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The ubiquitin E2 variant domain of TSG101 (TSG101‐UEV) plays a pivotal role in protein sorting and virus budding by recognizing PTAP motifs within ubiquitinated proteins. Disruption of TSG101‐UEV/PTAP interactions has emerged as a promising strategy for the development of host‐oriented broad‐spectrum antivirals with low susceptibility to resistance. TSG101 is a challenging target characterized by an extended and flat binding interface, low affinity for PTAP ligands, and complex binding energetics. Here, we assess the druggability of the TSG101‐UEV/PTAP binding interface by searching for drug‐like inhibitors and evaluating their ability to block PTAP recognition, impair budding, and inhibit viral proliferation. A discovery workflow was established by combining in vitro miniaturized HTS assays and a set of cell‐based activity assays including high‐content bimolecular complementation, virus‐like particle release measurement, and antiviral testing in live virus infection. This approach has allowed us to identify a set of chemically diverse molecules that block TSG101‐UEV/PTAP binding with IC50s in the low μM range and are able to disrupt the interaction between full‐length TSG101 and viral proteins in human cells and inhibit viral replication. State‐of‐the‐art molecular docking studies reveal that the active compounds exploit binding hotspots at the PTAP binding site, unlocking the full binding potential of the TSG101‐UEV binding pockets. These inhibitors represent promising hits for the development of novel broad‐spectrum antivirals through targeted optimization and are also valuable tools for investigating the involvement of ESCRT in the proliferation of different virus families and study the secondary effects induced by the disruption of ESCRT/virus interactions. [ABSTRACT FROM AUTHOR]

Theresa Klett,1,* Martin Schwer,1,* Larissa N Ernst,1,* Marc U Engelhardt,1 Simon J Jaag,2 Benedikt Masberg,2 Cornelius Knappe,2 Michael Lämmerhofer,2 Matthias Gehringer,3,4 Frank M Boeckler1,5 1Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 2Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 3Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 4Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany; 5Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany*These authors contributed equally to this workCorrespondence: Frank M Boeckler, Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8 (Haus B), Tübingen, D – 72076, Germany, Tel +49 7071 29 74567, Email frank.boeckler@uni-tuebingen.dePurpose: Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN).Methods: After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5’-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS).Results: In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53.Conclusion: The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and − 9.1 °C. Keywords: covalent fragment-based drug discovery, differential scanning fluorimetry, 5,5’-dithiobis-(2-nitrobenzoic acid), intact protein mass spectrometry, glutathione

Sodium–calcium exchanger (NCX) proteins are ubiquitously expressed and play a pivotal role in cellular calcium homeostasis by mediating uphill calcium efflux across the cell membrane. Intracellular calcium allosterically regulates the exchange activity by binding to two cytoplasmic calcium‐binding domains, CBD1 and CBD2. However, the calcium‐binding affinities of these domains are seemingly inadequate to sense physiological calcium oscillations. Previously, magnesium binding to either domain was shown to tune their affinity for calcium, bringing it into the physiological range. However, while the magnesium‐binding site of CBD2 was identified, the identity of the CBD1 magnesium site remains elusive. Here, using molecular dynamics in combination with differential scanning fluorimetry and mutational analysis, we pinpoint the magnesium‐binding site in CBD1. Specifically, among four calcium‐binding sites (Ca1–Ca4) in this domain, only Ca1 can accommodate magnesium with an affinity similar to its free intracellular concentration. Moreover, our results provide mechanistic insights into the modulation of the regulatory calcium affinity by magnesium, which allows an adequate NCX activity level throughout varying physiological needs. [ABSTRACT FROM AUTHOR]

