Background/Objectives: Protein kinases represent major therapeutic targets because dysregulation of their phosphorylation activity is associated with several diseases, including cancer, diabetes, and inflammatory disorders. Thus, many researchers in the pharmaceutical filed are making significant effort to design potent new protein kinase inhibitors (PKIs) as potential drugs. In this context, we aimed to identify new alternatives by exploiting the chemical space defined by ligands of the nucleotide-binding protein family for the discovery of novel protein kinase inhibitors. Protein kinases bind the nucleotide adenosine triphosphate (ATP) and belong to the nucleotide-binding protein group. Methods: All ligands of the nucleotide-binding protein family, excluding known kinase inhibitors, that were identified in the ChEMBL database were used in a structure-based virtual screening approach. From this set, we aimed to identify novel nucleotide-binding protein inhibitors (NBPIs) as novel kinase inhibitors. A total of 19,709 NBPI compounds that were dissimilar to known PKIs were docked on five protein kinases, and the 200 best scoring docking poses were retained for potential purchase. Results: Only 25 compounds were commercially available in stock and were evaluated experimentally on a panel of 10 diverse protein kinases. Three NBPI compounds, one of which had originally been identified as active against the ATP-binding cassette transporter ABCG2, were identified as Haspin kinase inhibitors with micromolar activity. Conclusions: This study presents an efficient computational approach to identifying novel kinase inhibitors from a database of ligands of the nucleotide-binding protein family, and the protocol could be applied to other protein target families.

There are currently no antiviral drugs available to treat or prevent life-threatening human non-poliovirus enterovirus infections, such as those caused by CV-B3, EV-A71 or EV-D68. Our aim is to develop novel inhibitors that target the non-structural ATPase/Helicase 2C protein, which is involved in the RNA replication process that is essential for enterovirus replication, among other functions. In this study, we describe the optimization of (S)-fluoxetine, a promising hit identified through drug repurposing that binds to an allosteric site on the CV-B3 2C ATPase domain. Our optimization process was guided by rational design, X-ray crystallographic structures, computational docking, and validation by enzyme and cell-based assays, leading to several new inhibitors, among which compound 53 (CV-B3 EC50 = 0.5 μM and EV-D68 EC50 = 0.4 μM), a novel anti-enterovirus with higher selectivity indexes than (S)-fluoxetine.

CLK1 is one of the four human isoforms of the cdc2-like (CLK) kinases that has been suggested as a therapeutic target in diverse diseases based on its important role regulating mRNA splicing. For example, CLKs and closely related kinases such as DYRK1A have been targeted in Alzheimer’s disease and other diseases in which splice site selection contributes to the disease development. Here we have developed an efficient in silico fragment-based ligand design approach to identify novel CLK1 inhibitors with excellent ligand efficiency based on an imidazo[2,1-b][1,3,4]thiadiazole fragment. More than one million docking poses were generated from 26,225 unique virtual compounds, and after applying several filtering steps, 11 compounds were selected, synthesized and their CLK1 inhibition and cellular potency were evaluated. Gratifyingly, inhibitor potencies were in excellent agreement with predicted values and crystallographic data of an inhibitor bound to CLK1 confirmed the unusual binding mode of the compounds.

Background/Objectives: Fragment-based approaches in the field of drug discovery and design have been widely developed and employed in both academia and industry. We present here an innovative in silico fragment-based drug design approach aimed at designing new inhibitors in the ATP-binding site of protein kinases. Methods: This tool, named Frags2Drugs (F2D), relies on a three-dimensional fragment library obtained from co-crystallized ligands. This library is stored in a graph-oriented database containing the required information to link fragments together. F2D builds every possible molecule that fits into the given cavity on a minute scale. Molecules are then filtered to keep those presenting the best predicted affinity. Several specific molecular filters can be applied, including protein kinase inhibitor-like filters. Results: We validated our method by reconstructing existing co-crystallized ligands and known kinase inhibitors. In this study, we provide several examples of its use to retrieve known or design new type I, type I1/2, type II, and macrocyclic inhibitors on several protein kinases. Conclusions: We have developed an in silico fragment-based ligand design tool able to identify novel kinase inhibitors by growing any scaffolds positioned in the ATP-binding site..

