Structural characteristics of thermostable immunogenic outer membrane protein from Salmonella enterica serovar Typhi

Cytotoxic pyrrole-based gold(III) chelates target human topoisomerase II as dual-mode inhibitors and interact with human serum albumin

Topoisomerase IIα (Top II) is a critical enzyme that resolves DNA topology during transcription and replication. Inhibitors of Top II are used as anticancer agents and are classified as interfacial poisons (IFPs) or catalytic inhibitors (CICs). Here, we report a novel class of cytotoxic, stable cationic gold(III) Schiff base chelates (AuL1, AuL2, and AuL3) with DNA-intercalating properties. In the NCI-60 screen, AuL1 and AuL3 exhibited potent cytotoxicity (mean GI50 values of 11 (7) μM and 14 (9) μM, respectively), whereas AuL2 showed minimal cytotoxicity. Cluster analysis aligned AuL1 and AuL3 with the Top II poison etoposide. Mechanistic studies revealed that AuL1 acts as an IFP at concentrations between 0.5 and 50 μM and as a CIC at concentrations between 50 and 500 μM. Further investigations demonstrated that all three gold(III) chelates bind to and intercalate DNA, the main substrate for Top II. Finally, binding studies with human serum albumin (HSA) indicated that the chelates have moderate affinity for the protein. Thermodynamic analysis indicates entropically driven binding, with minimal structural disruption observed via UV-CD spectroscopy. These findings highlight the dual mode Top II inhibition mechanism delineated for the gold(III) chelates and their favourable pharmacodynamic interactions with HSA, underscoring their potential as promising anticancer agents.

TMB Stab-pred: Predicting the stability of transmembrane β-barrel proteins using their sequence and structural signatures

Understanding the folding and stability of transmembrane β-barrel proteins (TMBs) provides insights into their structural integrity, functional mechanisms, and implications for disease states. In this work, we have characterized the important features that influence the folding and stability of TMBs. Our results showed that lipid accessible surface area and transition energy are important for understanding the stability of TMBs. Further, this information was utilized to develop a linear regression-based method for predicting the stability of TMBs. Our method achieved a correlation and mean absolute error (MAE) of 0.96 and 0.94 kcal/mol on the jack-knife test. Moreover, we compared the stability of TMBs with globular all-β proteins and observed that long-range interactions and energetic properties are crucial for maintaining the stability of both β-barrel membrane and all-β globular proteins. On the other hand, side-chain - side-chain hydrogen bonds and lipid accessible surface area are specific to membrane proteins. These features are critical for membrane proteins because they influence a protein to embed within the membrane environment. Further, we have developed a web server, TMB Stab-pred for predicting the stability of TMBs, and it is accessible at https://web.iitm.ac.in/bioinfo2/TMBB/index.html.

Insight into the effect of ZIF-8 on the interaction between drugs and protein/cell

Understanding the impact of nanomaterials on drug-protein/cell interactions is crucial for comprehending their in vivo biological effects. We investigated the impact of zeolitic imidazolate framework (ZIF)-8 on the interaction between curcumin (Cur) and human serum albumin (HSA) using various spectroscopic techniques and molecular docking. Additionally, we examined its effect on drug-cell interaction using HepG2 cells and Escherichia coli (E. coli). The UV-vis spectra and fluorescence results demonstrated the occurrence of an interaction between Cur-HSA and ZIF-8, potentially resulting in the formation of ground-state complexes. ZIF-8 did not alter the static quenching mechanism, interaction force type, and binding stoichiometry between Cur and HSA, but it induced subtle changes in the secondary structure and esterase activity of HSA. Cur predominantly binds in the site I of HSA. Molecular docking analysis confirmed the results. The incorporation of ZIF-8 enhanced the antitumor activity of Cur-HSA and the antibacterial efficacy of ciprofloxacin (CIP)-HSA, while concurrently enhancing the uptake of CIP by E. coli. These results indicate that the influence of ZIF-8 on drug-protein interactions may consequently exert a significant impact on drug efficacy.

α-Synuclein Iron-Responsive-Element RNA and Iron Regulatory Protein Affinity Is Specifically Reduced by Iron in Parkinson's Disease

α-Synuclein (α-Syn) is implicated in the pathophysiology of Parkinson's disease (PD) and plays a significant role in neuronal degeneration. Iron response proteins (IRPs) bind to iron response elements (IREs) found in the 5'-untranslated regions (5'-UTRs) of the messenger RNA that encode the α-Syn gene. This study used multi-spectroscopic approach techniques to investigate the impact of iron on α-Syn IRE RNA binding to IRP1. The formation of a stable complex between α-Syn RNA and IRP1 was suggested by fluorescence quenching results. Fluorescence measurements showed that α-Syn RNA and IRP1 had a strong interaction, with a binding constant (Ka) of 21.0 × 106 M-1 and 1:1 binding stoichiometry. About one binding site per IRP1 molecule was suggested by the α-Syn RNA binding. The Ka for α-Syn RNA•IRP1 with added Fe2+ (50 μM) was 6.4 μM-1. When Fe2+ was added, the Ka of α-Syn RNA•IRP1 was reduced by 3.3 times. These acquired Ka values were used to further understand the thermodynamic characteristics of α-Syn RNA•IRP1 interactions. The thermodynamic properties clearly suggested that α-Syn RNA binding to IRP1 was an entropy-favored and enthalpy-driven event, with significant negative ΔH and small positive ΔS. For α-Syn RNA•IRP1, the Gibbs free energy (ΔG) was -43.7 ± 2.7 kJ/mol, but in the presence of Fe2+, it was -36.3 ± 2.1 kJ/mol. These thermodynamic calculations indicated that hydrogen bonding as well as van der Waals interactions might help to stabilize the complex formation. Additionally, far-UV CD spectra verified α-Syn RNA•IRP1 complex formation, and α-Syn RNA and Fe2+ induce secondary structural alteration of IRP1. According to our findings, iron alters the hydrogen bonding in α-Syn RNA•IRP1 complexes and induces a structural change in IRP1. This suggests that iron selectively affects the thermodynamics of these RNA-protein interactions.