Per- and polyfluoroalkyl substances (PFAS) are a class of over 8000 chemicals, many of which are persistent, bioaccumulative, and toxic to humans, livestock, and wildlife. Serum protein binding affinity is instrumental in understanding PFAS toxicity, yet experimental binding data is limited to only a few PFAS congeners. Previously, we demonstrated the usefulness of a high-throughput, in vitro differential scanning fluorimetry assay for determination of relative binding affinities of human serum albumin for 24 PFAS congeners from 6 chemical classes. In the current study, we used this assay to comparatively examine differences in human, bovine, porcine, and rat serum albumin binding of 8 structurally informative PFAS congeners from 5 chemical classes. With the exception of the fluorotelomer alcohol 1H, 1H, 2H, 2H-perfluorooctanol (6:2 FTOH), each PFAS congener bound by human serum albumin was also bound by bovine, porcine, and rat serum albumin. The critical role of the charged functional headgroup in albumin binding was supported by the inability of albumin of each species tested to bind 6:2 FTOH. Significant interspecies differences in serum albumin binding affinities were identified for each of the bound PFAS congeners. Relative to human albumin, perfluoroalkyl carboxylic and sulfonic acids were bound with greater affinity by porcine and rat serum albumin, and the perfluoroalkyl ether acid congener bound with lower affinity to porcine and bovine serum albumin. These comparative affinity data for PFAS binding by serum albumin from human, experimental model, and livestock species reduce critical interspecies uncertainty and improve accuracy of predictive bioaccumulation and toxicity assessments for PFAS. [ABSTRACT FROM AUTHOR]

The focus of our attention is directed towards the small molecule of oxaloacetate. This work is dedicated to the investigation of the role played by natural intermediates as metabolism switches in intermolecular interactions. The full range of biological activity for oxaloacetate has been unveiled through the utilization of computer modeling methods. Furthermore, the interaction partner proteins have been characterized. It has been demonstrated that small molecules act as metabolic intermediates, serving as points of intersection for numerous metabolic pathways encompassing protein, carbohydrate, and lipid metabolism. Concurrently, a coordinating role is assumed by these molecules in the execution and modulation of mediator, hormonal, receptor responses, immunological, inflammatory, antibacterial, and antiviral reactions, thus manifesting anticarcinogenic properties. Through the application of differential scanning fluorimetry and microcapillary thermophoresis, the interaction between lactate dehydrogenase and ligands of endogenous origin has been established. The calculated Kd value obtained for the interaction between oxaloacetate and lactate dehydrogenase was determined to be 0.5±0.01 μM. The thermalstability of LDH is enhanced by final concentrations of oxaloacetate ranging from 0.5 to 1 µM, whereas a concentration of 16 µM of the metabolite diminishes its thermostable characteristics. In intermolecular processes in in vitro cell culture, the stimulating effect of oxaloacetate 33,8 % (p=0.028) on the primary culture of human dermal fibroblasts was shown. [ABSTRACT FROM AUTHOR]

Mastering selective molecule trafficking across human cell membranes poses a formidable challenge in healthcare biotechnology while offering the prospect of breakthroughs in drug delivery, gene therapy, and diagnostic imaging. The cholera toxin B-subunit (CTB) has the potential to be a useful cargo transporter for these applications. CTB is a robust protein that is amenable to reengineering for diverse applications; however, protein redesign has mostly focused on modifications of the N- and C-termini of the protein. Exploiting the full power of rational redesign requires a detailed understanding of the contributions of the surface residues to protein stability and binding activity. Here, we employed Rosetta-based computational saturation scans on 58 surface residues of CTB, including the GM1 binding site, to analyze both ligand-bound and ligand-free structures to decipher mutational effects on protein stability and GM1 affinity. Complimentary experimental results from differential scanning fluorimetry and isothermal titration calorimetry provided melting temperatures and GM1 binding affinities for 40 alanine mutants among these positions. The results showed that CTB can accommodate diverse mutations while maintaining its stability and ligand binding affinity. These mutations could potentially allow modification of the oligosaccharide binding specificity to change its cellular targeting, alter the B-subunit intracellular routing, or impact its shelf-life and in vivo half-life through changes to protein stability. We anticipate that the mutational space maps presented here will serve as a cornerstone for future CTB redesigns, paving the way for the development of innovative biotechnological tools. [ABSTRACT FROM AUTHOR]

