Molecular scaffold-based design and comparison of combinatorial libraries focused on the ATP-binding site of protein kinases

Advances in Cancer Therapy: A Comprehensive Review of CDK and EGFR Inhibitors

Protein kinases have essential responsibilities in controlling several cellular processes, and their abnormal regulation is strongly related to the development of cancer. The implementation of protein kinase inhibitors has significantly transformed cancer therapy by modifying treatment strategies. These inhibitors have received substantial FDA clearance in recent decades. Protein kinases have emerged as primary objectives for therapeutic interventions, particularly in the context of cancer treatment. At present, 69 therapeutics have been approved by the FDA that target approximately 24 protein kinases, which are specifically prescribed for the treatment of neoplastic illnesses. These novel agents specifically inhibit certain protein kinases, such as receptor protein-tyrosine kinases, protein-serine/threonine kinases, dual-specificity kinases, nonreceptor protein-tyrosine kinases, and receptor protein-tyrosine kinases. This review presents a comprehensive overview of novel targets of kinase inhibitors, with a specific focus on cyclin-dependent kinases (CDKs) and epidermal growth factor receptor (EGFR). The majority of the reviewed studies commenced with an assessment of cancer cell lines and concluded with a comprehensive biological evaluation of individual kinase targets. The reviewed articles provide detailed information on the structural features of potent anticancer agents and their specific activity, which refers to their ability to selectively inhibit cancer-promoting kinases including CDKs and EGFR. Additionally, the latest FDA-approved anticancer agents targeting these enzymes were highlighted accordingly.

Deep scaffold hopping with multimodal transformer neural networks

Scaffold hopping is a central task of modern medicinal chemistry for rational drug design, which aims to design molecules of novel scaffolds sharing similar target biological activities toward known hit molecules. Traditionally, scaffolding hopping depends on searching databases of available compounds that can't exploit vast chemical space. In this study, we have re-formulated this task as a supervised molecule-to-molecule translation to generate hopped molecules novel in 2D structure but similar in 3D structure, as inspired by the fact that candidate compounds bind with their targets through 3D conformations. To efficiently train the model, we curated over 50 thousand pairs of molecules with increased bioactivity, similar 3D structure, but different 2D structure from public bioactivity database, which spanned 40 kinases commonly investigated by medicinal chemists. Moreover, we have designed a multimodal molecular transformer architecture by integrating molecular 3D conformer through a spatial graph neural network and protein sequence information through Transformer. The trained DeepHop model was shown able to generate around 70% molecules having improved bioactivity together with high 3D similarity but low 2D scaffold similarity to the template molecules. This ratio was 1.9 times higher than other state-of-the-art deep learning methods and rule- and virtual screening-based methods. Furthermore, we demonstrated that the model could generalize to new target proteins through fine-tuning with a small set of active compounds. Case studies have also shown the advantages and usefulness of DeepHop in practical scaffold hopping scenarios.

In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality

A structurally diverse, high-quality, and kinase-focused database plays a critical role in finding hits or leads in kinase drug discovery. Here, we propose a workflow for designing a virtual kinase-focused combinatorial library using existing structures. Based on the analysis of known protein kinase inhibitors (PKIs), detailed fragment optimization, fragment selection, fragment linking, and a molecular filtering scheme were defined. Quick recognition of core fragments that can possibly form dual hydrogen bonds with the hinge region of the ATP-pocket was proposed. Furthermore, three diversity and four quality metrics were chosen for compound library analysis, which can be applied to databases with over 30 million structures. Compared with 13 commercial libraries, our protocol demonstrates a special advantage in terms of good skeleton diversity, acceptable fingerprint diversity, balanced scaffold distribution, and high quality, which can work well not only on existing PKIs, but also on four chosen commercial libraries. Overall, the strategy can greatly facilitate the expansion of a desirable chemical space for kinase drug discovery.

Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer

Multidrug resistance (MDR) is the major cause, by which cancer cells expel the drugs out, developing a challenge against the current chemotherapeutic drugs regime. This mechanism is attributed to the over expression of ABC transporters like MRP1 on the surface of cells. Since nucleotide binding domains (NBD) of ABC transporters are the site of ATP binding and hydrolysis, thereby in this study we have targeted NBD1 of MRP1using molecular docking and molecular dynamic simulations (MDS). The compounds present in the FDA approved library were docked against NBD1 of the human multidrug resistance associated protein 1 (PDB ID: 2CBZ). For the docking studies, Standard Precision and Extra Precision methods were employed. After the EP docking studies, ligands showed an extremely low docking score that was indicative of very high binding affinity of the ligands to the NBD. Apart from the low docking score, another short listing criterion in simulation studies was the interaction of incoming ligand with the desired conserved residues of NDB involved in ATP binding and hydrolysis. Based on these measures, potassium citrate (DB09125) and technetium Tc-99m medronate (DB09138) were chosen and subjected to 100 ns simulation studies. From the MDS study we concluded that between these two compounds, potassium citrate is a better candidate for targeting MRP1.

De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments

Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve as potential starting points for drug discovery. However, the discovery and development of novel inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding fragments that are synthetically feasible and can be elaborated to small molecule libraries. Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible with hinge-region binding, and docked into a panel of protein kinases. Fragments with a high consensus score were subsequently short-listed for synthesis. Application of this strategy led to a number of core fragments with no previously reported activity against kinases. Small libraries around the core fragments were synthesized, and representative compounds were tested against a large panel of protein kinases and subjected to co-crystallization experiments. Each of the tested compounds was active against at least one kinase, but not all kinases in the panel were inhibited. A number of compounds showed high ligand efficiencies for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1, SGK1, TAK1, and GCK for which only few inhibitors are reported in the literature.

Structure-based library design in efficient discovery of novel inhibitors

Structure-based library design employs both structure-based drug design (SBDD) and combinatorial library design. Combinatorial library design concepts have evolved over the past decade, and this chapter covers several novel aspects of structure-based library design together with successful case studies in the anti-viral drug design HCV target area. Discussions include reagent selections, diversity library designs, virtual screening, scoring/ranking, and post-docking pose filtering, in addition to the considerations of chemistry synthesis. Validation criteria for a successful design include an X-ray co-crystal complex structure, in vitro biological data, and the number of compounds to be made, and these are addressed in this chapter as well.

The design, annotation, and application of a kinase-targeted library

We present here a workflow for designing a kinase-targeted library (KTL) with the goal of capturing known kinase inhibitor chemical space. We validated our design retrospectively using recent, high-throughput screening data and found significant enrichment of kinase inhibitor hits while retaining majority of the active kinase inhibitor series. To further assist kinase projects in triaging KTL screen hits, we also developed a methodology to systematically annotate known kinase inhibitors in the KTL with regard to their binding modes.

Lessons for fragment library design: analysis of output from multiple screening campaigns

Over the past 8 years, we have developed, refined and applied a fragment based discovery approach to a range of protein targets. Here we report computational analyses of various aspects of our fragment library and the results obtained for fragment screening. We reinforce the finding of others that the experimentally observed hit rate for screening fragments can be related to a computationally defined druggability index for the target. In general, the physicochemical properties of the fragment hits display the same profile as the library, as is expected for a truly diverse library which probes the relevant chemical space. An analysis of the fragment hits against various protein classes has shown that the physicochemical properties of the fragments are complementary to the properties of the target binding site. The effectiveness of some fragments appears to be achieved by an appropriate mix of pharmacophore features and enhanced aromaticity, with hydrophobic interactions playing an important role. The analysis emphasizes that it is possible to identify small fragments that are specific for different binding sites. To conclude, we discuss how the results could inform further development and improvement of our fragment library.

