Design, synthesis, stereochemical determination, molecular docking study, in silico pre-ADMET prediction and anti-proliferative activities of indole-pyrimidine derivatives as Mcl-1 inhibitors

Imaging metabolic mechanisms and the binding behavior of nutrients/transporters of edible Matricaria flowers VOCs

To promote the consumption of flowers and to utilize the nutritional value of proteins, the efficacy of the beneficial components of flowers has been intensively studied. Anthemis nobilis was used as the study object, and all its volatile components (VOCs) were fingerprinted using headspace solid-phase micro-extraction gas-mass spectrometry (HS-SPME/GC-MS). GC-MS fingerprints of five parts of Anthemis nobilis were established using three proteins, bovine lactoferrin (BLF), bovine lactoglobulin (β-Lg), and human serum albumin (HSA), as nutrient transporters. The interactions between the volatile components from different parts of the mother chrysanthemum plant and the nutrient/transport proteins were investigated. The results of fingerprinting showed that the flavor components were dominated by alkenes. In addition, this study revealed that among the three nutrient transporters, the strongest binding to the adsorbed volatile components was HSA, followed by BLF, and β-Lg was second. In addition, a characteristic molecule, camphene, was screened. Integrated molecular simulation using fluorescence spectroscopy was used to validate the results of the interaction of the nutrient/transport proteins systems with characteristic molecule. The properties of the characteristic molecules such as absorption, distribution, metabolism, excretion and toxicity in vivo were analyzed using ADMET to provide a theoretical basis for the preparation of flower-flavored dairy products.

Design of new Mcl-1 inhibitors for cancer using fragments hybridization, molecular docking, and molecular dynamics studies

Apoptosis is a critical process that regulates cell survival and death and plays an essential role in cancer development. The Bcl-2 protein family, including myeloid leukemia 1 (Mcl-1), is a key regulator of the intrinsic apoptosis pathway, and its overexpression in many human cancers has prompted efforts to develop Mcl-1 inhibitors as potential anticancer agents. In this study, we aimed to design new Mcl-1 inhibitors using various computational techniques. First, we used the Mcl-1 receptor-ligand complex to build an e-pharmacophore hypothesis and screened a library of 567,000 fragments from the Enamine database. We obtained 410 fragments and used them to design 92,384 novel compounds, which we then docked into the Mcl-1 binding cavity using HTVS, SP, and XP docking modes of Glide. To assess their suitability as drug candidates, we conducted MM-GBSA calculations and ADME prediction, leading to the identification of 10 compounds with excellent binding affinity and favorable pharmacokinetic properties. To further investigate the interaction strength, we performed molecular dynamics simulations on the top three Mcl-1 receptor-ligand complexes to study their interaction stability. Overall, our findings suggest that these compounds have promising potential as anticancer agents, pending further experimental validation such as Mcl-1 apoptosis Assay. By combining experimental methods with various in silico approaches, these techniques prove to be invaluable for identifying novel drug candidates with distinct therapeutic applications using fragment-based drug design. This methodology has the potential to expedite the drug discovery process while also reducing its costs.Communicated by Ramaswamy H. Sarma.

Active Cu(II), Mn(II) and Ag(I) 1,10-phenanthroline/1,10-phenanthroline-5,6-dione/dicarboxylate chelates: effects on Scedosporium

Background: Scedosporium/Lomentospora species are human pathogens that are resistant to almost all antifungals currently available in clinical practice. Methods: The effects of 16 1,10-phenanthroline (phen)/1,10-phenanthroline-5,6-dione/dicarboxylate chelates containing Cu(II), Mn(II) and Ag(I) against Scedosporium apiospermum, Scedosporium minutisporum, Scedosporium aurantiacum and Lomentospora prolificans were evaluated. Results: To different degrees, all of the test chelates inhibited the viability of planktonic conidial cells, displaying MICs ranging from 0.029 to 72.08 μM. Generally, Mn(II)-containing chelates were the least toxic to lung epithelial cells, particularly [Mn2(oda)(phen)4(H2O)2][Mn2(oda)(phen)4(oda)2].4H2O (MICs: 1.62-3.25 μM: selectivity indexes >64). Moreover, this manganese-based chelate reduced the biofilm biomass formation and diminished the mature biofilm viability. Conclusion: [Mn2(oda)(phen)4(H2O)2][Mn2(oda)(phen)4(oda)2].4H2O opens a new chemotherapeutic avenue for the deactivation of these emergent, multidrug-resistant filamentous fungi.

