of Binding Mechanism with Different Fit; 2.5 Deviations from the Lock-and-Key Principle 2.5.1 Strain in Host-Guest Complexes2.5.2 Solvent Effects; 2.5.3 Enthalpy/Entropy Variations; 2.5.4 Loose Fit in Hydrophobically Driven Complex Formation; 2.6 Conformational Pre-organization: Flexible vs. Rigid Hosts; 2.7 Selectivity and Stability in Supramolecular Complexes; 2.8 Induced Fit, Cooperativity, and Allosteric Effects; 2.9 Quantification of Non-covalent Forces; 2.9.1 Ion Pairs and Electrostatic Donor-Acceptor Interactions; 2.9.2 Hydrogen Bonds; 2.9.3 Weak Hydrogen Bonds: The Use of Intramolecular ""Balances"; 2.9.4 Polarization Effects; 2.9.5 Dispersive Interactions 2.10 Conclusions2.11 References; 3 Experimental Approaches to Determine the Thermodynamics of Protein-Ligand Interactions; 3.1 Introduction; 3.2 Basic Thermodynamics of Protein-Ligand Interactions; 3.3 Measurement of Thermodynamic Parameters; 3.3.1 Calorimetric Determination of Thermodynamic Parameters; 3.3.2 van't Hoff Determination of Thermodynamic Parameters; 3.3.2.1 Relationship to Equilibrium Constant; 3.3.2.2 Obtaining the Equilibrium Constant; 3.4 Applications; 3.4.1 Calorimetric Determination of Thermodynamic Parameters; 3.4.2 van't Hoff Determination of Thermodynamic Parameters 3.5 Caveats3.6 Summary; 3.7 References; 4 The Biophore Concept; 4.1 Introduction; 4.2 Methodology for Pharmacophore Detection and Searching; 4.2.1 Definition of Pharmacophoric Groups; 4.2.2 Ligand-based Methods for Pharmacophore Perception; 4.2.3 Protein Structure-based Pharmacophore Perception; 4.2.4 Methods for Pharmacophore Searching; 4.3 Pharmacophore Fingerprints; 4.4 Applications of the Biophore Concept; 4.4.1 Lead Generation; 4.4.2 Multi-pharmacophore Descriptors in Diversity Analysis and Library Design; 4.4.3 Structure-based Design; 4.5 The Biophore Concept in ADME Prediction 4.6 Summary |
| Record Nr. | UNINA-9910876698703321 |
| Weinheim, : Cambridge, : Wiley-VCH, 2003 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Structure-based ligand design / / edited by Klaus Gubernator, Hans-Joachim Bohm
| Structure-based ligand design / / edited by Klaus Gubernator, Hans-Joachim Bohm |
| Pubbl/distr/stampa | Weinheim ; ; New York, : Wiley-VCH, c1998 |
| Descrizione fisica | 1 online resource (170 p.) |
| Disciplina | 615.19 |
| Altri autori (Persone) |
GubernatorKlaus
BohmHans-Joachim |
| Collana | Methods and principles in medicinal chemistry |
| Soggetto topico |
Ligand binding (Biochemistry)
Pharmaceutical chemistry QSAR (Biochemistry) Drugs - Design |
| ISBN |
1-282-01029-8
9786612010293 3-527-61217-3 3-527-61216-5 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Structure-Based Ligand Design; Preface; List of Contributors; Contents; 1 Rational Design of Bioactive Molecules; 1.1 Introduction; 1.1.1 From Ligand Design to Drug Discovery; 1.2 Source of Structural Information; 1.3 Classes of Therapeutic Agents; 1.4 Protein-Ligand Interaction; 1.4.1 Covalent versus Noncovalent Inhibitors; 1.4.2 Nonbonded Interactions in Protein-Ligand Complexes; 1.4.3 HydrogenBonds; 1.4.4 The Role of Solvent in Polar Protein-Ligand Interactions; 1.4.5 Lipophilic Interactions; 1.4.6 Criteria for Strong Protein-Ligand Interactions
