Preface xiii
1 Exploring Protein–Protein Interactions: Concepts, Methods, and Implications 1
mi Zhou and Renxiao Wang
1.1 General Concepts of Protein–Protein Interactions 1
1.1.1 Definition of Protein–Protein Interactions 1
1.1.2 Structural Properties of Protein–Protein Interactions 2
1.1.3 Diverse Types of Protein–Protein Interactions 3
1.1.3.1 Enzyme–Substrate Interactions 3
1.1.3.2 Receptor–Ligand Interactions 3
1.1.3.3 Antigen–Antibody Interactions 3
1.1.3.4 Chaperone–Client Interactions 4
1.1.3.5 Scaffold Interactions 4
1.2 Functional Significance of Protein–Protein Interactions 4
1.2.1 Cellular Signal Transduction 5
1.2.2 Regulation of Gene Expression 6
1.2.3 Immune Response 8
1.2.3.1 Immune Cell Migration 8
1.2.3.2 T-Cell Antigen Recognition and Activation 8
1.2.3.3 B-Cell Antigen Recognition and Activation 9
1.2.4 Protein Degradation Pathway 9
1.2.5 Disease Mechanisms 10
1.2.5.1 Cancer 10
1.2.5.2 Neurodegenerative Diseases 11
1.2.5.3 Infectious Disease 11
1.3 Methods for Analyzing Protein–Protein Interactions 12
1.3.1 Experimental Methods 12
1.3.1.1 Structure Determination 12
1.3.1.2 Affinity, Kinetics, and Thermodynamics Measurement 13
1.3.1.3 Large-Scale PPI Network Mapping 13
1.3.2 Computational Methods 14
1.3.2.1 Sequence-Based Methods 14
1.3.2.2 Structure-Based Methods 15
1.3.2.3 Network-Based Methods 15
1.4 Implications of the Basic Research on Protein–Protein Interactions 16
1.4.1 Advancing Disease Understanding and Diagnosis 16
1.4.2 Driving Target-Based Drug Discovery 17
1.4.3 Fostering Innovations in Biotechnology 17
1.5 Conclusions and Perspectives 19
References 19
2 Overview of Drug Discovery Targeting PPI Systems 29
Hao Ma and Jian Zhang
2.1 Introduction 29
2.2 Fundamentals of Protein–Protein Interactions 30
2.2.1 Basic Principles of Protein Structure and Function 30
2.2.2 Types of Protein–Protein Interactions 32
2.2.3 Significance of PPIs in Cellular Processes and Disease Pathways 32
2.3 Challenges in Targeting PPI Systems 33
2.3.1 Structural Complexities of PPI Interfaces 33
2.3.2 Dynamics and Flexibility of Protein Complexes 34
2.3.3 Druggability Issues Associated with PPI Targets 35
2.4 Approaches in Drug Discovery Targeting PPI Systems 35
2.4.1 High-Throughput Drug Design (HTS) Methods 35
2.4.2 Structure-Based Drug Design (SBDD) Techniques 36
2.4.3 Fragment-Based Drug Discovery (FBDD) Strategies 37
2.4.4 Computational Methods for Predicting PPI Inhibitors 38
2.5 Case Studies and Success Stories 40
2.5.1 BCL Family 40
2.5.1.1 Bcl- 2 40
2.5.1.2 Bcl-xL 42
2.5.1.3 Mcl- 1 42
2.5.2 p53–MDM 2 43
2.5.3 XIAP/c-IAP 1 44
2.5.4 Cd40-cd40l 45
2.5.5 Cyclin-Dependent Kinase (CDK) 46
2.5.6 Pd-/pd-l 1 47
2.5.7 Hsp90-Cdc 37 48
2.5.8 Menin-MLL 48
2.5.9 Kras-SOS 1 49
2.5.10 Keap1-Nrf2 PPI 49
2.6 Conclusion 51
References 53
3 Fluorescence Resonance Energy Transfer Technology and its Applications 61
Jing-Yu Lang
3.1 Introduction 61
3.2 Mechanism of FRET 61
3.3 Applications of FRET 63
3.3.1 Molecular Interactions 63
3.3.2 Conformational Changes 64
3.3.3 Cellular Imaging 64
3.3.4 Drug Discovery 64
3.3.5 Clinical Diagnosis 65
3.3.6 Structural Biology 66
3.3.7 Materials Science 66
3.3.8 Environmental and Agricultural Sciences 66
3.4 Advantages and Limitations 67
3.5 Recent Advances 68
3.6 Conclusion 70
Acknowledgements 71
References 71
4 Dissect Protein Interactions Using Mass Spectrometry 75
Bin Liao and Liang Zhang
