Probing the binding of anticancer drug topotecan with human hemoglobin: Structural and thermodynamic studies

Hemoglobin targeting potential of aminocarb pesticide: Investigation into dynamics, conformational stability, and energetics in solvent environment

Aminocarb (AMC), a carbamate pesticide, due to its prevalent usage exhibits increased accumulation in the environment affecting both insects and humans. It enters the human body via food grains and be transported through bloodstream. AMC's chemical structure, containing specific molecular frameworks and functional groups, enables it to bind with proteins like albumin and hemoglobin. Given that molecules with similar architecture are known to bind with hemoglobin, we aimed to explore Aminocarb's binding capability and the potential mechanism or mode of its interaction with hemoglobin. Hb being a tetramer with a profound interface between amino acid chains offers multiple binding sites. It is therefore important to investigate the structural aspects of binding of AMC by employing various spectroscopic and in-silico methods. The surface of the α1 chain near the α1β2 interface emerges as the preferred binding site for AMC, primarily due to its conformational restrictions. In its bound state, AMC tends to maintain a relaxed conformation, closely resembling its globally optimized geometry, and resides in close proximity to the α1 chain via multiple hydrophobic contacts and water bridge as observed in molecular dynamics (MD) simulations. Fluorescence quenching experiments showed moderate binding strength (7.7 × 10⁴ L M⁻1 at 288 K, 7.8 × 10⁴ L M⁻1 at 298 K, 7.9 × 10⁴ L M⁻1 at 308 K) and spontaneous binding, driven by hydrophobic and van der Waals interactions, as indicated by enthalpy (0.80-0.91 kJ mol⁻1), entropy (0.0970-0.0974 kJ mol⁻1), and Gibbs free energy (-27.13 to - 29.08 kJ mol⁻1). Circular dichroism experiments reveal no major structural changes in Hb. Quantum chemical calculations and MD simulations reveal conformation-dependent energy differences, enhancing our understanding of AMC's binding mechanism to Hb.

Probing the interaction of hesperidin showing antiproliferative activity in colorectal cancer cells and human hemoglobin

Hesperidin, a flavanone glycoside abundant in citrus is known to possess anti-carcinogenic properties. However, its main interaction with cancer cells and blood proteins is not well-studied yet. Here we have explored the interactions of hesperidin with human colorectal cancer cells, HCT116, and human hemoglobin (HHb) with several experimental and theoretical studies. Cellular assays showed that hesperidin interacted with colorectal cancer cells and induced membrane damage, colony formation inhibition, oxidative stress, mitochondrial dysfunction, Bax/Bcl-2, caspase-9, and caspase-3 upregulation, and cytochrome c release determined by cellular, qPCR and ELISA assays. The interaction of the hesperidin with HHb indicated the formation of a static complex mainly with the assistance of hydrogen bonds which lead to partial folding of protein determined by spectroscopy, molecular docking, and molecular dynamic studies. In conclusion, these findings show that hesperidin with potential binding affinity with a plasma protein model can also show promising anticancer activities against colorectal cancer cells.

New insights on the binding of butyl-paraben to trypsin: experimental and computational approaches

Butyl-paraben (BP) is one of the most widely used preservatives in numerous foodstuffs, skin care products, and a variety of drugs, and trypsin is the main digestive enzyme, the research on the binding between the two is essential for human health. In the present paper, the effect of BP on trypsin has been explored using experimental and computational techniques to evaluate BP toxicity at the protein level. The obtained results from molecular docking and kinetic assay revealed BP was embedded in the hydrophobic cavity-S1 binding pocket of the enzyme to inhibit its activity by a competitive model. Intrinsic fluorescence of trypsin after interaction with BP revealed the static mode of quenching. FRET indicated that the distance of the enzyme to BP is 1.89 nm with high energy efficiency. Thermodynamic results proved that BP spontaneously bound to trypsin in an enthalpy-driven manner, the van der Waals interactions and H-bonds serving as the predominant forces in binding processes. CD spectroscopy and molecular dynamics (MD) simulation revealed that the trypsin structure transformed from the β-Sheet structure to the unordered Coil structure upon interacting with BP. Resonance light scattering (RLS), synchronous fluorescence, and three-dimensional (3 D) spectroscopies further supported the alteration in the conformation of trypsin. Differential scanning calorimetry (DSC) showed that trypsin was somewhat destabilized in the presence of BP. Accordingly, all of the experimental data were confirmed by MD simulation.Communicated by Ramaswamy H. Sarma.

