Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein–protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein–protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.

Antiapoptotic Bcl-2 family proteins, such as Bcl-x_L, Bcl-2, and Mcl-1, are often overexpressed in tumor cells, which contributes to tumor cell resistance to chemotherapies and radiotherapies. Inhibitors of these proteins thus have potential applications in cancer treatment. We discovered, through structure-based virtual screening, a lead compound with micromolar binding affinity to Mcl-1 (inhibition constant (K_i)=3 μM). It contains a phenyltetrazole and a hydrazinecarbothioamide moiety, and it represents a structural scaffold not observed among known Bcl-2 inhibitors. This work presents the structural optimization of this lead compound. By following the scaffold-hopping strategy, we have designed and synthesized a total of 82 compounds in three sets. All of the compounds were evaluated in a fluorescence-polarization binding assay to measure their binding affinities to Bcl-x_L, Bcl-2, and Mcl-1. Some of the compounds with a 3-phenylthiophene-2-sulfonamide core moiety showed sub-micromolar binding affinities to Mcl-1 (K_i=0.3–0.4 μM) or Bcl-2 (K_i≈1 μM). They also showed obvious cytotoxicity on tumor cells (IC₅₀<10 μM). Two-dimensional heteronuclear single quantum coherence NMR spectra of three selected compounds, that is, YCW-E5, YCW-E10, and YCW-E11, indicated that they bind to the BH3-binding groove on Bcl-x_L in a similar mode to ABT-737. Several apoptotic assays conducted on HL-60 cells demonstrated that these compounds are able to induce cell apoptosis through the mitochondrial pathway. We propose that the compounds with the 3-phenylthiophene-2-sulfonamide core moiety are worth further optimization as effective apoptosis inducers with an interesting selectivity towards Mcl-1 and Bcl-2.

In a previous study we reported a class of compounds with a 2H-thiazolo[3,2-a]pyrimidine core structure as general inhibitors of anti-apoptotic Bcl-2 family proteins. However, the absolute stereochemical configuration of one carbon atom on the core structure remained unsolved, and its potential impact on the binding affinities of compounds in this class was unknown. In this study, we obtained pure R and S enantiomers of four selected compounds by HPLC separation and chiral synthesis. The absolute configurations of these enantiomers were determined by comparing their circular dichroism spectra to that of an appropriate reference compound. In addition, a crystal structure of one selected compound revealed the exocyclic double bond in these compounds to be in the Z configuration. The binding affinities of all four pairs of enantiomers to Bcl-x_L, Bcl-2, and Mcl-1 proteins were measured in a fluorescence-polarization-based binding assay, yielding inhibition constants (K_i values) ranging from 0.24 to 2.20 μM. Interestingly, our results indicate that most R and S enantiomers exhibit similar binding affinities for the three tested proteins. A binding mode for this compound class was derived by molecular docking and molecular dynamics simulations to provide a reasonable interpretation of this observation.

Autophagy is a highly conserved process in which damaged proteins and organelles are sequestered in double-membrane autophagosomes and delivered to lysosomes for degradation and recycling. As an efficient response to cellular stress, autophagy is essential for the maintenance of cellular homeostasis. Defective autophagy is associated with a variety of diseases, including cancer. This article summarizes current knowledge about the molecular mechanism of autophagy and its role in tumorigenesis. Particular focus is placed on the development of small-molecule regulators of autophagy and their potential application as anticancer therapeutic agents.

Considerable efforts have been made to the development of small-molecule inhibitors of antiapoptotic B-cell lymphoma 2 (Bcl-2) family proteins (such as Bcl-2, Bcl-x_L, and Mcl-1) as a new class of anticancer therapies. Unlike general inhibitors of the entire family, selective inhibitors of each member protein can hopefully reduce the adverse side effects in chemotherapy treatments of cancers overexpressing different Bcl-2 family proteins. In this study, we designed four series of benzylpiperazine derivatives as plausible Bcl-2 inhibitors based on the outcomes of a computational algorithm. A total of 81 compounds were synthesized, and their binding affinities to Bcl-2, Bcl-x_L, and Mcl-1 measured. Encouragingly, 22 compounds exhibited binding affinities in the micromolar range (K_i<20 μM) to at least one target protein. Moreover, some compounds were observed to be highly selective binders to Mcl-1 with no detectable binding to Bcl-2 or Bcl-x_L, among which the most potent one has a K_i value of 0.18 μM for Mcl-1. Binding modes of four selected compounds to Mcl-1 and Bcl-x_L were derived through molecular docking and molecular dynamics simulations. It seems that the binding affinity and selectivity of these compounds can be reasonably interpreted with these models. Our study demonstrated the possibility for obtaining selective Mcl-1 inhibitors with relatively simple chemical scaffolds. The active compounds identified by us could be used as lead compounds for developing even more potent selective Mcl-1 inhibitors with potential pharmaceutical applications.

Sphingomyelin synthase (SMS) produces sphingomyelin and diacylglycerol from ceramide and phosphatidylcholine. It plays an important role in cell survival and apoptosis, inflammation, and lipid homeostasis, and therefore has been noticed in recent years as a novel potential drug target. In this study, we combined homology modeling, molecular docking, molecular dynamics simulation, and normal mode analysis to derive a three-dimensional structure of human sphingomyelin synthase (hSMS1) in complex with sphingomyelin. Our model provides a reasonable explanation on the catalytic mechanism of hSMS1. It can also explain the high selectivity of hSMS1 towards phosphocholine and sphingomyelin as well as some other known experimental results about hSMS1. Moreover, we also derived a complex model of D609, the only known small-molecule inhibitor of hSMS1 so far. Our hSMS1 model may serve as a reasonable structural basis for the discovery of more effective small-molecule inhibitors of hSMS1.

A class of compounds with a common thiazolo[3,2-a]pyrimidinone motif has been developed as general inhibitors of Bcl-2 family proteins. The lead compound was originally identified in a random screening of a small compound library using a fluorescence polarization-based competitive binding assay. Its binding to the Bcl-x_L protein was further confirmed by ¹⁵N-HSQC NMR experiments. Structural modifications on the lead compound were guided by the outcomes of molecular modeling studies. Among the 42 compounds obtained, a number of them exhibited much improved binding affinities to Bcl-2 family proteins as compared to the lead compound. The most potent compound, BCL-LZH-40, inhibited the binding of BH3 peptides to Bcl-x_L, Bcl-2, and Mcl-1 with inhibition constants (K_i) of 17, 534, and 200 nM, respectively.

An automatic method has been developed for identifying antibody entries in the protein data bank (PDB). Our method, called KIAb (Keyword-based Identification of Antibodies), parses PDB-format files to search for particular keywords relevant to antibodies, and makes judgment accordingly. Our method identified 780 entries as antibodies on the entire PDB. Among them, 767 entries were confirmed by manual inspection, indicating a high success rate of 98.3%. Our method recovered basically all of the entries compiled in the Summary of Antibody Crystal Structures (SACS) database. It also identified a number of entries missed by SACS. Our method thus provides a more complete mining of antibody entries in PDB with a very low false positive rate.