Quantum chemical studies, spectroscopic NMR and FT-IR analysis, and molecular docking investigation of 3,3′-di-O-methyl ellagic acid (DMA) as a potent Mycobacterium tuberculosis agent

Tuberculosis which is mainly caused by Mycobacterium tuberculosis remains of public health importance due to the resistance of the causative pathogen to the present antibiotics used as treatment options. This resistance has led to the need for the discovery of new treatment options. Herein, the isolation, geometrical optimization, spectroscopic NMR and FT-IR analysis, a study of weak interactions, electronic properties, and the in-silico biological activity of 3,3′-di-O-methyl ellagic acid (DMA) were determined. In addition, the effect of solvent on the kinetic stability, reactivity, and other electronic properties of DMA was determined in three solvents; DMSO, methanol, and water. Also, the biological activity potential and the drug-likeness of DMA were determined using molecular docking protocol and ADMET studies. The studied compound was isolated using column and thin-layer chromatography techniques while characterization was done using spectroscopic techniques. Key vibrations in the compound are C = O vibrations, C = C vibrations, C-H vibrations, –CH3 vibrations, and O-H vibrations. A study of quantum descriptors revealed that DMA is more reactive in water with an energy gap of −3.162 eV and those in three solvents are −3.163, −3.944, and −4.3022 eV in methane, gas, and water respectively. The compound shows great optical potentials with dipole moments of 3.2415D, 5.221D, 5.2015D, and 4.469D in water, DMSO, methanol, and Gas-phase respectively which are greater than that of urea used in the comparison. The QTAIM analysis based on the bond ellipticity < 0.5 suggests the presence of covalent bonds within the atoms of the studied compound. The MESP result shows the presence of π- H bond interaction within the OCH3 and oxygen atom. Molecular docking studies of the studied compound were carried out employing proteins 1W2G, 1YWF, and 1F0N proteins for mycobacterial tuberculosis and the standard drug isoniazid. The result was compared with that of a standard drug. The binding affinities of −7.1, −6.9, and −7.1 kcal/mol for 1W2G, 1YWF, and 1F0N were obtained, and −5.9, −5.9 and −6.0 kcal/mol for the standard drug with 1W2G, 1YWF and 1F0N. These results show that the studied compound has greater biological activity against these proteins as compared to the standard drug. ADMET studies show that the studied compound has great drug-likeness and bioavailability since it did not violate any of Lipinski’s rule of five

Unraveling the impact of polar solvation on the molecular geometry, spectroscopy (FT-IR, UV, NMR), reactivity (ELF, NBO, HOMO-LUMO) and antiviral inhibitory potential of Cissampeline by molecular docking approach

Cissampeline, a highly promising natural substance derived from medicinal plants of the Cissampelos genus, has recently garnered significant interest due to its potent antiviral properties against a broad spectrum of viral infections. In this comprehensive study, we employed gd3bj-B3LYP/def2svp level of theory to investigate the impact of polar solvation on the molecular structure, dynamical stability, spectroscopy, nature of bonding, and antiviral inhibitory potential of Cissampeline. Our results demonstrated excellent agreement between the theoretically characterized structure and the experimentally determined one. Interestingly, we observed that in the absence of a solvent environment, the gas phase exhibited shorter bond angles compared to when different solvents were utilized, indicating reduced solvent interactions. Regarding solvation dynamics, we found that the total energy of the structure, when optimized in different solvents, followed the order DMSO > MeOH > Water > Gas, with corresponding total final energies of 1736.599 > 867.932 > 837.760 > 413.989 kcal/mol, respectively. Furthermore, NBO analysis revealed the strength of electron delocalization, with the order of perturbation energies being DMSO > MeOH > H2O > Gas phase, measured at 626.07 > 241.40 > 238.65 > 72.93 kcal/mol, respectively. Particularly noteworthy was the σ-σ* transition in the DMSO solvent phase, displaying the highest perturbation energy of 626.07 kcal/mol. FMO analysis provided insights into the energy levels of the studied species, with values of 4.5432 eV for Gas, 4.5250 eV for MeOH, 4.5247 eV for H2O, and 4.5242 eV for DMSO, respectively. Regarding the interaction of Cissampeline with amino acid residues, we found that the ligand exhibited the highest binding affinity with 3MX2 at -7.7 kcal/mol, followed by CMPL + 3T5N at -7.3 kcal/mol, and CMPL + 3MX5 at -6.0 kcal/mol. In comparison, the standard drug RIBAV only displayed successful interaction with 3MX2, showing the least binding affinity at -5.8 kcal/mol. This study showed highlights the remarkable potential of Cissampeline as an effective antiviral agent and sheds light on the importance of considering solvation effects in molecular investigations

Anti-inflammatory biomolecular activity of chlorinated-phenyldiazenyl-naphthalene-2-sulfonic acid derivatives: perception from DFT, molecular docking, and molecular dynamic simulation

In this study, two novel derivatives of naphthalene-2-sulfonic acid: 6-(((1S,5R)-3,5-dichloro-2,4,6-triazabicyclo [z3.1.0]hex-3-en-1-yl)amino)-5-((E)-phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS1) and (E)-6-((4,6-dichloro-1,3,5-triazine2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS2) have been synthesized and characterized using FT-IR, UV-vis, and NMR spectroscopic techniques. Applying density functional theory (DFT) at the B3LYP, APFD, PBEPBE, HCTH, TPSSTPSS, and ωB97XD/aug-cc-pVDZ level of theories for the electronic structural properties. In-vitro analysis, molecular docking, molecular dynamic (MD) simulation of the compounds was conducted to investigate the anti-inflammatory potential using COXs enzymes. Docking indicates binding affinity of −9.57, −9.60, −6.77 and −7.37 kcal/mol for DTPS1, DTPS2, Ibuprofen and Diclofenac which agrees with in-vitro assay. Results of MD simulation, indicates sulphonic group in DTPS1 has > 30% interaction with the hydroxyl and oxygen atoms in amino acid residues, but > 35% interaction with the DTPS2. It can be said that the DTPS1 and DTPS2 can induce inhibitory effect on COXs to halt biosynthesis of prostaglandins (PGs), a chief mediator of inflammation and pain in mammals. Communicated by Ramaswamy H. Sarma</p