Binding of norharmane with RNA reveals two thermodynamically different binding modes with opposing heat capacity changes

Probing the nucleobase-specific binding interaction of hydroxychloroquine sulfate with RNA and subsequent sequestration by a water-soluble molecular basket

A thorough understanding of the binding interactions of small molecules with genetic materials of the cell (DNA/RNA) has a persistent importance in pharmaceutical industries for the development of new drugs for treating various life-threatening ailments. Hydroxychloroquine sulfate (HCQS), an antimalarial drug, was potentially used for clinical trials with the hope of treating patients suffering from SARS-CoV-2 during the COVID-19 pandemic. Herein, we have extensively delineated the binding interactions of HCQS with RNA under physiological conditions using multi-spectroscopic and calorimetric approaches. Our results demonstrated that HCQS binds to RNA through the groove-binding mode in uridine- and cytidine-rich regions. The mode of binding was meticulously characterized by fluorescence quenching studies and circular dichroism spectroscopy, well complemented by other experiments. Our results obtained from isothermal titration calorimetry reveal the phenomenon of the release of bound water molecules when HCQS binds at the groove position of RNA, the process being entropically driven. Furthermore, we have employed the concept of host-guest chemistry for the sequestration of RNA-bound HCQS using a water-soluble, non-toxic, 4-sulfocalix[4]arene as a basket-type macrocyclic host. This investigation may be conducive to the development of safe RNA-based therapeutics like RNA-based vaccines that comprise small molecule-RNA interactions.

Insights into interaction of quaternary ammonium salt cationic surfactants with different branched-chain lengths and DNA: Multi-spectral analysis, viscosity method, and gel electrophoresis

In this study, the interactions between three quaternary ammonium salt (QAS) cationic surfactants with different branched-chain lengths (TMBAC, TEBAC, and TBBAC) and DNA are investigated by UV-vis absorption, fluorescence and CD spectroscopy, viscosity method, and gel electrophoresis. Berberine hydrochloride (BR) is utilized as a fluorescent probe. The three interaction modes and strengths are compared. The effects of surfactant concentrations, ratio of DNA and BR, and ionic strength on the interaction are estimated. DNA conformational changes are explored. The results indicate that three surfactants can interact with DNA through electrostatic interaction rather than groove and intercalation binding. The interaction results in DNA double helix compression. Also, interaction strength is TBBAC-DNA > TEBAC-DNA > TMBAC-DNA due to different branched-chain lengths. Moreover, fluorescence quenching extent is more obvious at 10.0:1.0 molar ratio (DNA: BR). The fluorescence quenching of three surfactant-DNA-BR systems is static. Three binding models are equal, and three interaction processes are spontaneous. The binding force of TBBAC-DNA is electrostatic, while that of TMBAC-DNA and TEBAC-DNA is Van der Waals forces and hydrogen bonding. Besides, DNA conformation keeps the B-form. It is expected to offer insights into the interaction of QAS cationic surfactants with different branched-chain lengths and DNA.

Photophysical and thermodynamic landscape of interaction of a styryl-based dye with DNA duplex: effect of medium ionic strength and live cell imaging

A red-emitting excited-state intramolecular charge transfer pyridinium dye, [4-((1E,3E)-4-(4-(dimethylamino)phenyl)buta-1,3-dien-1-yl)-1-methylpyridin-1-ium] (DAPBMP), was synthesized and characterized using NMR and ESIMS studies. Binding interaction between dye DAPBMP and genomic DNA were investigated using steady-state and time-resolved spectroscopic methods. The thermodynamics of the interaction process were characterized using isothermal titration calorimetry (ITC) which reveals the key role of the hydrophobic effect and electrostatic interaction between the positive charged dye and the negatively charged polyphosphate of DNA backbone. The binding of dye to the minor groove of the DNA double helix is confirmed by circular dichroism spectroscopy and molecular docking simulation study. The binding interaction is found to be strongly dependent on the ionic strength of the medium as demonstrated by a systematic study in the presence of various concentrations of NaCl. A detailed calorimetric study shows that polyelectrolytic contribution, ΔGpe, (a measure of the role of electrostatic force) to the total free energy change (ΔG) of interaction progressively decreases with increasing ionic strength of the medium due to weakening of the DAPBMP:DNA binding by screening of the electrostatic charges. The fluorescence of DAPBMP exhibits a remarkable emission enhancement of almost 15 times when the viscosity of the water-propylene glycol system increases. Fluorescent microscopy was performed with C2C12 mouse skeletal myoblast and A549 lung cancer cells in the presence of DAPBMP dye. The dye passed through the C2C12 cell membrane and binds the negatively charged nucleic acids, essentially double-stranded DNA which made the nuclear puncta along with perinuclear located mitochondria.