Lipopolysaccharide (LPS) synthesis in Gram‐negative bacteria is completed at the outer leaflet of the inner membrane (IM). Following synthesis, seven LPS transport (Lpt) proteins facilitate the movement of LPS to the outer membrane (OM), an essential process that if disrupted at any stage has lethal effects on bacterial viability. LptB2FG, the IM component of the Lpt bridge system, is a type VI ABC transporter that provides the driving force for LPS extraction from the IM and subsequent transport across a stable protein bridge to the outer leaflet of the OM. LptC is a periplasmic protein anchored to the IM by a single transmembrane (TM) helix intercalating within the lateral gate formed by LptF TM5 and LptG TM1. LptC facilitates the hand‐off of LPS from LptB2FG to the periplasmic protein LptA and has been shown to regulate the ATPase activity of LptB2FG. Here, using an engineered chromosomal knockout system in Escherichia coli to assess the effects of LptC mutations in vivo, we identified six partial loss of function LptC mutations in the first unbiased alanine screen of this essential protein. To investigate the functional effects of these mutations, nanoDSF (differential scanning fluorimetry) and site‐directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy in combination with an in vitro ATPase assay show that specific residues in the TM helix of LptC destabilize the LptB2FGC complex and regulate the ATPase activity of LptB. [ABSTRACT FROM AUTHOR]

Objective: Inflammation is a complex reaction present in numerous disorders. Indomethacin, a compound possessing an indoline core, is a Nonsteroidal Anti-Inflammatory Drug (NSAID) that is commonly prescribed for inflammation and pain. The actin network, plays a major role in cellular activities and it's regulated by by Rho GTPases has important implications for cellular dynamics and orientation. In this research, we explore the effects of indomethacin on the inflammatory response as mediated via RhoA and pyrin inflammatory complexes using an inflammatory disease model with relation actin cytoskeleton. Materials and Methods: This study used Western blotting to examine the impact of indomethacin on the assembly processes related to the pyrin inflammasome complex and the RhoA signaling pathway in Lipopolysaccharide-stimulated THP-1 cells. Actin-indomethacin interaction was analyzed by Differential Scanning Fluorimetry (DSF). Results: We found that while the expression levels of pyrin decreased, phosphorylated-RhoA increased but overall RhoA levels did not change. The equilibrium dissociation constant (KD) for the G-actin-indomethacin complex was calculated to be 9.591± 1.608 ng/mL (R² = 0.8582) using ΔTm measurements of indomethacin by DSF. Conclusion: Moreover, the effects of indomethacin on inflammation pathways may provide insight into the molecular mechanisms of pyrin inflammasome formation in various autoimmune diseases. [ABSTRACT FROM AUTHOR]

The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5′RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15. [ABSTRACT FROM AUTHOR]

Influenza virus infections represent an ongoing public health threat as well as an economic burden. Although seasonal influenza vaccines have been available for some decades, efforts are being made to generate new efficient, flexible, and cost-effective technologies to be transferred into production. Our work describes the development of a model influenza hemagglutinin antigen that is capable of inducing protection against viral challenge in mice. High amounts of the H1 hemagglutinin ectodomain, HA18–528, were expressed in a bacterial system as insoluble inclusion bodies. Solubilization was followed by a thorough differential scanning fluorimetry (DSF)-guided optimization of refolding, which allows for fast and reliable screening of several refolding conditions, yielding tens of milligrams/L of folded protein. Structural and functional analysis revealed native-like folding as well as the presence of a mix of monomers and oligomers in solution. Mice immunized with HA18–528 were protected when exposed to influenza A virus as opposed to mice that received full-length denatured protein. Sera of mice immunized with HA18–528 showed both high titers of antigen-specific IgG1 and IgG2a isotypes as well as viral neutralization activity. These results prove the feasibility of the recombinant bacterial expression system coupled with DSF-guided refolding in providing influenza hemagglutinin for vaccine development. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome-causing coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) and main protease (Mpro) play an important role in viral replication events and are important targets for anti-coronavirus drug discovery. In search of these protease inhibitors, we screened a library of 1300 compounds using a fluorescence thermal shift assay (FTSA) and identified 53 hits that thermally stabilized or destabilized PLpro. The hit compounds structurally belonged to two classes of small molecules: thiazole derivatives and symmetrical disulfide compounds. Compound dissociation constants (Kd) were determined using an enzymatic inhibition method. Seven aromatic disulfide compounds were identified as efficient PLpro inhibitors with Kd values in the micromolar range. Two disulfides displayed six-fold higher potency for PLpro (Kd = 0.5 µM) than for Mpro. The disulfide derivatives bound covalently to both proteases, as confirmed through mass spectrometry. The identified compounds can serve as lead compounds for further chemical optimization toward anti-COVID-19 drugs. [ABSTRACT FROM AUTHOR]

