G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy

How Do Molecular Crowders Influence Ligand Binding Kinetics with G-Quadruplex DNA? The Role of Bound Water

Understanding the kinetics of ligand interaction with G-quadruplex DNA (GqDNA) in a crowded cell-like environment is of paramount importance in biology and pharmacology, as it elucidates the effect of molecular crowders on reaction rates governing these interactions─a process that largely remains unexplored. In this study, we investigate the binding/unbinding kinetics of a G-quadruplex stabilizing benzophenoxazine ligand, cresyl violet (CV), with a human telomeric hybrid GqDNA structure using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. Experiments are conducted with and without 10% and 20% (w/v) ethylene glycol (EG), PEG200 and PEG6000 crowders. The steady-state fluorescence results reveal a reduction in the ligand binding affinity to GqDNA as the size and concentration of the crowders increase. FCS data further demonstrate that the crowder-induced reduction in binding affinity is primarily driven by the viscosity-induced decrease in the association rate (k+) and a competing excluded volume effect, as well as a concomitant increase in the dissociation rate (k-) of the ligand. Atomistic MD simulations highlight the key role of strong electrostatic forces between the G-tetrad and π-stacked ligand, along with long-lived water-mediated hydrogen-bond bridges, in stabilizing the ligand/GqDNA complex in the absence of crowders. However, in the presence of EG/PEG crowders, the ligand binding mode is disrupted by hydrogen-bond interactions of the crowders with the ligand, causing rotation of the ligand's molecular plane relative to the G-tetrad. This disruption weakens the π-stacking electrostatic forces between the ligand and the G-tetrad and breaks the long-lived water-mediated hydrogen-bond bridges between the ligand and GqDNA, destabilizing the ligand/GqDNA complex. The current investigation underscores the prominent role of hydrogen-bond interactions of EG/PEG crowders, along with other factors, in affecting the stability of the ligand/GqDNA interaction in a crowded milieu.

Synergistic Chloroform-Methanol Binary Solvent Mixture Is Inherently Spatially and Dynamically Heterogeneous

Nonideality in a binary solvent mixture is manifested through anomalies in various physical properties like viscosity, dielectric constant, polarity, freezing point, boiling point, and so forth. Sometimes, such anomalies become much more prominent, leading to a synergistic behavior, where the physical property of the mixture is way different from its bulk counterparts. Various alcohols/chlorinated methane binary solvent mixtures show such a synergistic behavior. The reason is attributed to the unique but diverse interactions present in the system. We speculated that these diverse interactions must manifest heterogeneity in such a binary solvent mixture. Using the improved methodology developed by our group, we investigate the presence of dynamic and spatial heterogeneity in the chloroform/methanol synergistic binary solvent mixture. To our delight, we found that our projection is accurate, and indeed, the chloroform/methanol binary solvent mixtures are heterogeneous. Two maxima for the synergistic behavior have been observed for the chloroform/methanol binary solvent mixture (at ∼0.45 and 0.75 mole fractions of methanol in chloroform) in the literature, where the extent of heterogeneity was also found to be the highest. The present study portrays the intriguing complexity of simple binary solvent mixtures, and the findings may provide valuable insights into solvent engineering for diverse applications like extraction/purification media, reaction media, polymer processing, nanomaterial synthesis, pollutant extraction, active ingredient delivery, biofuel production, and battery technology.

Mechanistic Insights into the c-MYC G-Quadruplex and Berberine Binding inside an Aqueous Two-Phase System Mimicking Biomolecular Condensates

We investigated the binding between the c-MYC G-quadruplex (GQ) and berberine chloride (BCl) in an aqueous two-phase system (ATPS) with 12.3 wt % polyethylene glycol and 5.6 wt % dextran, mimicking the highly crowded intracellular biomolecular condensates formed via liquid-liquid phase separation. We found that in the ATPS, complex formation is significantly altered, leading to an increase in affinity and a change in the stoichiometry of the complex with respect to neat buffer conditions. Thermodynamic studies reveal that binding becomes more thermodynamically favorable in the ATPS due to entropic effects, as the strong excluded volume effect inside ATPS droplets reduces the entropic penalty associated with binding. Finally, the binding affinity of BCl for the c-MYC GQ is higher than those for other DNA structures, indicating potential specific interactions. Overall, these findings will be helpful in the design of potential drugs targeting the c-MYC GQ structures in cancer-related biocondensates.