Comparative analysis of cobalt ferrite and iron oxide nanoparticles using bimodal hyperthermia, along with physical and in silico interaction with human hemoglobin

Magnetic nanoparticles (MNPs) have captivated the scientific community towards biomedical applications owing to their numerous distinctive physio-chemical properties. In this work, cobalt ferrite (CFNPs) and iron oxide nanoparticles (IONPs) were synthesized using the thermal decomposition method and then functionalized with polyacrylic acid (PAA) for aqueous dispersion. Associated techniques, namely TEM, FESEM, DLS, XRD, and VSM, were used to characterize the synthesized nanoparticles. We also investigated the light-induced and magnetic-field-induced hyperthermia properties of the PAA-functionalized MNPs. It was found that the PAA-CFNPs show a high specific absorption rate (SAR) compared with the PAA-IONPs. Since blood plasma is essential for the delivery and targeting of drugs, studying biological interactions is crucial for effective therapeutic use. Therefore, we performed physical and in silico studies to probe into the mechanistic interaction of CFNPs and IONPs with human hemoglobin. From these studies, we inferred the successful binding between the nanoparticles and protein. Preliminary in vitro cytocompatibility and photothermal toxicity studies in breast cancer (MCF-7) cells treated with the nanoparticles revealed a low dark toxicity and significant laser-induced photothermal toxicity.

PROTEIN BINDING CHARACTERISTICS OF YOHIMBINE, A NATURAL INDOLE ALKALOID BASED DRUG FOR ERECTILE DYSFUNCTION

Even to this day, talking about sexual-dysfunctions largely remains a taboo. Hence less studies were recorded and fewer remedies given. Erectile dysfunction (ED) is one of the most commonly treated psychological disorders which leads to major distress, interpersonal limitation and reduces the quality of life & marriage. This study aimed to assess a plant-derived molecule, Yohimbine (Yoh, a β-carboline indole-alkaloid; often used for ED treatment) and its potential binding phenomenon with hemoglobin (Hb). Successful binding of the Yoh with Hb is evident from spectroscopic and molecular-docking results. Yoh quenched the fluorescence of Hb efficiently through static mode. The binding affinity was in the order of 10⁵ M^-1 with 1:1 stoichiometry. Thermodynamic analyses concluded that the protein-ligand association to be spontaneous and attributed by entropy-driven exothermic-binding. Non-polyelectrolytic factor was the core, dominating factor. The structural aspects have been deciphered through infra-red spectroscopy and computational-methods. The giant 3D-protein moiety was significantly perturbed through drug-binding. Hydrophobic forces and hydrogen bonding participation were stipulated by molecular modeling data. This study reveals the detailed interaction pattern and molecular mechanism of Hb-Yoh binding; correlating the structure-function relationship for the first time; therefore, holds enormous importance from the standpoint of rational and efficient drug-designing & development.

The discovery of berberine erythrocyte-hemoglobin self-assembly delivery system: a neglected carrier underlying its pharmacokinetics