Small molecule interactions with biomacromolecules: selective sensing of human serum albumin by a hexanuclear manganese complex - photophysical and biological studies

A covalently bonded hexanuclear neutral complex, [Mn6(μ3-O)2(3-MeO-salox)6(OAc)2(H2O)4] (1), has been synthesized and characterized by single crystal X-ray diffraction analysis along with IR and HRMS studies. Complex 1 has been found to selectively interact with human serum albumin (HSA), a model transport protein. The interaction of 1 with HSA was investigated by monitoring the change in the absorbance value of HSA at λ = 280 nm with increasing concentration of 1. Likewise, fluorescence titrations were carried out under two conditions: (i) titration of a 5 μM solution of complex 1 with the gradual addition of HSA, showing a ∼9-fold fluorescence intensity enhancement at 424 nm, upon excitation at 300 nm; and (ii) upon excitation at 295 nm, titration of 5 μM HSA solution with the incremental addition of complex 1, showing a quenching of fluorescence intensity at 334 nm, with simultaneous development of a new emission band at 424 nm. A linear form of the Stern-Volmer equation gives KSV = 9.77 × 104 M-1 and the Benesi-Hildebrand plot yields the binding constant as KBH = 1.98 × 105 M-1 at 298 K. The thermodynamic parameters, ΔS°, ΔH°, and ΔG°, were estimated by using the van't Hoff relationship which infer the major contribution of hydrophobic interactions between HSA and 1. It was observed that quenching of HSA emission arises mainly through a dynamic quenching mechanism as indicated by the dependence of average lifetime 〈τ〉 on the concentration of 1. The changes in the CD (circular dichroism) spectral pattern of HSA in the presence of 1 clearly establish the variation of HSA secondary structure on interaction with 1. The most probable interaction region in HSA for 1 was determined from molecular docking studies which establish the preferential trapping of 1 in the subdomain IIA of site I in HSA and substantiated by the results of site-specific marker studies. Complex 1 was further evaluated for its antiproliferative effects in lung cancer A549 cells, which strictly inhibits the growth of the cells in both 2D and 3D mammospheres, indicating its potential application as an anticancer drug.

Exploring the binding behaviors between nisoldipine and bovine serum albumin as a model protein by the aid of multi-spectroscopic approaches and in silico

Bovine serum albumin (BSA), a model protein was used to evaluate the binding behavior of nisoldipine and human serum albumin by a series of experiments and in silico in this article. The outcomes suggested that nisoldipine and BSA formed the nisoldipine-BSA complex with a molar ratio of 1:1, caused the fluorescence quenching of BSA, which quenching mechanism was attributable to static quenching. The binding constant of the nisoldipine-BSA complex was (1.3-3.0) × 104 M-1 at 298-310 K, indicating that nisoldipine on BSA protein had a moderate affinity. During the complexation of nisoldipine with BSA, nisoldipine can spontaneously insert into the site II (subdomain III A) of BSA and the distance of energy transfer from donor group in protein to acceptor group in nisoldipine was 3.21 nm, which led to the change in the hydrophobicity of the microenvironment surrounding Trp residues and in the secondary structure of BSA. Additionally, the findings also confirmed that the hydrogen bond and van der Waals force were responsible for forming the nisoldipine-BSA complex and the complexation process was a spontaneous exothermic process.Communicated by Ramaswamy H. Sarma.

Preserved structure and function of human serum albumin self-folded in the oxidative cytoplasm of Escherichia coli

Human serum albumin (HSA), a polypeptide featuring 17 disulfide bonds, acts as a crucial transport protein in human blood plasma. Its extended circulation half-life, mediated by FcRn (neonatal Fc receptor)-facilitated recycling, positions HSA as an excellent carrier for long-acting drug delivery. However, the conventional method of obtaining HSA from human blood faces limitations due to availability and potential contamination risks, such as blood-borne diseases. This study introduced SHuffle, an oxidative Escherichia coli (E. coli) expression system, for the production of recombinant HSA (rHSA) that spontaneously self-folds into its native conformation. This system ensures precise disulfide bond formation and correct folding of cysteine-rich rHSA, eliminating the need for chaperone co-expression or domain fusion of a folding enhancer. The purified rHSA underwent thorough physicochemical characterization, including mass spectrometry, circular dichroism spectroscopy, intrinsic fluorescence spectroscopy, esterase-like activity assay, and size exclusion chromatography, to assess critical quality attributes. Importantly, rHSA maintained native binding affinity to FcRn and the albumin-binding domain. Collectively, our analyses demonstrated a high comparability between rHSA and plasma-derived HSA. The expression of rHSA in E. coli with an oxidizing cytosol provides a secure and cost-effective approach, enhancing the potential of rHSA for diverse medical applications.

Interaction studies of cannabidiol with human serum albumin by surface plasmon resonance, spectroscopy, and molecular docking

The binding interaction of cannabidiol (CBD) and human serum albumin (HSA) under physiological blood pH conditions (pH 7.4) was conducted by surface plasmon resonance (SPR), fluorescence spectroscopy, UV-Visible spectrophotometry, and molecular docking. The responses from SPR measurement increased with the increase in CBD concentration until equilibrium was reached at the equilibrium dissociation constant (KD) of 9.8 × 10-4 M. The results from fluorescence and UV-Visible spectroscopy showed that CBD bound to HSA at one site in a spontaneous manner to form protein-CBD complexes. The quenching process involved both static and dynamic mechanisms while the static mechanism contributed predominantly to the binding between CBD and albumin. The binding constants estimated from the fluorescence studies were from 0.16 × 103 to 8.10 × 103 M-1, which were calculated at different temperature conditions using Stern-Volmer plots. The thermodynamic parameters demonstrated that the binding interaction was a spontaneous reaction as Gibbs free energy had negative values (ΔG = -12.57 to -23.20 kJ.mol-1). Positive ΔH and ΔS values (ΔH = 2.46 × 105 J.mol-1 and ΔS = 869.81 J.mol-1K-1) indicated that the hydrophobic force was the major binding interaction. Finally, confirmation of the type and extent of interaction was provided using UV-spectroscopy and molecular docking studies. The outcomes of this study are expected to serve as a platform to conduct future studies on binding interactions and toxicological research of CBD.Communicated by Ramaswamy H. Sarma.

An affordable label-free ultrasensitive immunosensor based on gold nanoparticles deposited on glassy carbon electrode for the transferrin receptor detection

In recent decades, there has been a concerning and consistent rise in the incidence of cancer, posing a significant threat to human health and overall quality of life. The transferrin receptor (TfR) is one of the most crucial protein biomarkers observed to be overexpressed in various cancers. This study reports on the development of a novel voltammetric immunosensor for TfR detection. The electrochemical platform was made up of a glassy carbon electrode (GCE) functionalized with gold nanoparticles (AuNPs), on which anti-TfR was immobilized. The surface characteristics and electrochemical behaviors of the modified electrodes were comprehensively investigated through scanning electron microscopy, XPS, Raman spectroscopy FT-IR, electrochemical cyclic voltammetry and impedance spectroscopy. The developed immunosensor exhibited robust analytical performance with TfR fortified buffer solution, showing a linear range (LR) response from 0.01 to 3000 μg/mL, with a limit of detection (LOD) of 0.01 μg/mL and reproducibility (RSD <4 %). The fabricated sensor demonstrated high reproducibility and selectivity when subjected to testing with various types of interfering proteins. The immunosensor designed for TfR detection demonstrated several advantageous features, such as being cost-effective and requiring a small volume of test sample making it highly suitable for point-of-care applications.