1.5 Approaches to Structure-Based Ligand Design1.5.1 Ligands Derived from Substrate or Natural Ligand; 1.5.2 Structures Derived from 3D Database Searches; 1.5.3 De-Novo Design of Ligands; 1.6 Methods and Toois used in Structure-Based Ligand Design; 1.7 Outlook and Future Developments; References; 2 Examples of Active Areas of Structure-Based-Design; 2.1 Thrombin Inhibitors; 2.2 Design of Orally Active Inhibitors of Elastase; 2.3 Dorzolamide:A Success Story of Structure-Based Drug Design; 2.4 Inhibitors of Serine Esterases; 2.4.1 Human Pancreatic Lipase (hPL) 2.4.2 Model of the Trilaurin Triglyceride Substrate Binding2.4.3 Tetrahydrolipstatin (THL); 2.5 Acetylcholinesterase (AChE); 2.5.1 Model of the Acetylcholine Substrate Binding; 2.5.2 Physostigmine; 2.5.3 Eisai E2020; References; 3 From Renin to HIV-1 Protease; 3.1 Introduction; 3.2 Renin; 3.2.1 Catalytic Site Binding; 3.2.2 Backbone Variations; 3.2.3 Subsite Interdependencies; 3.2.4 Renin Crystal Structure; 3.2.5 Summary - Renin Modeling; 3.3 HIV-1 Protease; 3.3.1 3D Structures of HIV-1 Protease; 3.3.2 HIV-1 Protease Nonpeptide Inhibitors 3.3.3 Docking/Modeling HIV-1 Protease Nonpeptide Inhibitors3.4 Summary: Comparison of HIV-1 Protease versus Renin Structure-Based Design; 3.5 Current Limitations/Future Perspective; 3.6 Conclusion; References; 4 Zinc Endoproteases: A Structural Superfamily; 4.1 Introduction; 4.2 Structural Classification of Zinc Endopeptidase Families; 4.2.1 Short Spacer or Metzincins Family; 4.2.2 Long Spacer or Gluzincins Family; 4.3 Overview of Inhibitor Design; 4.4 Current Limitations; 4.5 Future Prospects; References; 5 Structure-Based Design of Potent Beta-Lactamase Inhibitors; 5.1 Introduction 5.2 Structure of Citrobacter freundii Class C Beta-Lactamase5.3 Model of the Mechanism of Action: Cleavage of Penicillin G; 5.4 Structure of the Complex with Aztreonam; 5.5 Design of Inhibitors; 5.6 Kinetics of the Inhibition Reaction; 5.7 Hydrolysis by Class A Beta-Lactamases; 5.8 X-Ray Structure of the Complex with a Bridged Monobactam; 5.9 Structure-Activity Relationship among Bridged Monobactams; 5.10 Conclusion; References; 6 Inhibition of Sialidase; 6.1 Introduction; 6.2 Influenza: Disease and Virus; 6.3 Structure of Sialidase; 6.4 Mechanism of Catalysis 6.5 Binding of Substrate and Transition State Mimics |
| Record Nr. | UNINA-9910877485903321 |
| Weinheim ; ; New York, : Wiley-VCH, c1998 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Virtual screening for bioactive molecules / / edited by Hans-Joachim Bohm and Gisbert Schneider
| Virtual screening for bioactive molecules / / edited by Hans-Joachim Bohm and Gisbert Schneider |
| Pubbl/distr/stampa | Weinheim ; ; New York, : Wiley-VCH, c2000 |
| Descrizione fisica | 1 online resource (327 p.) |
| Disciplina | 615/.19 |
| Altri autori (Persone) |
BohmHans-Joachim
SchneiderGisbert <1965-> |
| Collana | Methods and principles in medicinal chemistry |
| Soggetto topico |
Drugs - Design - Computer simulation
Drugs - Testing - Computer simulation |
| ISBN |
1-282-01035-2
