Multi-spectroscopic and molecular modeling studies of interaction between two different angiotensin I converting enzyme inhibitory peptides from gluten hydrolysate and human serum albumin

Interaction of organophosphate pesticide chlorpyrifos with alpha-2-macroglobulin: Biophysical and molecular docking approach

Organophosphate class of pesticides causes neurotoxicity and carcinogenicity in humans. Once inside the human body, these pesticides often interact with plasma proteins, such as alpha-2-macroglobulin (α₂M) which is the key anti-proteinase. Our work focuses on the structural and functional alteration of α₂M by chlorpyrifos (CPF), a member of organophosphates. We explored the binding interaction between alpha-2-macroglobulin and CPF by using UV absorption and fluorescence spectroscopy (steady state and synchronous), circular dichroism and molecular docking approach. The functional activity of α₂M was analyzed by anti-proteinase trypsin inhibitory assay which showed dose-dependent decrease in alpha-2-macroglobulin antiproteolytic potential. UV absorption studies and fluorescence quenching experiments suggested the formation of a complex between α₂M and CPF. The CD spectra suggested a reduction in the beta helical (β helix) content of α₂M. Analysis of thermodynamic parameters suggested the process is spontaneous and endothermic with the ΔG and ΔH values being -5.501 kJ/mol, 11.49 kJ/mol, respectively. CPF binds with Ile-1390, Pro-1391, Leu-1392, Lys-1393, Val-1396, Lys-1397, Arg-1407, Thr-1408, Glu-1409, Val-1410, Asp-282, Glu-281 of α₂M as suggested by molecular docking.

Exploring the binding mechanisms of inorganic magnetic nanocarrier containing L-Dopa with HSA protein utilizing multi spectroscopic techniques

In this study, the interaction of Fe₃O₄@CaAl-LDH@L-Dopa nanoparticles (NPs) with human serum albumin (HSA) was investigated in simulated physiological conditions applying UV-visible, fluorescence, and circular dichroism (CD) spectroscopic techniques. The consequences of UV-vis and CD spectroscopy demonstrated that the interaction of HSA to Fe₃O₄@CaAl-LDH@L-Dopa NPs enforced some conformational alterations within HSA. The fluorescence spectroscopy analysis indicated that by enhancing temperature, the Stern-Volmer quenching constant (K_sv) was decreased, which is relevant to a static quenching mechanism. The binding constant (K_b) was 7.07 × 10⁴ M^-1 while the number of the binding site (n) was 0.94 which is in compromise with its binding constant. Also, thermodynamic parameters (ΔH° > 0, ΔG° < 0, and ΔS° > 0) have suggested that hydrophobic forces perform a key role in the interaction of HSA with Fe₃O₄@CaAl-LDH@L-Dopa NPs. Displacement studies successfully carried out using the Warfarin and Ibuprofen have predicted that the binding of Fe₃O₄@CaAl-LDH@L-Dopa NPs to HSA is situated at site II (subdomain IIIA).Communicated by Ramaswamy H. Sarma.

Understanding the structure and conformation of bovine hemoglobin in presence of the drug hydroxyurea: multi-spectroscopic studies supported by docking and molecular dynamics simulation

Binding interaction between the small antitumor drug Hydroxyurea (HU) and Bovine Hemoglobin (BHb) has been explored in details from multi-spectroscopic and computational studies. The formation of ground state complex between BHb and HU has been suggested from the electronic UV-Vis and steady-state fluorescence spectroscopic studies. The quenching in fluorescence of BHb in presence of HU at varied concentrations has been analyzed from the SV plots. Static type of quenching has been suggested from time-resolved fluorescence spectroscopic studies. Binding parameters associated with the BHb-HU complex have also been estimated from the temperature dependent fluorescence spectroscopic studies. Alterations in the micro-environment of the Tyr and Trp residues of BHb in presence of HU have been observed from the synchronous fluorescence measurement. The result obtained from CD spectroscopic measurements signify partial unfolding in the secondary structure of BHb due to binding with HU molecule. The experimental observations are supported by theoretical studies. Molecular docking and molecular dynamics simulations have been performed to investigate the structural stability and compactness of BHb in the binding interaction between BHb and HU. The interaction of BHb with HU is expected to provide fundamental insights towards understanding the therapeutic effectiveness of HU upon interaction with BHb used in chemo-, radio therpeutic procedures and also in the treatment of SCD.

