Investigation of Structural, Physicochemical, Pharmacokinetics, PASS Prediction, and Molecular Docking Analysis of Methyl 6-O-Myristoyl-α-D -Glucopyranoside Derivatives against SARS-CoV-2

Abstract

Monosaccharide derivatives are of importance in the field of carbohydrate chemistry because of their effectiveness in the synthesis of biologically active products. As a consequence, the chemistry and biochemistry of carbohydrate derivatives are an essential part of biochemical and medicinal research. In this work, we have explored the speciation of acylated methyl 6-O-myristoyl-α-D-glucopyranoside derivatives (2−9) to find the pharmacodynamics, toxicity profiles, and biological activities by using ADMET studies. PASS prediction also indicated that these acylated derivatives (2−9) are more potent as anticarcinogenic agents than as antioxidant agents. Quantum mechanical study employing density functional theory with B3LYP/6-31G(d,p) for investigating the enthalpies (ΔH), Gibbs free energies (ΔG), entropies (ΔS), and molecular orbital (HOMO−LUMO gap, hardness, softness, chemical potential, and electrophilicity index), dipole moment and natural bond orbital revealed that these derivatives are thermodynamically stable. The molecular docking study revealed that ivermectin has the highest binding affinity (−8.1 kcal mol−1) and, among the tested compounds, 2 and 3 (−5.7 kcal mol−1) showed the highest binding affinity, followed by 4 and 5 (−5.5 kcal mol−1). These results of acylated derivatives (2−9) could be useful for the development of drugs.

Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques

“…Frequency calculations were also carried out to confirm that all structures were in their energy minima. Previous studies [46] , [47] , [48] , [49] , [50] , [51] , [52] have demonstrated the accuracy and efficiency of using the B3LYP/6–31G(d,p) level of theory. The analysis of frontier molecular orbital (FMO) energy distribution, spanning from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO), along with the generation of molecular electrostatic potential (MEP) maps, was performed using GaussView 6 software.…”

Synthesis of New Derivatives of Benzylidinemalononitrile and Ethyl 2-Cyano-3-phenylacrylate: In Silico Anticancer Evaluation

“…39 The geometries and vibrational wave numbers of benzylidenemalononitrile and ethyl 2-cyano-3-phenylacrylate derivatives ( 1 – 6 ) were optimized using the B3LYP/6-31G(d,p) level of theory. The prior research 40 that our group conducted consisted of exploring the deamination reactions of a variety of different nitrogenous bases using a variety of different computational methodologies. The results obtained from G3MP2, G3MP2B3, G4MP2, G3B3, and CBS-QB3 methods agreed with each other within a range of 10 kJ mol –1 , while the B3LYP/6-31G(d,p) method had a deviation of up to 18 kJ mol –1 .…”

Design, Synthesis, In Silico and POM Studies for the Identification of the Pharmacophore Sites of Benzylidene Derivatives

“…The chemical reactivity indicators, such as HOMO, LUMO and gap energies were also evaluated [ 41 , 42 ]. Molecular docking studies performed on pathogenic fungal and bacterial proteins have helped to obtain more information about the biological applications of synthesized molecules [ 43 , 44 ]. Thus, their binding affinity and abilities with fungal proteins (PDB: 1KS5, 1R51) and bacterial proteins (PDB: 4A1J, 5IQR) were assessed, whereby the binding mode was then identified.…”