The SARS-CoV-2 E protein through its C-terminal PDZ-binding motif (PBM) interacts with several host PDZ-containing proteins, including Zonula occludens-1 (ZO-1) protein via its PDZ2 domain, thereby contributing to viral pathogenesis. Targeting this interaction represents a potential therapeutic strategy. In this study, we determined the X-ray structure of the E PBM peptide in complex with the ZO-1 PDZ2 domain at 1.7 Å resolution. The structure revealed a domain-swapped dimer conformation of ZO-1 PDZ2, with the E PBM peptide conventionally bound within the PDZ domain’s canonical binding groove, exhibiting key interactions characteristic of type II PBM/PDZ interactions. To identify potential inhibitors of the E PBM/ZO-1 PDZ2 interaction, we performed a Homogeneous Time-Resolved Fluorescence (HTRF) screening using a protein-protein interaction-focused library of 1000 compounds. This led to the identification of 36 hits that disrupted this interaction. Subsequent cytotoxicity and dose-response assays narrowed the selection to 14 promising compounds. Docking simulations showed that some compounds bind within or near the PBM-binding pocket, supporting a competitive mechanism of interaction inhibition, while others bind at a central interface between the two PDZ monomers, suggesting an inhibition of dimerization, which in turn prevents PBM binding. Thus, the E PBM/ZO-1 PDZ2 interaction can be inhibited through both direct and indirect mechanisms. Finally, antiviral assays using a NanoLuciferase-expressing recombinant SARS-CoV-2 demonstrated that one compound, C19, significantly reduced viral replication, highlighting its potential as a candidate for further therapeutic development.

A first access to mono-, di- and tri-(Het)arylated pyrazolo[5,1-b]oxazoles is reported. The series were generated from a library of 3-(Het)arylpyrazolo[5,1-b]oxazole platforms selectively functionalized through regioselective arylation procedures. The regioselective functionalization in C-2 and C-7 positions was investigated. Each Palladium-catalyzed cross-coupling condition was optimized and a representative library of the scope and limitations of the reactions was studied.

Computational approaches are nowadays largely applied in drug discovery projects. Among these, molecular docking is the most used for hit identification against a drug target protein. However, many scientists in the field shed light on the lack of availability and reproducibility of the data obtained from such studies to the whole community. Consequently, sustaining and developing the efforts toward a large and fully transparent sharing of those data could be beneficial for all researchers in drug discovery. The purpose of this article is first to propose guidelines and recommendations on the appropriate way to conduct virtual screening experiments and second to depict the current state of sharing molecular docking data. In conclusion, we have explored and proposed several prospects to enhance data sharing from docking experiment that could be developed in the foreseeable future.

A library of substituted indolo[2,3-c]quinolone-6-ones was developed as simplified Lamellarin isosters. Synthesis was achieved from indole after a four-step pathway sequence involving iodination, a Suzuki-Miyaura cross-coupling reaction, and a reduction/lactamization sequence. The inhibitory activity of the 22 novel derivatives was assessed on Haspin kinase. Two of them possessed an IC50 of 1 and 2 nM with selectivity towards a panel of 10 other kinases including the parent kinases DYRK1A and CLK1. The most selective compound exerted additionally a very interesting cell effect on the osteosarcoma U-2 OS cell line.

This work describes the synthesis, enzymatic activities on PI3K and mTOR, in silico docking and cellular activities of various uncommon 2,4,7 trisubstituted pyrido[3,2-d]pyrimidines. The series synthesized offers a chemical diversity in C-7 whereas C-2 (3-hydroxyphenyl) and C-4 groups (morpholine) remain unchanged, in order to provide a better understanding of the molecular determinants of PI3K selectivity or dual activity on PI3K and mTOR. Some C-7 substituents were shown to improve the efficiency on kinases compared to the 2,4-di-substituted pyrimidopyrimidine derivatives used as references. Six novel derivatives possess IC50 values on PI3Kα between 3 and 10 nM. The compounds with the best efficiencies on PI3K and mTOR induced micromolar cytotoxicity on cancer cell lines possessing an overactivated PI3K pathway.

The front cover picture, designed by El Kazzouli and co-workers, illustrates the site-selective C5 and C7 palladium-catalyzed C-H arylations of 4-azaindazole N-oxide. The 1,10-phenanthroline as ligand and Pd(OAc)2 as catalyst in toluene promoted the activation of C5 position, while the triphenyl phosphine as ligand and PdCl2 as catalyst in DMA directed the arylation at C7 position. This new method allows the synthesis of C5, C7-diarylated 4-azaindazole N-oxides as well as the C3, C5, C7-triarylated 4-azaindazoles. Details can be found in the Communication by El Kazzouli, Suzenet, Guillaumet and co-workers (S. Faarasse, S. El Kazzouli, O. Bourzikat, S. Bourg, S. Aci-Sèche, P. Bonnet, F. Suzenet, G. Guillaumet Adv. Synth. Catal. 2021, 363, 3937–3945; DOI: 10.1002/adsc.202001421).

