Targeting phosphatidylinositol 3-kinase gamma (PI3Kγ): Discovery and development of its selective inhibitors

Identification of novel covalent JAK3 inhibitors through consensus scoring virtual screening: integration of common feature pharmacophore and covalent docking

Accumulated research strongly indicates that Janus kinase 3 (JAK3) is intricately involved in the initiation and advancement of a diverse range of human diseases, underscoring JAK3 as a promising target for therapeutic intervention. However, JAK3 shows significant homology with other JAK family isoforms, posing substantial challenges in the development of JAK3 inhibitors. To address these limitations, one strategy is to design selective covalent JAK3 inhibitors. Therefore, this study introduces a virtual screening approach that combines common feature pharmacophore modeling, covalent docking, and consensus scoring to identify novel inhibitors for JAK3. First, common feature pharmacophore models were constructed based on a selection of representative covalent JAK3 inhibitors. The optimal qualitative pharmacophore model proved highly effective in distinguishing active and inactive compounds. Second, 14 crystal structures of the JAK3-covalent inhibitor complex were chosen for the covalent docking studies. Following validation of the screening performance, 5TTU was identified as the most suitable candidate for screening potential JAK3 inhibitors due to its higher predictive accuracy. Finally, a virtual screening protocol based on consensus scoring was conducted, integrating pharmacophore mapping and covalent docking. This approach resulted in the discovery of multiple compounds with notable potential as effective JAK3 inhibitors. We hope that the developed virtual screening strategy will provide valuable guidance in the discovery of novel covalent JAK3 inhibitors.

Designing Small Molecule PI3Kγ Inhibitors: A Review of Structure-Based Methods and Computational Approaches

The PI3K/AKT/mTOR pathway plays critical roles in a wide array of biological processes. Phosphatidylinositol 3-kinase gamma (PI3Kγ), a class IB PI3K family member, represents a potential therapeutic opportunity for the treatment of cancer, inflammation, and autoimmunity. In this Perspective, we provide a comprehensive overview of the structure, biological function, and regulation of PI3Kγ. We also focus on the development of PI3Kγ inhibitors over the past decade and emphasize their binding modes, structure-activity relationships, and pharmacological activities. The application of computational technologies and artificial intelligence in the discovery of novel PI3Kγ inhibitors is also introduced. This review aims to provide a timely and updated overview on the strategies for targeting PI3Kγ.

Optimization of virtual screening against phosphoinositide 3-kinase delta: Integration of common feature pharmacophore and multicomplex-based molecular docking

Extensive research has accumulated which suggests that phosphatidylinositol 3-kinase delta (PI3Kδ) is closely related to the occurrence and development of various human diseases, making PI3Kδ a highly promising drug target. However, PI3Kδ exhibits high homology with other members of the PI3K family, which poses significant challenges to the development of PI3Kδ inhibitors. Therefore, in the present study, a hybrid virtual screening (VS) approach based on a ligand-based pharmacophore model and multicomplex-based molecular docking was developed to find novel PI3Kδ inhibitors. 13 crystal structures of the human PI3Kδ-inhibitor complex were collected to establish models. The inhibitors were extracted from the crystal structures to generate the common feature pharmacophore. The crystallographic protein structures were used to construct a naïve Bayesian classification model that integrates molecular docking based on multiple PI3Kδ conformations. Subsequently, three VS protocols involving sequential or parallel molecular docking and pharmacophore approaches were employed. External predictions demonstrated that the protocol combining molecular docking and pharmacophore resulted in a significant improvement in the enrichment of active PI3Kδ inhibitors. Finally, the optimal VS method was utilized for virtual screening against a large chemical database, and some potential hit compounds were identified. We hope that the developed VS strategy will provide valuable guidance for the discovery of novel PI3Kδ inhibitors.

