Stereoselective and domain-specific effects of ibuprofen on the thermal stability of human serum albumin

Thermal effects and drugs competition on the palmitate binding capacity of human serum albumin

Human serum albumin (HSA) is the most abundant plasma protein of the circulatory system. It is a multidomain, multifunctional protein that, combining diverse affinities and wide specificity, binds, stores, and transports a variety of biological compounds, pharmacores, and fatty acids. HSA is finding increasing uses in drug-delivery due to its ability to carry functionalized ligands and prodrugs. All this raises the question of competition for binding sites occupancy in case of multiple ligands, which in turn influences the protein structure/dynamic/function relationship and also has an impact on the biomedical applications. In this work, the effects of interactive binding of palmitic acid (PA), warfarin (War) and ibuprofen (Ibu) on the thermal stability of HSA were studied using DSC, ATR-FTIR, and EPR. PA is a high-affinity physiological ligand, while the two drugs are widely used for their anticoagulant (War) and anti-inflammatory (Ibu) efficacy, and are exogenous compounds that accommodate in the deputed drug site DS1 and DS2, respectively overlapping with some of the fatty acid binding sites. The results indicate that HSA acquires the highest thermal stability when it is fully saturated with PA. The binding of this physiological ligand does not hamper the binding of War or Ibu to the native state of the protein. In addition, the three ligands bind simultaneously, suggesting a synergic cooperative influence due to allosteric effects. The increased thermal stability subsequent to binary and multiple ligands binding moderates protein aggregation propensity and restricts protein dynamics. The biophysics findings provide interesting features about protein stability, aggregation, and dynamics in interaction with multiple ligands and are relevant in drug-delivery.

Role of the Human Serum Albumin Protein Corona in the Antimicrobial and Photothermal Activity of Metallic Nanoparticles against Escherichia coli Bacteria

The emergence of antibiotic-resistant bacteria has become a major public health concern, leading to growing interest in alternative antimicrobial agents. The antibacterial activity of metal nanoparticles (NPs) has been extensively studied, showing that they can effectively inhibit the growth of various bacteria, including both Gram-positive and -negative strains. The presence of a protein corona, formed by the adsorption of proteins onto the NP surface in biological fluids, can significantly affect their toxicity. Understanding the effect of the protein corona on the antimicrobial activity of metal NPs is crucial for their effective use as antimicrobial agents. In this study, the antimicrobial activity of noble metal NPs, such as platinum (Pt), silver (Ag), and gold (Au) with and without the human serum albumin (HSA) protein corona against Escherichia coli strains, was investigated. In addition, the plasmonic photothermal effect related to AuNPs, which resulted to be the most biocompatible compared to the other considered metals, was evaluated. The obtained results suggest that the HSA protein corona modulated the antimicrobial activity exerted by the metal NPs against E. coli bacteria. These findings may pave the way for the investigation and development of innovative nanoapproaches to face antibiotic resistance emergence.

Characterization of Climbazole-Bovine serum albumin interaction by experimental and in silico approaches

Interactive association of an antifungal drug, climbazole (CBZ) with the carrier protein in bovine circulation, bovine serum albumin (BSA) was explored by fluorescence and absorption spectroscopy along with in silico techniques. The fluorescence and absorption spectral alterations of the protein upon addition of CBZ affirmed the complex foration between CBZ and BSA. The inverse temperature dependence behaviour of the K_SV values as well as the hyperchromic result of the protein's absorption signals characterized CBZ-triggered quenching of BSA fluorescence as the static quenching. A weak binding affinity (K_a = 3.12-1.90-× 10³ M^-1) was reported towards the CBZ-BSA association process. Interpretation of thermodynamic data (entropy change = +14.68 J mol^-1 K^-1 and enthalpy change = -15.07 kJ mol^-1) and in silico analyses anticipated that hydrophobic forces, van der Waals forces and hydrogen bonds were the key intermolecular forces in the complex stabilization. Inclusion of CBZ to BSA produced microenvironmental perturbations around Tyr and Trp residues, and also significantly defended temperature-induced destabilization of BSA. The binding locus of CBZ was detected in the proximity of Sudlow's sites I (subdomain IIA) and II (subdomain IIIA) of BSA, exhibiting greater preference towards site II, as revealed by competitive site-marker displacement investigations and in silico analysis. The stability of the CBZ-BSA complex was further validated by the molecular dynamics simulation assessments.