Synthesis of two novel pyrazolo[1,5-a]pyrimidine compounds with antibacterial activity and biophysical insights into their interactions with plasma protein

Two novel water-soluble pyrazolo[1,5-a]pyrimidine derivatives, 5-chloro-7-(4-methyl-piperazin -1-yl)-pyrazolo[1,5-a]pyrimidine (CMPS) and N'-(5-chloro-pyrazolo[1,5-a]pyrimidin-7-yl)-N,N-dimethyl -propane-1,3-diamine (NCPS), were synthesized and characterized with antibacterial activity. Then, the interactions of these compounds with bovine serum albumin (BSA) were studied by fluorescence, time-resolved fluorescence, circular dichroism (CD) spectroscopy and molecular docking. The results indicate that both CMPS and NCPS could effectively quench the intrinsic fluorescence of BSA via a static quenching process. The energy transfer from BSA to CMPS and NCPS may occur with high probability. Both CMPS and NCPS bind in the site I of BSA. The hydrophobic force and hydrogen bonds play major roles in the complex formation. Binding constants for both systems show that the affinity of CMPS binding to BSA is stronger than that of NCPS. The results of three-dimensional fluorescence and CD spectra reveal that the binding of CMPS and NCPS to BSA can induce conformational changes of BSA, and the influence of CMPS is slightly stronger than that of NCPS.

Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources

Functional foods are emerging as essential healthy nutritional component due to their abundant wellbeing benefits. Especially the food-derived peptides are considered as key components for playing their biologically active roles. One such robust therapeutics that already exploited with food peptides that help treating high blood pressure via targeting Angiotensin-Converting Enzyme (ACE). This in silico study demonstrated the inhibitory potential of antihypertensive peptides derived from food sources. This study involves an intensive structure-based analysis of enzyme-peptide interactions using Molecular Dynamics (MD) simulations. Interestingly, this study will help us to get deeper understanding on how food peptides achieve successful inhibition of ACE. In this study, the peptide-enzyme complexes revealed two binding pockets, A and B, on either side of the active site Zn atom. Pocket B has a smaller binding site volume than pocket A, comprised of β-sheets and the active site opening cleft. The interface of the binding sites showed that the enzyme structure was negative to neutral charge, and the peptide structure was positive to neutral charge. The dynamics of complex structures of seven highly potential peptides were performed for 20 ns each at 300 K. Comparative analysis of RMSD, RMSF and binding energies show the enzyme-peptide complexes and the overall stability of apo-enzyme. Importantly, two peptides AFKAWAVAR and IWHHTF showed the highest variation in their RMSD as compared to the apo-enzyme. This study will further be useful for the assessment of the characteristics to predict novel inhibitory peptides that can be generated from food proteins.Communicated by Ramaswamy H. Sarma.

Investigation of the Interaction Mechanism between Salbutamol and Human Serum Albumin by Multispectroscopic and Molecular Docking

Salbutamol (SBAL), a kind of short-acting beta 2-adrenergic agonist, has been mainly used to treat bronchial asthma and other allergic airway diseases clinically. In this study, the interaction mechanism between salbutamol and human serum albumin was researched by the multispectral method and molecular docking. The fluorescence intensity of HSA could be regularly enhanced with the increase of SBAL concentration. Both the results of the multispectral method and molecular docking showed that SBAL could bind HSA with van der Waals force and hydrogen bonds. The binding mechanism was further analysed by UV-Vis and synchronous fluorescence spectra. The contents of the secondary structure of free HSA and SBAL-HSA complex were evaluated using CD spectra.

