Targeting Protein-Protein Interactions by Small Molecules

Protein-protein interactions (PPIs) provide a rich source of drug targets for the development of new generation of clinical therapeutics. However, targeting PPIs by small-molecule inhibitors remains a significant challenge due to large, flat, and hydrophobic features of the PPI interfaces. Recently, important advances have been made in the discovery and development of small-molecule PPI inhibitors. This chapter aims to give an overview of the structural features of PPIs as well as the design strategies of small-molecule PPI inhibitors. Moreover, PPI inhibitors under clinical development will be briefly introduced and two successful examples in PPI-based drug development (venetoclax and lifitegrast) will be highlighted.

High-throughput screening (HTS) is an important method to discover small-molecule inhibitors of protein-protein interactions. The construction of HTS compatible assays and compounds libraries plays a key role in successful identification of PPI inhibitors. Strategies for compound library design and assay establishment as well as their advantages and limitations will be introduced. Two successful case studies about HTS of p53–MDM2 and PDEδ–KRAS inhibitors are highlighted.

Protein-protein interactions (PPIs) are important targets for the development of chemical probes and therapeutic agents. From the initial discovery of the existence of hot spots at PPI interfaces, it has been proposed that hot spots might provide the key for developing small-molecule PPI inhibitors. However, there has been no review on the ways in which the knowledge of hot spots can be used to achieve inhibitor design, nor critical examination of successful examples. This chapter discusses the characteristics of hot spots and the identification of druggable hot spot pockets. An analysis of four examples of hot spot-based design reveals the importance of this strategy in discovering potent and selective PPI inhibitors. A general procedure for hot spot-based design of PPI inhibitors is outlined.

Protein-protein interactions (PPIs) play a vital role in directing various life processes and are responsible for both normal and aberrant cellular functions. Thus, PPIs serve as a large family of potential targets for drug discovery, which are yet to be fully explored. Due to the unique nature of PPIs, as well as certain technical difficulties, they are considered to be challenging targets for drug discovery. However, in the past two decades or so, significant progress has been made in both experimental and computational techniques applicable to this subject, and these developments have accelerated advances in the field. In this chapter, we review several typical computational methods that can be used for discovering small-molecule inhibitors of PPIs. In addition, several representative studies published in recent years in which these computational methods have been applied to the discovery of PPI inhibitors are briefly described.

Protein-protein interactions (PPIs) are implicated innumerous biological processes under physiological and pathophysiological conditions. They thus offer new opportunities for therapeutic intervention. Various experimental methods have been applied to the identification of small-molecule inhibitors targeting PPIs, which can be classified as biophysical, biochemical, and genetic methods. This chapter gives an overview of some widely applied experimental methods in each category, highlighting their principles, advantages, and disadvantages, as well as their recent developments.

Protein-protein interactions (PPIs) are important to every cellular process, from signaling pathways to protein post-translational modifications, as well as many cellular machines for complex biological functions. These interactions make up the so-called interactomics of the organism, and aberrant PPIs are the cause of multiple diseases, including aggregation-related Alzheimer’s disease and many types of cancers. Therefore, modulating the protein-protein interactions was considered as the precise way for pharmacological interventions. In this chapter, we first briefly introduced the fragment-based drug discovery and summarized the current consideration for constructing the fragment library and commonly adopted fragment screening methods. In the second part, we first classified the PPIs into four categories based on the interaction pattern and size of interfaces. Then we reviewed recent progress of utilizing the fragment-based drug discovery approach to develop antagonists of various interesting PPIs and organized these case studies into a biological function-oriented way.

Targeting protein-protein interactions by small molecule compounds is challenging; however, exciting achievements have been made over the past decade. New targets of PPIs were identified, and lots of small molecule modulators were developed. In this chapter, we make a brief review of the research into PPIs and their small molecule inhibitors. We focus on the progress in some new targets of PPIs involving in biological processes such as epigenetic modification, ubiquitin-mediated protein degradation, immune response, RTK signaling pathway, and copper transport. These case studies may provide researchers with a basic overview of this area. Several other promising targets are also discussed herein.