The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4

Plakophilin 1 (PKP1), a member of the armadillo repeat family of proteins, is a key structural component of cell-cell adhesion scaffolds, although it can also be found in other cell locations, including the cytoplasm and the nucleus. PADI4 (peptidyl-arginine deiminase 4) is one of the human isoforms of a family of enzymes engaged in the conversion of arginine to citrulline, and is present in monocytes, macrophages, granulocytes, and in several types of cancer cells. It is the only family member observed both within the nucleus and the cytoplasm under ordinary conditions. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with PADI4, by using several biophysical methods, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular simulations; furthermore, binding was also tested by Western-blot (WB) analyses. Our results show that there was binding between the two proteins, with a dissociation constant in the low micromolar range (∼ 1 μM). Molecular modelling provided additional information on the possible structure of the binding complex, and especially on the binding hot-spot predicted for PADI4. This is the first time that the interaction between these two proteins has been described and studied. Our findings could be of importance to understand the development of tumors, where PKP1 and PADI4 are involved. Moreover, our findings pave the way to describe the formation of neutrophil extracellular traps (NETs), whose construction is modulated by PADI4, and which mediate the proteolysis of cell-cell junctions where PKP1 intervenes.

Ibuprofen Favors Binding of Amyloid-β Peptide to Its Depot, Serum Albumin

The deposition of amyloid-β peptide (Aβ) in the brain is a critical event in the progression of Alzheimer’s disease (AD). This Aβ deposition could be prevented by directed enhancement of Aβ binding to its natural depot, human serum albumin (HSA). Previously, we revealed that specific endogenous ligands of HSA improve its affinity to monomeric Aβ. We show here that an exogenous HSA ligand, ibuprofen (IBU), exerts the analogous effect. Plasmon resonance spectroscopy data evidence that a therapeutic IBU level increases HSA affinity to monomeric Aβ₄₀/Aβ₄₂ by a factor of 3–5. Using thioflavin T fluorescence assay and transmission electron microcopy, we show that IBU favors the suppression of Aβ₄₀ fibrillation by HSA. Molecular docking data indicate partial overlap between the IBU/Aβ₄₀-binding sites of HSA. The revealed enhancement of the HSA–Aβ interaction by IBU and the strengthened inhibition of Aβ fibrillation by HSA in the presence of IBU could contribute to the neuroprotective effects of the latter, previously observed in mouse and human studies of AD.

Evaluating phospholipid- and protein-water partitioning of two groups of chemicals of emerging concern: Diastereo- and enantioselectivity

The partitioning between phospholipids/proteins and water can be used to predict the bioaccumulation potential of chemicals with better accuracy compared with n-octanol-water partition coefficient. However, such partitioning is poorly understood for chiral chemicals, many of which exhibit differential bioaccumulation and toxicity potential between enantiomers. In this study, the enantiospecific liposome-water and bovine serum albumin (BSA)-water partition coefficients (Klip/w and KBSA/w, determined at 25 ℃ and 37 ℃, respectively) were measured by equilibrium dialysis for α-, β-, and γ-hexabromocyclododecane (HBCD) and three β-blockers (propranolol, metoprolol, and sotalol). Raman and fluorescence analyses and molecular docking were conducted to provide additional insights into the partitioning process. Results showed α- and β-HBCD displayed stronger enantioselective partitioning to liposomes with the (-)-form, while (-)-α-HBCD, R-(+)-propranolol, R-(+)-metoprolol, and E2-sotalol favored partitioning to BSA compared with their antipodes. Raman spectra revealed α- and γ-HBCD enhanced and reduced the organization of liposome acyl chains, respectively, and polar interactions enhanced the liposome partitioning of β-blockers. Fluorescence spectra indicated the changed tryptophan microenvironment might influence the BSA steric effect toward HBCD, and electrostatic interactions dominated the formation of BSA-β-blocker complexes. Molecular docking results supported the difference in the thermodynamic nature of interaction between the studied enantiomers and BSA.

Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena

Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.

Interactive multiple binding of oleic acid, warfarin and ibuprofen with human serum albumin revealed by thermal and fluorescence studies

Human serum albumin binds a wide variety of drugs with different structure and affinity to two main binding sites, drug site 1 (DS1) and drug site 2 (DS2), which partially or totally overlap with fatty acid (FA) sites. Although multiple binding sites are available for endogenous compounds, FAs are the primary physiological ligands of albumin and their competition in the occupancy of DS1 and DS2 affects the binding of exogenous molecules, with a possible impact on drug delivery. In this work, we have investigated the simultaneous binding of oleic acid, warfarin and ibuprofen to albumin using differential scanning calorimetry and fluorescence to evaluate the impact on the conformational stability of the protein. The two drugs are widely used for their anticoagulant (warfarin) and anti-inflammatory (ibuprofen) properties, and can be also considered as site markers to probe DS1 and DS2, respectively. Oleic acid is one of the most important fatty acids from a physiological point of view for its role as a source of energy for cells, and also it binds albumin with the highest association constant. When complexed with oleic acid the calorimetric profile of albumin shows a biphasic trend whose line shape depends on the ligand concentration. The binding capacity of either warfarin or ibuprofen to albumin is modulated by oleate molecules in a concentration-dependent mode being synergic cooperative (warfarin) or competitive-like (ibuprofen). The overall results provide insights on the dynamics of albumin/ligands complex, which in turn may have important pharmacokinetic and pharmacodynamic implications.

Design of Inhibitors of the Intrinsically Disordered Protein NUPR1: Balance between Drug Affinity and Target Function

Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of several tumors. We have previously repurposed trifluoperazine (TFP) as a drug targeting NUPR1 and, by using a ligand-based approach, designed the drug ZZW-115 starting from the TFP scaffold. Such derivative compound hinders the development of pancreatic ductal adenocarcinoma (PDAC) in mice, by hampering nuclear translocation of NUPR1. Aiming to further improve the activity of ZZW-115, here we have used an indirect drug design approach to modify its chemical features, by changing the substituent attached to the piperazine ring. As a result, we have synthesized a series of compounds based on the same chemical scaffold. Isothermal titration calorimetry (ITC) showed that, with the exception of the compound preserving the same chemical moiety at the end of the alkyl chain as ZZW-115, an increase of the length by a single methylene group (i.e., ethyl to propyl) significantly decreased the affinity towards NUPR1 measured in vitro, whereas maintaining the same length of the alkyl chain and adding heterocycles favored the binding affinity. However, small improvements of the compound affinity towards NUPR1, as measured by ITC, did not result in a corresponding improvement in their inhibitory properties and in cellulo functions, as proved by measuring three different biological effects: hindrance of the nuclear translocation of the protein, sensitization of cells against DNA damage mediated by NUPR1, and prevention of cancer cell growth. Our findings suggest that a delicate compromise between favoring ligand affinity and controlling protein function may be required to successfully design drugs against NUPR1, and likely other IDPs.