4.1 Introduction 75
4.2 Affinity Purification Coupled with Mass Spectrometry (AP-MS) 76
4.3 Proximity Labeling 81
4.4 Cross-linking Mass Spectrometry (XL-MS) 84
4.5 Co-fractionation Coupled with Mass Spectrometry (CF-MS) 88
4.6 Thermal Proximity Co-aggregation (TPCA) 90
4.7 Limited Proteolysis–Mass Spectrometry (LiP–MS) 93
4.8 Conclusion and Outlook 95
Acknowledgements 96
References 96
5 Detection of Protein–Protein Interactions In Situ via Proximity Ligation Assay 105
Xinyue Zhou and Peng Zou
5.1 Introduction 105
5.2 Implementations of Proximity Ligation Assay 106
5.3 Applications of PLA for Detecting Protein–Protein Interactions 108
5.4 Conclusions and Outlooks 109
Acknowledgments 110
References 110
6 Application of Surface Plasmon Resonance in the Characterization of Protein–Protein Interactions 115
Yuanyuan Xie and Jianrong Xu
6.1 Introduction 115
6.1.1 Protein–Protein Interactions 115
6.1.2 Principle of Surface Plasmon Resonance 115
6.1.3 Advantage of SPR 116
6.2 Applications of SPR Assays in PPIs Characterization 117
6.2.1 SPR Application in Binary PPI Systems 117
6.2.1.1 SPR Assay in Verifying and Measuring PPIs 117
6.2.1.2 SPR-Guided Screening and Optimization in Drug Discovery 120
6.2.1.3 SPR in the Validation of PPI Interface 123
6.2.2 SPR Application in Ternary PPI Systems 126
6.2.2.1 SPR-Based Epitope Competition Assays 126
6.2.2.2 SPR-Based Drug Discovery of PPI Modulators 128
6.2.2.3 SPR Applications in Targeted Protein Degradation 130
6.3 Advantages and Limitations of SPR Application for PPIs 131
6.4 Future Directions 132
References 133
7 Computational Methods for Protein–Protein Interactions 139
Hao Li, Yurui Li, and Sheng-You Huang
7.1 Introduction 139
7.2 Protein–Protein Docking 140
7.2.1 Sampling 142
7.2.1.1 Traditional Search Algorithms 142
7.2.1.2 Deep Learning-Based Search Algorithms 144
7.2.2 Scoring 145
7.2.2.1 Traditional Scoring Function 145
7.2.2.2 Deep Learning-Based Scoring Function 146
7.2.3 Template-based Docking 147
7.3 End-to-end Structure Prediction 148
7.4 CAPRI Experiments 151
7.4.1 Casp13-capri 152
7.4.2 Casp14-capri 152
7.4.3 Casp15-capri 153
7.5 Challenges and Future Directions 154
Acknowledgments 155
Author Contributions 155
References 155
8 Foldamers as Inhibitors of Aberrant Protein–Protein Interactions 163
Nicholas H. Stillman, Ryan A. Dohoney, Charles Z. Baysah, and Sunil Kumar
8.1 Introduction 163
8.2 The Evolution of Hamilton’s Oligopyridylamides 164
8.3 Limitations of a Tedious Synthetic Route 165
8.4 OPs as Antagonists of Neurodegeneration 166
8.5 OPs Inhibit HIV Infection 168
8.6 OPs Targeting Type II Diabetes 169
8.7 OPs Targeting and Reactivating Mutant Protein in Cancer 171
8.8 Novel Synthesis of OPs and Alzheimer’s Disease 173
8.9 2d-fast 174
8.10 OQ Foldamers – Structure and Discovery 181
8.11 Synthesis of OQ Foldamers 182
8.12 OQs as Modulators of Type II Diabetes-Related aPPIs 183
8.13 Mechanistic Insights into OQ Manipulation of aPPIs 186
8.14 Chemical Diversity and Structure Modulate Efficacy of OQs 188
8.15 Modulation of Alzheimer’s Disease-Related Aβ 189
8.16 OQs for the Modulation of Synucleinopathies 191
8.17 Epilogue 194
Acknowledgement 194
References 195
9 Application of Sulfonyl-γ-AApeptides for PPI Drug Discovery 205
Jarais Fontaine and Jianfeng Cai
9.1 Introduction 205
9.2 Application of Sulfonyl-γ-AApeptides 206
