Protein-ligand interactions:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Weinheim
Wiley-VCH
2012
|
| Series: | Methods and principles in medicinal chemistry
53 |
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XX, 339 S. Ill., graph. Darst. 240 mm x 170 mm |
| ISBN: | 9783527329663 3527329668 |
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| 245 | 1 | 0 | |a Protein-ligand interactions |c ed. by Holger Gohlke |
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IMAGE 1
V
CONTENTS
LIST O F CONTRIBUTORS X I I I
PREFACE X V I I
A PERSONAL FOREWORD X I X
PART I BINDING THERMODYNAMICS 1
1 STATISTICAL THERMODYNAMICS O F BINDING A N D MOLECULAR
RECOGNITION MODELS 3 KIM A. SHARP 1.1 INTRODUCTORY R E M A R K S 3
1.2 T H E BINDING C O N S T A N T A N D FREE ENERGY 3
1.3 A STATISTICAL MECHANICAL T R E A T M E N T O F BINDING 4
1.3.1 BINDING I N A SQUARE WELL POTENTIAL 6
1.3.2 BINDING I N A H A R M O N I C POTENTIAL 7
1.4 STRATEGIES FOR CALCULATING BINDING FREE ENERGIES 9
1.4.1 DIRECT ASSOCIATION SIMULATIONS 9
1.4.2 T H E Q U A S I - H A R M O N I C APPROXIMATION 10
1.4.3 ESTIMATION O F ENTROPY CONTRIBUTIONS TO BINDING 11
1.4.4 T H E MOLECULE MECHANICS P O I S S O N - B O L T Z M A N N SURFACE
AREA METHOD 13 1.4.5 T H E R M O D Y N A M I C W O R K METHODS 14
1.4.6 LIGAND DECOUPLING 15
1.4.7 LINEAR INTERACTION METHODS 15
1.4.8 SALT EFFECTS O N BINDING 16
1.4.9 STATISTICAL POTENTIALS 17
1.4.10 EMPIRICAL POTENTIALS 18
REFERENCES 19
2 S O M E PRACTICAL RULES FOR T H E THERMODYNAMIC OPTIMIZATION
O F DRUG CANDIDATES 23
ERNESTO FREIRE
2.1 ENGINEERING BINDING CONTRIBUTIONS 2 5
2.2 ELIMINATING UNFAVORABLE ENTHALPY 2 5
2.3 IMPROVING BINDING ENTHALPY 2 6
HTTP://D-NB.INFO/1017774943
IMAGE 2
V I CONTENTS
2.4 IMPROVING BINDING AFFINITY 2 7
2.5 IMPROVING SELECTIVITY 28
2.6 T H E R M O D Y N A M I C OPTIMIZATION PLOT 2 8
ACKNOWLEDGMENTS 3 0 REFERENCES 3 1
3 ENTHALPY-ENTROPY COMPENSATION A S DEDUCED FROM M E A S U R E M E N T S
O F T E M P E R A T U R E DEPENDENCE 33 ATHEL CORNISH-BOWDEN 3.1
INTRODUCTION 33
3.2 T H E C U R R E N T STATUS O F ENTHALPY-ENTROPY C O M P E N S A T I
O N 3 4
3.3 M E A S U R E M E N T O F T H E ENTROPY A N D ENTHALPY O F
ACTIVATION 3 4
3.4 A N EXAMPLE 3 5
3.5 T H E C O M P E N S A T I O N T E M P E R A T U R E 3 8
3.6 EFFECT O F H I G H CORRELATION O N ESTIMATES O F ENTROPY A N D
ENTHALPY 3 9
3.7 EVOLUTIONARY CONSIDERATIONS 4 0
3.8 TEXTBOOKS 4 0
REFERENCES 4 2
PART II LEARNING FROM BIOPHYSICAL EXPERIMENTS 4 5
4 INTERACTION KINETIC DATA GENERATED BY SURFACE PLASMON RESONANCE
BIOSENSORS A N D T H E U S E O F KINETIC RATE CONSTANTS IN LEAD
GENERATION A N D OPTIMIZATION 4 7 U. HELENA DANIELSON 4.1 BACKGROUND 4 7
4.2 SPR BIOSENSOR TECHNOLOGY 4 8
4.2.1 PRINCIPLES 4 8
4.2.2 SENSITIVITY 4 9
4.2.3 KINETIC RESOLUTION 5 0
4.2.4 PERFORMANCE FOR D R U G DISCOVERY 51
4.3 F R O M INTERACTION MODELS TO KINETIC RATE CONSTANTS A N D AFFINITY
5 3
4.3.1 DETERMINATION O F INTERACTION KINETIC RATE CONSTANTS 5 3
4.3.2 DETERMINATION O F AFFINITIES 5 4
4.3.3 STEADY-STATE ANALYSIS VERSUS ANALYSIS O F COMPLETE S E N S O R G R
A M S 5 4 4.4 AFFINITY VERSUS KINETIC RATE CONSTANTS FOR EVALUATION O F
INTERACTIONS 5 5
4.5 FROM MODELS TO M E C H A N I S M S 5 6
4.5.1 IRREVERSIBLE INTERACTIONS 5 7
4.5.2 I N D U C E D FIT 5 7