Sub-Micromolar Inhibition of SARS-CoV-2 3CLpro by Natural Compounds

Inhibiting the main protease 3CLpro is the most common strategy in the search for antiviral drugs to fight the infection from SARS-CoV-2. We report that the natural compound eugenol is able to hamper in vitro the enzymatic activity of 3CLpro, the SARS-CoV-2 main protease, with an inhibition constant in the sub-micromolar range (K_i = 0.81 μM). Two phenylpropene analogs were also tested: the same effect was observed for estragole with a lower potency (K_i = 4.1 μM), whereas anethole was less active. The binding efficiency index of these compounds is remarkably favorable due also to their small molecular mass (MW < 165 Da). We envision that nanomolar inhibition of 3CLpro is widely accessible within the chemical space of simple natural compounds.

Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned randomly and distant from the binary complex (HSA-warfarin) in a physiologically relevant concentration. The results obtained from both approaches indicated that s-ibuprofen and ascorbic acid both displayed allosteric effects on the release of warfarin from HSA. Although ascorbic acid aided in warfarin release, leading to destabilization of HSA, ibuprofen demonstrated a stabilizing effect on releasing the anticoagulant drug through several noncovalent interactions, including hydrophobic, electrostatic, and hydrogen-bonding interactions with the protein. The calculated binding free energy and energy contribution of involved residues using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method, along with root mean square deviation (RMSD) values, protein gyration, and free energy surface (FES) mapping of the protein, provided valuable details on the nature of the interactions of each drug on the release of warfarin from HSA. These results can provide important information on the mechanisms of anticoagulant release that has not been revealed in molecular details previously.

Biomolecular interaction mechanism of an anticancer drug, pazopanib with human serum albumin: a multi-spectroscopic and computational approach

Pazopanib (PZP) is a multi-targeting tyrosine kinase inhibitor and is currently approved by FDA for the treatment of soft tissue sarcoma and renal cancer. Molecular interaction mechanism of PZP with human serum albumin (HSA) was explored under simulated physiological conditions (pH = 7.4), using fluorescence and UV absorption spectroscopy along with computational methods. Based on the inverse correlation between the Stern-Volmer constant (K_sv) and temperature, it was concluded that PZP quenched the protein fluorescence through static quenching mechanism. This was also confirmed from the UV-vis absorption spectral results. Moderate binding affinity between PZP and HSA was evident from the K_a values (5.51 - 1.05 × 10⁵ M^-1) while PZP-HSA complex formation was driven by hydrophobic and van der Waals interactions as well as hydrogen bonds, as revealed by positive entropy change (ΔS = +98.37 J mol^-1 K^-1) and negative enthalpy change (ΔH = -60.31 kJ mol^-1). Three-dimensional fluorescence spectral results disclosed microenvironmental perturbations around Trp and Tyr residues of the protein upon PZP binding. Interestingly, the addition of PZP to HSA significantly protected the protein against thermal stress. Competitive drug displacement results obtained with warfarin, phenylbutazone and diazepam elucidated Sudlow's Site I, positioned in subdomain IIA of HSA, as the preferred binding site of PZP which was well supported by molecular docking analysis, while molecular dynamics simulation results suggested the stability of the PZP-HSA complex.Communicated by Vsevolod Makeev.

The armadillo-repeat domain of plakophilin 1 binds the C-terminal sterile alpha motif (SAM) of p73

BACKGROUND

Plakophilin 1 (PKP1) is a component of desmosomes, which are key structural components for cell-cell adhesion, and can also be found in other cell locations. The p53, p63 and p73 proteins belong to the p53 family of transcription factors, playing crucial roles in tumour suppression. The α-splice variant of p73 (p73α) has at its C terminus a sterile alpha motif (SAM); such domain, SAMp73, is involved in the interaction with other macromolecules.

METHODS

We studied the binding of SAMp73 with the armadillo domain of PKP1 (ARM-PKP1) in the absence and the presence of 100 mM NaCl, by using several biophysical techniques, namely fluorescence, far-ultraviolet circular dichroism (CD), nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), and molecular docking and simulations.