Cyclodextrin Derivatives as Modulators for Enhanced Drug Delivery from Niosome Membrane: A Fluorescence Correlation Spectroscopy and Isothermal Titration Calorimetry Approach

Designing efficient drug delivery systems for optimum therapeutic outcomes and minimum adverse effects remains a pivotal focus in pharmaceutical research. Understanding the nature of interactions between drugs and drug carriers and the drug-release mechanism are the key aspects for the development of effective delivery systems. This work presents a detailed investigation into the intricate interactions between niosomes and the drug Phenosafranin (PSF), and the subsequent release induced by a variety of cyclodextrins (CDs) employing a multifaceted approach. Ensemble average spectroscopic and single molecular level investigations based on fluorescence correlation spectroscopy (FCS), are employed to explore the binding interactions of PSF with the niosome membrane. Subsequently, the release of the drug was studied by disrupting the niosome structure using various CDs, and their efficacy was accessed through steady-state and time-resolved photophysical responses. FCS experiments provided precise insights into the binding and drug release process at the single-molecule level through the variation in translational and diffusion characteristics of the drug. Additionally, isothermal titration calorimetric (ITC) investigations further revealed the thermodynamics governing the CD-niosome host:guest interactions and the varying potential of different CDs in disrupting the niosome to release the drug which were further validated by electron microscopy and confocal fluorescence microscopy analyses. A broader analysis of niosomes prepared with various nonionic surfactants highlighted the influence of cavitand size and structure on the interaction with different niosome constituents. This comprehensive analysis sheds light on the complex interplay of these components and their interactions, providing insights into drug delivery systems and their potential therapeutic applications.

Interaction between antidepressant drug trazodone with double-stranded DNA: Multi-spectroscopic and computational analysis

Trazodone (TZD) is an antidepressant drug used to treat major depressive and sleeping disorders. Elevated doses of trazodone are associated with central nervous system depression, which manifests as nausea, drowsiness, confusion, vertigo, exhaustion, etc. To develop a clinically viable active pharmaceutical compound with minimal adverse effects, it is imperative to possess a comprehensive knowledge of the drug's action mechanism on DNA. Hence, we investigate the mode of interaction between trazodone and DNA utilizing various spectroscopic and computational techniques. Studies using UV-vis titration showed that the DNA and trazodone have an effective interaction. The magnitude of the Stern-Volmer constant (KSV) has been calculated to be 5.84 × 106 M-1 by the Lehrer equation from a steady-state fluorescence study. UV-vis absorption, DNA melting, dye displacement, and circular dichroism studies suggested that trazodone binds with DNA in minor grooves. Molecular docking and molecular dynamic simulation demonstrated that the TZD-DNA system was stable, and the mode of binding was minor groove. Furthermore, ionic strength investigation demonstrates that DNA and trazodone do not have a substantial electrostatic binding interaction.

