Binding Constants Research Articles

Competitive Interaction of the SGFRKMAF Peptide with 3CLpro Dimerization Intermediates: A Brownian Dynamics Investigation.

The SGFRKMAF peptide is known to inhibit the dimerization of 3CLpro monomers, which is essential for SARS-CoV-2 replication. The mechanism behind this, however, is largely unknown. In this work, we used Brownian dynamics simulations to compare and contrast 3CLpro monomer-monomer interactions and 3CLpro monomer-SGFRKMAF peptide interactions. We found that formation of the 3CLpro wild-type dimer could potentially involve formation of three intermediates that are primarily stabilized by G11-G124, S1-S301, and T118-G278 interactions. Analysis of 3CLpro monomer interaction with the SGFRKMAF peptide, however, revealed the presence of eight basins of interactions where the peptide assumes the highest local densities at the 3CLPro monomer surface. The second highest-density basin was found to coincide with the interface region of the wild-type 3CLpro dimer, thereby directly blocking the 3CLpro dimer-dimer interactions. The other basins, however, were found to lie far from the interface region. Notably, we found that only 6% of the BD trajectories end up directly into the basin at the interface region and ∼39% of the trajectories end up into those basins lying away from the interface region, indicating a greater role for peptide binding at sites away from the dimer interface region. Importantly, the locations of the basins lying away from the interface were found to coincide with the 3CLpro residues involved in stabilization of the 3CLpro monomer-monomer intermediates. Given that the rate constant of the peptide reaching the monomer surface was found to be almost an order of magnitude higher than the rate constant of monomer-monomer association, the SGFRKMAF peptide has the potential to inhibit dimerization of 3CLpro monomers not only through blocking the interface region but also through blocking the formation of the intermediates involved in the dimerization process. This could potentially open new avenues for 3CLpro dimerization inhibitors that transcend traditional X-ray-based discovery approaches.

Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.

Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.

Synthesis, spectral elucidation and DNA binding studies of cadmium(II) carboxylates with nitrogen donor heteroligands

A new series of novel homoleptic and heteroleptic Cd(II) complexes using cyclopropanecarboxylic acid (HL1) and cyclopentanecarboxylic acid (HL2) as main ligands and N-donor species like 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), and 2,9-dimethyl-1,10-phenanthroline (Me2phen) as co-ligands were prepared and characterized by FT-IR, multinuclear (1H and 13C) NMR, and UV–Visible spectroscopies. Furthermore, the crystal structure of the Cd(II) complex coordinated by cyclopentanecarboxylic acid (HL2) and 1,10-phenanthroline (phen) was explored by single crystal X-ray diffraction (SC-XRD) analysis. The crystal structure was binuclear, in which the coordination geometry around each cadmium center was distorted pentagonal bipyramidal coordination geometry. Various intermolecular interactions were accountable for stabilizing the supramolecular associations, which were seen by Hirshfeld surface analysis in terms of interatomic contacts. The spectroanalytical data of the synthesized complexes confirm the absence of the –OH band in the spectra of complexes as compared to the spectra of the free ligands, which favour the formation of complexes. The nature of complex-DNA interaction and the effect of the coordination of heteroligands on the binding strength of complexes were probed through UV–Visible spectroscopy and cyclic voltammetry. The obtained data confirm that the interaction of DNA with the complexes is dual: intercalation as well as groove binding. The DNA binding constants (Kb) and Gibb’s free energy changes (ΔG) were also determined for these complexes. This study aims to project effective drugs with the least harmful effects that could be useful for mankind against dreadful diseases.