Effect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders

Actin, an ATPase superfamily protein, regulates some vital biological functions like cell locomotion, cytokinesis, synaptic plasticity and cell signaling in higher eukaryotes, and is dependent on the dynamics of actin polymerization process. Impaired regulation of actin polymerization has been implicated in the formation and deposition of rod-like paracrystalline structures called as Hirano bodies in neuronal cells of patients suffering from Alzheimer's disease, Pick's disease, Guam amyotrophic lateral sclerosis and parkinsonism-dementia complex. Aggregation of actin forming amorphous deposition in the brain cells is also associated with chronic alcoholism and aging of the neurons. In the current article, we propose the breaking of the highly amorphous and dysregulated actin aggregates using generic compounds like tetracycline, oxytetracycline, doxycycline and minocycline which are used as antibiotics against tuberculosis and infection caused due to various Gram-negative bacteria. We have investigated the effect and affinity of binding of these four compounds to that of actin aggregates using 90° light scattering, size exclusion chromatography, dynamic light scattering, circular dichroism, scanning electron microscopy, transmission electron microscopy imaging and kinetic analysis. The isothermal calorimetric measurements showed that the binding constant for the cycline family molecules used in this study range from 9.8 E4 M^-1 to 1.3 E4 M^-1. To understand the in vivo effect, we also studied the effect of these drugs on Saccharomyces cerevisiae Δend3 mutant cells. Our data suggest that these generic compounds can plausibly be used for the treatment of various neurodegenerative diseases occurring due to Hirano body formation in brain cells.Communicated by Ramaswamy H. Sarma.

Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors

The angiotensin-converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase, which has a direct involvement in the control of blood pressure by performing the hydrolysis of angiotensin I to produce angiotensin II. At the same time, ACE hydrolyzes other substrates such as the vasodilator peptide bradykinin and the anti-inflammatory peptide N-acetyl-SDKP. In this sense, ACE inhibitors are bioactive substances with potential use as medicinal products for treatment or prevention of hypertension, heart failures, myocardial infarction, and other important diseases. This review examined the most recent literature reporting ACE inhibitors with the help of molecular modeling. The examples exposed here demonstrate that molecular modeling methods, including docking, molecular dynamics (MD) simulations, quantitative structure-activity relationship (QSAR), etc, are essential for a complete structural picture of the mode of action of ACE inhibitors, where molecular docking has a key role. Examples show that too many works identified ACE inhibitory activities of natural peptides and peptides obtained from hydrolysates. In addition, other works report non-peptide compounds extracted from natural sources and synthetic compounds. In all these cases, molecular docking was used to provide explanation of the chemical interactions between inhibitors and the ACE binding sites. For docking applications, most of the examples exposed here do not consider that: (i) ACE has two domains (nACE and cACE) with available X-ray structures, which are relevant for the design of selective inhibitors, and (ii) nACE and cACE binding sites have large dimensions, which leads to non-reliable solutions during docking calculations. In support of the solution of these problems, the structural information found in Protein Data Bank (PDB) was used to perform an interaction fingerprints (IFPs) analysis applied on both nACE and cACE domains. This analysis provides plots that identify the chemical interactions between ligands and both ACE binding sites, which can be used to guide docking experiments in the search of selective natural components or novel drugs. In addition, the use of hydrogen bond constraints in the S₂ and S₂′ subsites of nACE and cACE are suggested to guarantee that docking solutions are reliable.

Potential of isoquercitrin as antisickling agent: a multi-spectroscopic, thermophoresis and molecular modeling approach

Sickle cell disease is an inherited disease caused by point mutation in hemoglobin (β-globin gene). Under oxygen saturation, sickle hemoglobin form polymers, leading to rigid erythrocytes. The transition of the blood vessels is altered and initiated by the adhesion of erythrocytes, neutrophils and endothelial cells. Sickle Hemoglobin (HbS) polymerization is a major cause in red blood cells (RBC), promoting sickling and destruction of RBCs. Isoquercitrin, a medicinal bioactive compound found in various medicinal plants, has multiple health benefits. The present study examines the potential of isoquercitrin as an anti-sickle agent, showing a significant decrease in the rate of polymerization as well as sickling of RBCs. Isoquercitrin-induced graded alteration in absorbance and fluorescence of HbS, confirmed their interaction. A negative value of ΔG° strongly suggests that it is a spontaneous exothermic reaction induced by entropy. Negative ΔH° and positive ΔS° predicted that hydrogen and hydrophobic binding forces interfered with a hydrophobic microenvironment of β6Val leading to polymerization inhibition of HbS. HbS-Isoquercitrin complex exhibits helical structural changes leading to destabilization of the HbS polymer as confirmed by CD spectroscopy. MST and DSC results indicate greater changes in thermophoretic mobility and thermal stability of sickle hemoglobin in the presence of isoquercitrin, respectively. These findings were also supported by molecular simulation studies using DOCK6 and GROMACS. Hence, we can conclude that isoquercitrin interacts with HbS through hydrogen bonding, which leads to polymerization inhibition. Consequently, isoquercitrin could potentially be used as a medication for the treatment of sickle cell disease.Communicated by Ramaswamy H. Sarma.

