Targeting Protein-Protein Interactions for Drug Discovery

Jian Zhang is a Distinguished Professor and Doctoral Supervisor at School of Medicine, Shanghai Jiao Tong University, China. He is also the Director of the Medicinal Bioinformatics Center. His fields of research include first-in-class drug design and chemical biology, mainly pertaining to protein-protein interactions and allostery and their application in drug discovery. He received a BM degree in Pharmacology from Peking University and a PhD from Shanghai Institute of Materia Medica, Chinese Academy of Sciences.

• Preface xiii1 Exploring Protein–Protein Interactions: Concepts, Methods, and Implications 1mi Zhou and Renxiao Wang1.1 General Concepts of Protein–Protein Interactions 11.1.1 Definition of Protein–Protein Interactions 11.1.2 Structural Properties of Protein–Protein Interactions 21.1.3 Diverse Types of Protein–Protein Interactions 31.1.3.1 Enzyme–Substrate Interactions 31.1.3.2 Receptor–Ligand Interactions 31.1.3.3 Antigen–Antibody Interactions 31.1.3.4 Chaperone–Client Interactions 41.1.3.5 Scaffold Interactions 41.2 Functional Significance of Protein–Protein Interactions 41.2.1 Cellular Signal Transduction 51.2.2 Regulation of Gene Expression 61.2.3 Immune Response 81.2.3.1 Immune Cell Migration 81.2.3.2 T-Cell Antigen Recognition and Activation 81.2.3.3 B-Cell Antigen Recognition and Activation 91.2.4 Protein Degradation Pathway 91.2.5 Disease Mechanisms 101.2.5.1 Cancer 101.2.5.2 Neurodegenerative Diseases 111.2.5.3 Infectious Disease 111.3 Methods for Analyzing Protein–Protein Interactions 121.3.1 Experimental Methods 121.3.1.1 Structure Determination 121.3.1.2 Affinity, Kinetics, and Thermodynamics Measurement 131.3.1.3 Large-Scale PPI Network Mapping 131.3.2 Computational Methods 141.3.2.1 Sequence-Based Methods 141.3.2.2 Structure-Based Methods 151.3.2.3 Network-Based Methods 151.4 Implications of the Basic Research on Protein–Protein Interactions 161.4.1 Advancing Disease Understanding and Diagnosis 161.4.2 Driving Target-Based Drug Discovery 171.4.3 Fostering Innovations in Biotechnology 171.5 Conclusions and Perspectives 19References 192 Overview of Drug Discovery Targeting PPI Systems 29Hao Ma and Jian Zhang2.1 Introduction 292.2 Fundamentals of Protein–Protein Interactions 302.2.1 Basic Principles of Protein Structure and Function 302.2.2 Types of Protein–Protein Interactions 322.2.3 Significance of PPIs in Cellular Processes and Disease Pathways 322.3 Challenges in Targeting PPI Systems 332.3.1 Structural Complexities of PPI Interfaces 332.3.2 Dynamics and Flexibility of Protein Complexes 342.3.3 Druggability Issues Associated with PPI Targets 352.4 Approaches in Drug Discovery Targeting PPI Systems 352.4.1 High-Throughput Drug Design (HTS) Methods 352.4.2 Structure-Based Drug Design (SBDD) Techniques 362.4.3 Fragment-Based Drug Discovery (FBDD) Strategies 372.4.4 Computational Methods for Predicting PPI Inhibitors 382.5 Case Studies and Success Stories 402.5.1 BCL Family 402.5.1.1 Bcl- 2 402.5.1.2 Bcl-xL 422.5.1.3 Mcl- 1 422.5.2 p53–MDM 2 432.5.3 XIAP/c-IAP 1 442.5.4 Cd40-cd40l 452.5.5 Cyclin-Dependent Kinase (CDK) 462.5.6 Pd-/pd-l 1 472.5.7 Hsp90-Cdc 37 482.5.8 Menin-MLL 482.5.9 Kras-SOS 1 492.5.10 Keap1-Nrf2 PPI 492.6 Conclusion 51References 533 Fluorescence Resonance Energy Transfer Technology and its Applications 61Jing-Yu Lang3.1 Introduction 613.2 Mechanism of FRET 613.3 Applications