Molecular Modelling Studies on Pyrazole Derivatives for the Design of Potent Rearranged during Transfection Kinase Inhibitors

Cheminformatics-based identification of phosphorylated RET tyrosine kinase inhibitors for human cancer

Background

Rearranged during transfection (RET), an oncogenic protein, is associated with various cancers, including non-small-cell lung cancer (NSCLC), papillary thyroid cancer (PTC), pancreatic cancer, medullary thyroid cancer (MTC), breast cancer, and colorectal cancer. Dysregulation of RET contributes to cancer development, highlighting the importance of identifying lead compounds targeting this protein due to its pivotal role in cancer progression. Therefore, this study aims to discover effective lead compounds targeting RET across different cancer types and evaluate their potential to inhibit cancer progression.

Methods

This study used a range of computational techniques, including Phase database creation, high-throughput virtual screening (HTVS), molecular docking, molecular mechanics with generalized Born surface area (MM-GBSA) solvation, assessment of pharmacokinetic (PK) properties, and molecular dynamics (MD) simulations, to identify potential lead compounds targeting RET.

Results

Initially, a high-throughput virtual screening of the ZINC database identified 2,550 compounds from a pool of 170,269. Subsequent molecular docking studies revealed 10 compounds with promising negative binding scores ranging from -8.458 to -7.791 kcal/mol. MM-GBSA analysis further confirmed the potential of four compounds to exhibit negative binding scores. MD simulations demonstrated the stability of CID 95842900, CID 137030374, CID 124958150, and CID 110126793 with the target receptors.

Conclusion

These findings suggest that these selected four compounds have the potential to inhibit phosphorylated RET (pRET) tyrosine kinase activity and may represent promising candidates for the treatment of various cancers.

α-Amylase and mycobacterium-TB H37Rv antagonistic efficacy of novel pyrazole-coumarin hybrids: an in vitro and in silico investigation

The present investigation of minutiae to acquire structural information of the novel pyrazole-coumarin hybrids (PC1-PC10) synthesized using ultrasound methods and characterized using different spectroscopic techniques: mass, 1H-NMR, 13 C-NMR and IR spectroscopy, and theoretically explored using the DFT approach with a B3LYP/6-311G (d, p) basis set, and there in vitro, antagonistic efficacy against α-amylase and mycobacterium-TB H37Rv are described in this article. Pyrazole-coumarin hybrids (PC1-PC10) showed α-amylase inhibition ranging from IC50 (0.32-0.58 mM) when compared with acarbose (IC50 = 0.34 mM). Similarly, Mycobacterium-TB H37Rv strain inhibition screening showed MIC values ranging from 62.5 to 1000 µg/mL when compared with rifampicin and isoniazid MIC = 0.25 and 0.20 µg/mL, respectively. Molecular docking and MD simulation studies were performed to determine the active sites and rationalize the activities of the active compounds. To investigate the binding conformation and dynamics responsible for their activity, the three most active compounds (PC1, PC3 and PC6) were docked into the porcine pancreatic α-amylase active site (PDB ID:1OSE), and mycobacterium-TB H37Rv active site (PDB ID: 4TZK). The binding interactions between PC1, PC3, and PC6 with α-amylase were like those responsible for inhibiting α-amylase by acarbose. Also, the mycobacterium-TB H37Rv inhibiting responsible residues were compared with standard isoniazid and rifampicin.Communicated by Ramaswamy H. Sarma.

Alpinumisoflavone against cancer pro-angiogenic targets: In silico, In vitro, and In ovo evaluation

BACKGROUND

Breast cancer is currently the world's most predominant malignancy. In cancer progression, angiogenesis is a requirement for tumor growth and metastasis.Alpinumisoflavone (AIF), a bioactive isoflavonoid, exhibited good binding affinity with the angiogenesis pathway's druggable target through molecular docking.

OBJECTIVES

To confirm AIF's angiogenesis inhibitory activity, cytotoxic potential toward breast cancer cells, and druggability.

METHODS

Antiangiogenic activity was evaluated in six pro-angiogenic proteins in vitro, duck chorioallantoic membrane (CAM) in ovo, molecular docking and druggability in silico.