4.5.3 CONFORMATIONAL SELECTION 5 8
4.5.4 UNIFIED MODEL FOR DYNAMIC TARGETS 5 8
4.5.5 HETEROGENEOUS SYSTEMS/PARALLEL REACTIONS 5 9
4.5.6 MECHANISM-BASED INHIBITORS 6 0
4.5.7 MULTIPLE BINDING SITES A N D INFLUENCE O F COFACTORS 61
4.6 STRUCTURAL INFORMATION 63
IMAGE 3
CONTENTS V I I
4.7 T H E U S E O F KINETIC RATE CONSTANTS I N LEAD GENERATION A N D
OPTIMIZATION 6 2
4.7.1 STRUCTURE-KINETIC RELATIONSHIPS 6 2
4.7.2 SELECTIVITY/SPECIFICITY A N D RESISTANCE 63
4.7.3 C H E M O D Y N A M I C S 63
4.7.4 T H E R M O D Y N A M I C S 6 4
4.8 DESIGNING C O M P O U N D S WITH OPTIMAL PROPERTIES 6 5
4.8.1 CORRELATION BETWEEN KINETIC A N D T H E R M O D Y N A M I C
PARAMETERS A N D PHARMACOLOGICAL EFFICACY 6 5 4.8.2 STRUCTURAL MODELING
66
4.9 CONCLUSIONS 6 7
ACKNOWLEDGMENTS 6 7 REFERENCES 6 7
5 NMR METHODS FOR T H E DETERMINATION O F PROTEIN-LIGAND INTERACTIONS 71
BERND W. KOENIG, SVEN SCHIINKE, MATTHIAS STOLDT, A N D DIETER WILLBOLD
5.1 EXPERIMENTAL PARAMETERS F R O M N M R 7 2
5.2 ASPECTS O F PROTEIN-LIGAND INTERACTIONS T H A T C A N BE ADDRESSED
BY N M R 7 7
5.2.1 DETECTION A N D VERIFICATION O F LIGAND BINDING 7 7
5.2.2 INTERACTION SITE M A P P I N G 78
5.2.3 INTERACTION MODELS A N D BINDING AFFINITY 8 0
5.2.4 MOLECULAR RECOGNITION 81
5.2.5 STRUCTURE O F PROTEIN-LIGAND COMPLEXES 8 2
5.3 LIGAND-INDUCED CONFORMATIONAL C H A N G E S O F A CYCLIC NUCLEOTIDE
BINDING D O M A I N 8 4
5.4 LIGAND BINDING TO GABARAP BINDING SITE A N D AFFINITY M A P P I N G
86
5.5 TRANSIENT BINDING O F PEPTIDE LIGANDS TO M E M B R A N E PROTEINS 88
REFERENCES 9 0
PART III MODELING PROTEIN-LIGAND INTERACTIONS 99
6 POLARIZABLE FORCE FIELDS FOR SCORING PROTEIN-LIGAND INTERACTIONS 101
JIAJING ZHANG, YUE SHI, A N D PENGYU REN 6.1 INTRODUCTION A N D OVERVIEW
101
6.2 AMOEBA POLARIZABLE POTENTIAL ENERGY MODEL 102
6.2.1 BOND, ANGLE, A N D CROSS-ENERGY T E R M S 102
6.2.2 TORSIONAL ENERGY T E R M 103
6.2.3 VAN D E R WAALS INTERACTIONS 103
6.2.4 P E R M A N E N T ELECTROSTATIC INTERACTIONS 103
6.2.5 ELECTRONIC POLARIZATION 104
6.2.6 POLARIZATION ENERGY 105
6.3 AMOEBA EXPLICIT WATER SIMULATION APPLICATIONS 106
6.3.1 SMALL-MOLECULE HYDRATION FREE ENERGY CALCULATIONS 106 6.3.2 ION
SOLVATION T H E R M O D Y N A M I C S 108
IMAGE 4
V I I I CONTENTS
6.3.3 BINDING FREE ENERGY O F TRYPSIN A N D BENZAMIDINE ANALOGS 110
6.4 IMPLICIT SOLVENT CALCULATION USING AMOEBA POLARIZABLE FORCE FIELD
113 6.5 CONCLUSIONS A N D FUTURE DIRECTIONS 115
REFERENCES 116
7 Q U A N T U M MECHANICS IN STRUCTURE-BASED LIGAND DESIGN 121
PAR SODERHJELM, SAMUEL GENHEDEN, A N D ULF RYDE 7.1 INTRODUCTION 121
7.2 T H R E E MM-BASED METHODS 122
7.3 QM-BASED FORCE FIELDS 123
7.4 Q M CALCULATIONS O F LIGAND BINDING SITES 125
7.5 Q M / M M CALCULATIONS 126
7.6 Q M CALCULATIONS O F ENTIRE PROTEINS 127
7.6.1 LINEAR SCALING METHODS 128
7.6.2 FRAGMENTATION METHODS 129
7.7 CONCLUDING REMARKS 133
ACKNOWLEDGMENTS 134 REFERENCES 134
8 HYDROPHOBIC ASSOCIATION A N D VOLUME-CONFINED
WATER MOLECULES 145
RICCARDO BARON, PIOTR SETNY, A N D J. ANDREW M C C A M M O N 8.1
INTRODUCTION 145
8.2 WATER AS A WHOLE I N HYDROPHOBIC ASSOCIATION 146
8.2.1 BACKGROUND 146
8.2.2 COMPUTATIONAL MODELING O F HYDROPHOBIC ASSOCIATION 150 8.2.2.1
EXPLICIT VERSUS IMPLICIT SOLVENT: IS T H E COMPUTATIONAL COST MOTIVATED?