9786612010354 3-527-61308-0 3-527-61309-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Virtual Screening for Bioactive Molecules; Preface; A Personal Foreword; Contents; List of Contributors; Prologue; 1 High-Throughput Screening and Virtual Screening: Entry Points to Drug Discovery; 1.1 Introduction; 1.2 Miniaturization and Detection Strategies; 1.2.1 Screening Plate Format and Fluidics; 1.2.2 Detection Strategies; 1.2.3 Cell-Based Reporter Gene Assays; 1.2.4 Fluorescence Correlation Spectroscopy .; 1.2.5 Microchip Fabrication; 1.2.6 Remarks and Summary; 1.3 Compound Libraries; 1.4 Multi-Dimensional Optimization: Qualifying HTS Lead Candidates; 1.5 Conclusions; References
2 Library Filtering Systems and Prediction of Drug-Like Properties2.1 Introduction; 2.2 Simple Counting Methods to Predict Drug-Likeness; 2.3 Functional Group Filters; 2.4 "Chemistry Space" Methods; 2.5 Examination of Building Blocks in Known Drugs; 2.6 Other Methods; 2.7 Conclusions and Future Directions; References; 3 Prediction of Physicochemical Properties; 3.1 Introduction; 3.2 Prediction of Lipophilicity; 3.2.1 Fragment-Based Methods; 3.2.2 Methods Based on Molecular Properties; 3.2.3 Predictive Ability of Existing Techniques; 3.2.4 Other Solvent Systems; 3.2.5 Effect of Ionization 3.3 Prediction of Solubility3.3.1 Fragmental Approaches; 3.3.2 Property-Based Methods; 3.3.3 Conclusions; 3.4 Prediction of pKa; 3.4.1 Fragment-Based Methods; 3.4.2 Methods Based on Molecular Properties; 3.4.3 Conclusions; 3.5 Prediction of Protein Binding; 3.6 Conclusions; References; 4 Descriptor-Based Similarity Measures for Screening Chemical Databases; 4.1 Introduction; 4.2 Fragment-Based Similarity Searching; 4.3 Association and Distance Coefficients for Similarity Searching; 4.4 Structural Representations for Similarity Searching; 4.4.1 Descriptor Selection; 4.4.2 Descriptor Encoding 4.5 ConclusionsReferences; 5 Modelling Structure-Activity Relationships; 5.1 Introduction; 5.2 Hansch Analysis; 5.3 3-D QSAR; 5.4 Alignment-Free 3-D Descriptors; 5.5 Topological Descriptors; 5.6 Pharmacophores and Pharmacophoric Keys; 5.7 Conclusions; 5.8 Appendix - Statistical Techniques in QSAR and Pattern Recognition; 5.8.1 Data Reduction and Display; 5.8.1.1 Principal Component Analysis; 5.8.1.2 Non-Linear Mapping; 5.8.1.3 Neural Networks; 5.8.2 Regression Techniques; 5.8.2.1 Multiple Linear Regression; 5.8.2.2 Principal Component Regression and Partial Least Squares 5.8.3 Classification Techniques5.8.3.1 Linear Discriminant Analysis; 5.8.3.2 Soft Independent Modelling of Class Analogy; 5.8.3.3 Recursive Partitioning; References; 6 Database Profiling by Neural Networks; 6.1 "Drug-Likeness": A General Compound Property?; 6.2 Methods and Programs; 6.2.1 Databases; 6.2.2 Descriptors; 6.2.3 Classification Tools; 6.2.4 Complete Algorithm; 6.3 Applications; 6.3.1 Drug-Likeness and a Recipe for a Computational Filter; 6.3.2 Crop Protection Compounds; 6.3.3 Virtual High-Throughput Screens; 6.3.4 Optimization of Combinatorial Libraries; 6.4 Conclusions; References 7 Pharmacophore Pattern Application in Virtual Screening. Library Design and QSAR |
| Record Nr. | UNINA-9910877541403321 |
| Weinheim ; ; New York, : Wiley-VCH, c2000 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||