Design, synthesis, docking, molecular dynamics and bioevaluation studies on novel N-methylpicolinamide and thienopyrimidine derivatives with inhibiting NF-κB and TAK1 activities: Cheminformatics tools RDKit applied in drug design

Novel ALK inhibitors containing DAAP fragments: Rational drug design and anti-tumor activity research

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase belonging to the insulin receptor subfamily, involved in cellular signaling pathways associated with insulin. While ALK gene remains inactive in normal human tissues, it exhibits high expression specifically in the central nervous system. However, dysregulation of the ALK gene has been implicated in non-small cell lung cancer (NSCLC) development. Although commercially available ALK inhibitors demonstrate favorable clinical efficacy against most Ceritinib-resistant mutants, they exhibit resistance towards G1202R mutants. Therefore, developing novel ALK inhibitors is crucial for addressing drug resistance in patients. We designed and synthesized 48 novel 2,4-diarylpyrimidine-based ALK inhibitors and investigated their antitumor activities. Among them, Ld-10 showed significant inhibitory activity against ALK kinase with an IC50 value of 1135 nM and demonstrated excellent antiproliferative activity against lung cancer cells H2228 with an IC50 value of 1.35 ± 0.13 μM. To further validate the antitumor potential of Ld-10, we conducted a series of in vitro pharmacological experiments. These included a hemolysis assay to confirm its low toxicity profile, an AO assay, a JC-1 staining assay, and a Calcein-AM/PI cell double staining assay for assessing apoptosis induction. Additionally, we performed dose-dependent arrest at G0/G1 phase to evaluate inhibition of cell growth and carried out cell cycle analysis and cloning experiments to provide evidence for significant tumor growth inhibition by compound Ld-10. In vivo pharmacological experiments demonstrated effective tumor growth inhibition without any significant toxic effects on mouse organs caused by Ld-10 administration. Based on these comprehensive findings from our experimental investigations, it can be concluded that Ld-10 holds promising potential as a novel ALK inhibitor.

DICCA-DTA: Diffusion and Contextualized Capsule Attention guided Factorized Cross-Pooling for Drug-Target Affinity prediction

Drug-Target Affinity (DTA) prediction plays a crucial role in the drug discovery process by evaluating the strength of the interaction between a drug and its biological target, which is often a protein. Despite advancements in DTA prediction through deep learning, several fundamental challenges persist: (i) suboptimal information propagation in molecular graphs, limiting the effective representation of complex drug structures, (ii) accurately modeling the complex interactions between drug-binding sites and protein substructures, and (iii) prioritizing critical substructure interactions to enhance both accuracy and interpretability. To address these challenges, the DICCA-DTA framework is introduced, aiming to improve the contextual integration of molecular information and facilitate a more comprehensive representation of drug-target interactions in allopathic research. It employs a Diffused Isomorphic Network (DIN) to extract comprehensive drug features from molecular graphs, capturing both local substructures and global information. Furthermore, a Contextualized Capsule Attention Network (CCAN) module incorporates multi-head attention with capsule networks to capture both local and global protein sequence characteristics. The attention-guided Factorized Cross-Pooling (FCP) mechanism dynamically refines drug-protein interaction modeling by selectively emphasizing critical binding site interactions, thereby enhancing predictive accuracy. Explainable attention maps further reveal the most crucial drug-protein binding site interactions, providing transparent insights into the model's decision-making process. Comprehensive evaluations across the Davis, KIBA, Metz and BindingDB datasets demonstrate the superior performance of the DICCA-DTA framework over existing state-of-the-art models. A case study on cancer-related protein interactions from the DrugBank database further demonstrates the framework's precision in identifying key drug-protein affinities, reinforcing its potential to accelerate drug discovery and repurposing.

T6496 targeting EGFR mediated by T790M or C797S mutant: machine learning, virtual screening and bioactivity evaluation study