152
8.3 CONFINED WATER MOLECULES I N PROTEIN-LIGAND BINDING 153
8.3.1 PROTEIN HYDRATION SITES 153
8.3.2 T H E R M O D Y N A M I C S O F VOLUME-CONFINED WATER LOCALIZATION
154 8.3.3 COMPUTATIONAL MODELING O F VOLUME-CONFINED WATER MOLECULES 156
8.3.4 IDENTIFYING HYDRATION SITES 158
8.3.5 WATER I N PROTEIN-LIGAND DOCKING 160
ACKNOWLEDGMENTS 161 REFERENCES 161
9 IMPLICIT SOLVENT MODELS A N D ELECTROSTATICS IN MOLECULAR RECOGNITION
171
TYLER LUCHKO A N D DAVID A. CASE 9.1 INTRODUCTION 171
9.2 P O I S S O N - B O L T Z M A N N METHODS 173
9.3 T H E GENERALIZED.BORN MODEL 175
9.4 REFERENCE INTERACTION SITE MODEL O F MOLECULAR SOLVATION 176
9.5 APPLICATIONS 179
IMAGE 5
CONTENTS I X
9.5.1 T H E "MM-PBSA" MODEL 180
9.5.2 RESCORING DOCKING POSES 182
9.5.3 MM/3D-RISM 182
ACKNOWLEDGMENTS 185 REFERENCES 185
10 LIGAND A N D RECEPTOR CONFORMATIONAL ENERGIES 191
THEMIS LAZARIDIS
10.1 T H E T R E A T M E N T O F LIGAND A N D RECEPTOR CONFORMATIONAL
ENERGY I N VARIOUS THEORETICAL FORMULATIONS O F BINDING 191 10.1.1
DOUBLE DECOUPLING FREE ENERGY CALCULATIONS 192 10.1.2 MM-PB(GB)SA 192
10.1.3 M I N I N G M I N I M A 193
10.1.4 FREE ENERGY FUNCTIONAL APPROACH 194
10.1.5 LINEAR INTERACTION ENERGY M E T H O D S 195
10.1.6 SCORING FUNCTIONS 3 96
10.2 COMPUTATIONAL RESULTS O N LIGAND CONFORMATIONAL ENERGY 19 6
10.3 COMPUTATIONAL RESULTS O N RECEPTOR CONFORMATIONAL ENERGY 198
10.4 CONCLUDING REMARKS 199
ACKNOWLEDGMENTS 199 REFERENCES 199
11 FREE ENERGY CALCULATIONS IN DRUG LEAD OPTIMIZATION 207
THOMAS STEINBRECHER
11.1 M O D E R N D R U G DESIGN 2 0 7
11.1.1 IN SILICO D R U G DESIGN 2 1 0
11.2 FREE ENERGY CALCULATIONS 2 3 2
11.2.1 CONSIDERATIONS FOR ACCURATE A N D PRECISE RESULTS 215
11.3 EXAMPLE PROTOCOLS A N D APPLICATIONS 2 3 7
11.3.1 EXAMPLE 1: DISAPPEARING A N I O N 2 1 9
11.3.2 EXAMPLE 2: RELATIVE LIGAND BINDING STRENGTHS 223
11.3.3 APPLICATIONS 223
11.4 DISCUSSION 226
REFERENCES 2 2 7
12 SCORING FUNCTIONS FOR PROTEIN-LIGAND INTERACTIONS 237
CHRISTOPH SOTRIFFER
12.1 INTRODUCTION 237
12.2 SCORING PROTEIN-LIGAND INTERACTIONS: W H A T FOR A N D H O W TO?
237
12.2.1 KNOWLEDGE-BASED SCORING FUNCTIONS 238 12.2.2 FORCE FIELD-BASED