Effect of molecular crowders on ligand binding kinetics with G-quadruplex DNA probed by fluorescence correlation spectroscopy

Guanine-rich single-stranded DNA folds into G-quadruplex DNA (GqDNA) structures, which play crucial roles in various biological processes. These structures are also promising targets for ligands, potentially inducing antitumor effects. While thermodynamic parameters of ligand/DNA interactions are well-studied, the kinetics of ligand interaction with GqDNA, particularly in cell-like crowded environments, remain less explored. In this study, we investigate the impact of molecular crowding agents (glucose, sucrose, and ficoll 70) at physiologically relevant concentrations (20% w/v) on the association and dissociation rates of the benzophenoxazine-core based ligand, cresyl violet (CV), with human telomeric antiparallel-GqDNA. We utilized fluorescence correlation spectroscopy (FCS) along with other techniques. Our findings reveal that crowding agents decrease the binding affinity of CV to GqDNA, with the most significant effect-a nearly three-fold decrease-observed with ficoll 70. FCS measurements indicate that this decrease is primarily due to a viscosity-induced slowdown of ligand association in the crowded environment. Interestingly, dissociation rates remain largely unaffected by smaller crowders, with only small effect observed in presence of ficoll 70 due to direct but weak interaction between the ligand and ficoll. These results along with previously reported data provide valuable insights into ligand/GqDNA interactions in cellular contexts, suggesting a conserved mechanism of saccharide crowder influence, regardless of variations in GqDNA structure and ligand binding mode. This underscores the importance of considering crowding effects in the design and development of GqDNA-targeted drugs for potential cancer treatment.

Towards Computational Modeling of Ligand Binding to the ILPR G-Quadruplex

Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area.

Fluorescence monitoring of binding of a Zn (II) complex of a Schiff base with human serum albumin

Zn (II) complexes of Schiff bases have potential applications in biomedical sciences as imaging agents, cancer therapeutics and diagnostics. Thus, it is important to understand their interaction with carrier proteins, like serum albumins. The present paper focuses on the binding interactions between Human serum albumin (HSA) and Znsalampy, making use of fluorescence spectroscopic techniques at ensemble as well as at single molecular level. An idea about the binding constant is obtained from the quenching of the single Trp (Tryptophan) residue of HSA by Znsalampy. Fluorescence correlation spectroscopy (FCS) has also been used to monitor the protein-ligand binding. The location of Znsalampy in its complex with HSA is determined by competitive binding experiments and molecular docking calculations. The binding constant obtained from the Znsalampy-HSA interaction falls in the ideal range for biological applications and the location is found to be in the proximity of Sudlow's site I. The esterase activity of HSA is retained in the presence of the Znsalampy. Hence, it is concluded that this Znsalampy may be a potential probe and biomarker in biomedical applications.

Optimization of G-Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones)

G-quadruplexes (G4s), secondary structures adopted by guanine-rich DNA and RNA sequences, are implicated in numerous biological processes and have been suggested as potential drug targets. Accordingly, there is an increasing interest in developing high-throughput methods that allow the generation of congeneric series of G4-targeting molecules ("ligands") and investigating their interactions with the targets. We have developed an operationally simple method of parallel synthesis to generate "ready-to-screen" libraries of cationic acylhydrazones, a motif that we have previously identified as a promising scaffold for potent, biologically active G4 ligands. Combined with well-established screening techniques, such as fluorescence melting, this method enables the rapid synthesis and screening of combinatorial libraries of potential G4 ligands. Following this protocol, we synthesized a combinatorial library of 90 bis(acylhydrazones) and screened it against five different nucleic acid structures. This way, we were able to analyze the structure-activity relationships within this series of G4 ligands, and identified three novel promising ligands whose interactions with G4-DNAs of different topologies were studied in detail by a combination of several biophysical techniques, including native mass spectrometry, and molecular modeling.