Targeting the PI3K/AKT signaling pathway in anticancer research: a recent update on inhibitor design and clinical trials (2020-2023)

INTRODUCTION

Recent years have witnessed great achievements in drug design and development targeting the phosphatidylinositol 3-kinase/protein kinase-B (PI3K/AKT) signaling pathway, a pathway central to cell growth and proliferation. The nearest neighbor protein-protein interaction networks for PI3K and AKT show the interplays between these target proteins which can be harnessed for drug discovery. In this review, we discuss the drug design and clinical development of inhibitors of PI3K/AKT in the past three years. We review in detail the structures, selectivity, efficacy, and combination therapy of 35 inhibitors targeting these proteins, classified based on the target proteins. Approaches to overcoming drug resistance and to minimizing toxicities are discussed. Future research directions for developing combinational therapy and PROTACs of PI3K and AKT inhibitors are also discussed.

AREA COVERED

This review covers clinical trial reports and patent literature on inhibitors of PI3K and AKT published between 2020 and 2023.

EXPERT OPINION

To address drug resistance and drug toxicity of inhibitors of PI3K and AKT, it is highly desirable to design and develop subtype-selective PI3K inhibitors or subtype-selective AKT1 inhibitors to minimize toxicity or to develop allosteric drugs that can form covalent bonds. The development of PROTACs of PI3Kα or AKT helps to reduce off-target toxicities.

Development of PI3Kγ selective inhibitors: the strategies and application

The γ isoform of Class I PI3Ks (PI3Kγ) is primarily found in leukocytes and is essential for the function of myeloid cells, as it regulates the migration, differentiation, and activation of myeloid-lineage immune cells. Thus, PI3Kγ has been identified as a promising drug target for the treatment of inflammation, autoimmune disease, and immuno-oncology. Due to the high incidence of serious adverse events (AEs) associated with PI3K inhibitors, in the development of PI3Kγ inhibitors, isoform selectivity was deemed crucial. In this review, an overview of the development of PI3Kγ selective inhibitors in the past years is provided. The isoform selectivity of related drugs was achieved by different strategies, including inducing a specificity pocket by a propeller-shape structure, targeting steric differences in the solvent channel, and modulating the conformation of the Asp-Phe-Gly DFG motif, which have been demonstrated feasible by several successful cases. The insights in this manuscript may provide a potential direction for rational drug design and accelerate the discovery of PI3Kγ selective inhibitors.

Fucoidan's Molecular Targets: A Comprehensive Review of Its Unique and Multiple Targets Accounting for Promising Bioactivities Supported by In Silico Studies

Fucoidan is a class of multifunctional polysaccharides derived from marine organisms. Its unique and diversified physicochemical and chemical properties have qualified them for potential and promising pharmacological uses in human diseases, including inflammation, tumors, immunity disorders, kidney diseases, and diabetes. Physicochemical and chemical properties are the main contributors to these bioactivities. The previous literature has attributed such activities to its ability to target key enzymes and receptors involved in potential disease pathways, either directly or indirectly, where the anionic sulfate ester groups are mainly involved in these interactions. These findings also confirm the advantageous pharmacological uses of sulfated versus non-sulfated polysaccharides. The current review shall highlight the molecular targets of fucoidans, especially enzymes, and the subsequent responses via either the upregulation or downregulation of mediators' expression in various tissue abnormalities. In addition, in silico studies will be applied to support the previous findings and show the significant contributors. The current review may help in understanding the molecular mechanisms of fucoidan. Also, the findings of this review may be utilized in the design of specific oligomers inspired by fucoidan with the purpose of treating life-threatening human diseases effectively.