Cofactor chemogenomics

Cofactors are organic molecules, most of them originating from vitamins, that bind to enzymes making them able to catalyze defined reactions. A cofactor-based chemogenomics approach exploits the presence of a cofactor-binding domain to develop compound scaffolds tailored to mimic the cofactor and to replace it within target enzyme classes. As a result, a loss of function is observed. An expansion of the cofactor scaffold to include structural/chemical features derived from the substrate, that usually binds at cofactor adjacent sites, increases the specificity of the enzyme fishing. This approach has been so far applied only to NAD(P)(+)-dependent enzymes. However, it is suitable for all other cofactors, with difficulties, for some of them, originated by very tight binding. In the case of cofactors covalently bound to the enzyme, the competition between the natural cofactor and the cofactor scaffold mimic can only occur during enzyme folding.

Sequence and structural analysis of kinase ATP pocket residues

Protein kinases represent one of the largest known families of enzymes. Most kinases bind ATP and most synthetic kinase inhibitors are ATP-competitive, which makes selectivity a potential problem. However, despite the high sequence similarity in the ATP binding pocket, several groups including ours have been able to develop highly potent and selective ATP-competitive inhibitors. To systematically aid the design of specific inhibitors in our protein kinase projects, we aligned all known three-dimensional structures and all known sequences of human protein kinases. We identified a set of 38 residues that make up the ATP pocket and analyzed the variability among these residues. The most variable residues in the ATP pocket are targeted to design specificity into inhibitors in our various kinase projects.

Exploring biology with small organic molecules

Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore 'biological-activity space'. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars--uncharted territory is explored using a system of coordinates that describes where each new feature lies.

Design and Characterization of Libraries of Molecular Fragments for Use in NMR Screening against Protein Targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.

Designing screens: how to make your hits a hit

The basic goal of small-molecule screening is the identification of chemically 'interesting' starting points for elaboration towards a drug. A number of innovative approaches for pursuing this goal have evolved, and the right approach is dictated by the target class being pursued and the capabilities of the organization involved. A recent trend in high-throughput screening has been to place less emphasis on the number of data points that can be produced, and to focus instead on the quality of the data obtained. Several computational and technological advances have aided in the selection of compounds for screening and widened the variety of assay formats available for screening. The effect on the efficiency of the screening process is discussed.

Inhibition of protein kinase CK2 by anthraquinone-related compounds. A structural insight

Protein kinases play key roles in signal transduction and therefore are among the most attractive targets for drug design. The pharmacological aptitude of protein kinase inhibitors is highlighted by the observation that various diseases with special reference to cancer are because of the abnormal expression/activity of individual kinases. The resolution of the three-dimensional structure of the target kinase in complex with inhibitors is often the starting point for the rational design of this kind of drugs, some of which are already in advanced clinical trial or even in clinical practice. Here we present and discuss three new crystal structures of ATP site-directed inhibitors in complex with "casein kinase-2" (CK2), a constitutively active protein kinase implicated in a variety of cellular functions and misfunctions. With the help of theoretical calculations, we disclose some key features underlying the inhibitory efficiency of anthraquinone derivatives, outlining three different binding modes into the active site. In particular, we show that a nitro group in a hydroxyanthraquinone scaffold decreases the inhibitory constants K(i) because of electron-withdrawing and resonance effects that enhance the polarization of hydroxylic substituents in paraposition.

Development of inhibitors for protein tyrosine kinases

In the last 5 years, through combinatorial chemistry, high-throughput screening, computational chemistry, and traditional medicinal chemistry, numerous inhibitors for various protein tyrosine kinases (PTKs) have been developed. The majority of these compounds are small molecules that compete at the ATP binding site of the catalytic domain of the enzymes. Some compounds such as pseudosubstrate-based peptide inhibitor binds to the peptide/protein substrate site of the catalytic domain. Some inhibitors, primarily monoclonal antibodies, bind to the extracellular domain of receptor tyrosine kinases. Some of these inhibitors are highly potent and selective. Several are currently undergoing clinical trials for a number of diseases such as cancer.