Exploiting σ-hole interaction to design small uncharged ligand molecules to stabilize G-quadruplex-DNA: a computational study

Small neutral seleno molecules were designed to stabilize G-quadruplex-DNA to accelerate the death of cancer cells. A new approach was considered in this study to design new ligands to stabilize G-quadruplex-DNA using the non-covalent σ-hole interaction. The systematic study has been performed with ligands in the absence and presence of σ-hole interaction to stabilize G-tetrad. Fluorine-substituted seleno ligands interact with the bases of G-quadruplex strongly with the σ-holes present in the ligands. The binding of the fluorinated ligands FSeCF₂SeCF₂ SeF2(4) (~75.0 kcal/mol) is stronger than that of BRACO-19 (~70.0 kcal/mol) calculated at the same level of theory with G-tetrad. It is reported that BRACO-19 is employed to inhibit the enzymatic activity of telomerase. The calculated results also reveal the importance of optimum chain length of ligands to achieve a better binding ability with G-tetrad. The MESP calculations and AIM analysis corroborate the trends of binding of these ligand molecules with G-quadruplexes. The small neutral molecules possess considerable advantage to pass through the lipid bilayer of the cell membrane by passive transport and are of choice in biological research and for clinical trials. Graphical AbtractSmall neutral ligands with σ-holes can stabilize G-quadruplex to inhibit enzymatic activity of telomerase.

A new strategy to generate super and hyper acids with simple organic molecules exploiting σ-hole interaction

Super and hyper acidity can be achieved using σ-hole non-covalent interactions with simple organic systems. The σ-hole interaction can stabilize the conjugate base of acids to such an extent that cyclopentadiene yields a ΔH_acid of 256 kcal mol^-1, which is ∼100 kcal mol^-1 lower than the reported results. The hyper acidic value of 209.0 kcal mol^-1 of organic acids has been achieved without electron-withdrawing substituents rather exploiting only σ-hole interaction. Remarkably, the 1st and 2nd acidity values (∼229 kcal mol^-1) of comparable strength in the hyperacid range have been observed for the first time using DFT computations. The simple organic acids were predicted to reach the pK_a values in the range of -7.3 to -7.8 in DMSO, which is remarkably lower than previous reports. These stable anions can be a potential candidate for application as an effective electrolyte in lithium-ion batteries.

Tuning the ring strain effect in acridine derivatives on binding affinity with G-quadruplex-DNA: A computational and experimental study

Search for inhibitors to stabilize the telomeric G-quadruplex in order to deter telomerase activity is an active area of research. Inhibitors play an important role to initiate the tumor cell mortalization process. This work reports for the first time of acridine derivative with four membered ammonium rings at the side chain to surpass the binding ability against BRACO-19 with G-quadruplex-DNA. It is known in the literature that acridine based molecule BRACO-19 can effectively bind with G-quadruplex-DNA. The computational study performed in this study revealed that the binding ability of acridine based molecule can be augmented with subtle variation in the molecular structure of the drug like candidates. Steered molecular dynamics (SMD) performed with the acridine derivatives and G-quadruplex DNA showed the importance of ring strain to the side chain of those ligand molecules. The rupture force analysis, hydrogen bonding interactions and the calculated free energies in MM-PBSA method suggest that ligand 3 is superior than that of BRACO-19. The synthesized ligand 3 and BRACO-19 showed the binding constants obtained from ITC measurements are 4 × 10⁶ mol^-1 and 2.6 × 10⁶, which corroborates the computational findings.

Impact of "half-crown/two carbonyl"-Ca2+ metal ion interactions of a low molecular weight gelator (LMWG) on its fiber to nanosphere morphology transformation with a gel-to-sol phase transition

We report here a smart functional low molecular weight gelator (LMWG) L, containing an unusual metal ion coordination site, i.e. "half-crown/two carbonyl". The gelator L shows excellent gelation behavior with typical fibrillar morphology in acetonitrile, methanol and ethanol media. Upon Ca2+ ion binding with its "half-crown/two carbonyl" coordination site, the acetonitrile gel of L exhibits a fiber to nanosphere morphology transformation along with a gel-to-sol phase transition as confirmed by microscopic investigation and by direct naked eye visualization, respectively. The mechanism involved in this morphology transformation and gel-to-sol phase transition process was studied thoroughly with the help of computational calculations and various spectroscopic experiments and discussed.

Computational predictions turning the isomers of alanine to generate distinct morphs of free-flowing salt crystals

The morphology of salt crystals has been an active area of research for decades and remains largely empirical. This study reveals the computational modeling guides to arrive at the correct answer, even for complex problems, such as the morphology of salt crystals with additives. There is no report on the two different morphologies of rock-salt crystals with two isomers of a single additive. Alanine isomers (α- and β-) can induce octahedron and rhombic dodecahedron morphologies in salt crystals. The computational study demonstrated that α-alanine preferentially interacts with {111} and β-alanine with {110} planes to yield such morphologies. The change in morphology with alanine can greatly influence the problem of the free-flowing issue of salt crystals.

The effect of σ/π, σ and π donors on the basicity of silylene superbases: a density functional theory study

In this study, we examined computationally that the combination of π-and σ-donor substituents results in higher basicity of silylene compounds compared to the usage of π-donor substituents alone.

A DFT study to design super- and hyperacids with 1-(cyclopenta-2,4-dien-1-yl)-4-nitrobenzene and 3-(cyclopenta-2,4-dien-1-ylmethylene)-6-methylenecyclohexa-1,4-diene molecules

DFT calculations reveal that poly-cyano-substituted 1-(cyclopenta-2,4-dien-1-yl)-4-nitrobenzene and 3-(cyclopenta-2,4-dien-1-ylmethylene)-6-methylenecyclohexa-1,4-diene can function as super- to hyper-acids.

Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study

This report reveals that hydrogen bonding interactions between the ligand and G-quadruplex can initiate an alternative binding motif to typical π-stacking interactions.

Computational evidence that hyperconjugative orbital interactions are responsible for the stability of intramolecular Te⋯O/Te⋯S non-covalent interactions and comparable to hydrogen bonds in quasi-cyclic systems

The intramolecular secondary bonding interactions involving quasi-cyclic tellurium are comparable to H-bond strength and partially governed by orbital interactions.