The transcription factor STAT5 catalyzes Mannich ligation reactions yielding inhibitors of leukemic cell proliferation

Targeted small molecule inhibitors blocking the cytolytic effects of pneumolysin and homologous toxins

Pneumolysin (PLY) is a cholesterol-dependent cytolysin (CDC) from Streptococcus pneumoniae, the main cause for bacterial pneumonia. Liberation of PLY during infection leads to compromised immune system and cytolytic cell death. Here, we report discovery, development, and validation of targeted small molecule inhibitors of PLY (pore-blockers, PB). PB-1 is a virtual screening hit inhibiting PLY-mediated hemolysis. Structural optimization provides PB-2 with improved efficacy. Cryo-electron tomography reveals that PB-2 blocks PLY-binding to cholesterol-containing membranes and subsequent pore formation. Scaffold-hopping delivers PB-3 with superior chemical stability and solubility. PB-3, formed in a protein-templated reaction, binds to Cys428 adjacent to the cholesterol recognition domain of PLY with a KD of 256 nM and a residence time of 2000 s. It acts as anti-virulence factor preventing human lung epithelial cells from PLY-mediated cytolysis and cell death during infection with Streptococcus pneumoniae and is active against the homologous Cys-containing CDC perfringolysin (PFO) as well.

Protein-Templated Ugi Reactions versus In-Situ Ligation Screening: Two Roads to the Identification of SARS-CoV-2 Main Protease Inhibitors

Protein-templated fragment ligation was established as a method for the rapid identification of high affinity ligands, and multicomponent reactions (MCR) such as the Ugi four-component reaction (Ugi 4CR) have been efficient in the synthesis of drug candidates. Thus, the combination of both strategies should provide a powerful approach to drug discovery. Here, we investigate protein-templated Ugi 4CR quantitatively using a fluorescence-based enzyme assay, HPLC-QTOF mass spectrometry (MS), and native protein MS with SARS-CoV-2 main protease as template. Ugi reactions were analyzed in aqueous buffer at varying pH and fragment concentration. Potent inhibitors of the protease were formed in presence of the protein via Ugi 4CR together with Ugi three-component reaction (Ugi 3CR) products. Binding of inhibitors to the protease was confirmed by native MS and resulted in the dimerization of the protein target. Formation of Ugi products was, however, more efficient in the non-templated reaction, apparently due to interactions of the protein with the isocyanide and imine fragments. Consequently, in-situ ligation screening of Ugi 4CR products was identified as a superior approach to the discovery of SARS-CoV-2 protease inhibitors.

Identification and Optimization of Protein Tyrosine Phosphatase Inhibitors Via Fragment Ligation

Phosphotyrosine biomimetics are starting points for potent inhibitors of protein tyrosine phosphatases (PTPs) and, thus, crucial for drug development. Their identification, however, has been heavily driven by rational design, limiting the discovery of diverse, novel, and improved mimetics. In this chapter, we describe two screening approaches utilizing fragment ligation methods: one to identify new mimetics and the other to optimize existing mimetics into more potent and selective inhibitors.

Shotgun Kinetic Target-Guided Synthesis Approach Enables the Discovery of Small-Molecule Inhibitors against Pathogenic Free-Living Amoeba Glucokinases

Pathogenic free-living amoebae (pFLA) can cause life-threatening central nervous system (CNS) infections and warrant the investigation of new chemical agents to combat the rise of infection from these pathogens. Naegleria fowleri glucokinase (NfGlck), a key metabolic enzyme involved in generating glucose-6-phosphate, was previously identified as a potential target due to its limited sequence similarity with human Glck (HsGlck). Herein, we used our previously demonstrated multifragment kinetic target-guided synthesis (KTGS) screening strategy to identify inhibitors against pFLA glucokinases. Unlike the majority of previous KTGS reports, our current study implements a "shotgun" approach, where fragments were not biased by predetermined binding potentials. The study resulted in the identification of 12 inhibitors against 3 pFLA glucokinase enzymes─NfGlck, Balamuthia mandrillaris Glck (BmGlck), and Acanthamoeba castellanii Glck (AcGlck). This work demonstrates the utility of KTGS to identify small-molecule binders for biological targets where resolved X-ray crystal structures are not readily accessible.

Going beyond Binary: Rapid Identification of Protein-Protein Interaction Modulators Using a Multifragment Kinetic Target-Guided Synthesis Approach

Kinetic target-guided synthesis (KTGS) is a powerful screening approach that enables identification of small molecule modulators for biomolecules. While many KTGS variants have emerged, a majority of the examples suffer from limited throughput and a poor signal/noise ratio, hampering reliable hit detection. Herein, we present our optimized multifragment KTGS screening strategy that tackles these limitations. This approach utilizes selected reaction monitoring liquid chromatography tandem mass spectrometry for hit detection, enabling the incubation of 190 fragment combinations per screening well. Consequentially, our fragment library was expanded from 81 possible combinations to 1710, representing the largest KTGS screening library assembled to date. The expanded library was screened against Mcl-1, leading to the discovery of 24 inhibitors. This work unveils the true potential of KTGS with respect to the rapid and reliable identification of hits, further highlighting its utility as a complement to the existing repertoire of screening methods used in drug discovery.