The role of hydrophobic interactions in the molten globule state of globular protein modulated by surfactants

In order to highlight the role of hydrophobic interactions in the molten globule (MG) state of globular protein modulated by surfactants, the interactions of bovine α-lactalbumin (α-LA) with alkyl trimethylammonium bromides (CnTAB, n = 10, 12, 14, and 16) have been studied by experimental and theoretical techniques. Isothermal titration calorimetry (ITC) showed that the enthalpy changes (ΔH) and area of the enthalpogram increased with increasing the chain length of CnTAB. The result of fluorescence, circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectrum suggested that C10TAB and C12TAB unfolded α-LA partially, C14TAB reconstructed protein with a native-like secondary structure content, and C16TAB induced an MG state α-LA. The SAXS results confirmed that the tertiary structure of α-LA was disrupted by C16TAB forming an MG state complex with a micelle-like structure even at the surfactants concentrations below CMC. As indicated by MD results, the β-domain and unstructured region(s) were involved in the MG state α-LA modulated by CnTAB. This work not only provides molecular insights into the role of hydrophobic interactions in the MG state of a globular protein but also helps understand the mechanism of preparing α-LA based biomacromolecule modulated by hydrophobic interactions.

Preferential Binding of Epirubicin Hydrochloride with Single Nucleotide Mismatched DNA and Subsequent Sequestration by a Mixed Micelle

Targeting mismatched base pairs containing DNA using small molecules and exploring the underlying mechanism involved during the binding interactions is one of the fundamental aspects of drug design. These molecules in turn are used in nucleic acid targeted therapeutics and cancer diagnosis. In this work, we systematically delineate the binding of the anticancer drug, epirubicin hydrochloride (EPR) with 20-mer duplex DNA, having both natural nucleobase pairing and thermodynamically least stable non-Watson-Crick base pairing. From the thermal denaturation studies, we observed that EPR can remarkably enhance the thermal stability of cytosine-cytosine (CC) and cytosine-thymine (CT) mismatched (MM) DNA over other 20-mer duplex DNA. From steady-state fluorescence spectroscopy and isothermal titration calorimetry studies, we concluded that EPR binds strongly with the mismatched duplex DNA through the intercalation binding mode. The interaction of EPR and duplex DNA has also been monitored at a single molecular resolution using fluorescence correlation spectroscopy (FCS). Dynamic quantitates such as diffusion coefficients and hydrodynamic radii obtained from an FCS study along with association and dissociation rate constants estimated from intensity time trace analyses further substantiate the stronger binding affinity of EPR to the thermally less stable mismatched DNA, formed by the most discriminating nucleobase (viz. cytosine). Additionally, we have shown that EPR can be sequestered from nucleic acids using a mixed micellar system of an anionic surfactant and a triblock copolymer. From thermal denaturation studies and circular dichroism spectroscopy, we found that the extent of drug sequestration depends on the binding affinity of EPR to the duplex DNA, and this mixed micellar system can be employed for the removal of excess drug in the case of a drug overdose.

Exploring the Nucleobase-Specific Hydrophobic Interaction of Cryptolepine Hydrate with RNA and Its Subsequent Sequestration

The study of the interactions of drug molecules with genetic materials plays a key role underlying the development of new drugs for many life-threatening diseases in pharmaceutical industries. Understanding their fundamental base-specific and/or groove-binding interaction is crucial to target the genetic material with an external drug, which can pave the way to curing diseases related to the genetic material. Here, we studied the interaction of cryptolepine hydrate (CRYP) with RNA under physiological conditions knowing the antimalarial and anticancer activities of the drug. Our experiments explicitly demonstrate that CRYP interacts with the guanine- and adenine-rich region within the RNA duplex. The pivotal role of the hydrophobic interaction governing the interaction is substantiated by temperature-dependent isothermal titration calorimetry experiments and spectroscopic studies. Circular dichroism study underpins a principally intercalative mode of binding of CRYP with RNA. This interaction is found to be drastically affected in the presence of magnesium salt, which has a strong propensity to coordinate with RNA nucleobases, which can in turn modulate the interaction of the drug with RNA. The temperature-dependent calorimetric results substantiate the occurrence of entropy-enthalpy compensation, which enabled us to rule out the possibility of groove binding of the drug with RNA. Furthermore, our results also show the application of host-guest chemistry in sequestering the RNA-bound drug, which is crucial to the development of safer therapeutic applications.