Fabrication of an affordable and sensitive corticosteroid-binding globulin immunosensor based on electrodeposited gold nanoparticles modified glassy carbon electrode

Herein, we fabricated an ultrasensitive electrochemical immunosensor for the quantitative detection of corticosteroid-binding globulin (CBG). CBG is a protein that regulates glucocorticoid levels and is an important biomarker for inflammation. A decrease in CBG levels is a key biomarker for inflammatory diseases, such as septic shock. To enhance the electrochemical performance and provide a large surface area for anti-CBG immobilization, we functionalized the glassy carbon electrode surface with AuNPs. Electrochemical characterization methods including cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to examine the construction of the fabricated immunosensor. The electrochemical signal demonstrated a remarkable sensitivity to the CBG antigen, with a detection range from 0.01 to 100 μg/mL and a limit of detection of 0.012 μg/mL, making it suitable for both clinical and research applications. This label-free immunosensor offers significant advantages, including high sensitivity, low detection limits and excellent selectivity, making it a promising tool for detecting CBG in complex biological samples. Its potential applications include early disease diagnosis, treatment monitoring and studying CBG-related physiological processes.

Interactions of ferulic acid and ferulic acid methyl ester with endogenous proteins: Determination using the multi-methods

Ferulic acid (FA) and ferulic acid methyl ester (FAM) are important phenolic compounds in Baijiu. In this study, the interaction of FA and FAM with human serum albumin (HSA) and lysozyme (LZM) was investigated using multispectral methods and molecular dynamics simulation. FA and FAM could interact with HSA and LZM, changing the conformation and hydrophilicity of the protein. The quenching mechanisms of FA-HSA, FA-LZM, FAM-HSA, and FAM-LZM were all static-quenching. In the FA-HSA, FAM-HSA, and FA-LZM systems, the interaction forces were mainly hydrophobic interactions and hydrogen bonding. In the FAM-LZM system, the interaction forces were mainly hydrophobic interactions, hydrogen bonding, and van der Waals force. Common metal ions such as K+, Ca2+, Cu2+, Mg2+, and Mn2+ could affect the binding ability of FA and FAM to HSA and LZM. Moreover, FA and FAM could increase the stability of HSA and LZM, and the protein bound to FA/FAM was more stable than the free protein. FA and FAM had varying degrees of impact on the physiological activities of HSA and LZM. This study provides relevant information on the interactions and metabolic mechanisms of FA and its derivatives with endogenous proteins.

Binding interactions of Vildagliptin with pepsin: A multi-spectroscopic and in-silico approach and a comparative account with metformin

Vildagliptin (VDG) and Metformin (Met) belong to a class of dipeptidylpeptidase-4 (DPP-4) inhibitor and biguanide, respectively and used for the management of diabetes mellitus type II (DMTII). Both the drugs are orally available which leads to various side effects due to its oral ingestion. Occurrence of these side effects might be due to some interactions with pepsin at a molecular level. Therefore, in order to investigate these interactions, multi-spectroscopic and in-silico techniques have been extensively studied to identify the binding characteristics of VDG with pepsin. Fluorescence data suggested that the quenching is due to dynamic and static mechanism and static was dominant one. However, fluorescence and UV-Vis spectroscopic measurement analysis suggested that VDG tends to associate with pepsin, via ground-state complex formation. Fluorescence study revealed the binding-constant value which was found to be 0.559 × 103 M-1 at 298.15 K that is non-covalent in nature. VDG-pepsin complex shows exothermic and spontaneous binding as confirmed by the calculated values of ΔH, ΔS, and ΔG, are majorly caused by van der Waals forces and H-bonding interactions. CD spectra of pepsin in presence of VDG confirmed post binding conformational change. Enzyme-activity assay showed that activity of pepsin was decreased by upto 28 %. FRET analysis suggested that energy transfer efficiency is negligible for VDG-pepsin interaction. In-silico analysis reveals that H-bonding and electrostatic negative forces are the significant driving forces involved in the interaction of VDG and pepsin.

Comparing the interactions of nitrendipine with lysozyme or human serum albumin and the effects of vitamin C and naringin on these interactions by spectroscopy and molecular docking methods

The interactions between drugs and proteins play a pivotal role in determining the pharmacological effects and disposition of drugs within the human body. This study focuses on exploring the interaction between nitrendipine and lysozyme/human serum albumin. Spectroscopic analysis indicated a compound static quenching, indicative of the formation of stable complexes between the drug and proteins. The addition of vitamin C or naringin resulted in a decrease of the binding constant between nitrendipine and lysozyme/human serum albumin. The presence of these compounds may disrupt the interactions between the drug and proteins, potentially leading to an increased concentration of free nitrendipine in the bloodstream. Nitrendipine binds more easily to human serum albumin at 310 K, and human serum albumin has an average binding site ratio with nitrendipine approximately 0.1 higher than that with lysozyme. Vitamin C has a greater impact on the binding constant of nitrendipine to human serum albumin and lysozyme. Compared to the binary system of proteins with the drug, the ternary system with the addition of vitamin C at 310 K reduces the binding constants of lysozyme and human serum albumin by 85%. In conclusion, this study explores the significance of considering drug-protein interactions in understanding drug behavior and potential drug-food interactions.

Multi-cavity molecular descriptor interconnections: Enhanced protocol for prediction of serum albumin drug binding

The role of human serum albumin (HSA) in the transport of molecules predicates its involvement in the determination of drug distribution and metabolism. Optimization of ADME properties are analogous to HSA binding thus this is imperative to the drug discovery process. Currently, various in silico predictive tools exist to complement the drug discovery process, however, the prediction of possible ligand-binding sites on HSA has posed several challenges. Herein, we present a strong and deeper-than-surface case for the prediction of HSA-ligand binding sites using multi-cavity molecular descriptors by exploiting all experimentally available and crystallized HSA-bound drugs. Unlike previously proposed models found in literature, we established an in-depth correlation between the physicochemical properties of available crystallized HSA-bound drugs and different HSA binding site characteristics to precisely predict the binding sites of investigational molecules. Molecular descriptors such as the number of hydrogen bond donors (nHD), number of heteroatoms (nHet), topological polar surface area (TPSA), molecular weight (MW), and distribution coefficient (LogD) were correlated against HSA binding site characteristics, including hydrophobicity, hydrophilicity, enclosure, exposure, contact, site volume, and donor/acceptor ratio. Molecular descriptors nHD, TPSA, LogD, nHet, and MW were found to possess the most inherent capacities providing baseline information for the prediction of serum albumin binding site. We believe that these associations may form the bedrock for establishing a solid correlation between the physicochemical properties and Albumin binding site architecture. Information presented in this report would serve as critical in provisions of rational drug designing as well as drug delivery, bioavailability, and pharmacokinetics.