Pentafluorophosphato‐Phenylalanines: Amphiphilic Phosphotyrosine Mimetics Displaying Fluorine‐Specific Protein Interactions

Phosphotyrosine residues are essential functional switches in health and disease. Thus, phosphotyrosine biomimetics are crucial for the development of chemical tools and drug molecules. We report here the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. A mild acidic pentafluorination protocol was developed and two PF₅‐amino acids were prepared and employed in peptide synthesis. Their structures, reactivities, and fluorine‐specific interactions were studied by NMR and IR spectroscopy, X‐ray diffraction, and in bioactivity assays. The mono‐anionic PF₅ motif displayed an amphiphilic character binding to hydrophobic surfaces, to water molecules, and to protein‐binding sites, exploiting charge and H−F‐bonding interactions. The novel motifs bind 25‐ to 30‐fold stronger to the phosphotyrosine binding site of the protein tyrosine phosphatase PTP1B than the best current biomimetics, as rationalized by computational methods, including molecular dynamics simulations.

Chemical Evolution of Antivirals Against Enterovirus D68 through Protein-Templated Knoevenagel Reactions

The generation of bioactive molecules from inactive precursors is a crucial step in the chemical evolution of life, however, mechanistic insights into this aspect of abiogenesis are scarce. Here, we investigate the protein-catalyzed formation of antivirals by the 3C-protease of enterovirus D68. The enzyme induces aldol condensations yielding inhibitors with antiviral activity in cells. Kinetic and thermodynamic analyses reveal that the bioactivity emerges from a dynamic reaction system including inhibitor formation, alkylation of the protein target by the inhibitors, and competitive addition of non-protein nucleophiles to the inhibitors. The most active antivirals are slowly reversible inhibitors with elongated target residence times. The study reveals first examples for the chemical evolution of bio-actives through protein-catalyzed, non-enzymatic C-C couplings. The discovered mechanism works under physiological conditions and might constitute a native process of drug development.

Tailored Bioorthogonal and Bioconjugate Chemistry: A Source of Inspiration for Developing Kinetic Target-Guided Synthesis Strategies

Kinetic target-guided synthesis (KTGS) is a promising tool for the discovery of biologically active compounds. It relies on the identification of potent ligands that are covalently assembled by the biological targets themselves from a pool of reagents. Significant effort is devoted to developing new KTGS strategies; however, only a handful of biocompatible reactions are available, which may be insufficient to meet the specificities (stability, dynamics, active site topology, etc.) of a wide range of biological targets with therapeutic potential. This Topical Review proposes a retrospective analysis of existing KTGS ligation tools, in terms of their kinetics and analogy with other biocompatible reactions, and provides new clues to expand the KTGS toolkit. By way of examples, a nonexhaustive selection of such chemical ligation tools belonging to different classes of reactions as promising candidate reactions for KTGS are suggested.

Protein-Templated Hit Identification through an Ugi Four-Component Reaction*

Kinetic target-guided synthesis represents an efficient hit-identification strategy, in which the protein assembles its own inhibitors from a pool of complementary building blocks via an irreversible reaction. Herein, we pioneered an in situ Ugi reaction for the identification of novel inhibitors of a model enzyme and binders for an important drug target, namely, the aspartic protease endothiapepsin and the bacterial β-sliding clamp DnaN, respectively. Highly sensitive mass-spectrometry methods enabled monitoring of the protein-templated reaction of four complementary reaction partners, which occurred in a background-free manner for endothiapepsin or with a clear amplification of two binders in the presence of DnaN. The Ugi products we identified show low micromolar activity on endothiapepsin or moderate affinity for the β-sliding clamp. We succeeded in expanding the portfolio of chemical reactions and biological targets and demonstrated the efficiency and sensitivity of this approach, which can find application on any drug target.

Recent advances in synthetic and medicinal chemistry of phosphotyrosine and phosphonate-based phosphotyrosine analogues

Phosphotyrosine-containing compounds attract significant attention due to their potential to modulate signalling pathways by binding to phospho-writers, erasers and readers such as SH2 and PTB domain containing proteins. Phosphotyrosine derivatives provide useful chemical tools to study protein phosphorylation/dephosphorylation, and as such represent attractive starting points for the development of binding ligands and chemical probes to study biology, and for inhibitor and degrader drug design. To overcome enzymatic lability of the phosphate group, physiologically stable phosphonate-based phosphotyrosine analogues find utility in a wide range of applications. This review covers advances over the last decade in the design of phosphotyrosine and its phosphonate-based derivatives, highlights the improved and expanded synthetic toolbox, and illustrates applications in medicinal chemistry.

