Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N'-hydroxy-pyrimidine-2-carboximidamide by DFT approach

Spectroscopic characterization, DFT, antimicrobial activity and molecular docking studies on 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole

The newly synthesized imidazole derivative namely, 4,5-bis[(E)-2-phenylethenyl]-1H,1'H-2,2'-biimidazole (KA1), was studied for its molecular geometry, docking studies, spectral analysis and density functional theory (DFT) studies. Experimental vibrational frequencies were compared with scaled ones. The reactivity sites were determined using average localized ionization analysis (ALIE), electron localized function (ELF), localized orbital locator (LOL), reduced density gradient (RDG), Fukui functions and frontier molecular orbital (FMO). Due to the solvent effect, a lower gas phase energy gap was observed. Through utilization of the noncovalent interaction (NCI) method, the hydrogen bond interaction, steric effect and Vander Walls interaction were investigated. Molecular docking simulations were employed to determine the specific atom inside the molecules that exhibits a preference for binding with protein. The parameters for the molecular electrostatic potential (MESP) and global reactivity descriptors were also determined. The thermodynamic characteristics were determined through calculations employing the B3LYP/cc-pVDZ basis set. Antimicrobial activity was carried out using the five different microorganisms like Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Candida albicans.

Comparison study (experimental and theoretical), hydrogen bond interaction through water, donor acceptor investigation and molecular docking study of 3,3-((1,2-phenylenebis (azaneylylidene)) bis (methaneylylidene)) diphenol

The novel Schiff's base (CS6) was synthesized and confirmed by various studies. The B3LYP/cc-pVDZ basis set was used for theoretical study and the results indicated that both the theoretical and experimental studies correlated well. The interaction energy of CS6-water complex calculated by using the local energy decomposition analysis was found to be -7.28 kcal/mol. The TD-TFT method was used for the calculation of electronic absorption spectrum. This study confirmed that the observed wavelength and the simulated wavelength in the electronic spectra were almost similar. The electrophilic and nucleophilic attacking sites of the titled compound were identified by using FMO and MEP studies. The highest stabilization energy (30.19 kcal/mol) formed by LP (2) O24 to anti-bonding σ*(C18-C19) was confirmed by the NBO study. The localized and delocalized electrons were confirmed by ELF and LOL studies. The hydrogen bond interaction as well as the physical and chemical properties of CS6 indicated that it showed a moderate similarity to the drugs. The docking study confirmed that the dehydro-L-gulonate decarboxylase inhibitor (1Q6O) could interact with CS6 compound with the binding energy of -5.26 kcal/mol.Communicated by Ramaswamy H. Sarma.

De Novo Potent Peptide Nucleic Acid Antisense Oligomer Inhibitors Targeting SARS-CoV-2 RNA-Dependent RNA Polymerase via Structure-Guided Drug Design

Global reports of novel SARS-CoV-2 variants and recurrence cases continue despite substantial vaccination campaigns, raising severe concerns about COVID-19. While repurposed drugs offer some treatment options for COVID-19, notably, nucleoside inhibitors like Remdesivir stand out as curative therapies for COVID-19 that are approved by the US Food and Drug Administration (FDA). The emergence of highly contagious SARS-CoV-2 variants underscores the imperative for antiviral drugs adaptable to evolving viral mutations. RNA-dependent RNA polymerase (RdRp) plays a key role in viral genome replication. Currently, inhibiting viral RdRp function remains a pivotal strategy to tackle the notorious virus. Peptide nucleic acid (PNA) therapy shows promise by effectively targeting specific genome regions, reducing viral replication, and inhibiting infection. In our study, we designed PNA antisense oligomers conjugated with cell-penetrating peptides (CPP) aiming to evaluate their antiviral effects against RdRp target using structure-guided drug design, which involves molecular docking simulations, drug likeliness and pharmacokinetic evaluations, molecular dynamics simulations, and computing binding free energy. The in silico analysis predicts that chemically modified PNAs might act as antisense molecules in order to disrupt ribosome assembly at RdRp's translation start site, and their chemically stable and neutral backbone might enhance sequence-specific RNA binding interaction. Notably, our findings demonstrate that PNA-peptide conjugates might be the most promising inhibitors of SARS-CoV-2 RdRp, with superior binding free energy compared to Remdesivir in the current COVID-19 medication. Specifically, PNA-CPP-1 could bind simultaneously to the active site residues of RdRp protein and sequence-specific RdRp-RNA target in order to control viral replication.

Identification of a Pentasaccharide Lead Compound with High Affinity to the SARS-CoV-2 Spike Protein via In Silico Screening

The spike (S) protein on the surface of the SARS-CoV-2 virus is critical to mediate fusion with the host cell membrane through interaction with angiotensin-converting enzyme 2 (ACE2). Additionally, heparan sulfate (HS) on the host cell surface acts as an attachment factor to facilitate the binding of the S receptor binding domain (RBD) to the ACE2 receptor. Aiming at interfering with the HS-RBD interaction to protect against SARS-CoV-2 infection, we have established a pentasaccharide library composed of 14,112 compounds covering the possible sulfate substitutions on the three sugar units (GlcA, IdoA, and GlcN) of HS. The library was used for virtual screening against RBD domains of SARS-CoV-2. Molecular modeling was carried out to evaluate the potential antiviral properties of the top-hit pentasaccharide focusing on the interactive regions around the interface of RBD-HS-ACE2. The lead pentasaccharide with the highest affinity for RBD was analyzed via drug-likeness calculations, showing better predicted druggable profiles than those currently reported for RBD-binding HS mimetics. The results provide significant information for the development of HS-mimetics as anti-SARS-CoV-2 agents.