Acquired resistance to EGFR is a major impediment in lung cancer treatment, highlighting the urgent need to discover novel compounds to overcome EGFR drug resistance. In this study, we utilized in silico methods and bioactivity evaluation for drug discovery to identify novel active anticancer agents targeting EGFRT790M/L858R and EGFRT790M/C797S/L858R. Firstly, we employed ROC-guided machine learning to retrieve nearly 7,765 compounds from a collection of three libraries (comprising over 220,000 compounds). Next, virtual screening, cluster analysis, and binding model analysis were employed to identify six potential compounds. Additionally, the kinase assay revealed that these six compounds demonstrated higher sensitivity to EGFR than c-Met. Among these compounds, T6496 inhibited both EGFRT790M/L858R and EGFRT790M/C797S/L858R kinases, with an IC50 of 3.30 and 8.72 μM. Furthermore, we evaluated the antitumor effects of the six selected compounds, and compound T6496 exhibited the strongest anticancer activity against H1975 cell lines, with an IC50 value of 2.7 μM. These results suggest that T6496 may mitigate EGFR resistance caused by T790M or C797S mutations. Moreover, the AO staining assay, JC-1 staining, ROS experiment and hemolytic toxicity evaluation revealed that T6496 could induce apoptosis in H1975 cell lines in a time-dependent and concentration-dependent manner, and is a potential compound for further structural optimization.

ROC-guided virtual screening, molecular dynamics simulation, and bioactivity validation assessment Z195914464 as a 3CL Mpro inhibitor

Discovering novel class anti-SARS-CoV-2 compounds with novel backbones is essential for preventing and controlling SARS-CoV-2 transmission, which poses a substantial threat to the health and social sustainable development of the global population because of its high pathogenicity and high transmissibility. Although the potential mutation of SARS-CoV-2 might diminish the therapeutic efficacy of drugs, 3CL Mpro is the target highly conservative in contrast with other targets. It is an essential enzyme for coronavirus replication. Based on this, this study utilized the drug discovery strategy of Knime molecular filtering framework, ROC-guided virtual screening, clustering analysis, binding mode analysis, and activity evaluation approaches to identify compound Z195914464 (IC50: 7.19 μM) is a novel class inhibitor of anti-SARS-CoV-2 against the 3CL Mpro target. In addition, based on molecular dynamics simulations and MMPBSA analyses, discovered that compound Z195914464 can interact with more key residues and lower bonding energies, which explains why it exhibited more activity than the other three compounds. In summary, this study developed a method for the rapid and accurate discovery of active compounds and can also be applied in the discovery of active compounds in other targets.

Screening and evaluation of novel DPP-IV inhibitory peptides in goat milk based on molecular docking and molecular dynamics simulation

Virtual screening techniques have gained much attention as a means of studying bioactive peptides. This study aimed to screen DPP-IV inhibitor peptides in goat milk after simulated digestion in vitro combined with molecular docking and dynamics simulations. By evaluating the docking energy and active sites, and by analyzing RMSD, RMSF, and Rg values, two novel peptides, GPFPLL and LPYPY, were successfully screened and identified. GPFPLL and LPYPY were found to exhibit high inhibitory activity against DPP-IV (IC50 of 130.68 ± 10.38 μM and 179.52 ± 18.89 μM, respectively). Both GPFPLL and LPYPY stably bound to S1 and S1' in DPP-IV, and both demonstrated competitive inhibition of DPP-IV. The inhibition of DPP-IV by GPFPLL and LPYPY after in vitro digestion reached 31.90 % ± 1.80 % and 39.37 % ± 0.90 %, respectively. In a Caco-2 cell experiment, GPFPLL and LPYPY exhibited significant inhibition of DPP-IV, reaching 46.53 % ± 3.48 % and 65.98 % ± 2.87 %, respectively, when the concentration of each peptide was 2 mg/mL. The results of this study suggest that using molecular docking and dynamics simulations to screen novel peptides is an effective approach, and the identified peptides GPFPLL and LPYPY show potential for diabetes management.

In silico method and bioactivity evaluation to discover novel antimicrobial agents targeting FtsZ protein: Machine learning, virtual screening and antibacterial mechanism study

This research paper utilizes a fused-in-silico approach alongside bioactivity evaluation to identify active FtsZ inhibitors for drug discovery. Initially, ROC-guided machine learning was employed to obtain almost 13182 compounds from three libraries. After conducting virtual screening to assess the affinity of 2621 acquired compounds, cluster analysis and bonding model analysis led to the discovery of five hit compounds. Additionally, antibacterial activity assays and time-killing kinetics revealed that T3995 could eliminate Staphylococcus aureus ATCC6538 and Bacillus subtilis ATCC9732, with MIC values of 32 and 2 μg/mL. Further morphology and FtsZ polymerization assays indicated that T3995 could be an antimicrobial inhibitor by targeting FtsZ protein. Moreover, hemolytic toxicity evaluation demonstrated that T3995 is safe at or below 16 ug/mL concentration. Additionally, bonding model analysis explained how the compound T3995 can display antimicrobial activity by targeting the FtsZ protein. In conclusion, this study presents a promising FtsZ inhibitor that was discovered through a fused computer method and bioactivity evaluation.