The Selectivity of Fosfosal for STAT5b over STAT5a is Mediated by Arg566 in the Linker Domain

Fosfosal is the O-phosphorylated derivative of salicylic acid, with documented clinical use as a prodrug for the treatment of inflammatory diseases. We recently discovered that fosfosal itself inhibits the protein-protein interaction domain, the SH2 domain, of the tumor-related transcription factor STAT5b. Here, we demonstrate that fosfosal is selective for STAT5b over its close homologue STAT5a. This selectivity is mediated by the STAT5b residue Arg566, located in the SH2 domain-adjacent linker domain. Our data provide further evidence for the role of the STAT linker domain in determining the activity of small molecules against the SH2 domain. We present a refined binding model for fosfosal and STAT5b, which can serve as the basis for the development of fosfosal-based STAT5b inhibitors.

Shikonin is a novel and selective IMPDH2 inhibitor that target triple-negative breast cancer

Triple-negative breast cancer (TNBC) is heterogeneous disease with a poor prognosis. It is therefore important to explore novel therapeutic agents to improve the clinical efficacy for TNBC. The inosine 5'-monophosphate dehydrogenase 2 (IMPDH2) is a rate-limiting enzyme in the de novo synthesis of guanine nucleotides. It is always overexpressed in many types of tumors, including TNBC and regarded as a potential target for cancer therapy. Through screening a library of natural products, we identified shikonin, a natural bioactive component of Lithospermum erythrorhizon, is a novel and selective IMPDH2 inhibitor. Enzymatic analysis using Lineweaver-Burk plot indicates that shikonin is a competitive inhibitor of IMPDH2. The interaction between shikonin and IMDPH2 was further investigated by thermal shift assay, fluorescence quenching, and molecular docking simulation. Shikonin treatment effectively inhibits the growth of human TNBC cell line MDA-MB-231, and murine TNBC cell line, 4T1 in a dose-dependent manner, which is impaired by exogenous supplementation of guanosine, a salvage pathway of purine nucleotides. Most importantly, IMPDH2 knockdown significantly reduced cell proliferation and conferred resistance to shikonin in TNBC. Collectively, our findings showed the natural product shikonin as a selective inhibitor of IMPDH2 with anti-TNBC activity, impelling its further study in clinical trials.

Pentagram-Shaped Ag@Pt Core-Shell Nanostructures as High-Performance Catalysts for Formaldehyde Detection

High-performance HCHO sensors are of great importance in various application fields such as indoor air quality assessments. Herein, bimetallic Ag-Pt nanoparticles are synthesized as high-performance catalysts for ZnO-based gas sensors. Spherical aberration (Cs)-corrected transmission electron microscopy images with atomic resolution clearly indicate that the prepared nanoparticles exhibit a novel Ag@Pt core-shell nanostructure with a pentagram shape. For high-performance HCHO sensor construction, integrated micro-electrodes are first fabricated with the microelectromechanical system (MEMS) technology. Then, the hydrothermal route is used to self-assemble well-aligned ZnO nanowire arrays onto the sensing microregion. After that, the pentagram-shaped Ag@Pt nanoparticles are loaded onto the surface of ZnO nanowires with the inkjet printing technique to form MEMS sensors with Ag@Pt@ZnO as the sensing material. The thoroughly sensing experiments indicate that the Ag@Pt nanoparticles exhibit satisfied catalytic activation to HCHO molecules. The experimental observed detection limit of our sensor to HCHO reaches the parts per billion level. To elucidate the HCHO-sensing mechanism, the online mass spectrum (online MS) is utilized to analyze the components of exhaust gas stream of HCHO flowing through the Ag@Pt@ZnO material. The online MS indicates that with the Ag@Pt catalyst, HCHO molecules are partially oxidized to HCOOH molecules at low temperatures and are completely oxidized to CO₂ molecules at high temperatures.

A novel artificial intelligence protocol for finding potential inhibitors of acute myeloid leukemia

There is currently no effective treatment for acute myeloid leukemia, and surgery is also ineffective as an important treatment for most tumors. Rapidly developing artificial intelligence technology can be applied to different aspects of drug development, and it plays a key role in drug discovery. Based on network pharmacology and virtual screening, candidates were selected from the molecular database. Nine artificial intelligence algorithm models were used to further verify the candidates' potential. The 350 training results of the deep learning model showed higher credibility, and the R-square of the training set and test set of the optimal model reached 0.89 and 0.84, respectively. The random forest model has an R-square of 0.91 and a mean square error of only 0.003. The R-square of the Adaptive Boosting model and the Bagging model reached 0.92 and 0.88, respectively. Molecular dynamics simulation evaluated the stability of the ligand-protein complex and achieved good results. Artificial intelligence models had unearthed the promising candidates for STAT3 inhibitors, and the good performance of most models showed that they still had practical value on small data sets.