Unveiling the molecular interactions between alkyl imidazolium ionic liquids and human serum albumin: Implications for toxicological significance

Alkyl imidazolium-based ionic liquids (ILs) are promising for diverse industrial applications; however, their growing prevalence has raised concerns regarding human exposure and potential health implications. A critical aspect to be clarified to address the adverse health effects associated with ILs exposure is their binding mode to human serum albumin (HSA). In this study, we delved into the binding interactions between three alkyl imidazolium ILs (1-hexyl-3-methyl-imidazolium (C6[MIM]), 1-ethyl-3-methyl-imidazolium chloride (C8[MIM]) and 1-decyl-3-methyl-imidazolium (C10[MIM]) and human serum albumins (HSAs) using a comprehensive approach encompassing molecular docking and multi-spectroscopy (UV-visible, Fluorescence, Circular Dichroism, FTIR). Furthermore, for the first time, we developed an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) approach time to quantify plasma protein binding rates. Our results revealed that the ILs primarily bind to the hydrophobic cavity of HSA through hydrogen bonding and van der Waals forces, forming stable complexes via static quenching. This affected HSA's secondary structure, reducing α-helical content, particularly around specific residues. Equilibrium dialysis and ultrafiltration coupled with UPLC-MS/MS analysis showed modest plasma protein binding rates (17.84%-31.85%) for the three ILs, with no significant influence from alkyl chain effects or concentration relationship. Lower plasma protein binding rates can affect bioavailability and distribution of ILs, potentially influencing their toxicity. These findings provide critical insights into the potential toxicological implications at the molecular level, thereby contributing to continuous efforts to evaluate the risk profiles and ensure the safe utilization of these compounds.

Exploring thyroxine binding globulin structural changes and its release from human hepatoblastoma cells upon interaction with silica particles: A prelude to unrevealing the mechanism of thyroid hormone dysregulation

Endocrine dysregulation in the presence of environmental chemical risk factors is a global adverse health concern. The aim of this investigation was to explore the structural changes and binding affinity of thyroxine (T4) binding protein (TBG) upon interaction with SiO2 particles as the second largest mineral in the Earth's crust and one of the most important constituents of rock, soil, and dust. Therefore, the interaction of TBG with SiO2 particles was assessed by fluorescence quenching, molecular docking, ANS and synchronous fluorescence, and far-UV CD analyses. Also, the release of TBG from human hepatoblastoma cell line, Hep G2, was assessed by ELISA assay. The results displayed that the value of stoichiometry of binding site (n) of TBG for T4 was approximately equal to one, which was reduced to 0.36 in the presence of SiO2 particles. Also, the binding affinity (Kb) values revealed that the binding affinity between T4 and TBG was strong (97.90 × 105 L/mol), while the presence of SiO2 particles resulted in the calculation of a Kb around 0.00159 × 105 L/mol, which was significantly lower than that of the absence of SiO2 particles. This data was also verified by molecular docking analyses which indicated that SiO2 particles interacted with the T4 binding pocket of TBG. Moreover, further studies exhibited that although the equimolar concentration of T4 to TBG resulted in the superior stability of TBG-T4 complex relative to free TBG, the presence of SiO2 particles with the same concentration led to denaturation of the secondary structure of TBG. Furthermore, it was seen that the amount of released TBG in the cell culture medium of Hep G2 was about 2.21 ng/mL protein, whereas this amount in SiO2 particles-treated cell group was significantly reduced to 1.71 ng/mL protein (*P < 0.05). In conclusion, this study implies that SiO2 particles show the potential to result in inhibition of TBG release, TBG denaturation, and interfere with TBG binding affinity which may lead to dysregulation of the thyroid hormone transport and associated signaling pathways.

Biophysical and docking study on the interaction of anticancer drugs encorafenib and binimetinib with human serum albumin

The utilization of BRAF and MEK inhibitors in combination therapy has demonstrated superior outcomes in the treatment of melanoma as compared to monotherapy. In the present scenario, the combination therapy of Encorafenib (ENC), a BRAF inhibitor, and Binimetinib (BINI), a MEK inhibitor, has been identified as one of the most efficacious treatment modalities for this malignancy. Investigations of protein binding, particularly with human serum albumin (HSA), are essential to understand drug performance and enhance therapeutic outcomes. The investigation of the interplay between small molecule drugs and HSA is of paramount importance, given that such interactions can exert a substantial influence on the pharmacokinetics of these therapeutic agents. The present study aims to bridge these lacunae by implementing a comprehensive approach that integrates fluorescence spectroscopy (FS), isothermal titration calorimetry (ITC), far-ultraviolet circular dichroism (far-UV CD), and molecular simulations. Through analysis of the fluorescence quenching of HSA at three distinct temperatures, it was ascertained that the association constants for the complexes formed between drugs and HSA were of the magnitude of 104 M-1. This suggests that the interactions between the compounds and albumin were moderate and comparable. Simultaneously, the investigation of fluorescence indicated a contrasting binding mechanism for the two inhibitors: ENC predominantly binds to HSA through enthalpic interaction, while BINI/HSA is stabilized by entropic contributions. The data obtained was confirmed through experimental procedures conducted using the ITC method. The results of ligand-competitive displacement experiments indicate that ENC and BINI can bind to HSA within subdomain IIA, specifically Sudlow site I. However, far-UV CD studies show that there are no notable alterations in the structure of HSA upon binding with either of the two inhibitors. Ultimately, the results were supported by computational molecular analysis, which identified the key interactions that contribute to the stabilization of the two ligand/HSA complexes.

Comparison of proanthocyanidins A2 and B2 on IgE-reactivity and epitopes in Gly m 6 using multispectral, LC/MS-MS and molecular docking

This study comparatively analyzed the changes in IgE-reactivity and epitopes in proanthocyanidins A2- (PA-Gly m 6) and B2-Gly m 6 (PB-Gly m 6) conjugates prepared by alkali treatment at 80 °C for 20 min. Similar to the western blot, ELISA also showed a higher reduced IgE-reactivity in PA-Gly m 6 (70.12 %) than PB-Gly m 6 (63.17 %). SDS-PAGE demonstrated that proanthocyanidins A2 caused more formation of >180 kDa polymers than proanthocyanidins B2. Multispectral analyses revealed that PA-Gly m 6 exhibited more structural alteration (e.g., a decrease of α-helical content and ANS fluorescence intensity) to unfold protein structure than proanthocyanidins B2, improving the accessibility to modify Gly m 6 for shielding or destroying conformational epitopes. LC/MS-MS revealed that PA-Gly m 6 conjugates had a lower abundance of allergens, peptides and linear epitopes than PB-Gly m 6 conjugates. Molecular docking showed that proanthocyanidins A2 and B2 reacted with Gln-317 and Asn-94 of epitopes, respectively. Overall, proanthocyanidins A2 is more effective than proanthocyanidins B2 to decrease the IgE-reactivity of Gly m 6 due to more shielding or destruction of conformational epitopes and lower content allergens and linear epitopes, which was attributed to more protein-crosslinks formation and structural changes in PA-Gly m 6 conjugates.