Tetraphenylborate enhanced enzymatic production of γ-cyclodextrin: System construction and its mechanism

γ-Cyclodextrin (γ-CD) is an attractive material among the natural cyclodextrins owing to its excellent properties. γ-CD is primarily produced from starch by γ-cyclodextrin glycosyltransferase (γ-CGTase) in a controlled system. However, difficulty in separation and low conversion rate leads to high production costs for γ-CD. In this study, γ-CGTase from Bacillus sp. G-825-6 STB17 was used in γ-CD production from cassava starch. With the introduction of sodium tetraphenylborate (NaBPh4), the total conversion rate was promoted from an initial 18.07 % to 50.49 % and the γ-CD ratio reached 78.81 % with a yield of 39.79 g/L. Furthermore, the mechanism was conducted via the determination of binding constant, which indicated that γ-CD exhibited much stronger binding strength with NaBPh4 than β-CD. The reformation of water molecules and the chaotropic effect might be the main driving forces for the interaction. Additionally, the conformations of CD complexes were depicted by NMR and molecular docking. The results further verified different binding patterns between CDs and tetraphenylborate ions, which might be the primary reason for the specific binding. This system not only guides γ-CD production with an efficient and easy-to-remove production aid but also offers a new perspective on the selection of complexing agents in CD production.

Detection of intrinsically disordered peptides by biological nanopore.

Intrinsically disordered protein regions (IDPRs) are pivotal in the regulation of transcription and the facilitation of signal transduction. Because of their multiple conformational states of structure, characterizing the highly flexible structures of IDPRs becomes challenging. Herein, we employed the wild-type (WT) aerolysin nanopore as a real-time biosensor for the identification and monitoring of long peptides containing IDPRs. This sensor successfully identified three intrinsically disordered peptides, with the lengths up to 43 amino acids, by leveraging the unique signatures of blockade current and translocation duration time. The analysis of the binding constant revealed that interactions between the nanopore and peptide are critical for peptide translocation, suggesting that mechanisms beyond mere volume exclusion are at play. Furthermore, by examining the detailed current traces of blockade events, we were able to compare the conformational stabilities of various IDPRs. Our approach can detect the conformational changes of IDPR in a confined nanopore space. These insights broaden the understanding of peptide structural changes under the confined space. This nanopore biosensor showed the potential to study the conformations change of IDPRs, IDPRs transmembrane interactions, and protein drug discovery.

Influence of millimeter range electromagnetic waves on bovine serum albumin interaction with acridine orange

ABSTRACT The effect of non-ionizing millimeter range electromagnetic waves (MM EMW) (30–300 GHz) on the bovine serum albumin (BSA) interaction peculiarities with acridine orange (AO) has been studied in vitro. The frequencies 41.8 and 50.3 GHz were chosen, since the first one is nonresonant frequency for the water, while the second one is resonant for water. The binding constant and number of binding sites were calculated at both irradiation presence and absence. AO was revealed to bind to BSA, while after the protein irradiation the interaction force strengthens. However, it was also shown that there are differences of the interaction parameters while irradiating by 41.8 or 50.3 GHz. AO binds to BSA, irradiated by MM EMW with the frequency 41.8 GHz much more weaker, than to that, irradiated by MM EMW with the frequency 50.3 GHz.

Steady State and Time-Resolved Fluorescence Spectroscopy of Cinchonine Dication in Sodium Dodecylsulphate Micellar System.

This paper reports the influence of surface charge of the micelles on to the photophysical properties of a cinchonine dication (C2+) fluorophore in anionic, sodium dodecylsulphate (SDS), surfactant at premicellar, micellar and post-micellar concentrations in aqueous phase at room temperature. The magnitude of edge excitation red shift (EERS) in the fluorescence maximum of C2+ in bulk water solution is 1897cm- 1 whereas, in the case of SDS it is observed to be 1984cm- 1. The fluorescence decay curve of C2+ fits with multi exponential functions in the micellar system. The increase in lifetime of C2+ in SDS has been attributed to the increase in radiative rate due to the incorporation of C2+ at the micelle -water interface. The value of dynamic quenching constant determined is 16.9 M- 1. The location of the probe molecule in micellar systems has been justified by a variety of spectral parameters such as dielectric constant, ET (30), viscosity, EERS, average fluorescence decay time, radiative and non-radiative rate constants. All experimental results suggest that the C2+ molecule binds strongly with the SDS micelles and resides at micellar-water interface. The binding constant (Kb) calculated (3.85 × 105 M- 1) for C2+ in SDS revealed that the electrostatic forces mediate charge probe-micelle association.