METHODS 2 4 0
12.2.3 EMPIRICAL SCORING FUNCTIONS 2 4 2
12.2.4 FURTHER APPROACHES 244
12.3 APPLICATION O F SCORING FUNCTIONS: W H A T IS POSSIBLE A N D
W H A T IS NOT? 246
IMAGE 6
CONTENTS
12.4 T H E R M O D Y N A M I C CONTRIBUTIONS A N D INTERMOLECULAR
INTERACTIONS:
W H I C H ARE ACCOUNTED FOR A N D W H I C H ARE NOT? 248 12.5
CONCLUSIONS O R W H A T R E M A I N S TO B E D O N E A N D W H A T
C A N B E EXPECTED? 254 ACKNOWLEDGMENTS 255 REFERENCES 255
PART IV CHALLENGES IN MOLECULAR RECOGNITION 2 6 5
13 DRAGGABILITY PREDICTION 2 6 7
DANIEL ALVAREZ-CARCIA, JESUS SECO, PETER SCHMIDTKE, A N D XAVIER BARRIL
13.1 INTRODUCTION 2 6 7
13.2 DRUGGABILITY: LIGAND PROPERTIES 2 6 7
13.3 DRUGGABILITY: LIGAND BINDING 2 6 8
13.4 DRUGGABILITY PREDICTION BY PROTEIN CLASS 2 7 0
13.5 DRUGGABILITY PREDICTIONS: EXPERIMENTAL METHODS 270
13.5.1 H I G H - T H R O U G H P U T SCREENING 270
13.5.2 FRAGMENT SCREENING 271
13.5.3 MULTIPLE SOLVENT CRYSTALLOGRAPHIC SCREENING 2 7 2 13.6
DRUGGABILITY PREDICTIONS: COMPUTATIONAL METHODS 2 7 2
13.6.1 CAVITY DETECTION ALGORITHMS 2 7 2
13.6.2 EMPIRICAL MODELS 273
13.6.2.1 TRAINING SETS 273
13.6.2.2 APPLICABILITY A N D PREDICTION PERFORMANCE 2 7 4 13.6.3
PHYSICAL C H E M I S T R Y PREDICTIONS 2 7 5
13.7 A TEST CASE: P T P I B 276
13.8 OUTLOOK A N D CONCLUDING REMARKS 278
REFERENCES 278
14 EMBRACING PROTEIN PLASTICITY IN LIGAND DOCKING 283
MANUEL RUEDA A N D RUBEN ABAGYAN 14.1 INTRODUCTION 283
14.2 DOCKING BY SAMPLING INTERNAL COORDINATES 284
14.3 FAST DOCKING TO MULTIPLE RECEPTOR CONFORMATIONS 285
14.4 SINGLE RECEPTOR C O N F O R M A T I O N 2 8 5
14.5 MULTIPLE RECEPTOR CONFORMATIONS 286
14.5.1 EXPLOITING EXISTING EXPERIMENTAL CONFORMATIONAL DIVERSITY 286
14.5.2 SELECTING "IMPORTANT" CONFORMATIONS 288
14.5.3 GENERATING I N SILICO MODELS 288
14.6 IMPROVING POOR HOMOLOGY MODELS O F T H E BINDING POCKET 289
14.7 STATE O F T H E ART: G P C R DOCK 2010 MODELING A N D DOCKING
A S S E S S M E N T 2 9 0
14.8 CONCLUSIONS A N D OUTLOOK 2 9 0
ACKNOWLEDGMENTS 292 REFERENCES 2 9 2
IMAGE 7
15 PROSPECTS O F MODULATING PROTEIN-PROTEIN INTERACTIONS 2 9 5
SHIJUN ZHONG, TAIJI OASHI, WENBO YU, PAUL SHAPIRO, AND ALEXANDER D.