NADP/H binding nearly doubles the stability of a Mycobacterium drug target: an unfolding study

Mycobacterium Aspartate beta semialdehyde dehydrogenase (ASADH) was studied using various spectroscopic techniques and size exclusion chromatography to examine the unfolding of free (apo) and NADP/H-bound (holo) forms of ASADH. Non-cooperative guanidinium chloride (GdnHCl)-induced unfolding of the apo ASADH was discovered, and no partially folded intermediate structures were stabilized. On the other hand, it was observed that GdnHCl's unfolding of holoenzyme was a cooperative process without any stable intermediate structure. The native form of holoenzyme is found to be stable against the lower concentration of GdnHCl only (namely up to 1.25 M GdnHCl). The tryptophan environment appears to unfold cooperatively in case of the holoenzyme and is in well coordination with the overall unfolding of the holoenzyme. The presence of NADP/H shows a stabilizing effect on the tryptophan environment as well as on the native NADP/H-bound enzyme. Δ G Solvent o values reveal nearly two-fold (∼1.9) conformationally more stable folded holoenzyme compared to its native apo state. The Cm for the apo and holo forms of ASADH are 1.3 and 1.9 M, respectively. Novel drug leads targeting the NADP/H binding domain of ASADH could offer promising drugs against extremely infective Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.

Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study

Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO22+). A total of six sets of initial coordinates are used for Zn2+-HSA and UO22+-HSA system at pH = 4, 7.4 and 9, respectively. Enhance sampling method, namely, well-tempered meta-dynamics (WT-MtD) is employed to study the binding and un-binding processes of UO22+ and Zn2+ ions. Potential of mean force (PMF) profiles are generated for all the six sets of complexes from the converged WT-MtD run. Various basins and barriers are observed along the (un)binding pathways. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run at each basins and barriers for both the ions at all pH values. The binding of UO22+ ion with HSA is the result of the dynamical balance between UO22+-HSA and UO22+-water short range Coulomb interactions. Zn2+ ion interact more strongly than UO22+ at all pH through short range Coulomb interactions. PMF values further concludes that UO22+ cannot associate to the Zn2+ bound HSA protein but can be captured by free HSA at all pH values i.e. endosomal, alkaline and physiological pH.Communicated by Ramaswamy H. Sarma.

Comparative Molecular Analysis and Antigenicity Prediction of an Outer Membrane Protein (ompC) of Non-typhoidal Salmonella Serovars Isolated from Different Food Animals in Lagos, Nigeria

Non-typhoidal Salmonella (NTS) infections occur globally with high morbidity and mortality. The public health challenge caused is exacerbated by increasing rate of antibiotic resistance and absence of NTS vaccine. In this study, we characterized the outer membrane protein C (OmpC) serovars isolated from different food animals and predicted antigenicity. ompC of 27 NTS serovars were amplified by polymerase chain reaction (PCR) and sequenced. Sequence data were analysed and B-cell epitope prediction was done by BepiPred tool. T-cell epitope prediction was done by determining peptide-binding affinities of major histocompatibility complex (MHC) classes I and II using NetMHC pan 2.8 and NetMHC-II pan 3.2, respectively. ompC sequence analysis revealed conserved region among ompCs of Salmonella Serovars. A total of 66.7% of ompCs were stable with instability index value < 40 and molecular weight that ranged from 27 745.47 to 32 714.32 kDa. All ompCs were thermostable and hydrophilic with the exception of S. Pomona (14p) isolate that had ompC with GRAVY value of 0.028 making it hydrophobic. Linear B-cell epitope prediction revealed ability of ompC to elicit humoral immunity. Multiple B-cell epitopes that were exposed and buried were observed on several positions on the ompC sequences. T-cell epitope prediction revealed epitopes with strong binding affinity to MHC-I and -II. Strong binding to human leukocyte antigen (HLA-A) ligands, including HLA-A03:1, HLA-A24:02 and HLA-A26:01 in the case of MHC-I were observed. While binding affinity to H-2 IAs, H-2 IAq and H-2 IAu (H-2 mouse molecules) were strongest in the case of MHC-II. ompCs of NTS serovars isolated from different food animal sources indicated ability to elicit humoral and cell-mediated immunity. Hence, ompCs of NTS serovars are potential candidate for production of NTS vaccines.

The effect of novel tyrosine-modified polyethyleneimines on human albumin structure - Thermodynamic and spectroscopic study

The interaction of proteins with nanoparticle components are crucial for the evaluation of nanoparticle function, toxicity and biodistribution. Polyethyleneimines (PEIs) with defined tyrosine modifications are a class of novel polymers designed for improved siRNA delivery. Their interactions with biomacromolecules are still poorly described. This paper analyzes the interaction of different tyrosine-modified PEIs with human serum albumin as the most abundant serum protein. The ability of tyrosine modified, linear or branched PEIs to bind human serum albumin (HSA) was analyzed and further characterized. The interaction with hydrophobic parts of protein were studied using 1- nilinonaphthalene-8-sulfonic acid (ANS) and changes in the HSA secondary structure were evaluated using circular dichroism (CD). Complex formation and sizes were studied by transmission electron microscopy (TEM) and dynamic light scattering methods (DLS). We demonstrate that tyrosine modified PEIs are able to bind human serum albumin. Based on thermodynamic studies, van der Waals interaction, H-bonding and hydrophobic interactions are determined as main molecular forces involved in complex formation. Analysis of secondary structures revealed that the polymers decreased α-helix content, while increasing levels of randomly folded structures. Complex formation was confirmed by TEM and DLS. These findings are crucial for understanding polymer-protein interactions and the properties of nanoparticles.

Recombinant protein expression: Challenges in production and folding related matters

Protein folding is a biophysical process by which proteins reach a specific three-dimensional structure. The amino acid sequence of a polypeptide chain contains all the information needed to determine the final three-dimensional structure of a protein. When producing a recombinant protein, several problems can occur, including proteolysis, incorrect folding, formation of inclusion bodies, or protein aggregation, whereby the protein loses its natural structure. To overcome such limitations, several strategies have been developed to address each specific issue. Identification of proper protein refolding conditions can be challenging, and to tackle this high throughput screening for different recombinant protein folding conditions can prove a sound solution. Different approaches have emerged to tackle refolding issues. One particular approach to address folding issues involves molecular chaperones, highly conserved proteins that contribute to proper folding by shielding folding proteins from other proteins that could hinder the process. Proper protein folding is one of the main prerequisites for post-translational modifications. Incorrect folding, if not dealt with, can lead to a buildup of protein misfoldings that damage cells and cause widespread abnormalities. Said post-translational modifications, widespread in eukaryotes, are critical for protein structure, function and biological activity. Incorrect post-translational protein modifications may lead to individual consequences or aggregation of therapeutic proteins. In this review article, we have tried to examine some key aspects of recombinant protein expression. Accordingly, the relevance of these proteins is highlighted, major problems related to the production of recombinant protein and to refolding issues are pinpointed and suggested solutions are presented. An overview of post-translational modification, their biological significance and methods of identification are also provided. Overall, the work is expected to illustrate challenges in recombinant protein expression.