A 1,8-Naphthalimide-based Tripodal Fluorescent Chemosensor to Selectively Detect Copper Ions.

A 1,8-naphthalimide-based tripodal fluorescent ligand (L3) was synthesized through the copper (I) catalyzed Huisgen azide-alkyne cycloaddition reaction of 2-(2-azidoethyl)-6-morpholino-1H-benzo[de]isoquinoline-1,3(2H)-dione with triproparagylamine. Naphthalimide acts as the fluorophore while the triazole and amine nitrogens chelate the metal ion. L3 showed a selective fluorescence turn-off for Cu(II) over other metal ions in aqueous acetonitrile solution. A Job's plot, Benesi-Hildbrand plot and high-resolution mass spectrometry data confirm a 1:1 binding stoichiometry with a binding constant of 7.8 х105 M- 1 while addition of disodium EDTA demonstrates its reversibility. The structure and stability of the complex was supported by theoretical calculations. The limit of detection for Cu(II) was calculated to be 0.3 µM which is considerably lower than WHO recommended Cu(II) limit in drinking water.

Thiazole-based metalloligands and their heteroleptic MOFs: Chromogenic and fluorometric detection of tryptophan and Z-l-phenylalanine using Cu(II)-complex and Cu(II)-Zn(II) MOF

Two thiazole-containing metalloligands based on the Cu(II) (P1) and Zn(II) (P2) comprising 2-(2-Pyridyl)-4-methylthiazole-5-carboxylic acid (HL1) and their extended heteroleptic metal-organic frameworks (MOFs) (CP1-CP2) have been prepared and further explored toward sensing. These compounds have been characterized through various spectro-analytical techniques, including elemental analysis, FT-IR, ESI-MS, SEM with EDX, PXRD, TGA, DSC/DTG, UV/vis and fluorescence spectroscopy. Structure of P1 has been confirmed by X-ray single crystal analysis. These compounds have been examined as chromogenic and fluorescent probes toward a series of amino acids wherein, P1 and CP1 showed highly selective chromogenic changes and fluorescence enhancement with Z-l-phenylalanine, respectively in aqueous-DMSO media. Notably, the association constant and detection limit were determined to be 2.25 × 105 M−1, 7.0 × 105 M−1 and 5.88 ppb, 0.39 ppb, respectively. Job's plot analysis, MALDI-TOF mass spectrometry and HRMS studies suggested the plausible interaction/ binding of Z-l-phenylalanine with P1 and CP1.

Prediction of the binding interactions between rosmarinic acid and cysteinyl leukotriene receptor type 1 by molecular docking and immobilized receptor chromatography.

Drug-protein interaction analysis is still at the center of research efforts to illustrate binding mechanisms and provide valuable information for selecting drug candidates with ideal properties in the early drug discovery stage. We present the prediction of the binding of rosmarinic acid (RA) to cysteinyl leukotriene receptor type1 (CysLTR1) by molecular docking. According to our findings, CysLTR1 is a potential anti-inflammatory target of RA. Under this assumption, we prepared the immobilized CysLTR1 column via a one-step method and characterized the immobilized CysLTR1 by fluorescent and chromatographic analyses. Furthermore, we used the immobilized CysLTR1 column to evaluate the binding interactions between RA and the immobilized receptor. Molecular docking showed that Tyr 249, Phe 174, Thr 280, Pro 177, and Thr 100 are the main sites for RA to interact with CysLTR1. The main forces that drive the findings are hydrogen bonds and hydrophobic interactions. Characterization results show that CysLTR1 is successfully immobilized with high specificity and stability. Almost no non-specific binding is observed on the immobilized CysLTR1 gels. The association constant and the binding sites are calculated to be 7.268 × 105 L mol-1 and 1.237 × 10-8 mol L-1 by injection amount-dependent method. These results, taken together, confirm the potential target of RA on the anti-inflammatory effect. We believe that it can provide valuable reference information on the in-depth exploration of drug-protein interaction mechanisms, and lead compound screening by this method.