9.2.1 Modulation of PPIs Involved in Cancer 206
9.2.1.1 Inhibition of β-catenin/B-cell lymphoma 9 PPIs 206
9.2.1.2 p53-MDM2/MDMX PPIs Inhibitor 208
9.2.1.3 HIF-1α PPI’s Inhibitor 209
9.2.2 Anti-Viral 210
9.2.2.1 HIV Fusion Inhibitor 210
9.2.2.2 Pan-Coronavirus Fusion inhibitor 212
9.2.3 Aβ-Oligomerization Modulation 213
9.2.4 Diabetes Therapeutics 216
9.3 Future Directions/Conclusion 216
Acknowledgments 217
References 217
10 Introduction of the Application of Stapled Peptides in Protein–Protein Interactions Drug Discovery and Their Successful Examples 219
Maxwell J. Austin and Danny Hung-Chieh Chou
10.1 Introduction 219
10.1.1 Stapled Peptides as a Solution to PPI Challenges 219
10.1.2 Growing Importance of PPIs in Drug Discovery 220
10.1.3 Early Development and Success of Stapled Peptides 220
10.1.4 Overview of the Chapter 221
10.2 Stapled Peptides: Structure Features and Benefits 221
10.2.1 Importance of α-Helical Structures in PPIs 221
10.2.2 Designing Stapled Peptides: Mechanism of Stapling 221
10.2.3 Additional Stapling Strategies 222
10.2.3.1 Lactamization Between Lysine and Glutamate/Aspartate 222
10.2.3.2 Azide–Alkyne Cycloaddition 223
10.2.3.3 C—H Activation 224
10.2.3.4 Cys–Cys Initiated Stapling Strategy 224
10.2.3.5 Tyrosine Stapling 224
10.2.4 Advantages of Stapled Peptides in Drug Discovery 225
10.2.4.1 Enhanced Proteolytic Stability 225
10.2.4.2 Improved Cell Permeability 226
10.2.4.3 Ability to Target Previously “Undruggable” PPIs 226
10.2.4.4 Specificity and Affinity Considerations 227
10.3 Successful Applications of Stapled Peptides in Drug Discovery 227
10.3.1 Targeting the MDM2–p53 Interaction 227
10.3.2 Targeting BCL-2 Family Proteins 228
10.3.3 Targeting the β-Catenin/TCF Interaction 229
10.3.4 Infectious Diseases 230
10.3.5 Clinical Progress and Future Directions 231
10.4 Challenges and Limitations 232
10.4.1 Manufacturing and Cost Considerations 232
10.4.2 Delivery Issues: Overcoming Biological Barriers 232
10.4.3 Off-Target Effects and Safety Concerns 233
10.4.4 Resistance Mechanisms 233
10.5 Future Directions 234
10.5.1 Expansion into New Disease Areas 234
10.5.2 Integration with Other Therapeutic Modalities 235
10.5.3 Emerging Delivery Technologies 235
10.5.4 Summary 236
Acknowledgments 237
References 237
11 Cyclic Peptides for PPI Drug Discovery 243
Hong-Gang Hu and Xiang li
11.1 Introduction 243
11.2 α-Helix Cyclic Peptides (Stapled Peptides) 244
11.2.1 Antitumor Stapled Peptides 245
11.2.2 Antiviral Stapled Peptides 251
11.2.3 Anti-osteoporosis Stapled Peptides 252
11.2.4 Anti-inflammation Stapled Peptides 253
11.2.5 Anti-diabetes Stapled Peptides 253
11.3 β-Hairpin Cyclic Peptides 253
11.4 Macrocyclic Peptides 255
11.5 Summary and Outlook 255
References 256
12 Small Molecule Inhibitors Targeting Protein–Protein Interactions in the BCL Protein 263
Wenhua Zhu, Yangbo He, Gang Chen, and Di Zhu
12.1 Introduction 263
12.2 Inhibitors of BCL-2 Family Antiapoptotic Proteins 264
12.2.1 Members and Structure of BCL-2 Family Proteins 264
12.2.2 Binding Sites and Key Interactions of BCL-2 Family Proteins 266
12.2.3 Antiapoptotic Proteins of the BCL-2 Family and Cancer 267
12.2.4 BCL-2 Family Antiapoptotic Protein Inhibitors 267
12.2.4.1 Selective Bcl-2/Bcl-xL Inhibitors 268
12.2.4.2 Selective Mcl-1 Inhibitor 280
12.2.4.3 Compounds 54-59 292
12.3 Inhibitors of β-catenin/BCL 9 300
12.3.1 Physiological Functions of BCL 9 300