Evaluation of the anti-inflammatory effects of PI3Kδ/γ inhibitors for treating acute lung injury

Phosphatidylinositol 3-kinase delta (PI3Kδ) and gamma (PI3Kγ) are predominantly located in immune and hematopoietic cells. It is well-established that PI3Kδ/γ plays important roles in the immune system and participates in inflammation; hence, it could be a potential target for anti-inflammatory therapy. Currently, several PI3K inhibitors are used clinically to treat cancers with aberrant PI3K signaling; however, their role in treating acute respiratory inflammatory diseases has rarely been explored. Herein, we investigated the potential anti-inflammatory activities of several pharmacological PI3K inhibitors, including marketed drugs idelalisib (PI3Kδ), duvelisib (PI3Kδ/γ), and copanlisib (pan-PI3K with preferential α/δ) and the clinical drug eganelisib (PI3Kγ), for treating acute lung injury (ALI). In the lipopolysaccharide-induced RAW264.7 macrophage inflammatory model, the four inhibitors significantly suppressed proinflammatory cytokine expression by inhibiting the PI3K signaling pathway. Oral administration of PI3K inhibitors markedly improved lung injury in a murine model of ALI. PI3K pathway inhibition decreased inflammatory cell infiltration and totalprotein levels, as well as reduced the expression of associated lung inflammatory factors. Collectively, all four representative PI3K inhibitors exerted prominent anti-inflammatory properties, indicating that PI3K δ and/or γ inhibition could be ideal targets to treat respiratory inflammatory diseases by reducing the inflammatory response. The findings of the current study provide a new basis for utilizing PI3K inhibitors to treat acute respiratory inflammatory diseases.

Exploring the molecular interactions and binding affinity of resveratrol and calcitriol with RAGE and its intracellular proteins and kinases involved in colorectal cancer

Colorectal cancer (CRC) burden is progressively increasing in young population due to dietary and lifestyle pattern. Advanced glycation end products (AGEs), one of the dietary compounds, form complex aggregates with proteins, lipids, and nucleic acids distorting their structure and function. AGE's pro-tumorigenic role is mediated through the receptor for AGEs (RAGE) triggering an array of signaling pathways. The current study aimed to target AGE-RAGE axis signaling proteins and kinases at multiple levels with calcitriol (CAL) and trans-resveratrol (RES) through in silico analysis using molecular docking (MD), molecular dynamic simulation(MDS), MM-PBSA analysis, and in vitro study. In silico analysis of CAL and RES showed significant binding affinity toward RAGE and its signaling proteins such as NF-kB, PI3K/AKT, ERK1/2, and PKC compared to its reference inhibitors through better hydrogen, hydrophobic, pi-pi stacking interactions. MD and MDS studies have revealed stable and compact protein-ligand complexes. Binding free energies of protein-ligand complex were estimated using MM/PBSA analysis thatprovided an assessment of overall interacting free energies of complexes and revealed the presence of low binding energy within the active site. Furthermore, in the in vitro study, methylglyoxal (MG), an AGE-precursor showed a proliferative effect on HCT116, however, CAL and RES showed an inhibitory effect against MG induced effect with an IC50 value of 51 nM and 110 µM respectively. Thus, the study suggests the possible target binding sites of AGE-RAGE signaling proteins and kinases with CAL and RES, thereby exploiting it for developing CAL with RES as adjuvant therapy along with chemo drug for CRC.Communicated by Ramaswamy H. Sarma.

Molecular modeling strategy for detailing the primary mechanism of action of copanlisib to PI3K: combined ligand-based and target-based approach

Since dysregulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3K has emerged as an attractive target for drug development. Although copanlisib is the first pan-PI3K inhibitor to be approved for clinical use, the precise mechanism by which it acts on PI3K has not been fully elucidated. To reveal the binding mechanisms and structure-activity relationship between PI3K and copanlisib, a comprehensive modeling approach that combines 3D-quantitative structure-activity relationship (3D-QSAR), pharmacophore model, and molecular dynamics (MD) simulation was utilized. Initially, the structure-activity relationship of copanlisib and its derivatives were explored by constructing a 3D-QSAR. Then, the key chemical characteristics were identified by building common feature pharmacophore models. Finally, MD simulations were performed to elucidate the important interactions between copanlisib and different PI3K subtypes, and highlight the key residues for tight-binding inhibitors. The present study uncovered the principal mechanism of copanlisib's action on PI3K at the theoretical level, and these findings might provide guidance for the rational design of pan-PI3K inhibitors.Communicated by Ramaswamy H. Sarma.