Berberine (BBR) has extremely low concentration and high tissue distribution. However, current pharmacokinetic studies predominantly focus on its concentration in plasma, which could hardly make a comprehensive understanding of its pharmacokinetic process. This study made a pioneering endeavor to explore the erythrocyte-hemoglobin (Hb) self-assembly system of BBR by exploring the interaction of BBR with erythrocyte and the combination of BBR with Hb. Results showed that BBR had a low bioavailability (C₀ = 2.833 μg/mL via intravenous administration of 2.5 mg/kg BBR and C_max = 0.260 μg/mL via oral administration of 400 mg/kg BBR). Besides, BBR achieved higher concentrations in erythrocytes than plasma, and the erythrocytes count and Hb content were significantly decreased after intravenous administration. Hemolysis rate indicated the BBR-erythrocyte system (with 2% erythrocytes) was relatively stable without hemolysis at the concentration of 1.00 mg/mL. And the maximum percentage of drug loading was 100% when the BBR-erythrocyte concentration was 0.185 μg/mL. Furthermore, incubation of BBR and erythrocytes resulted in internalization of the erythrocyte membrane and the formation of intracellular vacuoles. The thermodynamic parameters indicated that the binding process of bovine hemoglobin (BHB) and BBR was spontaneous. UV-vis absorption spectra, synchronous fluorescence, circular dichroism and Raman spectra collectively indicated that BBR showed strong binding affinity toward BHB and affected the molecular environment of residues like tryptophan and tyrosine in BHB, resulting in the conformational changes of its secondary and tertiary structure. Molecular docking indicated BBR interacted with Arg-141 residue of BHB via hydrogen bond with the bond length of 2.55 Å. The ΔG value of the BHB-BBR system was −31.79 kJ/mol. Molecular dynamics simulation indicated the root mean square derivation of BBR-BHB was <0.025 nm, suggestive of stable conformation. Cumulatively, there was an erythrocyte-Hb self-assembled drug delivery system after oral or intravenous administration of BBR, which conceivably gained novel insight into the discrepancy between the extremely low plasma concentration and relatively high tissue concentration of BBR.

Conformational dynamics of myoglobin in the presence of vitamin B12: A spectroscopic and in silico investigation

Myoglobin is an essential transport protein of heart and muscle tissues that acts as a local oxygen reservoir and a marker in different diseased conditions. On the other hand, Vitamin B12 is a vital nutrient that helps synthesize red blood cells, DNA, and proteins. To understand the ability of vitamin B12 to bind to the excess of myoglobin produced in the body under certain conditions (muscle injuries, severe trauma, etc.), it is essential to dig into the interaction between them. Therefore, the present study reports the binding interaction of vitamin B12 and myoglobin employing different spectroscopic and computational methods. The myoglobin's intrinsic fluorescence is quenched by vitamin B12 via static nature as observed from steady-state as well as time-resolved fluorescence measurements. The microenvironment of myoglobin's tryptophan residue gets affected, but there is no change observed in its α-helical content by vitamin B12 as seen from synchronous fluorescence and circular dichroism measurements. The probable binding of vitamin B12 on myoglobin was elucidated through molecular docking, and the interaction stability was studied by molecular dynamics simulation. The determination of vitamin B12's affinity to myoglobin and its effect on the conformational transitions of myoglobin might afford valuable insight for clinical pharmacology.

Spectroscopic and computational insight into the conformational dynamics of hemoglobin in the presence of vitamin B12

Protein-ligand interactions play a significant role in all living organisms, thereby affecting the design and application of drugs and other biomaterials. The current study reports the binding of vitamin B12 to hemoglobin, employing optical spectroscopy and computational methods. It is observed that vitamin B12 quenched the intrinsic fluorescence of hemoglobin. The nature of quenching appears to be static according to the steady-state and time-resolved fluorescence measurements. The conformational changes of hemoglobin caused by vitamin B12 interactions were studied by synchronous fluorescence spectroscopy and protein secondary structure analyses. The synchronous fluorescence spectra indicate the tryptophan residue microenvironment change while no secondary structural change is observed from circular dichroism spectra and molecular dynamics (MD) simulation study. The computational molecular docking elucidated the probable binding of vitamin B12 at the active site of hemoglobin, whereas the stability of the hemoglobin-vitamin B12 complex was studied by MD simulation. The study might be helpful for the treatment of pernicious anemia, hereditary transcobalamin deficiency, and performance enhancement of elite athletes.

Ex vivo binding studies of the anti-cancer drug noscapine with human hemoglobin: a spectroscopic and molecular docking study

Noscapine binds human hemoglobin spontaneously forming a stable complex that affects noscapine's ADMET profile, bioavailability and toxicity.

