Binding interaction of sodium-N-dodecanoyl sarcosinate with hemoglobin and myoglobin: Physicochemical and spectroscopic studies with molecular docking analysis

Rudra, Suparna; Dasmandal, Somnath; Mahapatra, Ambikesh

doi:10.1016/j.jcis.2017.02.035

Cited by 26 publications

(8 citation statements)

References 31 publications

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“…Interestingly, when hematin is placed as a sandwich configuration between the GMC and chitosan on GCE electrode as GCE/GMC@hematin-Chit (Scheme D), a well-defined redox peak at an apparent standard electrode potential, E °′ = −0.39 ± 0.02 V versus Ag/AgCl in N 2 -purged pH 7 PBS, was noticed. The E °′ value obtained here is comparable with the E °′ value of several heme-based proteins, hemoglobin (−0.29, −0.34, −0.37 V vs Ag/AgCl), − cytrochrome C (−0.16 to −0.4 V vs Ag/AgCl), , and naked heme complex (−0.38 V vs Ag/AgCl) ,,,,− systems indicating the efficient electron-transfer behavior of the hematin on the sandwiched configuration system. The position of the redox peak obtained here has some special meaning.…”

Section: Resultssupporting

confidence: 81%

“…Inspired by nature, mimicking the intricacy of naturally occurring enzymes has been a long-term goal of researchers. Biomimetic electrocatalytic reductions of O 2 and H 2 O 2 are of great importance in the fields of electrochemistry, electroanalytical chemistry, biomedical, energy, , and food science industry. , In this connection, synthetic bioinspired molecules reduce the gap between the natural and artificial enzymes/proteins. − Hematin (Hemat), an iron porphyrin derivative, is a well-known active center of heme proteins, and it has the ability to mimic the active site of various heme-proteins/enzymes such as catalases, peroxidases, hemoglobin (Hb), and myoglobins. − Because it has Fe 3+ as a central metal atom to which a hydroxyl (−OH) group is linked, in general, it is referred to as oxyheme or hydroxyheme. One of the major functions of Hemat is that it triggers the production of globulin in the body .…”

Section: Introductionmentioning

confidence: 99%

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Highly Redox-Active Hematin-Functionalized Carbon Mesoporous Nanomaterial for Electrocatalytic Reduction Applications in Neutral Media

Amreen

Kumar

2018

ACS Appl. Nano Mater.

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Hematin is a hydroxyl group linked heme site (hydroxyl heme) of the natural enzymes/proteins like hemoglobin, cytochrome c, catalase, and horseradish peroxidase, and it has an important role in the physiological function. Because of problems like poor electron-transfer functionality (on solid electrodes), poor solubility, and molecular aggregation in aqueous solution, limited electrochemical studies have been reported in the literature. A new electrode modification method for hematin using graphitized mesoporous carbon nanomaterial and chitosan for enhanced redox-active and efficient electrocatalytic reductions of hydrogen peroxide and dissolved oxygen in neutral pH was demonstrated in this work. The hematin-modified electrode showed a highly stable redox peak at E°′ = −0.390 V versus Ag/AgCl with a heterogeneous rate constant value of 1.34 s–1. Calculated hematin-active loading concentration (Γhemat = 126 × 10–10 mol cm–2) is ∼20 times higher than the reported values. Physicochemical and electrochemical characterizations revealed trapping of the hematin via axial bond coordination and intermolecular hydrogen bonding with amino functional groups of chitosan and π–π interactions with the graphitic site of mesoporous carbon within the matrix. The new hematin electrode showed ∼400 mV reduction in the overpotential with current sensitivity/detection range of 570 nA μM–1/100–900 μM and 6.7 μA ppm–1/1–10 ppm, respectively, for H2O2 and dissolved oxygen reduction reactions in pH 7 phosphate buffer solution. Michaelis–Menten kinetics were applied for the H2O2 reduction reaction and estimated the rate constant values as K M = 0.78 mM and k s = 1.15 s–1. No marked interference was noticed with common biochemicals such as nitrite, nitrate, glucose, uric acid, ascorbic acid, xanthine, hypoxanthine, cysteine, and dopamine on amperometric i–t detection of H2O2 indicating the activity similar to the heme-based proteins/enzymes.