Developing new PI3Kγ inhibitors by combining pharmacophore modeling, molecular dynamic simulation, molecular docking, fragment-based drug design, and virtual screening

Since dysregulation of the phosphatidylinositol 3-kinase gamma (PI3Kγ) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3Kγ has emerged as an attractive target for drug development. IPI-549 is the only selective PI3Kγ inhibitor that has advanced to clinical trials, thus, IPI-549 could serve as a promising template for designing novel PI3Kγ inhibitors. In this present study, a modeling strategy consisting of common feature pharmacophore modeling, receptor-ligand pharmacophore modeling, and molecular dynamics simulation was utilized to identify the key pharmacodynamic characteristic elements of the target compound and the key residue information of the PI3Kγ interaction with the inhibitors. Then, 10 molecules were designed based on the structure-activity relationships, and some of them exhibited satisfactory predicted binding affinities to PI3Kγ. Finally, a hierarchical multistage virtual screening method, involving the developed common feature and receptor-ligand pharmacophore model and molecular docking, was constructed for screening the potential PI3Kγ inhibitors. Overall, we hope these findings would provide some guidance for the development of novel PI3Kγ inhibitors.

Recent advances in PI3K/PKB/mTOR inhibitors as new anticancer agents

The biochemical role of the PI3K/PKB/mTOR signalling pathway in cell-cycle regulation is now well known. During the onset and development of different forms of cancer it becomes overactive reducing apoptosis and allowing cell proliferation. Therefore, this pathway has become an important target for the treatment of various forms of malignant tumors, including breast cancer and follicular lymphoma. Recently, several more or less selective inhibitors targeting these proteins have been identified. In general, drugs that act on multiple targets within the entire pathway are more efficient than single targeting inhibitors. Multiple inhibitors exhibit high potency and limited drug resistance, resulting in promising anticancer agents. In this context, the present survey focuses on small molecule drugs capable of modulating the PI3K/PKB/mTOR signalling pathway, thus representing drugs or drug candidates to be used in the pharmacological treatment of different forms of cancer.

Investigation into the anti-airway inflammatory role of the PI3Kγ inhibitor JN-PK1: An in vitro and in vivo study

Phosphatidylinositol 3-kinase gamma (PI3Kγ) has been proven to be a potential target for the treatment of inflammatory diseases of the airway; however, there are few reports of selective PI3Kγ inhibitors being used in the field of airway inflammation thus far. Herein, a study employing in vitro and in vivo methodologies was carried out to assess the anti-airway inflammatory effects of JN-PK1, a selective PI3Kγ inhibitor. In RAW264.7 macrophages, JN-PK1 inhibited PI3Kγ-dependent, cellular C5a-induced AKT Ser473 phosphorylation in a concentration- and time-dependent manner and had no significant effect on cell viability.Furthermore, JN-PK1 significantly suppressed LPS-induced, proinflammatory cytokine expression and nitric oxide production through inhibition of the PI3K signaling pathway in RAW264.7 cells. Then, a murine asthma model was established to evaluate the anti-airway inflammation effect of JN-PK1. BALB/c mice were sensitized and challenged with ovalbumin (OVA) to develop an inflammatory response, fibrosis formation, and other airway changes similar to the symptomatology of asthma in humans. Oral administration of JN-PK1 remarkably attenuated OVA-induced asthma in association with the inhibition of the PI3K signaling pathway. That is to say, the oral administration significantly inhibited increases in inflammatory cell counts and reduced T-helper type 2 cytokine production in bronchoalveolar lavage fluid. Pulmonary histological studies showed that oral administration of JN-PK1 not only reduced the infiltration of inflammatory cells but also retarded airway inflammation and fibration. Taken together, JN-PK1 could be developed as a promising candidate for inflammation therapy, and our findings support some potential for therapeutic inhibition of PI3Kγ to treat inflammatory airway diseases.