Iron response elements (IREs)-mRNA of Alzheimer's amyloid precursor protein binding to iron regulatory protein (IRP1): a combined molecular docking and spectroscopic approach

The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP IRE mRNA∙IRP1 reveals that 11 residues are involved in hydrogen bonding as the main driving force for the interaction. Fluorescence binding results revealed a strong interaction between APP IRE mRNA and IRP1 with a binding affinity and an average binding sites of 31.3 × 10⁶ M^-1 and 1.0, respectively. Addition of Fe²⁺(anaerobic) showed a decreased (3.3-fold) binding affinity of APP mRNA∙IRP1. Further, thermodynamic parameters of APP mRNA∙IRP1 interactions were an enthalpy-driven and entropy-favored event, with a large negative ΔH (-25.7 ± 2.5 kJ/mol) and a positive ΔS (65.0 ± 3.7 J/mol·K). A negative ΔH value for the complex formation suggested the contribution of hydrogen bonds and van der Waals forces. The addition of iron increased the enthalpic contribution by 38% and decreased the entropic influence by 97%. Furthermore, the stopped-flow kinetics of APP IRE mRNA∙IRP1 also confirmed the complex formation, having the rate of association (k_on) and the rate of dissociation (k_off) as 341 μM^-1 s^-1, and 11 s^-1, respectively. The addition of Fe²⁺ has decreased the rate of association (k_on) by ~ three-fold, whereas the rate of dissociation (k_off) has increased by ~ two-fold. The activation energy for APP mRNA∙IRP1 complex was 52.5 ± 2.1 kJ/mol. The addition of Fe²⁺ changed appreciably the activation energy for the binding of APP mRNA with IRP1. Moreover, circular dichroism spectroscopy has confirmed further the APP mRNA∙IRP1 complex formation and IRP1 secondary structure change with the addition of APP mRNA. In the interaction between APP mRNA and IRP1, iron promotes structural changes in the APP IRE mRNA∙IRP1 complexes by changing the number of hydrogen bonds and promoting a conformational change in the IRP1 structure when it is bound to the APP IRE mRNA. It further illustrates how IRE stem-loop structure influences selectively the thermodynamics and kinetics of these protein-RNA interactions.

Binding order and apparent binding affinity in the bisubstrate activity of strictosidine synthase

The Rauvolfia serpentina strictosidine synthase (RsSTR) enzyme with a bisubstrate activity is central to monoterpenoid indole alkaloid (MIA) biosynthesis pathways, as it stereoselectively condenses the terpenoid and indole metabolites, secologanin and tryptamine, respectively, into strictosidine. Here, cooperativity was aimed to be deciphered by proxy with help of a non-substrate tryptamine analog (decoy compound) to allow a bisubstrate binding without reaction, facilitating an isothermal titration calorimetry (ITC)-based analysis of the effect of the presence of one substrate on the binding of the other. Tryptamine and tryptamine analog bound to RsSTR with similar binding affinities (Kd). On the contrary, ITC revealed an exothermic titration of secologanin to RsSTR but could not fully quantify it because of weak binding. Interestingly, secologanin bound to RsSTR with an apparent binding affinity (Kd,app) of 212.1 μM in the presence of the decoy compound, as opposed to a lack of binding to RsSTR alone, strongly suggesting a "tryptamine-first" mode of binding. Conversely, binding of tryptamine analog in the presence of secologanin was enhanced >3-fold. Further, molecular dynamics simulation (MDS) analyses revealed the conformational flexibility needed for such cooperativity. Our binding studies complemented with the computational analyses suggested cooperativity in the ordered bisubstrate binding to RsSTR. Therefore, understanding thermodynamics and cooperativity in the binding of substrates or ligands would help to unravel the mechanism of enzyme catalysis and ligand-receptor interactions, and would guide the redesign of enzymes for enhanced properties and the design of inhibitors against enzymes and receptors.Communicated by Ramaswamy H. Sarma.

Molecular interactions between bovine serum albumin (BSA) and trihalophenol: Insights from spectroscopic, calorimetric and molecular modeling studies

The issue of disinfection byproducts (DBPs) in the water has received critical attention due to the health effects on humans. In the water environment, interactions between bovine serum albumins (BSA), the most abundant water-soluble protein, and DBPs unavoidably occur. In this study, comparative binding interactions of two aromatic DBPs - 2,4,6-trichlorophenol (TCP) and 2,4,6-tribromophenol (TBP) with BSA were investigated systematically utilizing fluorescence spectrometry, UV absorption spectrometry, isothermal titration calorimetry and molecular docking approach. The fluorescence quenching results indicated that TCP/TBP could quench the endogenous fluorescence of BSA through static quenching mechanisms, and TBP showed a more substantial quenching effect. The binding constants were determined for TCP-BSA (3.638 × 10⁵ L/mol, 303 K) and TBP-BSA (6.394 × 10⁵ L/mol, 303 K) complexes, with TBP showing higher binding affinity than TCP. The thermodynamic study and docking analysis suggested that hydrogen bonding and van der Waals forces were the primary interaction forces. Both of TCP and TBP were located in the subdomain IIIA of BSA, and TBP could form more stable complex than TCP. The results of the present study contributed valuable information on the environmental behaviors of halophenols in water environment from perspectives of binding with BSA.

Multi technique investigation on interaction between 5-(2-thiazolylazo)-2,4,6-triaminopyrimidine and HSA and BSA

In research laboratories and in various industries, azo compounds are among the most effective and commonly used organic dyes. The association between human (HSA) and bovine (BSA) serum albumins with 5-(2-thiazolylazo)-2,4,6-triaminopyrimidine (TTP) was investigated in this research using spectroscopy methods and molecular modeling study. The fluorescence quenching results showed that the quenching mechanisms were static and dynamic processes for HSA and BSA, respectively. From the thermodynamic observations, it is clear that the binding process is a spontaneous molecular interaction, in which van der Waals and hydrogen bonding interactions for HSA and hydrophobic interaction for BSA play the major roles. According to Förster energy transfer, non-radiative energy transferred from HSA and BSA to TTP, is provided by close distance (r₀) between TTP and Trp residues of HSA and BSA. The synchronous fluorescence spectroscopy, FT-IR findings and UV-Vis absorption data confirm that TTP can induce conformational and micro environmental changes in both the proteins. Furthermore, docking results predicted the probable binding site of TTP in subdomain IIA of HSA and BSA molecules where Trp residues are located. Types of amino acid residues surrounding the TTP molecule supported that van der Waals forces, hydrophobic forces and electrostatic forces play important roles in stabilization of drug-protein complexes formed.Communicated by Ramaswamy H. Sarma.