MACKERELL JR. 15.1 INTRODUCTION 2 9 5
15.2 T H E R M O D Y N A M I C S O F P R O T E I N - P R O T E I N
INTERACTIONS 2 9 7
15.3 C A D D METHODS FOR T H E IDENTIFICATION A N D OPTIMIZATION
O F SMALL-MOLECULE INHIBITORS O F PPIS 298 15.3.1 IDENTIFYING INHIBITORS
O F P P I S U S I N G SBDD 299
15.3.1.1 PROTEIN STRUCTURE PREPARATION 2 9 9
15.3.1.2 BINDING SITE IDENTIFICATION 3 0 0
15.3.1.3 VIRTUAL CHEMICAL DATABASE 3 0 2
15.3.1.4 VIRTUAL SCREENING O F C O M P O U N D DATABASE 3 0 2 15.3.1.5
RESCORING 3 0 4
15.3.1.6 FINAL SELECTION O F LIGANDS FOR EXPERIMENTAL ASSAY 3 0 6 15.3.2
LEAD OPTIMIZATION 3 0 7
15.3.2.1 LIGAND-BASED OPTIMIZATION 307 15.3.2.2 C O M P U T A T I O N O
F BINDING FREE ENERGY 308 15.4 EXAMPLES O F C A D D APPLIED TO PPIS 308
15.4.1 ERK 3 0 9
15.4.2 BCL6 311
15.4.3 S100B 313
15.4.4 P56LCK KINASE S H 2 D O M A I N 313
15.5 S U M M A R Y 3 1 5
ACKNOWLEDGMENTS 315 REFERENCES 3 1 5
INDEX 331 |
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| author_GND | (DE-588)122454359 |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV039847317 |
| illustrated | Illustrated |
| indexdate | 2024-07-21T00:22:25Z |
| institution | BVB |
| isbn | 9783527329663 3527329668 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-024707120 |
| oclc_num | 773431439 |
| open_access_boolean | |
| owner | DE-91G DE-BY-TUM DE-11 DE-355 DE-BY-UBR DE-M49 DE-BY-TUM DE-19 DE-BY-UBM DE-20 |
| owner_facet | DE-91G DE-BY-TUM DE-11 DE-355 DE-BY-UBR DE-M49 DE-BY-TUM DE-19 DE-BY-UBM DE-20 |
| physical | XX, 339 S. Ill., graph. Darst. 240 mm x 170 mm |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Wiley-VCH |
| record_format | marc |
| series | Methods and principles in medicinal chemistry |
| series2 | Methods and principles in medicinal chemistry |
| spelling | Protein-ligand interactions ed. by Holger Gohlke Weinheim Wiley-VCH 2012 XX, 339 S. Ill., graph. Darst. 240 mm x 170 mm txt rdacontent n rdamedia nc rdacarrier Methods and principles in medicinal chemistry 53 Proteine (DE-588)4076388-2 gnd rswk-swf Wechselwirkung (DE-588)4064937-4 gnd rswk-swf Ligand Biochemie (DE-588)4606532-5 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Proteine (DE-588)4076388-2 s Ligand Biochemie (DE-588)4606532-5 s Wechselwirkung (DE-588)4064937-4 s DE-604 Gohlke, Holger 1972- Sonstige (DE-588)122454359 oth Methods and principles in medicinal chemistry 53 (DE-604)BV035418617 53 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3932617&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024707120&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein-ligand interactions Methods and principles in medicinal chemistry Proteine (DE-588)4076388-2 gnd Wechselwirkung (DE-588)4064937-4 gnd Ligand Biochemie (DE-588)4606532-5 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4064937-4 (DE-588)4606532-5 (DE-588)4143413-4 |
| title | Protein-ligand interactions |
| title_auth | Protein-ligand interactions |
| title_exact_search | Protein-ligand interactions |
| title_full | Protein-ligand interactions ed. by Holger Gohlke |
| title_fullStr | Protein-ligand interactions ed. by Holger Gohlke |
| title_full_unstemmed | Protein-ligand interactions ed. by Holger Gohlke |
| title_short | Protein-ligand interactions |
| title_sort | protein ligand interactions |
| topic | Proteine (DE-588)4076388-2 gnd Wechselwirkung (DE-588)4064937-4 gnd Ligand Biochemie (DE-588)4606532-5 gnd |
| topic_facet | Proteine Wechselwirkung Ligand Biochemie Aufsatzsammlung |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=3932617&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024707120&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035418617 |
| work_keys_str_mv | AT gohlkeholger proteinligandinteractions |