Direct and site-selective C5 and C7 palladium-catalyzed C-H arylations of 4-azaindazole N-oxide have been achieved. A bidentate ligand and Pd(OAc)(2) catalyst in toluene promoted the activation of C5 position, while a phosphine ligand and PdCl2 catalyst in DMA directed the arylation at C7 position. Using this new method, the synthesis of C5, C7-diarylated 4-azaindazole N-oxides as well as the C3, C5, C7-triarylated 4-azaindazoles was achieved towards future medicinal compounds development.

Protein-protein interactions (PPIs) mediate nearly every cellular process and represent attractive targets for modulating disease states but are challenging to target with small molecules. Despite this, several PPI inhibitors (iPPIs) have entered clinical trials, and a growing number of PPIs have become validated drug targets. However, high-throughput screening efforts still endure low hit rates mainly because of the use of unsuitable screening libraries. Here, we describe the collective effort of a French consortium to build, select, and store in plates a unique chemical library dedicated to the inhibition of PPIs. Using two independent predictive models and two updated databases of experimentally confirmed PPI inhibitors developed by members of the consortium, we built models based on different training sets, molecular descriptors, and machine learning methods. Independent statistical models were used to select putative PPI inhibitors from large commercial compound collections showing great complementarity. Medicinal chemistry filters were applied to remove undesirable structures from this set (such as PAINS, frequent hitters, and toxic compounds) and to improve drug likeness. The remaining compounds were subjected to a clustering procedure to reduce the final size of the library while maintaining its chemical diversity. In practice, the library showed a 46-fold activity rate enhancement when compared to a non-iPPI-enriched diversity library in high-throughput screening against the CD47-SIRPα PPI. The Fr-PPIChem library is plated in 384-well plates and will be distributed on demand to the scientific community as a powerful tool for discovering new chemical probes and early hits for the development of potential therapeutic drugs.

Drug discovery is a challenging and expensive field. Hence, novel in silico tools have been developed in early discovery stage to identify and prioritize novel molecules with suitable physicochemical properties. In many in silico drug design projects, molecular databases are screened by virtual screening tools to search for potential bioactive molecules. The preparation of the molecules is therefore a key step in the success of well-established techniques such as docking, similarity or pharmacophore searching. We review here the lists of several toolkits used in different steps during the cleaning of molecular databases, integrated within a KNIME workflow. During the first step of the automatic workflow, salts are removed, and mixtures are split to get one compound per entry. Then compounds with unwanted features are filtered. Duplicated entries are then deleted while considering stereochemistry. As a compromise between exhaustiveness and computational time, most distributed tautomers at physiological pH are computed. Additionally, various flags are applied to molecules by using either classical molecular descriptors, similarity search to known libraries or substructure search rules. Moreover, stereoisomers are enumerated depending on the unassigned chiral centers. Then, three-dimensional coordinates, and optionally conformers, are generated. This workflow has been already applied to several drug design projects and can be used for molecular database preparation upon request.

Chiralpak ZWIX(+) and ZWIX(-), are brush-type bonded-silica chiral stationary phases (CSPs), based on complex diastereomeric Cinchona alkaloids derivatives bearing both a positive and a negative charge. In the present study, we aimed to improve the understanding of retention and enantioseparation mechanisms of these CSPs employed in supercritical fluid chromatography (SFC). For this purpose, 9 other stationary phases were used as comparison systems: two of them are commercially available and bear only a positive charge (Chiralpak QN-AX and QD-AX) and the 7 others were designed purposely to be structurally similar to the parent ZWIX phases, but miss some portion of the complex ligand. First, cluster analysis was employed to identify similar and dissimilar behavior among the 11 stationary phases, where ionic interactions appeared to dominate the observed differences. Secondly, the stationary phases were characterized with linear solvation energy relationships (LSER) based on the SFC analysis of 161 achiral analytes and a modified version of the solvation parameter model to include ionic interactions. This served to compare the interaction capabilities for the 11 stationary phases and showed in particular the contribution of attractive and repulsive ionic interactions. Then the ZWIX phases were characterized for their enantioseparation capabilities with a set of 58 racemic probes. Discriminant analysis was applied to explore the molecular structural features that are useful to successful enantioseparation on the ZWIX phases. In particular, it appeared that the presence of positive charges in the analyte is causing increased retention but is not necessarily a favorable feature to enantiorecognition. On the opposite, the presence of negative charges in the analyte favors early elution and enantiorecognition. Finally, a smaller set of 30 pairs of enantiomers, selected by their structural diversity and different enantioseparation values on the ZWIX phases, were analyzed on all chiral phases to observe the contribution of each structural fragment of the chiral ligand on enantioselectivity. Molecular modelling of the ligands also helped in understanding the three-dimensional arrangement of each ligand, notably the intra-molecular hydrogen bonding or the possible contribution of ionic interactions. In the end, each structural element in the ZWIX phases appeared to be a significant contributor to successful enantioresolution, whether they contribute as direct interaction groups (ion-exchange functions) or as steric constraints to orientate the interacting groups towards the analytes.