Thermofluor-Based Optimization Strategy for the Stabilization of Recombinant Human Soluble Catechol-O-Methyltransferase

Catechol-O-methyltransferase (COMT) has been involved in a number of medical conditions including catechol-estrogen-induced cancers and a great range of cardiovascular and neurodegenerative diseases such as Parkinson's disease. Currently, Parkinson's disease treatment relies on a triple prophylaxis, involving dopamine replacement by levodopa, the use of aromatic L-amino acid decarboxylase inhibitors, and the use of COMT inhibitors. Typically, COMT is highly thermolabile, and its soluble isoform (SCOMT) loses biological activity within a short time span preventing further structural and functional trials. Herein, we characterized the thermal stability profile of lysate cells from Komagataella pastoris containing human recombinant SCOMT (hSCOMT) and enzyme-purified fractions (by Immobilized Metal Affinity Chromatography-IMAC) upon interaction with several buffers and additives by Thermal Shift Assay (TSA) and a biological activity assessment. Based on the obtained results, potential conditions able to increase the thermal stability of hSCOMT have been found through the analysis of melting temperature (T_m) variations. Moreover, the use of the ionic liquid 1-butyl-3-methylimidazolium chloride [C₄mim]Cl (along with cysteine, trehalose, and glycerol) ensures complete protein solubilization as well as an increment in the protein Tm of approximately 10 °C. Thus, the developed formulation enhances hSCOMT stability with an increment in the percentage of activity recovery of 200% and 70% when the protein was stored at 4 °C and -80 °C, respectively, for 12 h. The formation of metanephrine over time confirmed that the enzyme showed twice the productivity in the presence of the additive. These outstanding achievements might pave the way for the development of future hSCOMT structural and biophysical studies, which are fundamental for the design of novel therapeutic molecules.

Interactions between stipuol enantiomers and human serum albumin

Natural polyacetylenes occur in food and herbal plants, have a wide range of bioactivities, and are recognized as important nutraceuticals. Stipuol is a natural polyacetylene present in the edible plant Panax notoginseng. The present study was aimed to study interactions of rac-stipuol and its enantiomers with human serum albumin (HSA) using multi-spectroscopic, molecular modeling and microscale thermophoresis. Steady-state and time-resolved fluorescence spectra manifest that the fluorescence quenching mechanism is mainly static in type. The bindings of (S)-stipuol, (R)-stipuol, rac-stipuol lead to some microenvironmental and slight conformational changes of HSA. Competitive ligand displacement experiments and molecular modeling studies revealed that stipuol enantiomers bind to HSA at subdomain III (site IIA). The calculated values of K_a and K_d showed that (R)-stipuol had a stronger binding affinity than (S)-stipuol. The results are informative for use of stipuol as a nutraceutical to improve human health.

An insight into the interaction between Indisulam and human serum albumin: Spectroscopic method, computer simulation and in vitro cytotoxicity assay

Indisulam (IDM) is a sulfanilamide anticancer agent and has been identified as a molecular glue recently. It shows potential for novel therapies development and brings more hope for curing human diseases. The affinity between molecular glues and plasma protein makes it significant to understand the characteristics of such substances. Therefore, the interaction between IDM and human serum albumin (HSA) was explored through solvent experiments, computer simulation experiments, enzyme kinetics experiments, and cell viability assay. The results revealed that IDM and HSA spontaneously formed stable binary complex with the binding constant of the order 10⁵ M^-1. IDM inserted in the site I of HSA, resulting the change in HSA secondary structure. And π electrons in IDM's benzene rings, as well as van der Waals forces and the H-bond, all helped to stabilize the HSA-IDM complex. The results of molecular dynamic simulation (MD) corresponded with the results from solvent experiment well. For instance, there were approximately 1-5 H-bonds between IDM and HSA. Lys199 and Arg218 were crucial energy contributors in the binding process. The esterase-like activity experiment confirmed that IDM inhibited the catalytic activity of HSA. In addition, cell experiment revealed that serum albumin can significantly reduce the cytotoxicity of IDM towards human embryonic kidney 293T (HEK293T) cells.

Probing the potential toxicity by characterizing the binding mechanism of sodium dehydroacetate to human serum albumin

BACKGROUND

Sodium dehydroacetate (DHA-S) is a common food additive, which can combine with serum proteins in the plasma, but the interaction mechanism between DHA-S and human serum albumin (HSA) is unclear. In this study, multiple spectroscopy techniques, isothermal titration calorimetry (ITC), molecular docking and esterase activity test were employed to investigate the interaction mechanism of DHA-S and HSA.

RESULTS

A DHA-S-HSA complex was formed and the structure of HSA were altered by DHA-S. Since DHA-S changed the tight structure of the hydrophobic subdomain IIA where tryptophan (Trp) was placed, the hydrophobicity of the microenvironment of HSA was enhanced. With the addition of DHA-S, the skeleton structure of HSA became loose and the solvent shell on the HSA surface was destroyed. DHA-S altered the secondary structure of HSA, resulting in the decreased α-helix and increased β-sheet contents. The interaction was exothermic and spontaneous driven by van der Waals and hydrogen bonding. DHA-S inhibited the esterase activity of HSA. Molecular docking demonstrated that the binding site of DHA-S on HSA located at the cavity of subdomains IIA and IIIA, but the amino acids related to esterase activity of HSA were not in the binding pocket, indicating that the mechanism by which DHA-S inhibited HSA esterase activity was the change in protein structure.

CONCLUSION

This study illustrated that DHA-S interacted with HSA and the structure and function of HSA were affected by DHA-S. This research could help to understand the toxicity of DHA-S and provide basic data for safe use of food additives. © 2021 Society of Chemical Industry.