Effect of non-covalent binding of tannins to sodium caseinate on the stability of high-internal-phase fish oil emulsions

In this study, we designed the noncovalent binding of sodium caseinate (SC) to tannic acid (TA) to stabilize high internal phase emulsions (HIPEs) used as fish oil delivery systems. Hydrogen bonding was the dominant binding force, followed by weak hydrophobic interaction and weak van der Waals forces, as demonstrated by FTIR, fluorescence spectroscopy, and molecular docking experiments, with a binding constant of 3.25 × 106, a binding site of 1.2, and a static quenching of the binding. Increasing SC:TA from SC to 2:1 decreased the particle size from 107.37 ± 10.66 to 76.07 ± 2.77 nm and the zeta potential from −6.99 ± 2.71 to −22 ± 2.42 mV. TA increased the interfacial tension of SC, decreased the surface hydrophobicity from 1.3 × 104 to 1.6 × 103 and improved the oxidation resistance of SC. The particle size of high internal phase emulsions stabilized by complexes with different mass ratios (SC:TA from 1:0 to 2:1) increased from 4.9 ± 0.02 to 12.9 μm, the potential increased from −32.37 ± 2.7 to −35.07 ± 2.58 mV, and the instability index decreased from 0.75 to 0.02. Thicker interfacial layers could be observed by laser confocal microscopy, and an increase in the storage modulus indicated a formation of a stronger gel network. SC:TA of 1:0 showed emulsion breakage after 14 d of storage at room temperature. SC:TA of 2:1 showed the lowest degree of oil-water separation after freeze-thaw treatment. Especially, the most stable high endo-phase emulsion (at SC:TA of 2:1) prepared at each mass ratio was selected for further stability exploration. The emulsion particle size increased only from 15.63 ± 0.06 to 22.27 ± 0.35 μm at salt ion concentrations of 50–200 mM and to 249.33 ± 31.79 μm at 300 mM. The instability index and storage modulus of the high endo-phase emulsions increased gradually with increasing salt ion concentrations. At different heating temperatures (55–85 °C), the instability index of the high internal phase emulsion gradually decreased and the storage modulus gradually increased. Meanwhile, at 50 °C for 15 d of accelerated oxidation, the content of hydroperoxide decreased from 53.32 ± 0.18 to 37.48 ± 0.77 nmol/g, about 29.7 %, and the thiobarbituric acid value decreased from 1.06 × 103 to 0.8 × 103, about 24.5 %, in the high endo-phase emulsions prepared by 2:1 SC:TA compared to the fish oils, and the SC-stabilized high endo-phase only emulsion broke at the sixth day of oxidation. From the above findings, it was concluded that the high internal phase emulsion prepared with SC:TA of 2:1 can be used as a good delivery system for fish oil.

Biophysical studies of human serum albumin with cocaine and cocaethylene: Understanding the drug-protein interaction in simulated physiological conditions

In this study, HSA was used as a transport protein model to simulate the transport dynamics and availability of cocaine (COC) and its pharmacologically active metabolite, cocaethylene (CE). In the interaction studies between the alkaloids and HSA, the binding constant (Kb) values were higher for CE (2.92 to 8.33 × 104 M−1) than COC (1.15 to 3.77 × 104 M−1) at different temperatures. Thermodynamic parameter calculations indicate that COC preferentially interacts through van der Waals forces and hydrogen bonds, while CE interacts hydrophobically. Competition studies using the ANS probe confirmed the more hydrophobic characteristics of CE. Synchronized fluorescence indicated that both compounds preferentially interact in the microregion of the Trp214 residue. Based on 3D fluorescence, UV–vis, and circular dichroic results, changes in the secondary structure of the protein were confirmed. Studies to assess the HSA binding site were carried out using warfarin (site I), diazepam (site II), and digitoxin (subdomain IIIB) as markers, and it was verified that both compounds interact preferentially at the site I. Finally, based on the 1H NMR and theoretical studies, it was possible to propose the alkaloid epitope in the interaction with HSA. In conclusion, when compared to COC, CE presented greater HSA protein affinity, justifying its longer plasma lifetime and increasing the drug’s effects on the body.