Novel N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide as anticancer agent: Synthesis, drug-likeness, ADMET profile, DFT and molecular modelling against EGFR target

A novel compound N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide (DHFP) was synthesized by addition, rearrangement, and intramolecular cyclization reactions. The three-dimensional geometry of DHFP has been determined by density functional theory calculations in the gas phase. Thus, the geometrical properties of DHFP such as the bond lengths, bond angles, and dihedral bond angles have been determined in the optimized molecular configuration. Also, the HOMO-LUMO energies were calculated. The charge distribution of the DHFP has been calculated by Natural Population Analysis (NPA) approach. NMR and FTIR spectra were calculated and compared with their experimental corresponding to confirm the synthesis of the DHFP. The anticancer activities of the DHFP were also determined on human colon cancer (HT29) and prostate cancer (DU145) cell lines. Molecular docking studies of the DHFP with EGFR tyrosine kinase, which is responsible for cancer cell proliferation and growth, were performed and it was observed that docking interaction took place. The DHFP has the potential to be a drug, as it is determined that DHFP obeys Lipinski's five rules, can cross the blood-brain barrier, and can be rapidly absorbed from the gastrointestinal wall.

Identification of bicyclic compounds that act as dual inhibitors of Bcl-2 and Mcl-1

Elevated expression of anti-apoptotic proteins, such as Bcl-2 and Mcl-1 contributes to poor prognosis and resistance to current treatment modalities in multiple cancers. Here, we report the design, synthesis and characterization of benzimidazole chalcone and flavonoid scaffold-derived bicyclic compounds targeting both Bcl-2 and Mcl-1 by optimizing the structural differences in the binding sites of both these proteins. Initial docking screen of Bcl-2 and Mcl-1 with pro-apoptotic protein Bim revealed possible hits with optimal binding energies. All the optimized bicyclic compounds were screened for their in vitro cytotoxic activity against two oral cancer cell lines (AW8507 and AW13516) which express high levels of Bcl-2 and Mcl-1. Compound 4d from the benzimidazole chalcone series and compound 6d from the flavonoid series exhibited significant cytotoxic activity (IC₅₀ 7.12 μM and 17.18 μM, respectively) against AW13516 cell line. Time Resolved-Fluorescence Resonance Energy Transfer (TR-FRET) analysis further demonstrated that compound 4d and compound 6d could effectively inhibit the Bcl-2 and Mcl-1 proteins by displacing their BH3 binding partners. Both compounds exhibited potent activation of canonical pathway of apoptosis evident from appearance of cleaved Caspase-3 and PARP. Further, treatment of oral cancer cells with the inhibitors induced dissociation of the BH3 only protein Bim from Mcl-1 and Bak from Bcl-2 but failed to release Bax from Bcl-xL thereby confirming the nature of compounds as BH3-mimetics selectively targeting Bcl-2 and Mcl-1. Our study thus identifies bicyclic compounds as promising candidates for anti-apoptotic Bcl-2/Mcl-1 dual inhibitors with a potential for further development.

Computational identification of bioactive compounds from Cydonia oblonga Mill. against hepatocellular carcinoma by targeting pTEN and HBx-interacting protein

Phytochemicals derived from Cydonia oblonga have been investigated for their anti-oxidant and anti-cancer activities in various cancer cell lines. The reported bioactive compounds are evaluated in silico to develop a novel antagonist against pTEN (phosphatase and tensin homolog) and HBx (hepatitis B X-interacting protein) to target hepatocellular carcinoma. Lower expression of pTEN or higher expression of HBx represents the progression of hepatocellular carcinoma. This research is intended to identify the best candidate who interacts with our target proteins (pTEN and HBx) from the quince seeds by using computational methodologies. The ternary structures of the proteins and phytochemicals are retrieved from the online databases (RCSB and PubChem). The drug likeness analysis of the reported seventeen compounds was done, but only five follow the selection criteria. ADMET profiling of these five compounds was done, followed by docking analysis and molecular dynamics study of the best complexes to determine the stability of the complexes. A docking study revealed that caffeoylquinic acids (CQA) derivatives have the significant inhibitory potential of 3-O-caffeoylquinic acid (3CQA) and 5-O-caffeoylquinic acid (5CQA) with binding affinity of - 7.53 and - 7.49 against pTEN and - 5.94 and - 6.01 against HBx in comparison to the doxorubicin. The average root mean square deviation and root mean square fluctuation values for protein-ligand complexes were found quite stable compared to the standard, while parameters like gyration and SASA (solvent-accessible surface area) supported the complexes significant binding and stability. The results obtained from the evaluation show that 3CQA and 5CQA have the best stability, especially with the pTEN protein target. Hence, these compounds have to be considered for detailed experimental studies to understand their biological function against hepato-carcinoma.