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Section: Resultssupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Highly Redox-Active Hematin-Functionalized Carbon Mesoporous Nanomaterial for Electrocatalytic Reduction Applications in Neutral Media

Amreen

Kumar

2018

ACS Appl. Nano Mater.

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“…These subunits are connected through turns with an oxygen-binding heme group at the centre and a hydrophobic core. 98,99 Results from "Swissdock" on SMZ-Hb and SDZ−Mb Complexes. The docking exercises performed at the Swissdock web server for SMZ−Mb binding resulted in 32 ligand binding sites, out of which only five sites were found with higher densities of ligand occupancy or clustering in comparison to the remaining surface area (Figure 11).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods

et al. 2022

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Protein–ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure–function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 104 M–1. SMZ with two additional methyl (−CH3) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand–protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.

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“…In the secondary structure of proteins, α‐helix content represents the ordering of protein molecules, while β‐sheet, β‐turn and random coil reflect the looseness of protein molecules. The displacement of the chromophore absorption spectrum mainly depends on the effect of hydrophilic or hydrophobic microenvironment . Comparing the CD spectrum of Mb to that of IA–Mb solutions (Figure ), negative peaks were observed at 208 nm (π–π*) and 222 nm (n–π*).…”

Section: Resultsmentioning

confidence: 99%

“…The displacement of the chromophore absorption spectrum mainly depends on the effect of hydrophilic or hydrophobic microenvironment. [40][41][42] Comparing the CD spectrum of Mb to that of IA-Mb solutions ( Figure 6), negative peaks were observed at 208 nm (π-π*) and 222 nm (n-π*). This demonstrated that the secondary structure conformation of Mb was mainly α-helix, which supported the highly spiral state of Mb with a large number of α-helices in the natural state.…”

Section: Discussionmentioning

confidence: 99%

Interactions of indole alkaloids with myoglobin: A mass spectrometry based spectrometric and computational method

Chi

Feng

et al. 2020

Rapid Comm Mass Spectrometry

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Rationale Interactions of drug molecules and proteins play important roles in physiological and pathological processes in vivo. It is of significance to establish a reliable strategy for studying protein–drug ligand interactions and would be helpful for the design and screening of new drugs in pharmacological research. Methods The interactions between four indole alkaloids (IAs) extracted from Ophiorrhiza japonica (O. japonica) and myoglobin (Mb) protein were investigated using a multi‐spectrometric and computational method of native electrospray ionization mass spectrometry (native ESI‐MS), hydrogen/deuterium exchange mass spectrometry (HDX‐MS), circular dichroism (CD) and molecular docking (MD). Results The IA‐bound Mb complexes were analyzed using native ESI‐MS, with the obtained protein‐to‐ligand stoichiometry at 1:1, 1:2 and 1:3. Binding constants were measured according to the interpretation of MS spectra. MD complemented MS measurements, probing the binding sites and modes of the four IAs to Mb. Analyses involving CD and HDX‐MS demonstrated that exposure to IAs could affect the conformation of Mb by decreasing the α‐helix content and made Mb more susceptible to HDX at the backbone. Conclusions A new MS‐based integrated analysis method has been developed to successfully study the interactions of Mb and IAs extracted from O. japonica. The experimental and calculation results have good consistency, revealing all of the four IA molecules could bind to Mb to form 1:1, 1:2 and 1:3 Mb–IA complexes. The order of binding ability of these IAs to Mb was ophiorrhine B > compound C > ophiorrhine A > compound D. CD and HDX‐MS results indicated that binding with IAs destabilizes Mb. HDX‐MS analysis suggests that Mb becomes more susceptible to HDX, indicating that binding with IAs destabilizes the structure of Mb. In addition, the interaction with IAs affected the overall structure of Mb, ascribed to the decrease of α‐helix content and less folding of the backbone.

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Binding interaction of sodium-N-dodecanoyl sarcosinate with hemoglobin and myoglobin: Physicochemical and spectroscopic studies with molecular docking analysis

Cited by 26 publications

References 31 publications

Highly Redox-Active Hematin-Functionalized Carbon Mesoporous Nanomaterial for Electrocatalytic Reduction Applications in Neutral Media

Highly Redox-Active Hematin-Functionalized Carbon Mesoporous Nanomaterial for Electrocatalytic Reduction Applications in Neutral Media

Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods

Interactions of indole alkaloids with myoglobin: A mass spectrometry based spectrometric and computational method

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