of FRET 633.3.1 Molecular Interactions 633.3.2 Conformational Changes 643.3.3 Cellular Imaging 643.3.4 Drug Discovery 643.3.5 Clinical Diagnosis 653.3.6 Structural Biology 663.3.7 Materials Science 663.3.8 Environmental and Agricultural Sciences 663.4 Advantages and Limitations 673.5 Recent Advances 683.6 Conclusion 70Acknowledgements 71References 714 Dissect Protein Interactions Using Mass Spectrometry 75Bin Liao and Liang Zhang4.1 Introduction 754.2 Affinity Purification Coupled with Mass Spectrometry (AP-MS) 764.3 Proximity Labeling 814.4 Cross-linking Mass Spectrometry (XL-MS) 844.5 Co-fractionation Coupled with Mass Spectrometry (CF-MS) 884.6 Thermal Proximity Co-aggregation (TPCA) 904.7 Limited Proteolysis–Mass Spectrometry (LiP–MS) 934.8 Conclusion and Outlook 95Acknowledgements 96References 965 Detection of Protein–Protein Interactions In Situ via Proximity Ligation Assay 105Xinyue Zhou and Peng Zou5.1 Introduction 1055.2 Implementations of Proximity Ligation Assay 1065.3 Applications of PLA for Detecting Protein–Protein Interactions 1085.4 Conclusions and Outlooks 109Acknowledgments 110References 1106 Application of Surface Plasmon Resonance in the Characterization of Protein–Protein Interactions 115Yuanyuan Xie and Jianrong Xu6.1 Introduction 1156.1.1 Protein–Protein Interactions 1156.1.2 Principle of Surface Plasmon Resonance 1156.1.3 Advantage of SPR 1166.2 Applications of SPR Assays in PPIs Characterization 1176.2.1 SPR Application in Binary PPI Systems 1176.2.1.1 SPR Assay in Verifying and Measuring PPIs 1176.2.1.2 SPR-Guided Screening and Optimization in Drug Discovery 1206.2.1.3 SPR in the Validation of PPI Interface 1236.2.2 SPR Application in Ternary PPI Systems 1266.2.2.1 SPR-Based Epitope Competition Assays 1266.2.2.2 SPR-Based Drug Discovery of PPI Modulators 1286.2.2.3 SPR Applications in Targeted Protein Degradation 1306.3 Advantages and Limitations of SPR Application for PPIs 1316.4 Future Directions 132References 1337 Computational Methods for Protein–Protein Interactions 139Hao Li, Yurui Li, and Sheng-You Huang7.1 Introduction 1397.2 Protein–Protein Docking 1407.2.1 Sampling 1427.2.1.1 Traditional Search Algorithms 1427.2.1.2 Deep Learning-Based Search Algorithms 1447.2.2 Scoring 1457.2.2.1 Traditional Scoring Function 1457.2.2.2 Deep Learning-Based Scoring Function 1467.2.3 Template-based Docking 1477.3 End-to-end Structure Prediction 1487.4 CAPRI Experiments 1517.4.1 Casp13-capri 1527.4.2 Casp14-capri 1527.4.3 Casp15-capri 1537.5 Challenges and Future Directions 154Acknowledgments 155Author Contributions 155References 1558 Foldamers as Inhibitors of Aberrant Protein–Protein Interactions 163Nicholas H. Stillman, Ryan A. Dohoney, Charles Z. Baysah, and Sunil Kumar8.1 Introduction 1638.2 The Evolution of Hamilton’s Oligopyridylamides 1648.3 Limitations of a Tedious Synthetic Route 1658.4 OPs as Antagonists of Neurodegeneration 1668.5 OPs Inhibit HIV Infection 1688.6 OPs Targeting Type II Diabetes 1698.7 OPs Targeting and Reactivating Mutant Protein in Cancer 1718.8 Novel Synthesis of OPs and Alzheimer’s Disease 1738.9 2d-fast 1748.10 OQ Foldamers – Structure and Discovery 1818.11 Synthesis of OQ Foldamers 1828.12 OQs as Modulators of Type II Diabetes-Related aPPIs 1838.13 Mechanistic Insights into OQ Manipulation of aPPIs 1868.14 Chemical Diversity and Structure Modulate Efficacy of OQs 1888.15 Modulation of Alzheimer’s Disease-Related Aβ 