Since the first approval of a protein kinase inhibitor (PKI) by the Food and Drug Administration (FDA) in 2001, 55 new PKIs have reached the market, and many inhibitors are currently being evaluated in clinical trials. This is a clear indication that protein kinases still represent major drug targets for the pharmaceutical industry. In a previous work, we have introduced PKIDB, a publicly available database, gathering PKIs that have already been approved (Phase 4), as well as those currently in clinical trials (Phases 0 to 3). This database is updated frequently, and an analysis of the new data is presented here. In addition, we compared the set of PKIs present in PKIDB with the PKIs in early preclinical studies found in ChEMBL, the largest publicly available chemical database. For each dataset, the distribution of physicochemical descriptors related to drug-likeness is presented. From these results, updated guidelines to prioritize compounds for targeting protein kinases are proposed. The results of a principal component analysis (PCA) show that the PKIDB dataset is fully encompassed within all PKIs found in the public database. This observation is reinforced by a principal moments of inertia (PMI) analysis of all molecules. Interestingly, we notice that PKIs in clinical trials tend to explore new 3D chemical space. While a great majority of PKIs is located on the area of "flatland", we find few compounds exploring the 3D structural space. Finally, a scaffold diversity analysis of the two datasets, based on frequency counts was performed. The results give insight into the chemical space of PKIs, and can guide researchers to reach out new unexplored areas. PKIDB is freely accessible from the following website: http://www.icoa.fr/pkidb.

DNA glycosylases are emerging as relevant pharmacological targets in inflammation, cancer and neurodegenerative diseases. Consequently, the search for inhibitors of these enzymes has become a very active research field. As a continuation of previous work that showed that 2-thioxanthine (2TX) is an irreversible inhibitor of zinc finger (ZnF)-containing Fpg/Nei DNA glycosylases, we designed and synthesized a mini-library of 2TX-derivatives (TXn) and evaluated their ability to inhibit Fpg/Nei enzymes. Among forty compounds, four TXn were better inhibitors than 2TX for Fpg. Unexpectedly, but very interestingly, two dithiolated derivatives more selectively and efficiently inhibit the zincless finger (ZnLF)-containing enzymes (human and mimivirus Neil1 DNA glycosylases hNeil1 and MvNei1, respectively). By combining chemistry, biochemistry, mass spectrometry, blind and flexible docking and X-ray structure analysis, we localized new TXn binding sites on Fpg/Nei enzymes. This endeavor allowed us to decipher at the atomic level the mode of action for the best TXn inhibitors on the ZnF-containing enzymes. We discovered an original inhibition mechanism for the ZnLF-containing Fpg/Nei DNA glycosylases by disulfide cyclic trimeric forms of dithiopurines. This work paves the way for the design and synthesis of a new structural class of inhibitors for selective pharmacological targeting of hNeil1 in cancer and neurodegenerative diseases.

The number of protein kinase inhibitors (PKIs) approved worldwide continues to grow steadily, with 39 drugs approved in the period between 2001 and January 2018. PKIs on the market have been the subject of many reviews, and structure-property relationships specific to this class of drugs have been inferred. However, the large number of PKIs under development is often overlooked. In this paper, we present PKIDB (Protein Kinase Inhibitor Database), a monthly-updated database gathering approved PKIs as well as PKIs currently in clinical trials. The database compiles currently 180 inhibitors ranging from phase 0 to 4 clinical trials along with annotations extracted from seven public resources. The distribution and property ranges of standard physicochemical properties are presented. They can be used as filters to better prioritize compound selection for future screening campaigns. Interestingly, more than one-third of the kinase inhibitors violate at least one Lipinski's rule. A Principal Component Analysis (PCA) reveals that Type-II inhibitors are mapped to a distinct chemical space as compared to orally administrated drugs as well as to other types of kinase inhibitors. Using a Principal Moment of Inertia (PMI) analysis, we show that PKIs under development tend to explore new shape territories as compared to approved PKIs. In order to facilitate the analysis of the protein space, the kinome tree has been annotated with all protein kinases being targeted by PKIs. Finally, we analyzed the pipeline of the pharmaceutical companies having PKIs on the market or still under development. We hope that this work will assist researchers in the kinase field in identifying and designing the next generation of kinase inhibitors for still untargeted kinases. The PKIDB database is freely accessible from a website at http://www.icoa.fr/pkidb and can be easily browsed through a user-friendly spreadsheet-like interface.