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 Ta.