12.3.2 β-catenin/BCL9 PPI 300
12.3.3 Targeting β-catenin/BCL9 Small Molecule Inhibitors 301
12.3.3.1 Natural Products and Their Derivatives 301
12.3.3.2 Phenyl-piperidine Derivatives 303
12.3.3.3 3-(4-fluorophenyl)-N-phenylbenzamide Derivatives 305
12.3.3.4 Other β-catenin/BCL9 Small Molecule Inhibitors 307
12.4 Targeting BCL-6 Small Molecule Inhibitors 307
12.4.1 Biological Functions of BCL 6 307
12.4.2 Structural Characteristics of the BCL6 BTB/POZ Domain 308
12.4.3 BCL6-targeted Diseases 309
12.4.4 BCL6 Inhibitor 310
12.4.4.1 79-6, FX1 and AP-4- 287 310
12.4.4.2 BI3812 and TMX- 2164 310
12.4.4.3 BCL6-i and Compound 107 316
12.4.4.4 Compounds 109, 111, WK500B, and GSK 137 316
12.4.4.5 CCT369347, CCT372064, and OICR 12694 317
12.5 BCL-3 Inhibitors 318
12.5.1 Structural Characteristics of BCL- 3 318
12.5.2 Biological Functions of BCL- 3 318
12.5.3 BCL-3/P50 Inhibitors 320
12.6 BCL-10 Inhibitors 320
12.6.1 Biological Functions of BCL- 10 320
12.6.2 Structural Characteristics of BCL- 10 321
12.6.3 BCL-10 and Cancer 322
12.7 Summary 322
References 323
13 Molecular Glues as Activators for PPI 343
Xiangbing Qi
13.1 Introduction 343
13.1.1 Significance of PPI in Biology and Disease 343
13.1.2 Opportunities and Challenges for PPI Drug Discovery 344
13.1.3 Four Classes of PPI Modulators 344
13.2 Molecular Glues as Orthosteric PPI Stabilizers/Activators 347
13.2.1 Design Principles of MG 347
13.2.2 Classification of MGs 347
13.2.2.1 MG Degraders (MGDs) 347
13.2.2.2 MG Stabilizers 354
13.2.2.3 MG Inhibitors 357
13.3 Methods for MG Discovery 358
13.3.1 Modifications of E3 Ligands: Discovery of New CRBN Ligands 360
13.3.2 Phenotype-Based Screening 361
13.3.2.1 Scalable Chemical Profiling 361
13.3.2.2 Proteomics-Based Screening 362
13.3.3 Target-Based Screening 363
13.3.3.1 HTS for PPI Stabilizers 363
13.3.3.2 Rational Design: Discovery of KRAS-CYPA Molecular Glue 363
13.4 Conclusions and Outlook 364
Contributors 364
References 364
14 Targeting APC–Asef Protein–Protein Interaction for Drug Discovery in Colorectal Cancer Therapy 373
Jie Zhong and Xiuyan Yang
14.1 Introduction 373
14.2 Structural Insights into APC–Asef Interaction 375
14.3 Current APC–Asef Inhibitors 376
14.3.1 Peptides 376
14.3.1.1 Minimal Asef Sequence for APC 376
14.3.1.2 MAI-150–Derived Peptidomimetic Inhibitors 377
14.3.1.3 MAI-203 as the First-in-Class Inhibitor of APC–Asef PPI with Anti-CRC Migration Activity 377
14.3.1.4 Intramolecular Hydrogen Bond Strategy Leading to the Best-in-Class Inhibitor MAI-400 379
14.3.1.5 A More Sensitive FP Assay Led to the Discovery of a Highly Efficient and Potent Inhibitor, MAI-516 380
14.3.1.6 Computer-Aided Design of Tripeptide Inhibitors Disrupting APC–Asef Interaction 381
14.3.2 Small Molecule Inhibitors of APC–Asef PPI 381
14.4 A More Sensitive FP Method for Identifying Highly Active APC–Asef Inhibitors 382
14.5 Conclusions and Outlook 383
References 385
15 Computational Methods Applied to Drug Discovery of Protein–Protein Interaction Systems 389
Zhiyong Gu and Xi Cheng
15.1 Introduction 389
15.2 Computational Methods for PPI Prediction 390
15.2.1 PPI Network Mapping 390
15.2.2 Protein Complex Prediction 394
15.2.3 PPI Modulator Discovery 395
15.2.3.1 Small Molecules 397
15.2.3.2 Peptides and Protein Mimics 400
15.2.3.3 Antibodies 401
15.3 Conclusions and Outlook 401
References 402
Index 409
