Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.     

Influence of Substitutional Defects in ZIF-8 Membranes on Reverse Osmosis Desalination: A Molecular Dynamics Study

In this study, molecular dynamics simulation is used to investigate the effects of water-based substitutional defects in zeolitic imidazolate frameworks (ZIF)-8 membranes on their reverse osmosis (RO) desalination performance. ZIF-8 unit cells containing up to three defect sites are used to construct the membranes. These substitutional defects can either be Zn defects or linker defects. The RO desalination performance of the membranes is assessed in terms of the water flux and ion rejection rate. The effects of defects on the interactions between the ZIF-8 membranes and NaCl are investigated and explained with respect to the radial distribution function (RDF) and ion density distribution. The results show that ion adsorption on the membranes occurs at either the nitrogen atoms or the defect sites. Complete NaCl rejection can be achieved by introducing defects to change the size of the pores. It has also been discovered that the presence of linker defects increases membrane hydrophilicity. Overall, molecular dynamics simulations have been used in this study to show that water-based substitutional defects in a ZIF-8 structure reduce the water flux and influence its hydrophilicity and ion adsorption performance, which is useful in predicting the type and number of defect sites per unit cell required for RO applications. Of the seven ZIF-8 structures tested, pristine ZIF-8 exhibits the best RO desalination performance.     

Monitoring the Reaction of the Body State to Antibiotic Treatment against Helicobacter pylori via Infrared Spectroscopy: A Case Study

The current understanding of deviations of human microbiota caused by antibiotic treatment is poor. In an attempt to improve it, a proof-of-principle spectroscopic study of the breath of one volunteer affected by a course of antibiotics for Helicobacter pylori eradication was performed. Fourier transform spectroscopy enabled searching for the absorption spectral structures sensitive to the treatment in the entire mid-infrared region. Two spectral ranges were found where the corresponding structures strongly correlated with the beginning and end of the treatment. The structures were identified as methyl ester of butyric acid and ethyl ester of pyruvic acid. Both acids generated by bacteria in the gut are involved in fundamental processes of human metabolism. Being confirmed by other studies, measurement of the methyl butyrate deviation could be a promising way for monitoring acute gastritis and anti-Helicobacter pylori antibiotic treatment.     

From Electronegativity towards Reactivity—Searching for a Measure of Atomic Reactivity

Pauling introduced the concept of electronegativity of an atom which has played an important role in understanding the polarity and ionic character of bonds between atoms. We set out to define a related concept of atomic reactivity in such a way that it can be quantified and used to predict the stability of covalent bonds in molecules. Guided by the early definition of electronegativity by Mulliken in terms of first ionization energies and Pauling in terms of bond energies, we propose corresponding definitions of atomic reactivity. The main goal of clearly distinguishing the inert gas atoms as nonreactive is fulfilled by three different proposed measures of atomic reactivity. The measure likely to be found most useful is based on the bond energies in atomic hydrides, which are related to atomic reactivities by a geometric average. The origin of the atomic reactivity is found in the symmetry of the atomic environment and related conservation laws which are also the origin of the shell structure of atoms and the periodic table. The reactive atoms are characterized by degenerate or nearly degenerate (several states of the same or nearly the same energy) ground states, while the inert atoms have nondegenerate ground states and no near-degeneracies. We show how to extend the use of the Aufbau model of atomic structure to qualitatively describe atomic reactivity in terms of ground state degeneracy. The symmetry and related conservation laws of atomic electron structures produce a strain (energy increase) in the structure, which we estimate by use of the Thomas-Fermi form of DFT implemented approximately with and without the symmetry and conservation constraints. This simplified and approximate analysis indicates that the total strain energy of an atom correlates strongly with the corresponding atomic reactivity measures but antibonding mechanisms prevent full conversion of strain relaxation to bonding.     

Effect of the Nanotube Radius and the Volume Fraction on the Mechanical Properties of Carbon Nanotube-Reinforced Aluminum Metal Matrix Composites

By using the advantages of carbon nanotubes (CNTs), such as their excellent mechanical properties and low density, CNT-reinforced metal matrix composites (MMCs) are expected to overcome the limitations of conventional metal materials, i.e., their high density and low ductility. To understand the behavior of composite materials, it is necessary to observe the behavior at the molecular level and to understand the effect of various factors, such as the radius and content of CNTs. Therefore, in this study, the effect of the CNT radius and content on the mechanical properties of CNT-Al composites was observed using a series of molecular dynamics simulations, particularly focusing on MMCs with a high CNT content and large CNT diameter. The mechanical properties, such as the strength and stiffness, were increased with an increasing CNT radius. As the CNT content increased, the strength and stiffness increased; however, the fracture strain was not affected. The behavior of double-walled carbon nanotubes (DWNTs) and single-walled carbon nanotubes (SWNTs) was compared through the decomposition of the stress–strain curve and observations of the atomic stress field. The fracture strain increased significantly for SWNT-Al as the tensile force was applied in the axial direction of the armchair CNTs. In the case of DWNTs, an early failure was initiated at the inner CNTs. In addition, the change in the elastic modulus according to the CNT content was predicted using the modified rule of mixture. This study is expected to be useful for the design and development of high-performance MMCs reinforced by CNTs.     

Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.     

Phenolics Profiling of Carpobrotus edulis (L.) N.E.Br. and Insights into Molecular Dynamics of Their Significance in Type 2 Diabetes Therapy and Its Retinopathy Complication

Adverse effects associated with synthetic drugs in diabetes therapy has prompted the search for novel natural lead compounds with little or no side effects. Effects of phenolic compounds from Carpobrotus edulis on carbohydrate-metabolizing enzymes through in vitro and in silico methods were assessed. Based on the half-maximal inhibitory concentrations (IC₅₀), the phenolic extract of the plant had significant (p < 0.05) in vitro inhibitory effect on the specific activity of alpha-amylase (0.51 mg/mL), alpha-glucosidase (0.062 mg/mL) and aldose reductase (0.75 mg/mL), compared with the reference standards (0.55, 0.72 and 7.05 mg/mL, respectively). Molecular interactions established between the 11 phenolic compounds identifiable from the HPLC chromatogram of the extract and active site residues of the enzymes revealed higher binding affinity and more structural compactness with procyanidin (−69.834 ± 6.574 kcal/mol) and 1,3-dicaffeoxyl quinic acid (−42.630 ± 4.076 kcal/mol) as potential inhibitors of alpha-amylase and alpha-glucosidase, respectively, while isorhamnetin-3-O-rutinoside (−45.398 ± 4.568 kcal/mol) and luteolin-7-O-beta-d-glucoside (−45.102 ± 4.024 kcal/mol) for aldose reductase relative to respective reference standards. Put together, the findings are suggestive of the compounds as potential constituents of C. edulis phenolic extract responsible for the significant hypoglycemic effect in vitro; hence, they could be exploited in the development of novel therapeutic agents for type-2 diabetes and its retinopathy complication.     

Discovery of New Coumarin-Based Lead with Potential Anticancer,CDK4 Inhibition and Selective Radiotheranostic Effect: Synthesis, 2D & 3D QSAR,Molecular Dynamics,In Vitro Cytotoxicity,Radioiodination, and Biodistribution Studies

Novel 6-bromo-coumarin-ethylidene-hydrazonyl-thiazolyl and 6-bromo-coumarin-thiazolyl-based derivatives were synthesized. A quantitative structure activity relationship (QSAR) model with high predictive power r² = 0.92, and RMSE = 0.44 predicted five compounds; 2b, 3b, 5a, 9a and 9i to have potential anticancer activities. Compound 2b achieved the best ΔG of –15.34 kcal/mol with an affinity of 40.05 pki. In a molecular dynamic study 2b showed an equilibrium at 0.8 Å after 3.5 ns, while flavopiridol did so at 0.5 Å after the same time (3.5 ns). 2b showed an IC₅₀ of 0.0136 µM, 0.015 µM, and 0.054 µM against MCF-7, A-549, and CHO-K1 cell lines, respectively. The CDK4 enzyme assay revealed the significant CDK4 inhibitory activity of compound 2b with IC₅₀ of 0.036 µM. The selectivity of the newly discovered lead compound 2b toward localization in tumor cells was confirmed by a radioiodination biological assay that was done via electrophilic substitution reaction utilizing the oxidative effect of chloramine-t. ¹³¹I-2b showed good in vitro stability up to 4 h. In solid tumor bearing mice, the values of tumor uptake reached a height of 5.97 ± 0.82%ID/g at 60 min p.i. ¹³¹I-2b can be considered as a selective radiotheranostic agent for solid tumors with promising anticancer activity.     

Computational Approaches for the Design of Novel Anticancer Compounds Based on Pyrazolo[3,4-d]pyrimidine Derivatives as TRAP1 Inhibitor

In the present in-silico study, various computational techniques were applied to determine potent compounds against TRAP1 kinase. The pharmacophore hypothesis DHHRR_1 consists of important features required for activity. The 3D QSAR study showed a statistically significant model with R² = 0.96 and Q² = 0.57. Leave one out (LOO) cross-validation (R² CV = 0.58) was used to validate the QSAR model. The molecular docking study showed maximum XP docking scores (−11.265, −10.532, −10.422, −10.827, −10.753 kcal/mol) for potent pyrazole analogs (42, 46, 49, 56, 43), respectively, with significant interactions with amino acid residues (ASP 594, CYS 532, PHE 583, SER 536) against TRAP1 kinase receptors (PDB ID: 5Y3N). Furthermore, the docking results were validated using the 100 ns MD simulations performed for the selected five docked complexes. The selected inhibitors showed relatively higher binding affinities than the TRAP1 inhibitor molecules present in the literature. The ZINC database was used for a virtual screening study that screened ZINC05297837, ZINC05434822, and ZINC72286418, which showed similar binding interactions to those shown by potent ligands. Absorption, distribution, metabolism, and excretion (ADME) analysis showed noticeable results. The results of the study may be helpful for the further development of potent TRAP1 inhibitors