Advances in structural identification of some thieno[2,3-d]pyrimidine scaffolds as antitumor molecules: Synthetic approaches and control programmed cancer cell death potential

Thieno[2,3-d]pyrimidine fragment is not only bioistostere to quinazoline ring but also to purines which exist in nucleic acids responsible for several key biological processes of the living cells, thus it is of a great interest for many researchers. Thieno[2,3-d]pyrimidine ring has become an important scaffold for different compounds with versatile pharmacological activities including anticancer. These compounds exert their anticancer activity through variant mechanisms of action; one of these is the induction of different programmed cell death types as apoptosis and necroptosis which is an effective approach for cancer treatment. This review highlights the different synthetic approaches of recent thieno[2,3-d]pyrimidine analogs along with their anticancer significance through induction of apoptotic or necroptotic cell death with illustration of the structure-activity relationship (SAR).

Identification of TAK-756, A Potent TAK1 Inhibitor for the Treatment of Osteoarthritis through Intra-Articular Administration

Osteoarthritis (OA) is a chronic and degenerative joint disease affecting more than 500 million patients worldwide with no disease-modifying treatment approved to date. Several publications report on the transforming growth factor β-activated kinase 1 (TAK1) as a potential molecular target for OA, with complementary anti-catabolic and anti-inflammatory effects. We report herein on the development of TAK1 inhibitors with physicochemical properties suitable for intra-articular injection, with the aim to achieve high drug concentration at the affected joint, while avoiding severe toxicity associated with systemic inhibition. More specifically, reducing solubility by increasing crystallinity, while maintaining moderate lipophilicity proved to be a good compromise to ensure high and sustained free drug exposures in the joint. Furthermore, structure-based design allowed for an improvement of selectivity versus interleukin-1 receptor-associated kinases 1 and 4 (IRAK1/4). Finally, TAK-756 was discovered as a potent TAK1 inhibitor with good selectivity versus IRAK1/4 as well as excellent intra-articular pharmacokinetic properties.

Prediction of Mycobacterium tuberculosis cell wall permeability using machine learning methods

Tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis (M. tb), continues to pose a significant worldwide health threat. The advent of drug-resistant strains of the disease highlights the critical need for novel treatments. The unique cell wall of M. tb provides an extra layer of protection for the bacteria and hence only compounds that can penetrate this barrier can reach their targets within the bacterial cell wall. The creation of a reliable machine learning (ML) model to predict the mycobacterial cell wall permeability of small molecules is presented in this work and four ML algorithms, including Random Forest, Support Vector Machines (SVM), k-nearest Neighbour (k-NN) and Logistic Regression were trained on a dataset of 5368 compounds. RDKit and Mordred toolkits were used to calculate features. To determine the most effective model, various performance metrics were used such as accuracy, precision, recall, F1 score, and area under the receiver operating characteristic curve. The best-performing model was further refined with hyperparameter tuning and tenfold cross-validation. The SVM model with filtering outperformed the other machine learning models and demonstrated 80.26% and 81.13% accuracy on the test and validation datasets, respectively. The study also provided insights into the molecular descriptors that play the most important role in predicting the ability of a molecule to pass the M. tb cell wall, which could guide future compound design. The model is available at https://github.com/PGlab-NIPER/MTB_Permeability .

Design, synthesis, and evaluation of antitumor activity of Mobocertinib derivatives, a third-generation EGFR inhibitor

Mobocertinib, as a structural analog of the third generation TKI Osimertinib, can selectively act on the EGFRex20 mutation. We have structurally modified Mobocertinib to obtain new EGFR inhibitors. In this paper, we chose Mobocertinib as a lead compound for structural modification to investigate the effect of Mobocertinib derivatives on EGFRT790M mutation. We designed and synthesized 63 Mobocertinib derivatives by structural modification using the structural similarity strategy and the bioelectronic isoarrangement principle. Then, we evaluated the in vitro antitumor activity of the 63 Mobocertinib derivatives and found that the IC50 of compound H-13 against EGFRL858R/T790M mutated H1975 cells was 3.91 μM, and in further kinase activity evaluation, the IC50 of H-13 against EGFRL858R/T790M kinase was 395.2 nM. In addition, the preferred compound H-13 was able to promote apoptosis of H1975 tumor cells and block the proliferation of H1975 cells in the G0/G1 phase; meanwhile, it was able to significantly inhibit the migratory ability of H1975 tumor cells and inhibit the growth of H1975 cells in a time-concentration-dependent manner. In the in vivo anti-tumor activity study, the preferred compound H-13 had no obvious toxicity to normal mice, and the tumor inhibition effect on H1975 cell-loaded nude mice was close to that of Mobocertinib. Finally, molecular dynamics simulations showed that the binding energy between compound H-13 and 3IKA protein was calculated to be -162.417 ± 14.559 kJ/mol. In summary, the preferred compound H-13 can be a potential third-generation EGFR inhibitor.