Developing a novel ultraselective and ultrasensitive label-free direct spectrofluorimetric nanobiosensor for direct highly fast field detection of explosive triacetone triperoxide

BackgroundDirect detection of the notorious explosive triacetone triperoxide (TATP) is very difficult because it lacks facile ionization and UV absorbance or fluorescence. Besides, the current indirect methods are time-consuming and need a pre-step for TATP cleavage to hydrogen peroxide. Moreover, they commonly show significant false-positive results in the presence of some camouflage which limits their field applications. Herein, for the first time, a novel label-free field-applicable spectrofluorimetric nanobiosensor was developed for direct TATP detection using a novel activated-protein protected gold nanocluster (ABSA-AuNCs; QY = 28.3 %) synthesized by a combined protein-assisted-ultrasonication procedure. ResultsThe ABSA-AuNCs revealed a fluorescence spectrum centered at 330.0 nm which was significantly quenched by TATP (binding constant = 154.06 M-1; ΔG = −12.5 kJ mol−1; E(%) = 88.5 %). This phenomenon was used as a basis for direct TATP quantification, providing a working range of 0.01–40.0 mg L−1 and a detection limit of 6.7 μg L−1 which is the lowest LOD provided for TATP detection up to now. A %RSD of 0.9 % and 1.56 % was obtained for repeatability and inter-day reproducibility, respectively. The selectivity was checked against a variety of camouflages, revealing ultra-selectivity. Several synthetic samples prepared by several camouflages and real samples (clay soil and real water media) were analyzed, revealing quantitative recoveries of TATP. SignificanceDuring the production of the notorious explosive TATP, it can be discharged into water and soil. This novel method eliminated the false-positive results of traditional methods and is applicable for direct quantitative detection of camouflaged TATP and its residues in real soil and water samples in a highly short response time (2 min). The camouflaged TATP analysis is important for tracking the terrorist attacks in field conditions and analysis of soil and water can provide a first indication of the location of the production site.

Pyrrole-based acyclic hexapodal aldehyde for anion recognition

A novel acyclic hexapodal host (4a) featuring with multiple formyl groups, pyrrole cores, and ester linkages has been prepared and characterized through 1H NMR, 13C NMR, high-resolution mass spectrometry and single-crystal X-ray diffraction techniques. This versatile host molecule exhibits robust anion recognition for CN−, F−, SO42−, HSO4−, H2PO4−, and HP2O73− with the binding constants spanning 0.18 × 105 M−1 to 7.72 × 105 M−1. Interactions with these anions were elucidated through UV–visible and 1H NMR titrations, complemented by DFT calculations. At low guest concentrations (5- to 100-fold excess), a 1:1 complexation is predominant. However, at high concentrations (1000-fold excess), the host's flexibility promotes the assembly of other host-guest complexes. Comparative studies with related pyrrole-based hexapodal ester 4b and tetrapodal aldehyde 4c highlight the importance of peripheral formyl groups, pyrrolic NH groups, the number of pendant arms, and conformational adaptability in anion recognition. These insights underscore the potential of acyclic multipodal hosts in advancing supramolecular chemistry and anion recognition.

The Delayed Box: Biphenyl Bisimide Cyclophane, a Supramolecular Nano-environment for the Efficient Generation of Delayed Fluorescence.