Two novel rhodamine-based fluorescent probes for the rapid and sensitive detection of Fe3+: Experimental and DFT calculations

Fe³⁺ ions play an important role in both biological and environmental field. In this work, two novel rhodamine-based colorimetric and fluorescent probes (RBA2 and RBA3) were designed and synthesized for the efficient detection of Fe³⁺. Upon the addition of Fe³⁺, the fluorescence intensity of RBA2 and RBA3 enhanced 108-fold and 222-fold, respectively. RBA2 and RBA3 exhibited a low detection limit which could achieve 12.8 nM and 11.0 nM. In addition, the binding modes of RBA2 and RBA3 with Fe³⁺ were proved to be 1:1 stoichiometry in the complexes by Job's plot, ESI-MS and ¹H NMR results. The complexing ability of RBA3 with Fe³⁺ excessed to that of RBA2 that was determined by the binding association constants, and highly consistent with DFT calculations results. Furthermore, RBA2 and RBA3 were further utilized to detect Fe³⁺ in living cells and real water samples, indicating their promising prospects in biological and environmental field.

A combined experimental and theoretical investigation of ruthenium(II)-hydrazone complex with DNA: Spectroscopic, nuclease activity, topoisomerase inhibition and molecular docking

A new Dichlorotetra(4-hydroxy-N'-(pyridin-4-ylmethylene)benzohydrazone)Ru(II) complex 1 has been synthesized and characterized using spectroscopic techniques. The structure of complex 1 has been optimized through ORCA computational programme package using B3LYP functionals. The complex binds efficiently with calf thymus DNA (CT-DNA) as monitored by UV-visible titrations (K_b = 4.8 × 10⁵), ethidium bromide displacement studies (K_sv = 1.39) as well as Circular Dichroism (CD) titrations. The complex intercalates with DNA base pairs. It shows cleavage of supercoiled (SC) DNA into nicked circular (NC) DNA efficiently via oxidative pathway. Complex 1 also inhibits Topoisomerase I (Topo I) relaxation activity at concentration < 20 μM. The molecular docking studies support that Topo I inhibition occur via blocking religation of G11 hydroxyl group.

Titanium oxide nanoparticles fabrication, hemoglobin interaction, white blood cells cytotoxicity, and antibacterial studies

This study is focused on the fabrication and characterization of titanium oxide (TiO₂) NPs. Afterwards; the interaction of TiO₂ NPs with human hemoglobin (Hb) was investigated by FTIR spectroscopy, fluorescence spectroscopy, and molecular docking studies. Also, the cytotoxic effect of fabricated TiO₂ NPs against human white blood cells (WBCs) was considered by MTT assay. The antibacterial effect of synthesized NPs was examined on Pseudomonas aeruginosa (ATCC 27853); Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923). TEM and DLS investigations showed that the synthesized TiO₂ NPs have a narrow nano-sized distribution. XRD pattern of the fabricated NPs exhibited that the TiO₂ NPs contain anatase phase. Similarity in amide I and II signal intensities showed that secondary structure of the adsorbed Hb is preserved. The intrinsic fluorescence study revealed that the fluorescence quenching of Hb was done by complex formation between Hb and TiO₂ NPs trough the hydrogen bond and van der Waals interactions. Synchronous fluorescence spectroscopy determined that interaction of TiO₂ NPs with Hb did not unfold the Hb structure in the vicinity of the Tyr and Trp residues. Molecular docking study depicted that Glu-95, Thr-134 and Tyr-140 are involved in the formation of hydrophilic bonds. MTT data and antibacterial assays indicated that TiO₂ NPs endow distinguished antibacterial activities against Gram-negative and Gram positive strains at safe concentrations. This study may reveal that fabricated TiO₂ NP can be used as a safe and potent antibacterial agent. Communicated by Ramaswamy H. Sarma.