Design, synthesis, and biological evaluation of 4-(2-fluorophenoxy)-7-methoxyquinazoline derivatives as dual EGFR/c-Met inhibitors for the treatment of NSCLC

In non-small cell lung cancer (NSCLC) treatment, aberrant expression of c-mesenchymal-epithelial transition factor (c-Met) has been identified as a driving factor in epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) resistance. Unfortunately, none of the EGFR/c-Met dual-target inhibitors have successfully passed clinical trials. Hence, based on molecular docking analysis and combination principles of EGFR and c-Met inhibitors, three series of 4-(2-fluorophenoxy)-7-methoxyquinazoline derivatives as new EGFR/c-Met inhibitors were designed, synthesized, and evaluated for their biological activities. Among these compounds, TS-41 displayed the best inhibitory activity against EGFRL858R and c-Met kinases, with an IC50 value of 68.1 nM and 0.26 nM respectively. Moreover, it also showed excellent inhibitory activity on three NSCLC cell lines A549-P, H1975 and PC-9 with IC50 values ranging from 1.48 to 2.76 μM. Flow cytometry assays demonstrated that TS-41 induced apoptosis and cell cycle arrest of A549-P cells in a concentration-dependent manner, corresponding to JC-1 staining assay results. Western blot analysis revealed that TS-41 significantly downregulated the phosphorylation of EGFR, c-Met, and downstream AKT at molecular level. Importantly, TS-41 exhibited potent in vivo anticancer efficacy in an A549-P-bearing allograft nude mouse model at a dose of 60 mg/kg with a tumor growth inhibition rate of 55.3 % compared with Afatinib (46.4 %), as well as low hemolytic toxicity and organ toxicity. Molecular docking results showed that TS-41 was well embedded into the cavity of EGFR (PDB: 5GMP) and c-Met (PDB: 3LQ8) proteins, respectively. In summary, TS-41 is a high-efficiency and low-toxicity EGFR/c-Met inhibitor for the treatment of NSCLC and is worthy of further exploration.

New insights into the suppression of inflammation and lipid accumulation by JAZF1

Atherosclerosis is one of the leading causes of disease and death worldwide. The identification of new therapeutic targets and agents is critical. JAZF1 is expressed in many tissues and is found at particularly high levels in adipose tissue (AT). JAZF1 suppresses inflammation (including IL-1β, IL-4, IL-6, IL-8, IL-10, TNFα, IFN-γ, IAR-20, COL3A1, laminin, and MCP-1) by reducing NF-κB pathway activation and AT immune cell infiltration. JAZF1 reduces lipid accumulation by regulating the liver X receptor response element (LXRE) of the SREBP-1c promoter, the cAMP-response element (CRE) of HMGCR, and the TR4 axis. LXRE and CRE sites are present in many cytokine and lipid metabolism gene promoters, which suggests that JAZF1 regulates these genes through these sites. NF-κB is the center of the JAZF1-mediated inhibition of the inflammatory response. JAZF1 suppresses NF-κB expression by suppressing TAK1 expression. Interestingly, TAK1 inhibition also decreases lipid accumulation. A dual-targeting strategy of NF-κB and TAK1 could inhibit both inflammation and lipid accumulation. Dual-target compounds (including prodrugs) 1-5 exhibit nanomolar inhibition by targeting NF-κB and TAK1, EGFR, or COX-2. However, the NF-κB suppressing activity of these compounds is relatively low (IC50 > 300 nM). Compounds 6-14 suppress NF-κB expression with IC50 values ranging from 1.8 nM to 38.6 nM. HS-276 is a highly selective, orally bioavailable TAK1 inhibitor. Combined structural modifications of compounds using a prodrug strategy may enhance NF-κB inhibition. This review focused on the role and mechanism of JAZF1 in inflammation and lipid accumulation for the identification of new anti-atherosclerotic targets.

