Investigations on experimental, theoretical spectroscopic, electronic excitations, molecular docking of Sulfaguanidine (SG): An antibiotic drug

Computational and experimental insights into the spectroscopy, electronic states, and molecular docking of (2S)-2,6-diaminohexanoic acid [DAHA]

This paper presents a theoretical analysis of the L-Lysine molecule using the DFT (density functional theory) method with a 6-311+ + G(d,p) basis set, a quantum-mechanical atomistic simulation method. The research encompasses the analysis of optimized chemical structure, vibrations, FMO, ELF, NLO, RDG, etc., to study the molecule's intensive properties, stability, and other biological activities. IR and UV spectra were analysed for the spectrochemical study, and the VEDA program was used to determine the PED values. The chemical reactivity of the molecule was identified through analysis of the Frontier molecular orbitals, Fukui, and molecular electrostatic potential. The electron localization function and reduced density gradient were determined to understand bonding and electronic structure. The temperature dependence on the properties of the molecule was estimated. The optical properties of the molecule were discussed by analyzing the non-linear optical property. The feasibility of the molecule as a therapeutic drug was examined using the drug likeness concept. Molecular docking analysis was conducted to acquire the best ligand-receptor complex and to study the molecule's biological activity.

Computational investigations on the anaesthetic drug, tetracaine (TCA) by DFT, TD-DFT, molecular docking, and molecular dynamic simulation analysis

The current investigation deals with the theoretical exploration of tetracaine (TCA) employing density function theory (DFT), time-dependent density function theory (TD-DFT), molecular docking (MD), and molecular dynamic simulation (MDS). The B3LYP method was utilised for this study in conjunction with a 6-31++G(d,p) basis set. We computed the charge distribution of the molecule tetracaine using molecular electrostatic potential (MEP) analysis, which indicate how molecules interact and what kinds of chemical bonds they have. Additionally, population analysis and Fukui function analysis have explored charges on the atoms. This comprehensive study also includes an assessment of various parameters such as chemical hardness, chemical softness, and electrophilicity index through the Frontier Molecular Orbital (FMO) investigation. The molecule's non-linear optical (NLO) properties were conducted to ascertain the hyperpolarizability and polarity values. Lastly, molecular docking was used to look at how a ligand and two protein receptors, named monoamine oxidase A (code: 2BXR) and monoamine oxidase B (code: 1OJD), interact with a ligand. The resulting binding energies were determined to be -7.7 and -7.6 kcal/mol, respectively. Following the completion of the docking process, an investigation of conformational behaviour was conducted with the assistance of molecular dynamic simulation (MDS). These findings indicate the possible applicability of this interaction in the field of medicine. This study has the potential to be utilized in the future to advance the creation of amphiphilic drugs.

Molecular Modeling of Vasodilatory Activity: Unveiling Novel Candidates Through Density Functional Theory, QSAR, and Molecular Dynamics

Cardiovascular diseases (CVD) pose a significant global health challenge, requiring innovative therapeutic strategies. Vasodilators, which are central to vasodilation and blood pressure reduction, play a crucial role in cardiovascular treatment. This study integrates quantitative structure- (QSAR) modeling and molecular dynamics (MD) simulations to predict the biological activity and interactions of vasodilatory compounds with the aim to repurpose drugs already known and estimateing their potential use as vasodilators. By exploring molecular descriptors, such as electronegativity, softness, and highest occupied molecular orbital (HOMO) energy, this study identifies key structural features influencing vasodilatory effects, as it seems molecules with the same mechanism of actions present similar frontier orbitals pattern. The QSAR model was built using fifty-four Food Drugs Administration-approved (FDA-approved) compounds used in cardiovascular treatment and their activities in rat thoracic aortic rings; several molecular descriptors, such as electronic, thermodynamics, and topographic were used. The best QSAR model was validated through robust training and test dataset split, demonstrating high predictive accuracy in drug design. The validated model was applied on the FDA dataset and molecules in the application domain with high predicted activity were retrieved and filtered. Thirty molecules with the best-predicted pKI50 were further analyzed employing molecular orbital frontiers and classified as angiotensin-I or β1-adrenergic inhibitors; then, the best scoring values obtained from molecular docking were used to perform a molecular dynamics simulation, providing insight into the dynamic interactions between vasodilatory compounds and their targets, elucidating the strength and stability of these interactions over time. According to the binding energies results, this study identifies novel vasodilatory candidates where Dasabuvir and Sertindole seem to have potent and selective activity, offering promising avenues for the development of next-generation cardiovascular therapies. Finally, this research bridges computational modelling with experimental validation, providing valuable insight for the design of optimized vasodilatory agents to address critical unmet needs in cardiovascular medicine.

Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine

Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.

Nature of Luminescence and Pharmacological Activity of Sulfaguanidine

Sulfonamides are one of the oldest groups of veterinary chemotherapeutic agents. Physico-chemical properties, the concentration and the nature of the environment are the factors responsible for the distribution of sulfonamides in the living organism. Although these drug compounds have been in use for more than half a century, knowledge about their behavior is still limited. Physiological activity is currently attributed to the sulfanyl radical. Our study is devoted to the spectral properties of aqueous solutions of sulfaguanidine, in which the formation of complexes with an H-bond and a protonated form takes place. The nature of the fluorescent state of sulfaguanidine was interpreted using computational chemistry, the electronic absorption method and the luminescence method. The structure of sulfaguanidine includes several active fragments: aniline, sulfonic and guanidine. To reveal the role of fragments in the physiological activity of the studied antibiotic, we calculated and compared the effective charges of the fragments of aniline and sulfaguanidine molecules. Chromophore groups were identified in molecules, which determine the intermolecular interaction between a molecule and a proton-donor solvent. The study also revealed the impact of sulfone and guanidine groups, as well as complexation, on the effective charge of the antibiotic fragment responsible for physiological activity and luminescent ability.

Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.

Design, Synthesis and Evaluation of Novel Antimicrobial Polymers Based on the Inclusion of Polyethylene Glycol/TiO2 Nanocomposites in Cyclodextrin as Drug Carriers for Sulfaguanidine

Polymers and their composites have recently attracted attention in both pharmaceutical and biomedical applications. Polyethylene glycol (PEG) is a versatile polymer extensively used in medicine. Herein, three novel PEG-based polymers that are pseudopolyrotaxane (PEG/α-CD) (1), titania–nanocomposite (PEG/TiO₂NPs) (2), and pseudopolyrotaxane–titania–nanocomposite (PEG/α-CD/TiO₂NPs) (3), were synthesized and characterized. The chemical structure, surface morphology, and optical properties of the newly materials were examined by FT-IR, ¹H-NMR, SEM, and UV–Vis., respectively. The prepared polymers were used as drug carriers of sulfaguanidine as PEG/α-CD/Drug (4), PEG/TiO₂NPs/Drug (5), and PEG/α-CD/TiO₂NPs/Drug (6). The influence of these drug-carrying formulations on the physical and chemical characteristics of sulfaguanidine including pharmacokinetic response, solubility, and tissue penetration was explored. Evaluation of the antibacterial and antibiofilm effect of sulfaguanidine was tested before and after loading onto the prepared polymers against some Gram-negative and positive bacteria (E. coli, Pseudomonas aeruginosa, and Staphylococcus aureus (MRSA)), as well. The results of this work turned out to be very promising as they confirmed that loading sulfaguanidine to the newly designed polymers not only showed superior antibacterial and antibiofilm efficacy compared to the pure drug, but also modified the properties of the sulfaguanidine drug itself.