Spiro compounds have drawn ever-increasing attention in drug discovery because of its prevalence in natural products/drugs and unique 3D structural features. A large number of spiro compounds have been proved to possess diverse bioactivities, and some of them have advanced into clinical trials for the treatment of diseases. The interruption of MDM2–p53 protein-protein interactions has been highly pursued as an attractive therapeutic strategy for cancer therapy. A large number of small-molecule inhibitors have been identified based on the well-defined MDM2–p53 interactions. Currently, several small-molecule inhibitors such as SAR405838, APG-115, MK-8242, DS-3032b, NVP-CGM097, RG7112, RG7388, and AMG 232 are undergoing clinical assessment for cancer therapy. In this chapter, we focus on the identification of spirooxindole containing small-molecule inhibitors (SAR405838, APG-115, RG7388, RO8994, RO2468, and RO5353), strategies employed for optimizations, structure–activity relationship studies (SARs) as well as their biochemical profiles. The identification of these lead compounds makes spirooxindoles promising scaffolds in designing potent inhibitors targeting MDM2–p53 interactions. Based on the SARs and the co-crystal structures of p53–MDM2 complexes, we first tentatively propose the prolinamide-based ‘3+1’ model for designing potential MDM2 inhibitors.

The aberrant activation of canonical Wnt signaling is strongly associated with the initiation and progression of many cancers. Cancer stem cells, which are resistant to conventional chemo- and radiotherapies and especially virulent, are also controlled by the hyperactivation of canonical Wnt signaling. Therefore, the disruption of this signaling pathway represents an attractive strategy for cancer therapy. The formation of the β-catenin/Tcf complex in the cell nucleus is the penultimate step of canonical Wnt signaling; hence, these protein-protein interactions (PPIs) were identified as an appealing therapeutic target for anticancer drug development. Herein, the approaches for the discovery of small-molecule inhibitors to disrupt the β-catenin/T cell factor protein-protein interaction, including high throughput screening (HTS), virtual screening, and hot spots-based rational design, were reviewed and the representative examples were presented. These novel inhibitors provide a good starting point for further research. Furthermore, the challenge and opportunity in this researching area, such as further improvement of the binding potency and selectivity, as well as the development of drug-like inhibitors for cell-based and in vivo studies were also discussed.

The transcription factor Nrf2 is in charge of the cellular defense system, and enhancing Nrf2 activity has potential usages in various inflammatory diseases. Recently, directly inhibiting Keap1-Nrf2 protein-protein interactions as a novel Nrf2-modulating strategy has many advantages over using electrophilic Nrf2 activators. The development of Keap1-Nrf2 protein-protein interaction inhibitors has become a topic of intense research, and potent inhibitors of this target have been identified. This chapter summarizes the progress in the discovery and development of Keap1-Nrf2 PPI inhibitors, including the Keap1-Nrf2 regulatory system, screening assay for inhibitor identification, different methods in the development of inhibitors. We also summarized the chemotypes of inhibitors, stated the structure–activity relationship, as well as discussed privileged structures.

As epigenetic readers, the bromodomain and extra-terminal domain (BET) protein family binds to acetyl-lysine (KAc) residues and regulates chromatin structure and gene expression. Inhibition of BET proteins by small-molecule inhibitors for a variety of therapeutic applications has garnered increasing interest, as many compounds have advanced into human clinical trials for various diseases. The BET bromodomain family is composed of BRD2, BRD3, BRD4, and testis-specific BRDT. Knockout studies in mice have validated Brdt-1 as a potential target for male non-hormonal contraception, and the pan-BET inhibitor JQ1 was identified as an effective and reversible contraceptive. Numerous small-molecule compounds with potent inhibitory activity against BET family proteins have been reported. However, most of these inhibitors show minimal intra-BET selectivity due to high levels of sequence homology among the BET subfamily members and shared common structural architecture. Therefore, the discovery of selective small-molecule inhibitors against BRDT for male contraception remains a challenge for the future. This review will cover the structure and function of BRDT, known BRDT inhibitors and discuss potential approaches to discover selective BRDT inhibitors.

Small GTPase is GDP-/GTP-binding proteins that serve as molecular switches to control a variety of essential processes inside cells. Misfunction of small GTPase is frequently discovered in diseases such as cancer, neurodegenerative disease, and other diseases. Controlling the activity of normal and mutated small GTPase are of great meaning in drug discovery. As small GTPases recruit large network of PPIs for signal transduction, rich PPIs are contained in small GTPase signaling pathways, such as small GTPase-GEF, small GTPase-effector interactions, and other PPIs. Targeting PPIs in small GTPase will serve as an effective way to modulate small GTPase activities and signal transduction. In this chapter, we will discuss a variety of approaches and novel strategies to target PPIs in small GTPases and recent advances with selected examples from last five years.