Investigation of inclusion complex of metformin into selective cyclic peptides as novel drug delivery system: Structure, electronic properties, AIM, and NBO study via DFT

Computational investigation of natural compounds as potential main protease (Mpro) inhibitors for SARS-CoV-2 virus

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (M^pro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.

In Silico Studies and Design of Scrupulous Novel Sensor for Nitro Aromatics Compounds and Metal Ions Detection

A Novel calix[4]pyrrole system bearing carboxylic acid functionality [ABuCP] has been synthesized and its interaction towards various nitroaromatics compounds [NACs] were investigated. ABuCP showed significant color change with 1,3-dinitro benzene (1,3-DNB) in comparison to the solution of other nitroaromatic compounds such as 2,3-dinitro toluene (2,3-DNT), 2,4-dinitro toluene (2,4-DNT), 2,6-dinitro toluene (2,6-DNT), 4-NBB (4-nitrobenzyl bromide) and 4-nitro toluene (4-NT). The ABuCP-1,3-DNB complex produces a red shift in absorption spectra based on charge transfer mediated recognition. Additionally, the density functional theory calculation confirmed the possible mechanism for the binding of 1,3-DNB as a guest is well supported by the calculation of other parameters such as hardness, stabilization energy, softness, electrophilicity index and chemical potential. The TDDFT calculation facilitates the understanding of the proper binding mechanism in reference to experimental results. Additionally we have also developed its derivative which acts as a new fluorescent sensor which can selectively recognize Sr(II) ions. In this view its aminoanthraquinone derivative of calix[4]pyrrole i.e. ABuCPTAA is synthesized which also results in generation of high fluorescence capability sensor.

Why Should Metformin Not Be Given in Advanced Kidney Disease? Potential Leads from Computer Simulations

Metformin is considered as the go-to drug in the treatment of diabetes. However, it is either prescribed in lower doses or not prescribed at all to patients with kidney problems. To find a potential explanation for this practice, we employed atomistic-level computer simulations to simulate the transport of metformin through multidrug and toxin extrusion 1 (MATE1), a protein known to play a key role in the expulsion of metformin into urine. Herein, we examine the hydrogen bonding between MATE1 and one or more metformin molecules. The simulation results indicate that metformin continuously forms and breaks off hydrogen bonds with MATE1 residues. However, the mean hydrogen bond lifetimes increase for an order of magnitude when three metformin molecules are inserted instead of one. This new insight into the metformin transport process may provide the molecular foundation behind the clinical practice of not prescribing metformin to kidney disease patients.