Exploring the interaction between Cry1Ac protein and Zn2+, Cd2+ metal ions by fluorescence quenching and molecular docking approaches

Bacillus Thuringiensis (Bt) protein has a strong ability to complex with metal ions, which may increase the transport of metal ions in the soil multi-media system. In this study, the interactions between Cry1Ac protein and metal ions (Zn²⁺ and Cd²⁺) were investigated through spectroscopies and molecular docking methods. The spectra results showed that both Zn²⁺ and Cd²⁺ quenched the fluorescence intensity of Cry1Ac protein through the static quenching. The binding constants with 4-5 orders of magnitude also indicated the interactions between the ions and the Cry1Ac protein. The thermodynamic analysis showed that hydrogen bonds and van der Waals forces were predominant during the processes. In terms of the Förster non-radiation energy transfer theory, the binding distances between metal ions and Cry1Ac protein were approximately 0.21-0.24 nm, indicating the existence of a non-radiative energy transfer between them. Furthermore, molecular docking revealed that the metal ions participated in ligand binding with the Cry1Ac at the locations Asp569, Thr560, Asn564 and Gln566. The present work provided reasonable models helping us further understand the transport effect of heavy metals in the presence of Cry1Ac. The results could provide mechanistic insights into the nature of metal ions-Cry1Ac interactions and offer important information on the toxicity risk of metal ions-Cry1Ac binding interactions.

Multi-Spectroscopic, thermodynamic and molecular docking studies to investigate the interaction of eplerenone with human serum albumin

The binding of small molecular drugs with human serum albumin (HSA) has a crucial influence on their pharmacokinetics. The binding interaction between the antihypertensive Eplerenone (EPL)and HSA was investigated using multi-spectroscopic techniques for the first time. These techniques include UV-Vis spectroscopy, Fourier Transform Infrared (FT-IR), native fluorescence spectroscopy, synchronous fluorescence spectroscopy and molecular docking approach. The fluorescence spectroscopic study showed that EPL quenched HSA inherent fluorescence. The mechanism for quenching of HSA by EPL has been determined to be static in nature and confirmed by UV absorption and fluorescence spectroscopy. The modified Stern-Volmer equation was used to estimate the binding constant (K_b ) as well as the number of bindings (n). The results indicated that the binding occurs at a single site (Kb;2.238 x 10³ L mol^-1 at 298 K). The enthalpy and entropy changes (∆H and ∆S) were 58.061 and 0.258 K J mol^-1 , respectively, illustrating that the principal intermolecular interactions stabilizing the EPL-HSA system are hydrophobic forces. Synchronous fluorescence spectroscopy revealed that EPL binding to HSA occurred around the tyrosine residue (Tyr) and this agreed with the molecular docking study. The FRET analysis confirmed the static quenching mechanism. The esterase enzyme activity of HSA was also evaluated showing its decrease in the presence of EPL. Furthermore, docking analysis and site-specific markers experiment revealed that EPL binds with HSA at subdomain IB (site III).

An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials

Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.

The inhibitory effects of natural antioxidants on protein glycation as well as aggregation induced by methylglyoxal and underlying mechanisms

The non-enzymatic glycation of protein can result in the formation of advanced glycation end-products (AGEs), leading to the deposition of amyloid proteins, and it's essential for the pathogenesis of diabetes complications and amyloid diseases. Reactive dicarbonyl compounds, such as methylglyoxal (MGO), are one of the most reactive glycating agents. Therefore, it's crucially necessary to inhibit protein glycation and aggregation induced by MGO. In the present study, we aimed to systemically investigate the anti-glycation and anti-fibrillization activities of eight natural antioxidants, including apigenin, quercetin (Que), catechin, resveratrol (Res), and gallic acid (GA), L-ascorbic acid (L-AA), limonene, and β-carotene, during MGO-induced protein glycation and aggregation. Furthermore, the underlying mechanisms were clarified. The formation of AGEs and the degree of protein aggregation were characterized by optical detection, flow cytometry, and so on. The results demonstrated that eight selected natural antioxidants could inhibit glycation and protein aggregation induced by MGO via the synergy of scavenging free radicals, capturing MGO, and interacting with proteins, among which GA (300 μM) and Res (15 μM) had higher inhibition rates on both argpyrimidine (specific fluorescent AGEs, 17% and 22%, respectively) and protein amyloid aggregation (42% and 29%, respectively). These findings suggested that antioxidants could act as potential inhibitors of AGEs and glycation-induced protein aggregation, which were expected to become a new strategy for the prevention and treatment of diabetes and amyloid diseases. Besides, these inhibition mechanisms provided valuable insights into the design and development of candidate drugs for the prevention and treatment of AGEs and protein aggregation-related diseases.

Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches

Sumatriptan (SUM), a serotonin activator used to treat migraines and cluster headaches. Molecular spectroscopic methods including fluorescence quenching, time dependent fluorescence, FRET, absorption, circular dichroism, differential scanning calorimetric and computational approaches were employed to unravel the interaction between sumatriptan and bovine serum albumin (BSA). The fluorescence quenching studies suggested the interaction between SUM and BSA with a moderate binding with the binding constant (K_b) in the order of 10⁴. The findings of temperature and time dependent fluorescence quenching studies confirmed the role of static quenching mechanism. Thermodynamic parameters suggested the key role of electrostatic force in the interaction of SUM with BSA. Absorption and CD spectral studies revealed the bioenvironmental changes around the Trp in BSA upon binding of SUM. Calorimetric based thermal denaturation results confirmed that the thermal stability of BSA was improved in the presence of SUM. resulted in the this decreased flexibility of protein chain. Site competitive studies indicated SUM was located in the hydrophobic cavity of site I which was further confirmed by the docking and dynamic simulation studies. Additionally, molecular dynamics simulations inferred the microenvironmental condition around the SUM and the amino acids and forces involved in the binding of SUM with BSA.Communicated by Ramaswamy H. Sarma.

Luminescence studies of binding affinity of vildagliptin with bovine serum albumin

Vildagliptin (VDG)is a frontier drug for diabetes mellitus. It is prescribed both in the monotherapy as well as in an amalgamation with other antidiabetic drugs. Drug-serum protein binding is an essential parameter which influences ADME properties of the drug. In current study, binding of VDG with serum protein (bovine serum albumin: BSA) was investigated using multi-spectroscopic techniques. A computational approach was also employed to identify the binding affinity of VDG with BSA at both Sudlow I and II sites. An enzyme activity assay specific for esterase was also investigated to know the post-binding consequences of VDG with BSA. Fluorescence spectra of BSA samples treated with VDG shows static quenching with binding parameters for VDG-BSA complex show single class of equivalent binding stoichiometry(n = 1.331) and binding constant 1.1 x 10⁴M^-1 at 298.15 K. The binding constant indicates important role of non-polar interactions in the binding process. Fluorescence resonance energy transfer (FRET) analysis of VDG absorption spectra and emission spectrum of BSA confirmed no significant resonance in energy transfer. Synchronous fluorescence of BSA after binding with VDG show maximum changes in emission intensity at tryptophan (Trp) residues. Post binding with VDG, BSA conformation changes as suggested by circular dichorism (CD) spectra of BSA and this lead to enhanced protein stability as indicated by a thermal melting curve of BSA.Communicated by Ramaswamy H. Sarma.