Toxicity of thimerosal in biological systems: Conformational changes in human hemoglobin, decrease of oxygen binding capacity, increase of protein glycation and amyloid's formation

Thimerosal (TH), an organomercurial compound, is used as a preservative in vaccines and cosmetics. Its interaction with human hemoglobin (Hb) was investigated under physiological conditions using biophysical and biological assays, aiming to evaluate hazardous effects. TH interacts spontaneously with Hb (stoichiometry 2:1, ligand-protein), preferably by electrostatic forces, with a binding constant of 1.41 × 10⁶ M^-1. Spectroscopic data allows to proposing that TH induces structural changes in Hg, through ethylmercury transfer to human Hb-Cys93 residues, forming thiosalicylic acid, which, in turn, interacts with the positive side of the amino acid in the Hb-HgEt adduct chain. As a consequence, inhibition of Hb-O₂ binding capacity up to 72% (human Hb), and 50% (human erythrocytes), was verified. Dose-dependent induction of TH forming advanced glycation end products (AGE) and protein aggregates (amyloids) was additionally observed. Finally, these results highlight the toxic potential of the use of TH in biological systems, with a consequent risk to human health.

Pharmacophore Modeling, Synthesis, Scaffold Hopping and Biological β- Hematin Inhibition Interaction Studies for Anti-malaria Compounds

Backgound:

Exploring potent compounds is critical to generating multi-target drug discovery. Hematin crystallization is an important mechanism of malaria.

Methods:

A series of chloroquine analogues were designed using a repositioning approach to develop new anticancer compounds. Protein-ligand interaction fingerprints and ADMET descriptors were used to assess docking performance in virtual screenings to design chloroquine hybrid β-hematin inhibitors. A PLS algorithm was applied to correlate the molecular descriptors to IC50 values. The modeling presented excellent predictive power with correlation coefficients for calibration and cross-validation of r2 = 0.93 and q2 = 0.72. Using the model, a series of 4-aminoquinlin hybrids were synthesized and evaluated for their biological activity as an external test series. These compounds were evaluated for cytotoxic cell lines and β-hematin inhibition.

Results:

The target compounds exhibited high β-hematin inhibition activity and were 3-9 times more active than the positive control. Furthermore, all the compounds exhibited moderate to high cytotoxic activity. The most potent compound in the dataset was docked with hemoglobin and its pharmacophore features were generated. These features were used as input to the Pharmit server for screening of six databases.

Conclusion:

The compound with the best score from ChEMBL was 2016904, previously reported as a VEGFR-2 inhibitor. The 11 compounds selected presented the best Gold scores with drug-like properties and can be used for drug development.

A biophysical probe on the binding of 2-mercaptothioazoline to bovine hemoglobin

2-Mercaptothiazoline (MTZ) is broadly present in daily use as an antifungal reagent, a brightening agent, and a corrosion inhibitor. MTZ is potentially harmful for human health. Although the toxic effects of MTZ on experimental animals have been reported, the effects of MTZ on the proteins in the circulatory system at the molecular level have not been identified previously. Here, we explored the interaction of MTZ with bovine hemoglobin (BHb) in vitro using multiple spectroscopic techniques and molecular docking. In this study, the binding capacity, acting force, binding sites, molecular docking simulation, and conformational changes were investigated. MTZ quenched the intrinsic emission of BHb via the static quenching process and could spontaneously bind with BHb mainly through van der Waals forces and hydrogen bond. The computational docking visualized that MTZ bound to the β2 subunit of BHb, which further led to some changes of the skeleton and secondary structure of BHb. This research provides valuable information about the molecular mechanisms on BHb induced by MTZ and is beneficial for clarifying the toxicological actions of MTZ in blood.

Interaction of promethazine and adiphenine to human hemoglobin: A comparative spectroscopic and computational analysis

The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra. The UV-Vis spectroscopy suggested ground state complex formation. The activation energy (E_a) was observed more in the case of Hb-ADP than Hb-PMT interaction system. The FRET result indicates the high probability of energy transfer from β Trp37 residue of Hb to the PMT (r=2.02nm) and ADP (r=2.33nm). The thermodynamic data reveal that binding of PMT with Hb are exothermic in nature involving hydrogen bonding and van der Waal interaction whereas in the case of ADP hydrophobic forces play the major role and binding process is endothermic in nature. The CD results show that both PMT and ADP, induced secondary structural changes of Hb and unfold the protein by losing a large helical content while the effect is more pronounced with ADP. Additionally, we also utilized computational approaches for deep insight into the binding of these drugs with Hb and the results are well matched with our experimental results.