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    Detailed Electronic Structure, Physico-Chemical Properties, Excited State Properties, Virtual Bioactivity Screening and SERS Analysis of Three Guanine Based Antiviral Drugs Valacyclovir HCl Hydrate, Acyclovir and Ganciclovir
    (Taylor & Francis Ltd, 2022) Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Thomas, Renjith; Kaya, Savas
    Valacyclovir HCl hydrate, acyclovir and ganciclovir are three commonly used anti viral drugs which are guanidine derivatives with ether side chain and all of them act by interfering with the viral DNA production. This manuscript tries to examine the structure and properties of these three purine based compounds using electronic structure methods and molecular mechanics. Density functional theory was used to optimize the ground state geometry of the molecules from frontier molecular orbitals are analyzed using B3LYP functional. They give wealth of information about the electronic properties and descriptors, which will enable to predict the bioactivity of the molecules. As the electrons interact with electromagnetic radiations, electronic excitations between different energy levels are analyzed in detail using TD-DFT with CAM-B3LYP orbital. Calculations shows that they are with excellent light-harvesting efficiency hence be used as photo sensitizers. Molecular docking studies predict the biological activity of the molecules against ADP-thymidine kinase, hence inhibits its action, subsequently affecting the viral DNA production. It is interesting to see that on adsorption with a graphene quantum dot surface, all adsorbed complex show enhancement in the Raman activity giving Surface Enhanced Raman Spectra (SERS) when studied using dispersion force corrected omega-B97XD functional. This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene drug molecular assembly shows enhanced biological activity when compared to individual drug molecules.
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    Spectral analysis and detailed quantum mechanical investigation of some acetanilide analogues and their self-assemblies with graphene and fullerene
    (Springer, 2020) Almuqrin, Aljawhara H.; Al-Otaibi, Jamelah S.; Mary, Y. Sheena; Thomas, Renjith; Kaya, Savas; Isin, Dilara Ozbakir
    Spectroscopic analysis and different quantum mechanical studies of four pharmaceutically active compounds phenacetin, p-acetanisidide, 4 '-butoxyacetanilide, and 4 '-(3-chloropropoxy)acetanilide are reported in this manuscript. Simulated IR spectrum of these compounds was compared with experimentally available data, and essential functional group assignments were made. We also report the frontier orbital properties and other derived local energy descriptors which talks about the relative stability and reactivity. Photovoltaic efficiency of the compounds was studied from the simulated electronic spectra. The compound was found to interact with graphene and fullerene, to form molecular self-assembly. These self-assemblies showed tremendous enhancement in various physicochemical properties when compared with its constituents. The nature of the interactions between studied chemical species was discussed with the help of chemical reactivity principles. Biological activity of the compounds was predicted using molecular docking studies. It is interesting to see that on adsorption with a graphene/fullerene surface, all adsorbed complex shows enhancement in the Raman activity giving surface enhanced Raman spectra (SERS). This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene/fullerene drug molecular assembly shows enhanced biological activity when compared with individual drug molecules.
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    Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins
    (Elsevier, 2023) Ilavarasi, Anbumani Velmurugan; Paularokiadoss, Francisxavier; Novena, L. Mary; Pooventhiran, T.; Erkan, Sultan; Celaya, Christian A.; Thomas, Renjith
    Electronic structure analysis of the alkaloid from scorpion venom (ASV) was studied at the B3LYP/6-311++G (d, p) level of theory. Vibrational analysis, molecular orbital analysis and the MEP and contour plot analysis show the reactivity and molecular stability of the compound. The measured frontier molecular orbital energy distance (ELUMO-EHOMO) is 4.12 eV. The reactive descriptors research found that the ASV molecule has a chemical hardness of 2.205 eV and an electronegativity of 3.325 eV, consistent with its biological activity. The calculated NLA parameters & mu;o, & alpha;o, and & beta;degrees values of the title molecule are 1.5009 Debye,-5.718 x 10-24 e.s.u, 2.984 x 10-30 e.s.u, respectively. The alkaloid from scorpion venom is found to form stable complexes with cyclodextrin. ASV was docked against the main proteases (MPro) and papain-like proteases (PLpro) of COVID-19. ASV has a Glide docking score of-8.017 kcal/mol with MPro and-5.091 kcal/mol with PLpro. ASV has a Prime MM-GBSA binding score of-51.74 kcal/mol with MPro and-32.19 kcal/mol with PLpro. The Glide and Prime results demonstrated that ASV has a stronger binding for MPro than PLpro protein. Furthermore, the major pharmacokinetic characteristics of ASV were predicted. ASV was found to have good drug-like properties with no violations. Since ASV binds to COVID-19 proteases, it could be used as an anti-COVID-19 agent. The outcomes of the study may have a substantial impact on the development of COVID-19 therapies.