The characterization of protein stability is essential for understanding the functions of proteins. Hydroxysteroid dehydrogenase is involved in the biosynthesis of steroid hormones and the detoxification of xenobiotic carbonyl compounds. However, the stability of hydroxysteroid dehydrogenases has not yet been characterized in detail. Here, we determined the changes in Gibbs free energy, enthalpy, entropy, and heat capacity of unfolding for 3α‐hydroxysteroid dehydrogenase/carbonyl reductase (3α‐HSD/CR) by varying the pH and urea concentration through differential scanning fluorimetry and presented pH‐dependent protein stability as a function of temperature. 3α‐HSD/CR shows the maximum stability of 30.79 kJ mol−1 at 26.4°C, pH 7.6 and decreases to 7.74 kJ mol−1 at 25.7°C, pH 4.5. The change of heat capacity of 30.25 ± 1.38 kJ mol−1 K−1 is obtained from the enthalpy of denaturation as a function of melting temperature at varied pH. Two proton uptakes are linked to protein unfolding from residues with differential pKa of 4.0 and 6.5 in the native and denatured states, respectively. The large positive heat capacity change indicated that hydrophobic interactions played an important role in the folding of 3α‐HSD/CR. These studies reveal the mechanism of protein unfolding in HSD and provide a convenient method to extract thermodynamic parameters for characterizing protein stability using differential scanning fluorimetry. [ABSTRACT FROM AUTHOR]

We concentrated and reformulated the anti-cocaine mAb, h2E2, to reduce the amount of sucrose and histidine buffer infused with the mAb, to satisfy FDA maximum exposure levels for those components for use in clinical trials. After concentration of the original 20 mg/ml mAb, 4 reformulation buffers were evaluated for suitability. The concentration of histidine was reduced from 10 mM to 3 or 0 mM, and the concentration of sucrose reduced from 10% to 2, 4, or 6%. The approximately 100 mg/ml reformulated mAb samples were analyzed for oligomer formation, aggregation, concentration of the emulsifier polysorbate 80, and thermal stability. These reformulated mAb samples were also assessed for their stability at 40°C from 1 day to 12 weeks. As expected, long term thermal resistance to oligomer formation increased as a function of increasing sucrose concentration. Interestingly, unbuffered reformulated mAb displayed a less than or equal to tendency to form oligomers and aggregates, compared to the histidine buffered samples. Importantly, even after 12 weeks at 40°C, all the reformulated samples displayed little aggregation, and bound their antigen (cocaine) with identical affinities and thermodynamics, as measured by isothermal titration calorimetry (ITC). These ITC thermodynamic binding parameters are consistent with recently published values for the original formulation of this mAb. In all reformulated samples there was a slight decrease in the number of cocaine binding sites after 12 weeks at 40°C, likely due to the parallel small increase in soluble oligomeric antibody, suggesting that soluble oligomeric mAb may no longer bind cocaine with high affinity. [Display omitted] • Formulated anti-cocaine h2E2 mAb was reformulated to reduce histidine and sucrose. • A formulation lacking a small molecule buffer was evaluated and proved effective. • Reformulated mAbs were evaluated by DSF and non-reducing SDS-PAGE. • Reformulated mAbs were thermally stressed for 1 day to 12 weeks at 40°C. • Stressed mAb evaluated for oligomer and aggregate formation as a function of time. • Stressed mAb was evaluated for antigen (cocaine) binding thermodynamics by ITC. [ABSTRACT FROM AUTHOR]