Kinetic Target-Guided Synthesis: Reaching the Age of Maturity

Kinetic target-guided synthesis (KTGS) is an original discovery strategy allowing a target to catalyze the irreversible synthesis of its own ligands from a pool of reagents. Although pioneered almost two decades ago, it only recently proved its usefulness in medicinal chemistry, as exemplified by the increasing number of protein targets used, the wider range of target and pocket types, and the diversity of therapeutic areas explored. In recent years, two new leads for in vivo studies were released. Amidations and multicomponent reactions expanded the armamentarium of reactions beyond triazole formation and two new examples of in cellulo KTGS were also disclosed. Herein, we analyze the origins and the chemical space of both KTGS ligands and warhead-bearing reagents. We review the KTGS timeline focusing on recent cases in order to give medicinal chemists the full scope of this strategy which has great potential for hit discovery and hit or lead optimization.

Direct Targeting Options for STAT3 and STAT5 in Cancer

Signal transducer and activator of transcription (STAT)3 and STAT5 are important transcription factors that are able to mediate or even drive cancer progression through hyperactivation or gain-of-function mutations. Mutated STAT3 is mainly associated with large granular lymphocytic T-cell leukemia, whereas mutated STAT5B is associated with T-cell prolymphocytic leukemia, T-cell acute lymphoblastic leukemia and γδ T-cell-derived lymphomas. Hyperactive STAT3 and STAT5 are also implicated in various hematopoietic and solid malignancies, such as chronic and acute myeloid leukemia, melanoma or prostate cancer. Classical understanding of STAT functions is linked to their phosphorylated parallel dimer conformation, in which they induce gene transcription. However, the functions of STAT proteins are not limited to their phosphorylated dimerization form. In this review, we discuss the functions and the roles of unphosphorylated STAT3/5 in the context of chromatin remodeling, as well as the impact of STAT5 oligomerization on differential gene expression in hematopoietic neoplasms. The central involvement of STAT3/5 in cancer has made these molecules attractive targets for small-molecule drug development, but currently there are no direct STAT3/5 inhibitors of clinical grade available. We summarize the development of inhibitors against the SH2 domains of STAT3/5 and discuss their applicability as cancer therapeutics.

Stafia-1: a STAT5a-Selective Inhibitor Developed via Docking-Based Screening of in Silico O-Phosphorylated Fragments

We present a new approach for the identification of inhibitors of phosphorylation-dependent protein-protein interaction domains, in which phenolic fragments are adapted by in silico O-phosphorylation before docking-based screening. From a database of 10 369 180 compounds, we identified 85 021 natural product-derived phenolic fragments, which were virtually O-phosphorylated and screened for in silico binding to the STAT3 SH2 domain. Nine screening hits were then synthesized, eight of which showed a degree of in vitro inhibition of STAT3. After analysis of its selectivity profile, the most potent inhibitor was then developed to Stafia-1, the first small molecule shown to preferentially inhibit the STAT family member STAT5a over the close homologue STAT5b. A phosphonate prodrug based on Stafia-1 inhibited STAT5a with selectivity over STAT5b in human leukemia cells, providing the first demonstration of selective in vitro and intracellular inhibition of STAT5a by a small-molecule inhibitor.

The STAT5b Linker Domain Mediates the Selectivity of Catechol Bisphosphates for STAT5b over STAT5a

STAT family proteins are important mediators of cell signaling and represent therapeutic targets for the treatment of human diseases. Most STAT inhibitors target the protein-protein interaction domain, the SH2 domain, but specificity for a single STAT protein is often limited. Recently, we developed catechol bisphosphates as the first inhibitors of STAT5b demonstrated to exhibit a high degree of selectivity over the close homologue STAT5a. Here, we show that the amino acid in position 566 of the linker domain, not the SH2 domain, is the main determinant of specificity. Arg566 in wild-type STAT5b favors tight binding of catechol bisphosphates, while Trp566 in wild-type STAT5a does not. Amino acid 566 also determines the affinity for a tyrosine-phosphorylated peptide derived from the EPO receptor for STAT5a and STAT5b, demonstrating the functional relevance of the STAT5 linker domain for the adjacent SH2 domain. These results provide the first demonstration that a residue in the linker domain can determine the affinity of nonpeptidic small-molecule inhibitors for the SH2 domain of STAT proteins. We propose targeting the interface between the SH2 domain and linker domain as a novel design approach for the development of potent and selective STAT inhibitors. In addition, our data suggest that the linker domain could contribute to the enigmatically divergent biological functions of the two STAT5 proteins.