RESULTS

Findings showed that AIF significantly inhibited (p =  < 0.001) the HER2(IC50 = 2.96 µM), VEGFR-2(IC50 = 4.80 µM), MMP-9(IC50 = 23.00 µM), FGFR4(IC50 = 57.65 µM), EGFR(IC50 = 92.06 µM) and RET(IC50 =  > 200 µM) activity in vitro.AIF at 25 µM-200 µM significantly inhibited (p =  < 0.001) the total number of branch points (IC50 = 14.25 μM) and mean length of tubule complexes (IC50 = 3.52 μM) of duck CAM comparable (p =  > 0.001) with the positive control 200 µM celecoxib on both parameters.AIF inhibited the growth of the estrogen-receptor-positive (ER +) human breast cancer cells (MCF-7) by 44.92 ± 1.79% at 100 µM while presenting less toxicity to human dermal fibroblast neonatal (HDFn) normal cells.The positive control 100 µM doxorubicin showed 86.66 ± 0.93% and 92.97 ± 1.27% inhibition with MCF-7 (IC50 = 3.62 μM) and HDFn, (IC50 = 27.16 μM) respectively.In docking, AIF has the greatest in silico binding affinity on HER2 (-10.9 kcal/mol) among the key angiogenic molecules tested. In silico rat oral LD50 calculation indicates that AIF is moderate to slightly toxic at 146.4 mg/kg with 1.1 g/kg and 20.1 mg/kg upper and lower 95% confidence limits. Lastly, it sufficiently complies with Lipinski's, Veber's, Egan's, Ghose's, and Muegge's Rule, supporting its oral drug-like property.

CONCLUSION

This study revealed that AIF possesses characteristics of a phytoestrogen compound with significant binding affinity, inhibitory activity against pro-angiogenic proteins, and cytotoxic potential against ER + breast cancer cells.The acceptable and considerable safety and drug-likeness profiles of AIF are worthy of further confirmation in vivo and advanced pre-clinical studies so that AIF can be elevated as a promising molecule for breast cancer therapy.

Investigating natural compounds against oncogenic RET tyrosine kinase using pharmacoinformatic approaches for cancer therapeutics

Rearranged during transfection (RET) tyrosine kinase is a transmembrane receptor tyrosine kinase regulating vital aspects of cellular proliferation, differentiation, and survival. An outstanding challenge in designing protein kinase inhibitors is due to the development of drug resistance. The “gain of function” mutations in the RET gate-keeper residue, Val804, confers resistance to the majority of known RET inhibitors, including vandetanib. To curtail this resistance, researchers developed selpercatinib (LOXO-292) against the RET gate-keeper mutant forms – V804M and V804L. In the present in silico investigation, a receptor–ligand pharmacophore model was generated to identify small molecule inhibitors effective for wild-type (WT) as well as mutant RET kinase variants. The generated model was employed to screen 144 766 natural products (NPs) available in the ZINC database and the retrieved NPs were filtered for their drug-likeness. The resulting 2696 drug-like NPs were subjected to molecular docking with the RET WT kinase domain and a total of 27 molecules displayed better dock scores than the reference inhibitors – vandetanib and selpercatinib. From 27 NPs, an aggregate of 12 compounds demonstrated better binding free energy (BFE) scores than the reference inhibitors, towards RET. Thus, the 12 NPs were also subjected to docking, simulation, and BFE estimation towards the constructed gate-keeper RET mutant structures. The BFE calculations revealed 3 hits with better BFE scores than the reference inhibitors towards WT, V804M, and V804L RET variants. Thus, the scaffolds of hit compounds presented in this study could act as potent RET inhibitors and further provide insights for drug optimization targeting aberrant activation of RET signaling, specifically the mutation of gate-keeper residue – Val804.

Identification of natural product inhibitors against rearranged during transfection (RET) tyrosine kinase as cancer therapeutics using combination of in silico techniques.

An update of new small-molecule anticancer drugs approved from 2015 to 2020

A high incidence of cancer has given rise to the development of more anti-tumor drugs. From 2015 to 2020, fifty-six new small-molecule anticancer drugs, divided into ten categories according to their anti-tumor target activities, have been approved. These include TKIs (30 drugs), MAPK inhibitors (3 drugs), CDK inhibitors (3 drugs), PARP inhibitors (3 drugs), PI3K inhibitors (3 drugs), SMO receptor antagonists (2 drugs), AR antagonists (2 drugs), SSTR inhibitors (2 drugs), IDH inhibitors (2 drugs) and others (6 drugs). Among them, PTK inhibitors (30/56) have led to a paradigm shift in cancer treatment with less toxicity and more potency. Each of their structures, approval statuses, applications, SAR analyses, and original research synthesis routes have been summarized, giving us a more comprehensive map for further efforts to design more specific targeted agents for reducing cancer in the future. We believe this review will help further research of potential antitumor agents in clinical usage.