Activating delayed fluorescence emission in a dilute solution via a non-covalent approach is a formidable challenge. In this report, we propose a strategy for efficient delayed fluorescence generation in dilute solution using a non-covalent approach via supramolecularly engineered cyclophane-based nanoenvironments that provide sufficient binding strength to π-conjugated guests and that can stabilize triplet excitons by reducing vibrational dissipation and lowering the singlet-triplet energy gap for efficient delayed fluorescence emission. Toward this goal, a novel biphenyl bisimide-derived cyclophane is introduced as an electron-deficient and efficient triplet-generating host. Upon encapsulation of various carbazole-derived guests inside the nanocavity of this cyclophane, emissive charge transfer (CT) states close to the triplet energy level of the biphenyl bisimide are generated. The experimental results of host-guest studies manifest high association constants up to 104 M-1 as the prerequisite for inclusion complex formation, the generation of emissive CT states, and triplet-state stabilization in a diluted solution state. By means of different carbazole guest molecules, we could realize tunable delayed fluorescence emission in this carbazole-encapsulated biphenyl bisimide cyclophane in methylcyclohexane/carbon tetrachloride solutions with a quantum yield (QY) of up to 15.6%. Crystal structure analyses and solid-state photophysical studies validate the conclusions from our solution studies and provide insights into the delayed fluorescence emission mechanism.

Pyranine Interaction with Amines in Micelles.

The fluorescence behavior of pyranine in anionic micellar system of sodium dodecyl sulphate was studied in the presence of selected amines. The amines included cyclopropylamine (CPA), ethylenediamine (EDA), benzylamine (BA), dibutylamine (DBA), cyclohexylamine (CHA), and polyethylenediamine (PEDA). All the studied amines quenched the intensity of pyranine. Study was performed in 0.05M and 0.1M SDS. The thermodynamic parameters were determined in order to understand the quenching of pyranine by the studied amines. Change in Gibbs free energy and quenching was found higher in 0.05M SDS concentration and was found lower when SDS concentration was increased to 0.1M SDS. Pyranine quenching by the amines studied were treated with an extended Stern-Volmer equation that produced the Stern-Volmer constant ([Formula: see text]). Binding constant (Kb), number of binding stoichiometry (n) and Gibbs free energy change (ΔGbinding) were found higher for lower surfactant concentration as compare to higher surfactant concentration. More negative (-ve) the Gibbs free energies more will be the quenching, higher will be the sensitivity and vice versa. The Gibbs free energies for all the studied amines were found in the order as cyclopropylamine > ethylenediamine > benzylamine > dibutylamine > cyclohexylamine > polyethylenediamine. Fluorescence quenching of pyranine by amines in aqueous SDS is reproducible and is useful for the determination of amines in environmental samples.

A Julolidine Aldehyde Dansyl Hydrazine Schiff Base as Fluorescence Chemosensor for Zn2+ ions Recognition and its Application.

The Schiff base fluorescent probe (Dz-Jul), containing julolidine aldehyde and dansyl hydrazine, was derived using a simple condensation. This chemosensor showed high selectivity towards Zn2+ and quick response (170s) in DMSO/H2O solutions (8/2, v/v, pH 7.2 buffer). A fluorometric titration determined that Dz-Jul-Zn2+ has a binding ratio of 1:1, and the association constant (Ka) is 1.03 × 105M-1. The Dz-Jul detection limit of Zn2+ ions was 15nM, much lower than the WHO standard (76.0nM). DFT, ESI mass, and FTIR spectral demonstrated a plausible complexation mode between Dz-Jul and Zn2+ ions. In actual water samples, Zn2+ has been detected with good detection performance using Dz-Jul. Additionally, Dz-Jul-coated test strips allowed for rapid and qualitative monitoring of Zn2+ ions in a visible manner.

DMNP as an Effective Cage for Ln3+: A Spectroscopic and Thermodynamic Study.

