Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of 1H NMR Chemical Shifts

Quantum Chemical NMR Spectroscopic Structural Analysis in Solution: The Investigation of 3-Indoleacetic Acid Dimer Formation in Chloroform and DMSO Solution

We present a DFT-PCM NMR study of 3-indoleacetic acid (3-IAA), used as a working example, including explicit solvent molecules, named PCM-nCHCl3, PCM-nDMSO (n = 0, 2, 4, 8, 14, 20, and 25), to investigate the dimer formation in solution. Apart from well-known cyclic (I) and open (II) acetic acid (AA) dimers, two new structures were located on DFT-PCM potential energy surface (PES) for 3-IAA named quasicyclic A (III) and quasicyclic B (IV), the last one having N-H…O hydrogen bond (instead of O-H…O). In addition, four other structures having π-π type interactions named V, VI, VII, and VIII were also obtained completing the sample on the PES. Our theoretical results and experimental 1H NMR data (CDCl3) strongly indicate that 3-IAA should exist in a quasicyclic form (III) in a chloroform solution different from AA. Solute-solvent interactions play a key role in O-H and N-H chemical shifts. The strong H-bond formation between the S=O and O-H and N-H groups produces large chemical shift value THAT masquerades the identification of dimer formation in DMSO solution based on 1H NMR chemical shift changes. However, analysis of 13C NMR and relative energy DFT-PCM-nDMSO results strongly indicate the presence of parallel ring interacting dimer having OH…benzene ring bond (VI). There can be a competition between solute-solute and solute-solvent interactions, and polar DMSO solvent can break the quasicyclic dimers (III and IV) intermolecular O-H…O and N-H…O bonds yielding two solvated monomeric species hydrogen bonded to O=S(CH3)2 groups, what may take place for other organic molecules in solution. However, it did not happen for the π-π interacting dimers and structure VI survived in DMSO solution.

Quantum Chemical Investigation of the Interaction of Thalidomide Monomeric, Dimeric, Trimeric, and Tetrameric Forms with Guanine DNA Nucleotide Basis in DMSO and Water Solution: A Thermodynamic and NMR Spectroscopy Analysis

Thalidomide (TLD) was used worldwide as a sedative, but it was revealed to cause teratogenicity when taken during early pregnancy. It has been stated that the (R) enantiomer of TLD has therapeutic effects, while the (S) form is teratogenic. Clinical studies, however, demonstrated the therapeutic efficacy of thalidomide in several intractable diseases, so TLD and its derivatives have played an important role in the development and therapy of anticancer drugs. Therefore, it is important to know the molecular mechanism of action of the TLD, although this is still not clear. In what molecular interactions are concerned, it is known that drug molecules can interact with DNA in different ways, for example, by intercalation between base pairs. Furthermore, the ability of the TLD to interact with DNA has been confirmed experimentally. In this work, we report a theoretical investigation of the interaction of the R and S enantiomers of TLD, in its monomeric, dimeric, trimeric, and tetrameric forms, with guanine (GUA) DNA nucleotide basis in solution using density functional theory (DFT). Our initial objective was to evaluate the interaction of TLD-R/S with GUA through thermodynamic and spectroscopic study in dimethyl sulfoxide (DMSO) solvent and an aqueous solution. Comparison of the experimental 1H nuclear magnetic resonance (NMR) spectrum in DMSO-d6 solution with calculated DFT-PCM-DMSO chemical shifts revealed that TLD can undergo molecular association in solution, and interaction of its dimeric form with a DNA base ((TLD)2-GUA and (TLD)2-2GUA, for example) through H-bond formation is likely to take place. Our results strongly indicated that we must consider the plausibility of the existence of TLD associations in solution when modeling the complexation of the TLD with biological targets. This is new information that may provide further insight into our understanding of drug binding to biological targets at the molecular level.

Quantum chemical investigation of predominant conformation of the antibiotic azithromycin in water and DMSO solutions: thermodynamic and NMR analysis

Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH … N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.

Exploring the permeability of covid-19 drugs within the cellular membrane: a molecular dynamics simulation study

The diffusion of drugs into the cellular membrane is an important step in the drug delivery systems. Furthermore, predicting the interaction and permeability of drugs across the cellular membrane could help scientists to design bioavailable and high-efficient drugs. Discovering the COVID-19 drugs has recently drawn remarkable attention to tackle its outbreak. Due to the rapid replication of the coronavirus in the human body, searching for highly permeable drugs into the cellular membrane is vital. Herein, we performed the molecular dynamics (MD) simulation and density functional (DFT) calculations to investigate the permeability of keto and enol tautomers of the favipiravir (FAV) as well as hydroxychloroquine (HCQ) COVID-19 drugs into the cellular membrane. Our results reveal that though both keto and enol tautomers of the FAV are feasible to transfer through the cellular membrane, the keto form moves faster and diffuses deeper; however, the HCQ molecules aggregate in the water phase and remain near the cellular membrane. It is worth pointing out that the obtained results are consistent with the reactivity trends projected by the calculated reactivity descriptors of the considered drugs. Despite the pair correlation function and H-bond analyses revealing the interactions between the membrane and HCQ, the aggregation of the HCQ molecules resists their passage through the cellular membrane. Besides, the lower free energy barrier of FAV confirms its higher permeability than HCQ. These findings suggest that due to the deeper permeability of the FAV drug, its effectiveness can be more than that of HCQ. These molecular insights might help with a better understanding of the interactions between COVID-19 drugs and cellular membranes. Moreover, these theoretical findings could help experimental researchers find high-efficient strategies for COVID-19 therapy.

An Investigation of the Predominant Structure of Antibiotic Azithromycin in Chloroform Solution through NMR and Thermodynamic Analysis

Azithromycin (AZM) is a well-known macrolide-type antibiotic that has been used in the treatment of infections and inflammations. Knowledge of the predominant molecular structure in solution is a prerequisite for...