RESULTS

Association was observed between the two proteins, with a dissociation constant of ~5 μM measured by ITC and fluorescence in the absence of NaCl. The binding region of SAMp73 involved residues of the so-called "middle-loop-end-helix" binding region (i.e., comprising the third helix, together with the C terminus of the second one, and the N-cap of the fourth), as shown by ¹⁵N, ¹H- HSQC-NMR spectra. Molecular modelling provided additional information on the possible structure of the binding complex.

CONCLUSIONS

This newly-observed interaction could have potential therapeutic relevance in the tumour pathways where PKP1 is involved, and under conditions when there is a possible inactivation of p53.

GENERAL SIGNIFICANCE

The discovery of the binding between SAMp73 and ARM-PKP1 suggests a functional role for their interaction, including the possibility that SAMp73 could assist PKP1 in signalling pathways.

Thermal Liquid Biopsy (TLB) of Blood Plasma as a Potential Tool to Help in the Early Diagnosis of Multiple Sclerosis

Background: Multiple sclerosis (MS) is frequently characterized by a variety of clinical signs, often exhibiting little specificity. The diagnosis requires a combination of medical observations and instrumental tests, and any support for its objective assessment is helpful. Objective: Herein, we describe the application of thermal liquid biopsy (TLB) of blood plasma samples, a methodology for predicting the occurrence of MS with a noninvasive, quick blood test. Methods: TLB allows one to define an index (TLB score), which provides information about overall real-time alterations in plasma proteome that may be indicative of MS. Results: This pilot study, based on 85 subjects (45 MS patients and 40 controls), showed good performance indexes (sensitivity and specificity both around 70%). The diagnostic methods better discriminate between early stage and low-burden MS patients, and it is not influenced by gender, age, or assumption of therapeutic drugs. TLB is more accurate for patients having low disability level (≤ 3.0, measured by the expanded disability status scale, EDSS) and a relapsing–remitting diagnosis. Conclusion: Our results suggest that TLB can be applied to MS, especially in an initial phase of the disease when diagnosis is difficult and yet more important (in such cases, accuracy of prediction is close to 80%), as well as in personalized patient periodic monitoring. The next step will be determining its utility in differentiating between MS and other disorders, in particular in inflammatory diseases.

Rutin Is a Low Micromolar Inhibitor of SARS-CoV-2 Main Protease 3CLpro: Implications for Drug Design of Quercetin Analogs

The pandemic, due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has stimulated the search for antivirals to tackle COVID-19 infection. Molecules with known pharmacokinetics and already approved for human use have been demonstrated or predicted to be suitable to be used either directly or as a base for a scaffold-based drug design. Among these substances, quercetin is known to be a potent in vitro inhibitor of 3CLpro, the SARS-CoV-2 main protease. However, its low in vivo bioavailability calls for modifications to its molecular structure. In this work, this issue is addressed by using rutin, a natural flavonoid that is the most common glycosylated conjugate of quercetin, as a model. Combining experimental (spectroscopy and calorimetry) and simulation techniques (docking and molecular dynamics simulations), we demonstrate that the sugar adduct does not hamper rutin binding to 3CLpro, and the conjugated compound preserves a high potency (inhibition constant in the low micromolar range, K_i = 11 μM). Although showing a disruption of the pseudo-symmetry in the chemical structure, a larger steric volume and molecular weight, and a higher solubility compared to quercetin, rutin is able to associate in the active site of 3CLpro, interacting with the catalytic dyad (His41/Cys145). The overall results have implications in the drug-design of quercetin analogs, and possibly other antivirals, to target the catalytic site of the SARS-CoV-2 3CLpro.