Dimethoxynitrophenyl-EDTA (DMNP) is a popular calcium cage that is frequently used to investigate the role of Ca2+ in signaling processes in vivo. Lanthanides have been used in Ca2+ biomimetics due to similarities in coordination properties of Ln3+ and Ca2+ that may enable fluorescence and NMR studies of functional and structural properties of Ca2+ binding proteins. In this study, we show that Tb3+, Eu3+, and Nd3+ bind strongly to DMNP in a 1:1 ratio. Isothermal titration calorimetric measurements of Ca2+ displacement by Ln3+ in DMNP provide the equilibrium binding constants for Ln3+DMNP complexation with association constants, K11 = (1.2 ± 0.7) × 1012 M-1 for Eu3+, (2.5 ± 1.7) × 1012 M-1 for Nd3+, and (2.8 ± 0.8) × 1012 M-1 for Tb3+. The kinetics and thermodynamics of Ca2+, Mg2+, and Tb3+ release from DMNP were characterized using photothermal beam deflection (PBD). Ligand release from the DMNP cage was rapid and occurred within 10 μs upon cage photofragmentation and was associated with similar reaction volume and enthalpy changes that can be attributed to the photoreleased ion solvation. In the case of Ca2+DMNP photodissociation at subsaturating Ca2+ concentrations, we observed a slower phase with a lifetime of 300 μs that we attribute to Ca2+ rebinding to unphotolyzed DMNP. These results demonstrate that DMNP can serve as an effective photolabile cage for oxophilic Ln3+ that has similar coordination properties to Ca2+ and Mg2+.

Multispectroscopic and Theoretical Investigation on the Binding Interaction of a Neurodegenerative Drug, Lobeline with Human Serum Albumin: Perturbation in Protein Conformation and Hydrophobic-Hydrophilic Surface.

Lobeline (LOB), a naturally occurring alkaloid, has a broad spectrum of pharmacological activities and therapeutic potential, including applications in central nervous system disorders, drug misuse, multidrug resistance, smoking cessation, depression, and epilepsy. LOB represents a promising compound for developing treatments in various medical fields. However, despite extensive pharmacological profiling, the biophysical interaction between the LOB and proteins remains largely unexplored. In the current article, a range of complementary photophysical and cheminformatics methodologies were applied to study the interaction mechanism between LOB and the carrier protein HSA. Steady-state fluorescence and fluorescence lifetime experiments confirmed the static-quenching mechanisms in the HSA-LOB system. "K" (binding constant) of the HSA-LOB system was determined to be 105 M-1, with a single preferable binding site in HSA. The forces governing the HSA-LOB stable complex were analyzed by thermodynamic parameters and electrostatic contribution. The research also investigated how various metal ions affect complex binding. Site-specific binding studies depict Site I as probable binding in HSA by LOB. We conducted synchronous fluorescence, 3D fluorescence, and circular dichroism studies to explore the structural alteration occurring in the microenvironment of amino acids. To understand the robustness of the HSA-LOB complex, we used theoretical approaches, including molecular docking and MD simulations, and analyzed the principal component analysis and free energy landscape. These comprehensive studies of the structural features of biomolecules in ligand binding are of paramount importance for designing targeted drugs and delivery systems.

Structural analysis of peptide identified from the 2KRR domain of the nucleolin protein with a c-Myc G4 structure using biophysical and biochemical methods.

For the first time, the c-Myc G4 structure is reported to be stabilized by binding of the peptide (derived from the 2KRR domain of the nucleolin protein called the Nu peptide) in the loop region of the G-quadruplex structure by stacking interactions. CD results showed the formation of parallel G4 structure in the presence of 100 mM Na+ or 100 mM K+ with the appearance of two isodichroic points at 229 nm, 254 nm and 252 nm in the presence of 100 mM Na+ or 100 mM K+, respectively. In addition, in UV thermal and CD melting studies, we observed drastic changes with an increase in the hyperchromicity at a DNA : peptide ratio of 1 : 50. On titrating the Nu peptide with c-Myc G4, we calculated the value of binding constant (K a) by plotting fluorescence intensity and DNA concentration as 0.1369 ± 0.008 μM and 0.1277 ± 0.073 μM in Na+ and K+, respectively, which confirms the strong association of Nu peptide with c-Myc G4. The Nu peptide showed preferential cytotoxicity against MDA-MB-231 cells with IC50 values of 5.020 μM and 5.501 μM after 72 and 96 hours. This approach suggests a novel strategy to target G4 structure using natural key peptide segments derived from G4 stabilizing protein.