Small Molecule Inhibitors in Adult High-Grade Glioma: From the Past to the Future

Glioblastoma is the most common primary malignant tumor in the brain and has a dismal prognosis despite patients accepting standard therapies. Alternation of genes and deregulation of proteins, such as receptor tyrosine kinase, PI3K/Akt, PKC, Ras/Raf/MEK, histone deacetylases, poly (ADP-ribose) polymerase (PARP), CDK4/6, branched-chain amino acid transaminase 1 (BCAT1), and Isocitrate dehydrogenase (IDH), play pivotal roles in the pathogenesis and progression of glioma. Simultaneously, the abnormalities change the cellular biological behavior and microenvironment of tumor cells. The differences between tumor cells and normal tissue become the vulnerability of tumor, which can be taken advantage of using targeted therapies. Small molecule inhibitors, as an important part of modern treatment for cancers, have shown significant efficacy in hematologic cancers and some solid tumors. To date, in glioblastoma, there have been more than 200 clinical trials completed or ongoing in which trial designers used small molecules as monotherapy or combination regimens to correct the abnormalities. In this review, we summarize the dysfunctional molecular mechanisms and highlight the outcomes of relevant clinical trials associated with small-molecule targeted therapies. Based on the outcomes, the main findings were that small-molecule inhibitors did not bring more benefit to newly diagnosed glioblastoma, but the clinical studies involving progressive glioblastoma usually claimed “noninferiority” compared with historical results. However, as to the clinical inferiority trial, similar dosing regimens should be avoided in future clinical trials.

Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome

Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.

QSAR analysis on a large and diverse set of potent phosphoinositide 3-kinase gamma (PI3Kγ) inhibitors using MLR and ANN methods

Phosphorylation of PI3Kγ as a member of lipid kinases-enzymes, plays a crucial role in regulating immune cells through the generation of intracellular signals. Deregulation of this pathway is involved in several tumors. In this research, diverse sets of potent and selective isoform-specific PI3Kγ inhibitors whose drug-likeness was confirmed based on Lipinski’s rule of five were used in the modeling process. Genetic algorithm (GA)-based multivariate analysis was employed on the half-maximal inhibitory concentration (IC₅₀) of them. In this way, multiple linear regression (MLR) and artificial neural network (ANN) algorithm, were used to QSAR models construction on 245 compounds with a wide range of pIC₅₀ (5.23–9.32). The stability and robustness of the models have been evaluated by external and internal validation methods (R² 0.623–0.642, RMSE 0.464–0.473, F 40.114, Q²_LOO 0.600, and R²_y-random 0.011). External verification using a wide variety of structures out of the training and test sets show that ANN is superior to MLR. The descriptors entered into the model are in good agreement with the X-ray structures of target-ligand complexes; so the model is interpretable. Finally, Williams plot-based analysis was applied to simultaneously compare the inhibitory activity and structural similarity of training, test and validation sets.

Structural Insights from Molecular Modeling of Isoindolin-1-One Derivatives as PI3Kγ Inhibitors against Gastric Carcinoma