[Display omitted] The structural maintenance of therapeutic proteins during formulation and/or storage is a critical aspect, particularly for multi-domain and/or multimeric proteins which usually exhibit intrinsic structural dynamics leading to aggregation with concomitant loss-of-function. Protein freeze-drying is a widely used technique to preserve protein structure and function during storage. To minimize chemical/physical stresses occurring during this process, protein stabilizers are usually included, their effect being strongly dependent on the target protein. Therefore, they should be screened for on a time-consuming case-by-case basis. Herein, differential scanning fluorimetry (DSF) and isothermal denaturation fluorimetry (ITDF) were employed to screen, among different classes of freeze-drying additives, for the most effective stabilizer of the model protein human phenylalanine hydroxylase (hPAH). Correlation studies among retrieved DSF and ITDF parameters with recovered enzyme amount and activity indicated ITDF as the most appropriate screening method. Biochemical and biophysical characterization of hPAH freeze-dried with ITDF-selected stabilizers and a long-term storage study (12 months, 5 ± 3 °C) showed that the selected compounds prevented protein aggregation and preserved hPAH structural and functional properties throughout time storage. Our results provide a solid basis towards the choice of ITDF as a high-throughput screening step for the identification of protein freeze-drying protectors. [ABSTRACT FROM AUTHOR]

Fluorescein isothiocyanate (FITC) is widely used to fluorescently label reactive lysine residues on proteins, including antibodies. The rate and extent of labeling varies with reaction conditions, concentration of label, and the concentration and nature of the protein. Fluorescently labeled proteins are very useful, and one use for FITC labeled mAbs is development of assays to measure anti-mAb antibodies produced in vivo during treatment with antibody therapeutics. Our laboratory has developed a humanized anti-cocaine mAb (h2E2) intended for the treatment of cocaine use disorders. Thus, a well characterized FITC labeled h2E2 mAb is needed to quantitate possible anti-mAb antibodies. The time course of labeling and the relative incorporation of FITC into the heavy and light chains, as well as into the Fab and Fc portions of the mAb, was assessed. A novel use of differential scanning fluorimetry in the absence of any extrinsic fluorophore was developed and demonstrated to be capable of measuring antigen (cocaine) binding. In addition, the effect of increasing degrees of labeling by FITC on the thermodynamic parameters driving the binding of cocaine to the mAb was assessed via isothermal titration calorimetry (ITC). This binding technique, unlike others developed recently to measure cocaine binding, is not dependent on, or subject to interference by, the absorbance or fluorescence of the incorporated FITC label. The methods and results reported herein guide the optimization of FITC labeling needed for anti-mAb assays and other assays important for the development of therapeutic mAbs, which are some of the most specific and clinically useful drugs available.

2′-Deoxyuridine 5′-triphosphate nucleotide hhydrolase (Dut) hydrolyzes dUTP to dUMP and pyrophosphate to prevent erroneous incorporation of dUMP from the dUTP metabolic pool into DNA. Dut is considered as a promising pharmacological target for antimetabolite therapy. Enzymatically active Dut is a trimer that binds the substrate at the interface between the subunits. High-speed nanoscale differential scanning fluorimetry (nanoDSF) was used to study how various physicochemical factors affect the stability of the Escherichia coli Dut trimer. Unlike with monomeric proteins, thermal unfolding of Dut occurred in two steps, the first one corresponding to dissociation of the trimer into monomeric subunits. Hydrophobic interactions and hydrogen bonds at the interfaces between the subunits were found to contribute most to trimer stabilization. The binding of nucleotide ligands partly stabilized the Dut trimer. In general, nanoDSF is a convenient assay for screening low-molecular-weight compounds for their ability to destabilize the active Dut trimer. [ABSTRACT FROM AUTHOR]