Biophysical and computational view on the in vitro combination between an anticancer drug, saracatinib and human serum albumin

Interaction behaviour of an anticancer drug, saracatinib (SCB) with human serum albumin (HSA), the major carrier protein in human blood circulation was investigated using fluorescence and absorption spectroscopy as well as computational methods. Analysis of the fluorescence quenching data along with absorption results confirmed the complex formation between SCB and HSA, based on the inverse correlation of the Stern-Volmer constant (K_SV) with temperature and hyperchromic effect in the absorption spectra. Moderate binding affinity between SCB and HSA was evident from the binding constant, K_a value (1.08-0.74 × 10⁴ M^-1), while the SCB-HSA complexation was anticipated to be stabilized by hydrophobic and van der Waals interactions along with hydrogen bonds, as revealed from the thermodynamic data (ΔS = + 29.40 J mol^-1 K^-1 and ΔH = - 13.90 kJ mol^-1). Addition of SCB to HSA significantly defended the thermal denaturation of the protein, though it perturbed the surrounding medium around Tyr and Trp residues. Site marker displacement results elucidated Sudlow's site I, positioned in subdomain IIA of HSA as the preferred binding site of SCB, which was well supported by molecular docking. Molecular dynamics simulation results suggested the stability of the SCB-HSA complex.Communicated by Ramaswamy H. Sarma.

Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution

BACKGROUND

Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility.

METHODS

We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD).

RESULTS

Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates.

CONCLUSIONS

The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species.

GENERAL SIGNIFICANCE

The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.

Anionic versus neutral Pt(II) complexes: The relevance of the charge for human serum albumin binding

The focus of this work is pointing out the different behavior of two structurally related Pt^(II) complexes, the anionic cyclometalated NBu₄[(Bzq)Pt(Thio)], 1 and the neutral [(Phen)Pt(Thio)], 2, (Bzq = benzo[h]quinoline, Phen = 1,10-phenantroline, Thio = 1,2-benzenedithiolate), on the interaction with human serum albumin (HSA), a key drug-delivery protein in the bloodstream. Being very limited the number of anionic Pt^(II) complexes reported to date, this is a pioneering example of report on a protein-ligand interaction involving a negatively charged platinum compound. The study was carried out by using fluorescence spectroscopy, differential scanning calorimetry and molecular docking simulations. The results revealed a strong binding affinity between the anionic compound and the protein, whereas a weak/moderate binding interaction was highlighted for the neutral one. Comparative studies with site specific ligands (warfarin and ibuprofen), allowed us to identify the protein binding sites of the two compounds. The work aims to shed light on the relevance of the charge in designing new drugs with a favorable binding affinity for HSA, which strongly contributes to influence their pharmacological and toxicological profile.

Thermal sensitivity as a quality control attribute for biotherapeutics: The L-asparaginase case

Thermal sensitivity, as a practical measure of thermostability, is an interesting quality attribute that can be used in the quality control (QC) release of biopharmaceuticals. This article investigates circular dichroism (CD) spectroscopy and nano-differential scanning fluorimetry (nano-DSF) to evaluate the thermal stability of E.coli L-asparaginase (L-ASNase) for QC purposes. In CD, molar ellipticity as a function of temperature (from 20 to 80°C) was measured at 222 nm. Different L-ASNase samples dissolved in different diluents were investigated by determining the melting temperature (T_m ) from the first derivative curve as well as the slope of the fitted sigmoidal function of the temperature gradient CD data. The obtained T_m values could be correlated with the L-ASNase sample origin as well as with the pH of the diluent. The T_m values obtained from the CD data were moreover consistent with the T_m values determined by nano-DSF, confirming their reliability. Next to the T_m value, also the slope of the fitted sigmoidal CD-function was able to differentiate different L-ASNase samples, including unstressed from stressed protein. By using both the T_m and the curve slope, the thermal stability of L-ASNase was investigated, demonstrating and recommending the use of this heat-stress characteristic as a QC quality attribute of proteins, which can be applied to detect substandard and falsified proteins.

Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.