1898.16 OQs for the Modulation of Synucleinopathies 1918.17 Epilogue 194Acknowledgement 194References 1959 Application of Sulfonyl-γ-AApeptides for PPI Drug Discovery 205Jarais Fontaine and Jianfeng Cai9.1 Introduction 2059.2 Application of Sulfonyl-γ-AApeptides 2069.2.1 Modulation of PPIs Involved in Cancer 2069.2.1.1 Inhibition of β-catenin/B-cell lymphoma 9 PPIs 2069.2.1.2 p53-MDM2/MDMX PPIs Inhibitor 2089.2.1.3 HIF-1α PPI’s Inhibitor 2099.2.2 Anti-Viral 2109.2.2.1 HIV Fusion Inhibitor 2109.2.2.2 Pan-Coronavirus Fusion inhibitor 2129.2.3 Aβ-Oligomerization Modulation 2139.2.4 Diabetes Therapeutics 2169.3 Future Directions/Conclusion 216Acknowledgments 217References 21710 Introduction of the Application of Stapled Peptides in Protein–Protein Interactions Drug Discovery and Their Successful Examples 219Maxwell J. Austin and Danny Hung-Chieh Chou10.1 Introduction 21910.1.1 Stapled Peptides as a Solution to PPI Challenges 21910.1.2 Growing Importance of PPIs in Drug Discovery 22010.1.3 Early Development and Success of Stapled Peptides 22010.1.4 Overview of the Chapter 22110.2 Stapled Peptides: Structure Features and Benefits 22110.2.1 Importance of α-Helical Structures in PPIs 22110.2.2 Designing Stapled Peptides: Mechanism of Stapling 22110.2.3 Additional Stapling Strategies 22210.2.3.1 Lactamization Between Lysine and Glutamate/Aspartate 22210.2.3.2 Azide–Alkyne Cycloaddition 22310.2.3.3 C—H Activation 22410.2.3.4 Cys–Cys Initiated Stapling Strategy 22410.2.3.5 Tyrosine Stapling 22410.2.4 Advantages of Stapled Peptides in Drug Discovery 22510.2.4.1 Enhanced Proteolytic Stability 22510.2.4.2 Improved Cell Permeability 22610.2.4.3 Ability to Target Previously “Undruggable” PPIs 22610.2.4.4 Specificity and Affinity Considerations 22710.3 Successful Applications of Stapled Peptides in Drug Discovery 22710.3.1 Targeting the MDM2–p53 Interaction 22710.3.2 Targeting BCL-2 Family Proteins 22810.3.3 Targeting the β-Catenin/TCF Interaction 22910.3.4 Infectious Diseases 23010.3.5 Clinical Progress and Future Directions 23110.4 Challenges and Limitations 23210.4.1 Manufacturing and Cost Considerations 23210.4.2 Delivery Issues: Overcoming Biological Barriers 23210.4.3 Off-Target Effects and Safety Concerns 23310.4.4 Resistance Mechanisms 23310.5 Future Directions 23410.5.1 Expansion into New Disease Areas 23410.5.2 Integration with Other Therapeutic Modalities 23510.5.3 Emerging Delivery Technologies 23510.5.4 Summary 236Acknowledgments 237References 23711 Cyclic Peptides for PPI Drug Discovery 243Hong-Gang Hu and Xiang li11.1 Introduction 24311.2 α-Helix Cyclic Peptides (Stapled Peptides) 24411.2.1 Antitumor Stapled Peptides 24511.2.2 Antiviral Stapled Peptides 25111.2.3 Anti-osteoporosis Stapled Peptides 25211.2.4 Anti-inflammation Stapled Peptides 25311.2.5 Anti-diabetes Stapled Peptides 25311.3 β-Hairpin Cyclic Peptides 25311.4 Macrocyclic Peptides 25511.5 Summary and Outlook 255References 25612 Small Molecule Inhibitors Targeting Protein–Protein Interactions in the BCL Protein 263Wenhua Zhu, Yangbo He, Gang Chen, and Di Zhu12.1 Introduction 26312.2 Inhibitors of BCL-2 Family Antiapoptotic Proteins 26412.2.1 Members and Structure of BCL-2 Family Proteins 26412.2.2 Binding Sites and Key Interactions of BCL-2 Family Proteins 26612.2.3 Antiapoptotic Proteins of the BCL-2 Family and Cancer 26712.2.4 BCL-2 Family Antiapoptotic Protein Inhibitors 26712.2.4.1 Selective Bcl-2/Bcl-xL