Structural Compactness in Hen Egg White Lysozyme Induced by Bisphenol S: A Spectroscopic and Molecular Dynamics Simulation Approach

The endocrine disrupting compound Bisphenol and its analogues are widely used in food packaging products and can cause serious health hazards. The protein, Lysozyme (Lyz), showing anti-microbial properties, is used as a "natural" food and dairy preservative. Herein, we explored the interaction between Lyz and Bisphenol S (BPS) by multi-spectroscopic and theoretical approaches. Lyz interacts with BPS through static quenching, where hydrophobic force governed the underlying interaction. Molecular docking results reveal that tryptophan plays a vital role in binding, corroborated well with near UV-CD studies. A decrease in the radius of gyration (from 1.43 nm to 1.35 nm) of Lyz substantiates the compactness of the protein conformation owing to such an interaction. This structural alteration experienced by Lyz may alter its functional properties as a food preservative. Consequently, this can degrade the quality of the food products and thereby lead to severe health issues.

Comparative binding analysis of noscapine and piperine with tRNA: A structural perturbation and energetic study

In this study, we have exploring the binding mechanisms of the two anticancer alkaloid noscapine (NOS) and piperine (PIP) with tRNA using different spectroscopy and computational method. Absorbance and emission spectra revealed that both the drugs show strong binding with tRNA, where NOS intercalate between the base pairs of tRNA and PIP binds in the groove of tRNA. Competitive binding study and steady state anisotropy further confirms the intercalative mode of binding between NOS and tRNA and groove binding in PIP-tRNA complex. The observed thermodynamic parameters suggested that NOS-tRNA complex formation is endothermic and entropy driven, however it was exothermic, and enthalpy driven in case of PIP-tRNA complex. CD and time resolved fluorescence studies show the structural perturbations and conformational change in tRNA structure with NOS as well as PIP. Molecular docking studies are comparable with experimental results and further confirmed that the hydrophobic interactions involved in the NOS-tRNA binding, whereas hydrogen binding and van der Waals interactions play important role in the PIP-tRNA complex formation. This study can be useful to understand the potential binding and resultant tRNA damage by alkaloids and deigned new target specific anticancer drug.

Contrasting Thermodynamics Governs the Interaction of 3-Hydroxyflavone with the N-Isoform and B-Isoform of Human Serum Albumin

Herein we report the interaction of 3-hydroxyflavone (3HF) with various isomeric forms of Human Serum Albumin (HSA), namely, the N-isoform (or native HSA at pH 7.4) and the B-isoform (at pH 9.2). Spectroscopic signatures of 3HF reveal that the interaction of 3HF with the N-isoform of HSA results in significant lowering of absorbance of the neutral species (λ_abs ∼ 345 nm) with concomitant increase of the anionic species (λ_abs ∼ 416 nm) whereas interaction with the B-isoform of HSA leads to selective enhancement of absorbance of the anionic species. The fluorescence profile of 3HF displays marked increase of intensity of the proton transferred tautomer (λ_em ∼ 538 nm) as well as the anionic species (λ_em ∼ 501 nm) for both the forms of the protein. However, analyses of the associated thermodynamics through temperature-dependent isothermal titration calorimetric (ITC) indicate that the interaction of 3HF with the N-isoform of HSA is more enthalpic in the lower temperature limit while the entropy contribution predominates in the higher temperature limit. Consequently, the 3HF-HSA (N-isoform at pH 7.4) interaction reveals an unusual thermodynamic signature of a positive heat capacity change (ΔC_p = 3.84 kJ mol^-1K^-1) suggesting the instrumental role of hydrophobic hydration. On the contrary, the 3HF-HSA (B-isoform at pH 9.2) interaction shows qualitatively reverse effect. Consequently, the interaction is found to be characterized by an enthalpy-dominated hydrophobic effect (negative heat capacity change, ΔC_p = -1.15 kJ mol^-1K^-1) which is rationalized on the basis of the nonclassical hydrophobic effect.