Coumarin derivative as a potent drug candidate against triple negative breast cancer targeting the frizzled receptor of wingless-related integration site signaling pathway

Triple negative breast cancer constitutes to about 21.8 percent of the total breast cancer related cases. Its ability to affect young ladies and in pre-menstrual stage makes this a disease of concern worldwide. The current treatment regimens involve chemotherapy which are used for treatment of other cancer types. In this regard, there is a need for specific and targeted drug candidate for its effective treatment. In the current study, assessment of coumarin derivative 2-(2-(6- Methyl-2-Oxo-2H-chromen-4-yl) acetamido)-3-phenylpropanoic acid is carried out both In-silico and In-vitro methods. Frizzled transmembrane proteins of Wingless-related integration site signaling pathway was targeted in which Frizzled-7 proved to a prospective target and showed a binding energy of -6.78 kcal/mol. The complex was subjected to molecular dynamics simulation for 200 ns and showed stable interaction with cysteine rich domain of the receptor. Cell proliferation, viability and apoptosis assay were performed on MDA-MB-231 and MDA-MB-468 cell lines with an IC₅₀ value of 81.23 and 84.68 µM, respectively. The results provide a drug candidate which is derivative of a natural compound with targeted TNBC inhibitory effect. Communicated by Ramaswamy H. Sarma.

Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells

Breast cancer, a heterogeneous disease, is among the most frequently diagnosed diseases and is the second leading cause of death due to cancer among women after lung cancer. Phytoactives (plant-based derivatives) and their derivatives are safer than synthetic compounds in combating chemoresistance. In the current work, a template-based design of the coumarin derivative was designed to target the ADP-sugar pyrophosphatase protein. The novel coumarin derivative (2R)-2-((S)-sec-butyl)-5-oxo-4-(2-oxochroman-4-yl)-2,5-dihydro-1H-pyrrol-3-olate was designed. Molecular docking studies provided a docking score of -6.574 kcal/mol and an MM-GBSA value of -29.15 kcal/mol. Molecular dynamics simulation studies were carried out for 500 ns, providing better insights into the interaction. An RMSD change of 2.4 Å proved that there was a stable interaction and that there was no conformational change induced to the receptor. Metadynamics studies were performed to calculate the unbinding energy of the principal compound with NUDT5, which was found to be -75.171 kcal/mol. In vitro validation via a cytotoxicity assay (MTT assay) of the principal compound was carried out with quercetin as a positive control in the MCF7 cell line and with an IC₅₀ value of 55.57 (+/-) 0.7 μg/mL. This work promoted the research of novel natural derivatives to discover their anticancer activity.

Synthesis, spectroscopic (FT-IR, FT-Raman, NMR & UV-Vis), reactive (ELF, LOL, Fukui), drug likeness and molecular docking insights on novel 4-[3-(3-methoxy-phenyl)-3-oxo-propenyl]-benzonitrile by experimental and computational methods

The spectroscopic analysis such as FT-IR, FT-Raman, UV-Vis and NMR are conducted for the synthesized molecule by both experimental and theoretical approach. The theoretical computations were achieved by DFT method with B3LYP functional and 6-311 ++ G (d, P) basis set. Firstly the geometrical parameters obtained by DFT are compared with the related experimental parameters. Experimental FT-IR and FT-Raman spectra of the title molecule have been acquired. The vibrational analysis is conducted and the assignments concerned to the observed bands are mentioned through the potential energy distribution (PED). The GIAO method was employed for theoretical NMR analysis and the results are compared with experimental chemical shifts. In accumulation to these analyses NLO, NBO, FMO and MEP analysis have been conducted to understand the nature of the molecule. ELF and LOL were performed. The drug likeness and molecular docking studies also conducted. The potency of inhibition of molecule against MPRO and PLPRO receptors has been performed using molecular docking studies.