Inhibitors 26812.2.4.2 Selective Mcl-1 Inhibitor 28012.2.4.3 Compounds 54-59 29212.3 Inhibitors of β-catenin/BCL 9 30012.3.1 Physiological Functions of BCL 9 30012.3.2 β-catenin/BCL9 PPI 30012.3.3 Targeting β-catenin/BCL9 Small Molecule Inhibitors 30112.3.3.1 Natural Products and Their Derivatives 30112.3.3.2 Phenyl-piperidine Derivatives 30312.3.3.3 3-(4-fluorophenyl)-N-phenylbenzamide Derivatives 30512.3.3.4 Other β-catenin/BCL9 Small Molecule Inhibitors 30712.4 Targeting BCL-6 Small Molecule Inhibitors 30712.4.1 Biological Functions of BCL 6 30712.4.2 Structural Characteristics of the BCL6 BTB/POZ Domain 30812.4.3 BCL6-targeted Diseases 30912.4.4 BCL6 Inhibitor 31012.4.4.1 79-6, FX1 and AP-4- 287 31012.4.4.2 BI3812 and TMX- 2164 31012.4.4.3 BCL6-i and Compound 107 31612.4.4.4 Compounds 109, 111, WK500B, and GSK 137 31612.4.4.5 CCT369347, CCT372064, and OICR 12694 31712.5 BCL-3 Inhibitors 31812.5.1 Structural Characteristics of BCL- 3 31812.5.2 Biological Functions of BCL- 3 31812.5.3 BCL-3/P50 Inhibitors 32012.6 BCL-10 Inhibitors 32012.6.1 Biological Functions of BCL- 10 32012.6.2 Structural Characteristics of BCL- 10 32112.6.3 BCL-10 and Cancer 32212.7 Summary 322References 32313 Molecular Glues as Activators for PPI 343Xiangbing Qi13.1 Introduction 34313.1.1 Significance of PPI in Biology and Disease 34313.1.2 Opportunities and Challenges for PPI Drug Discovery 34413.1.3 Four Classes of PPI Modulators 34413.2 Molecular Glues as Orthosteric PPI Stabilizers/Activators 34713.2.1 Design Principles of MG 34713.2.2 Classification of MGs 34713.2.2.1 MG Degraders (MGDs) 34713.2.2.2 MG Stabilizers 35413.2.2.3 MG Inhibitors 35713.3 Methods for MG Discovery 35813.3.1 Modifications of E3 Ligands: Discovery of New CRBN Ligands 36013.3.2 Phenotype-Based Screening 36113.3.2.1 Scalable Chemical Profiling 36113.3.2.2 Proteomics-Based Screening 36213.3.3 Target-Based Screening 36313.3.3.1 HTS for PPI Stabilizers 36313.3.3.2 Rational Design: Discovery of KRAS-CYPA Molecular Glue 36313.4 Conclusions and Outlook 364Contributors 364References 36414 Targeting APC–Asef Protein–Protein Interaction for Drug Discovery in Colorectal Cancer Therapy 373Jie Zhong and Xiuyan Yang14.1 Introduction 37314.2 Structural Insights into APC–Asef Interaction 37514.3 Current APC–Asef Inhibitors 37614.3.1 Peptides 37614.3.1.1 Minimal Asef Sequence for APC 37614.3.1.2 MAI-150–Derived Peptidomimetic Inhibitors 37714.3.1.3 MAI-203 as the First-in-Class Inhibitor of APC–Asef PPI with Anti-CRC Migration Activity 37714.3.1.4 Intramolecular Hydrogen Bond Strategy Leading to the Best-in-Class Inhibitor MAI-400 37914.3.1.5 A More Sensitive FP Assay Led to the Discovery of a Highly Efficient and Potent Inhibitor, MAI-516 38014.3.1.6 Computer-Aided Design of Tripeptide Inhibitors Disrupting APC–Asef Interaction 38114.3.2 Small Molecule Inhibitors of APC–Asef PPI 38114.4 A More Sensitive FP Method for Identifying Highly Active APC–Asef Inhibitors 38214.5 Conclusions and Outlook 383References 38515 Computational Methods Applied to Drug Discovery of Protein–Protein Interaction Systems 389Zhiyong Gu and Xi Cheng15.1 Introduction 38915.2 Computational Methods for PPI Prediction 39015.2.1 PPI Network Mapping 39015.2.2 Protein Complex Prediction 39415.2.3 PPI Modulator Discovery 39515.2.3.1 Small Molecules 39715.2.3.2 Peptides and Protein Mimics 40015.2.3.3 Antibodies 40115.3 Conclusions and Outlook 401References 402Index 409