Molecular interaction study of an anticancer drug, ponatinib with human serum albumin using spectroscopic and molecular docking methods

Binding of a potent anticancer agent, ponatinib (PTB) to human serum albumin (HSA), main ligand transporter in blood plasma was analyzed with several spectral techniques such as fluorescence, absorption and circular dichroism along with molecular docking studies. Decrease in the K_SV value with increasing temperature pointed towards PTB-induced quenching as the static quenching, thus affirming complexation between PTB and HSA. An intermediate binding affinity was found to stabilize the PTB-HSA complex, as suggested by the K_a value. Thermodynamic analysis of the binding phenomenon revealed participation of hydrophobic and van der Waals interactions along with hydrogen bonds, which was also supported by molecular docking analysis. Changes in both secondary and tertiary structures as well as in the microenvironment around Trp and Tyr residues of HSA were anticipated upon PTB binding to the protein, as manifested from circular dichroism and three-dimensional fluorescence spectra, respectively. Binding of PTB to HSA led to protein's thermal stabilization. Competitive ligand displacement experiments using different site markers such as warfarin, indomethacin and ketoprofen disclosed the binding site of PTB as Sudlow's site I in HSA, which was further confirmed by molecular docking analysis.

Stabilizing proteins to prevent conformational changes required for amyloid fibril formation

Amyloid fibrillation is associated with several human maladies, such as Alzheimer's, Parkinson's, Huntington's diseases, prions, amyotrophic lateral sclerosis, and type 2 diabetes diseases. Gaining insights into the mechanism of amyloid fibril formation and exploring novel approaches to fibrillation inhibition are crucial for preventing amyloid diseases. Here, we hypothesized that ligands capable of stabilizing the native state of query proteins might prevent protein unfolding, which, in turn, may reduce the propensity of proteins to form amyloid fibrils. We demonstrated the efficient inhibition of amyloid formation of the human serum albumin (HSA) (up to 85%) and human insulin (up to 80%) by a nonsteroidal anti-inflammatory drug, ibuprofen (IBFN). IBFN significantly increases the conformational stability of both HSA and insulin, as confirmed by differential scanning calorimetry (DSC). Moreover, increasing concentration of IBFN boosts its amyloid inhibitory propensity in a linear fashion by influencing the nucleation phase as assayed by thioflavin T fluorescence, transmission electron microscopy, and dynamic light scattering. Furthermore, circular dichroism analysis supported the DSC results, showing that IBFN binds to the native state of proteins and almost completely prevents their tendency to lose secondary and tertiary structures. Cell toxicity assay confirms that species formed in the presence of IBFN are less toxic to neuronal cells (SH-SY5Y). These results demonstrate the feasibility of using a small molecule to stabilize the native state of proteins, thereby preventing the amyloidogenic conformational changes, which appear to be the common link in several human amyloid diseases.

The Cyanobacterial Ribosomal-Associated Protein LrtA from Synechocystis sp. PCC 6803 Is an Oligomeric Protein in Solution with Chameleonic Sequence Properties

The LrtA protein of Synechocystis sp. PCC 6803 intervenes in cyanobacterial post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family of proteins, involved in protein synthesis. In this work, we studied the conformational preferences and stability of isolated LrtA in solution. At physiological conditions, as shown by hydrodynamic techniques, LrtA was involved in a self-association equilibrium. As indicated by Nuclear Magnetic Resonance (NMR), circular dichroism (CD) and fluorescence, the protein acquired a folded, native-like conformation between pH 6.0 and 9.0. However, that conformation was not very stable, as suggested by thermal and chemical denaturations followed by CD and fluorescence. Theoretical studies of its highly-charged sequence suggest that LrtA had a Janus sequence, with a context-dependent fold. Our modelling and molecular dynamics (MD) simulations indicate that the protein adopted the same fold observed in other members of the HPF family (β-α-β-β-β-α) at its N-terminal region (residues 1–100), whereas the C terminus (residues 100–197) appeared disordered and collapsed, supporting the overall percentage of overall secondary structure obtained by CD deconvolution. Then, LrtA has a chameleonic sequence and it is the first member of the HPF family involved in a self-association equilibrium, when isolated in solution.