Synthesis, Structural Characterizations, and Quantum Chemical Investigations on 1-(3-Methoxy-phenyl)-3-naphthalen-1-yl-propenone

In the present study, 1-(3-methoxy-phenyl)-3-naphthalen-1-yl-propenone (MPNP) is synthesized and characterized by several experimental techniques such as Fourier transform-infrared spectroscopy (FT-IR), FT-Raman, NMR and UV-vis spectral methods. The similar techniques are also investigated by the computational method using Gaussian software. The density functional theory (DFT) method is used to obtain the optimized structure using the B3LYP/6-311++G(d,p) basis set. This optimization procedure of the molecule gives the minimum energy confirmation of the structure. The computed geometrical parameters are compared with experimental data. The experimental FT-IR and FT-Raman spectra of MPNP are obtained in the regions 4000-400 and 4000-50 cm-1 respectively. The detailed vibrational assignments of the molecule are obtained with the support of potential energy distribution. The theoretical NMR (1H and 13C) analysis is conducted by the GIAO method for its structural characterization and compared with experimental chemical shifts. The experimental UV-vis spectrum is obtained in the dimethyl sulfoxide solvent and compared with the theoretically computed spectrum by the time-dependent DFT method. In addition to these studies, other analyses such as nonlinear optical, natural bonds orbital, frontier molecular orbital, molecular electrostatic potential, and NCI have been conducted to understand the nature of the molecule. The title molecule is docked and also the drug-likeness, ADMET studies were carried out. The RBD domain bound to the ACE2 receptor during the fusion makes spike glycoprotein an elusive therapeutic target in SARS-CoV-2 infection.

Application of Amino Acids in the Structural Modification of Natural Products: A Review

Natural products and their derivatives are important sources for drug discovery; however, they usually have poor solubility and low activity and require structural modification. Amino acids are highly soluble in water and have a wide range of activities. The introduction of amino acids into natural products is expected to improve the performance of these products and minimize their adverse effects. Therefore, this review summarizes the application of amino acids in the structural modification of natural products and provides a theoretical basis for the structural modification of natural products in the future. The articles were divided into six types based on the backbone structures of the natural products, and the related applications of amino acids in the structural modification of natural products were discussed in detail.

Investigation of interaction between boronic acids and sugar: effect of structural change of sugars on binding affinity using steady state and time resolved fluorescence spectroscopy and molecular docking

Binding interactions of boronic acid derivatives viz. 2-Methylphenylboronic acid (B1) and 3-Methoxyphenylboronic acid (B2) with mono saccharides (arabinose, fructose and galactose) and disaccharides (sucrose, lactose and maltose) in aqueous condition at pH 7.4 by means of fluorescence spectroscopy is reported in the present investigation. Sugar sensing as well as continuous glucose monitoring (CGM) plays a significant role in diabetes regulation. Sugar sensors mediated through enzymes have their own drawbacks, which led to encouragement to search for designing new sensors through alternate approaches. Among many, fluorescence-based sensors are drawing more attention. Boronic acid-based fluorescence sensors have the capacity to bind reversibly with diols, which makes their demand high in applications. Addition of sugar reduces fluorescence intensities. Change in intensities is associated to cleavage of intermolecular hydrogen bonding which leads in reduced stability of boronate ester. Lineweaver-Burk and Benesi-Hildebrand equation is used for analysing data. Mono sugars are estimated to have higher binding constants. Mutarotation leads to structural changes in saccharides which play a key role in binding interactions. Sugars in furanose form are found to be highly favoured for binding. Molecular docking of B1 and B2 with proteins with PDB ID: 2IPL and 2IPM being periplasmic was done with the help of Schrodinger Maestro 11.2 version. GLIDE scores terms are used for expressing binding affinity.

Understanding the binding interaction between phenyl boronic acid P1 and sugars: determination of association and dissociation constants using S-V plots, steady-state spectroscopic methods and molecular docking

Continuous monitoring of glucose and sugar sensing plays a vital role in diabetes control. The drawbacks of the present enzyme-based sugar sensors have encouraged the investigation into alternate approaches to design new sensors. The popularity of fluorescence sensors is due to their ability to bind reversibly to compounds containing diol. In this study we investigated the binding ability of phenyl boronic acid P1 for monosaccharides and disaccharides (sugars) in aqueous medium at physiological pH 7.4 using steady-state fluorescence and absorbance. P1 fluorescence was quenched due to formation of esters with sugars. Absorbance and fluorescence measurements led to results that indicated that the sugars studied could be ordered in terms of their affinity to P1, as stated: sucrose > lactose > galactose > xylose > ribose > arabinose. In each case, the slope of modified Stern-Volmer plots was nearly 1, indicating the presence of only a single binding site in boronic acids for sugars. Docking studies were carried out using Schrodinger Maestro v.11.2 software. The binding affinity of phenyl boronic acid P1 with periplasmic protein (PDB ID 2IPM and 2IPL) was estimated using GlideScore.