Reactive oxygen species generation and human serum albumin damage induced by the combined effects of ultrasonic irradiation and brilliant cresyl blue

In this paper, brilliant cresyl blue (BCB) was selected as a sonosensitizer. The sonodynamic damage to human serum albumin (HSA) in the presence of BCB and the mechanism were studied by means of fluorescence and absorption spectra. Firstly, BCB could quench the intrinsic fluorescence of HSA obviously and the quenching mechanism was static quenching due to the formation of HSA-BCB complex. The results of the displacement experiments and the molecular modeling suggested that the binding site of BCB on HSA was site I, and hydrophobic forces and hydrogen bonds played major roles in the interaction between HSA and BCB. Secondly, the damage of HSA induced by the combined effects of ultrasonic irradiation and BCB was more efficient than that only BCB or ultrasound irradiation, which confirmed that BCB had sonodynamic activity. The damage degree of HSA was positively correlated with reactive oxygen species (ROS) produced in the system, which indicated that ultrasound could activate BCB to produce ROS, and the kinds of ROS produced by the combined effects of ultrasonic irradiation and BCB were mainly hydroxyl free radical, singlet oxygen and superoxide anion radical.

Interaction of silica nanoparticles with tau proteins and PC12 cells: Colloidal stability, thermodynamic, docking, and cellular studies

Study on the side effects of the nanoparticles (NPs) can provide useful information regarding their biological and medical applications. Herein, the colloidal stability of the silicon dioxide NPs (SiO₂ NPs) in the absence and presence of tau was investigated by TEM and DLS techniques. Afterwards, the thermodynamic parameters of interaction between SiO₂ NPs and tau were determined by fluorescence spectroscopy and docking studies. Finally, the cytotoxic effects of SiO₂ NPs on the viability of PC12 cells were investigated by MTT, AO/EB staining and flow cytometry assays. TEM, DLS, and zeta potential investigations revealed that tau can reduce the colloidal stability of SiO₂ NPs. Fluorescence spectroscopy study indicated that SiO₂ NPs bound to the tau with high affinity through hydrogen bonds and van der Waals interactions. Docking study also determined that Ser, Thr and Tyr residues provide a polar microenvironment for SiO₂ NPs/tau interaction. Cellular studies demonstrated that SiO₂ NPs can induce cell mortality through both apoptosis and necrosis mechanisms. Therefore, it may be concluded that the biological systems such as nervous system proteins can affect the colloidal stability of NPs and vice versa NPs in the biological systems can bind to proteins and cell membranes non-specifically and may induce toxicity.

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.

Binding affinity of pyrano[3, 2-f]quinoline and DNA: spectroscopic and docking approach

The interaction between pyrano[3, 2-f]quinoline (PQ) and calf thymus DNA (CTDNA) using spectroscopic and molecular modeling approach has been presented here. Apparent association constant (1.05×10⁵ L/mol) calculated from UV-vis specta, indicates a moderate complex formation between CTDNA and PQ. The quenching phenomena as obtained from emission spectra of ethidium bromide (EB)-CTDNA by PQ was found to be a dynamic one and the binding constants found to be 8.64, 9.25, 11.17, 12.03 × 10⁴ L/mol at 293, 300, 308, and 315 K. Thermodynamic parameter enthalpy change (ΔH) and entropy change (ΔS), indicates weak force like van der Walls force and hydrogen bonds having the key role in this binding process. The results of circular dichroism (CD) demonstrate that PQ has not induced characteristic changed in CTDNA. Results achieved from UV absorption and fluorescence spectroscopy indicating the binding mode of PQ with DNA seems to be a nonintercalative binding. The theoretical results as originating from molecular modeling showed that PQ possibly will bind into the hydrophobic region of DNA having docking binding energy = -10.03 kcal/mol and the obtained results are in consonance with the inferences obtained from experimental data. This result is important for the better understanding of pharmaceutical aspects of binding affinity of PQ and CTDNA.