The upregulation of phosphoinositol-3-kinase γ (PI3Kγ) is deemed to be positively correlated with tumor-associated-macrophage (TAM)-mediated gastric carcinoma (GC). PI3Kγ suppresses tumor necrosis factor-alpha (TNF-α) and interleukin-12 (IL-12) through activation of the AKT/mTOR pathway, which promotes the immunosuppressant phenotype of TAM. Unlike α and β isoforms, δ and γ isoforms are primarily distributed in leucocytes and macrophages. Dual inhibitors against PI3Kδ and PI3Kγ have been proven to have merits in targeting solid tumors. Furthermore, it has been found that PI3Kδ is activated by cytokines, while PI3Kγ is activated by G-protein-coupled receptors (GPCRs). This facilitates determining the functional difference between these two isoforms. For this goal, selective inhibitors would be immensely helpful. In the current manuscript, we conducted various molecular modeling studies with a series of isoindolin-1-one derivatives as potent PI3Kγ inhibitors by combining molecular docking, molecular dynamics (MD), molecular mechanics, Poisson–Boltzmann/generalized Born surface area (MM-PB/GBSA) binding free energy calculation, and three-dimensional structure–activity relationship (3D-QSAR) study. To evaluate the selectivity of γ isoform over δ, the molecular modeling studies of idelalisib analogs reported as PI3Kδ inhibitors were also investigated. The contour polyhedrons were generated from the comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) around the ligand-bound active site for both isoforms, which could emphasize plausible explanations for the physicochemical factors that affect selective ligand recognition. The binding modalities of the two isoforms using CoMFA and MD models were compared, which suggested some key differences in the molecular interactions with the ligands and could be summarized as three subsites (one affinity subsite near the C-helix and DFG and two hydrophobic subsites). In the context of the structure–activity relationship (SAR), several new compounds were designed using a fragment-substitution strategy with the aim of selectively targeting PI3Kγ. The pIC50 values of the designed compounds were predicted by the 3D-QSAR models, followed by the MM-PB/GBSA binding energy estimation. The overall findings suggest that the designed compounds have the potential to be used as PI3Kγ inhibitors with a higher binding affinity and selectivity.

Evolution and Targeting of Myeloid Suppressor Cells in Cancer: A Translational Perspective

Simple Summary

Immunotherapy is achieving impressive results in the treatment of several cancers. While the main strategies aim to re-invigorate the specific lymphocyte anti-tumor response, many studies underline that altered myeloid cell frequency and functions can dramatically interfere with the responsiveness to cancer therapies. Therefore, many novel strategies targeting TAMs and MDSCs in combination with classical treatments are under continuous evolution at both pre-clinical and clinical levels, showing encouraging results. Herein, we depict a comprehensive overview of myeloid cell generation and function in a cancer setting, and the most relevant strategies for their targeting that are currently in clinical use or under pre-clinical development.

Abstract

In recent years, the immune system has emerged as a critical regulator of tumor development, progression and dissemination. Advanced therapeutic approaches targeting immune cells are currently under clinical use and improvement for the treatment of patients affected by advanced malignancies. Among these, anti-PD1/PD-L1 and anti-CTLA4 immune checkpoint inhibitors (ICIs) are the most effective immunotherapeutic drugs at present. In spite of these advances, great variability in responses to therapy exists among patients, probably due to the heterogeneity of both cancer cells and immune responses, which manifest in diverse forms in the tumor microenvironment (TME). The variability of the immune profile within TME and its prognostic significance largely depend on the frequency of the infiltrating myeloid cells, which often represent the predominant population, characterized by high phenotypic heterogeneity. The generation of heterogeneous myeloid populations endowed with tumor-promoting activities is typically promoted by growing tumors, indicating the sequential levels of myeloid reprogramming as possible antitumor targets. This work reviews the current knowledge on the events governing protumoral myelopoiesis, analyzing the mechanisms that drive the expansion of major myeloid subsets, as well as their functional properties, and highlighting recent translational strategies for clinical developments.

A multi-conformational virtual screening approach based on machine learning targeting PI3Kγ

Nowadays, more and more attention has been attracted to develop selective PI3Kγ inhibitors, but the unique structural features of PI3Kγ protein make it a very big challenge. In the present study, a virtual screening strategy based on machine learning with multiple PI3Kγ protein structures was developed to screen novel PI3Kγ inhibitors. First, six mainstream docking programs were chosen to evaluate their scoring power and screening power; CDOCKER and Glide show satisfactory reliability and accuracy against the PI3Kγ system. Next, virtual screening integrating multiple PI3Kγ protein structures was demonstrated to significantly improve the screening enrichment rate comparing to that with an individual protein structure. Last, a multi-conformational Naïve Bayesian Classification model with the optimal docking programs was constructed, and it performed a true capability in the screening of PI3Kγ inhibitors. Taken together, the current study could provide some guidance for the docking-based virtual screening to discover novel PI3Kγ inhibitors.