Novel tryptanthrin derivatives with benzenesulfonamide substituents: Design, synthesis, and anti-inflammatory evaluation

Herein, two series of tryptanthrin derivatives with benzenesulfonamide substituents were designed and synthesized to discover novel anti-inflammatory agents. The anti-inflammatory activities of all derivatives were screened by evaluating their inhibitory effects on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW264.7 cells. Among them, compound 8j exhibited the best NO inhibitory activity (IC₅₀ = 1.25 ± 0.21 μM), with no obvious toxicity. Further evaluation showed that 8j could also significantly reduce the levels of pro-inflammatory cytokines interleukin-1β (IL-1β, IC₅₀ = 8.48 ± 0.23 μM) and tumor necrosis factor-α (TNF-α, IC₅₀ = 11.53 ± 0.35 μM) and downregulate the LPS-induced expression of iNOS and COX-2. Reverse docking of 8j suggested p38α as the molecular target, which is a well-known crucial player in the p38 MAPK signaling pathway that controls the transcription of pro-inflammatory mediators. Cellular thermal shift assay showed that 8j efficiently stabilized p38α in LPS-treated RAW264.7 cells. Western blot showed that inflammatory response was inhibited by 8j through inhibiting the phosphorylation of p38α and MK2 in the p38 MAPK signaling pathway. Finally, In vivo studies showed that 8j could significantly ameliorate the degree of foot swelling and knee joint pathology in adjuvant-induced arthritis (AIA) rats and reduce levels of TNF-α and IL-1β in serum, achieving the effect of protecting synovial tissue and ameliorating arthritis. These findings suggested that 8j may be a promising compound for further development of anti-inflammatory agents.

XS-2, a novel potent dual PI3K/mTOR inhibitor, exhibits high in vitro and in vivo anti-breast cancer activity and low toxicity with the potential to inhibit the invasion and migration of triple-negative breast cancer

Breast cancer has become the most commonly diagnosed cancer, surpassing lung cancer, with 2.26 million new breast cancers worldwide in 2020. Hence, there is an urgent need to develop effective molecularly targeted therapeutic drugs to treat breast cancer. In this paper, we designed, synthesized and screened a novel thiophene-triazine derivative, XS-2, as a potent dual PI3K/mTOR inhibitor for the treatment of breast cancer. Also, XS-2 was found to be potentially effective against triple-negative breast cancer (TNBC) in vitro during the investigation. We evaluated the in vitro inhibitory effect of XS-2 on 10 cancer cell lines by MTT and 6 kinases to investigated its in vivo antitumor activity in MCF-7 xenograft tumor-bearing BALB/c nude mice. In addition, the in vitro/in vivo toxicity to mice was also assessed by hemolytic toxicity, H&E staining and blood biochemical analysis. In order to investigate the antitumor mechanism of XS-2, a series of experiments were carried out in vitro/in vivo animal model and molecular biological levels such as the cell cycle and the apoptosis assay, real-time PCR, western blot, docking and molecular simulations analysis, etc. What's more, wound healing assay, Transwell and Western Blot were applied to explore the ability of XS-2 to inhibit the cell invasion and migration. The results showed that XS-2 exhibited strong antitumor activity both in vitro and in vivo. The inhibitory activities of XS-2 on ten cancer cell lines were ranging from 1.07 ± 0.11 to 0.002 ± 0.001 μM, which were 1565 times better than that of the lead compound GDC-0941, inhibitory activities against PI3Kα and mTOR kinases were 291.0 and 60.8 nM, respectively. Notably, XS-2 not only showed significant in vivo antitumor activity and low toxicity, with the tumor inhibition rate of 57.0 %, but also exhibited strong inhibitory in the expression of related proteins of PI3K pathway in tumor tissues. In addition, XS-2 significantly inhibited breast cancer MCF-7 and MDA-MB-231 cells in a concentration- and time-dependent manner, and inhibited the migration and invasion ability of MDA-MB-231 and MCF-7 cells. More than that, XS-2 could inhibit the increase of the expression levels of N-cadherin and vimentin upregulated by EGF and reversed the E-cadherin expression down regulated by EGF, resulting in inhibiting EMT in MCF-7 and MDA-MB-231 cells. The results showed that XS-2 was expected to be successfully developed as a high-efficiency and low-toxicity breast cancer therapeutic drug with the potential to inhibit the invasion and migration of TNBC. This provides a new research idea for the treatment of TNBC, which is of great significance.