Accurate temperature control within biological and chemical reaction samples and instrument calibration are essential to the diagnostic, pharmaceutical and chemical industries. This is particularly challenging for microlitre-scale reactions typically used in real-time PCR applications and differential scanning fluorometry. Here, we describe the development of a simple, inexpensive ratiometric dual fluorescent protein temperature biosensor (DFPTB). A combination of cycle three green fluorescent protein and a monomeric red fluorescent protein enabled the quantification of relative temperature changes and the identification of temperature discrepancies across a wide temperature range of 4–70 °C. The maximal sensitivity of 6.7% °C−1 and precision of 0.1 °C were achieved in a biologically relevant temperature range of 25–42 °C in standard phosphate-buffered saline conditions at a pH of 7.2. Good temperature sensitivity was achieved in a variety of biological buffers and pH ranging from 4.8 to 9.1. The DFPTB can be used in either purified or mixed bacteria-encapsulated formats, paving the way for in vitro and in vivo applications for topologically precise temperature measurements. [ABSTRACT FROM AUTHOR]

Biotinylation of proteins, including antibodies, is a very useful and important modification for a variety of biochemical characterizations, including anti-drug antibody (ADA) assays used to detect antibodies raised against therapeutic antibodies. We assessed different degrees of biotin labeling of an anti-cocaine mAb currently under development for treating cocaine use disorder. We noted that higher levels of biotin labeling dramatically decreased mAb solubility, and increased the tendency to bind to surfaces, complicating characterization of the biotinylated antibody. Specifically, in phosphate buffered saline, labeling stoichiometries of more than about 3 biotin/mAb resulted in decreased recoveries due to increased binding to surfaces and decreased mAb solubility. Native gel agarose electrophoresis, differential scanning fluorimetry, and isothermal titration calorimetry all demonstrated changes in the mAb which became more pronounced above a labeling ratio of 3 biotin/mAb. At 3.0 biotin/mAb, there were minimal changes in solubility, adsorptivity, exposure of hydrophobic dye-binding sites, heat stability, and cocaine binding, in stark contrast to labeling with 5.6 biotin/mAb. Thus, the degree of biotinylation should be kept at about 3 biotin/mAb to maintain antigen binding and general structure, solubility, and stability of this mAb, a finding which may be important for other similar mAbs currently in use or under development. [Display omitted] • Anti-cocaine h2E2 mAb was biotinylated at levels from about 2 to 8 biotin/mAb. • Increasing biotinylation greatly reduced mAb solubility in PBS buffer. • At >3 biotin/mAb, reversible mAb adsorption caused variation in measured biotin/mAb. • DSF revealed large increases in hydrophobic mAb binding of Sypro dye at >3 biotin/mAb. • ITC revealed only small changes in mAb cocaine (antigen) binding at >3 biotin/mAb. [ABSTRACT FROM AUTHOR]

Simple Summary: The toolkit for diagnosing the most aggressive primary brain tumor glioblastoma (GBM) is very limited. We recently demonstrated that plasma denaturation profiles (PDPs) of GBM patients and healthy controls obtained with nanoDSF can be automatically classified using artificial intelligence (AI) algorithms. Since PDPs have been shown to be useful for subtype differentiation for lung cancer, we decided to investigate whether nanoDSF-derived PDPs could also be used to discriminate EGFR alterations in GBM, which is important for determining therapy strategies. We found that AI is able to discriminate EGFR alterations in GBM with an 81.5% accuracy. Thus, we have demonstrated that the use of plasma denaturation profiles could answer the unsatisfied neuro-oncology need for a predictive diagnostic biomarker, which could complete MRI and clinical data, allowing for a rapid orientation of patients for a definitive pathological diagnosis and treatment. Glioblastoma (GBM) is the most frequent and aggressive primary brain tumor in adults. Recently, we demonstrated that plasma denaturation profiles of glioblastoma patients obtained using Differential Scanning Fluorimetry can be automatically distinguished from healthy controls with the help of Artificial Intelligence (AI). Here, we used a set of machine-learning algorithms to automatically classify plasma denaturation profiles of glioblastoma patients according to their EGFR status. We found that Adaboost AI is able to discriminate EGFR alterations in GBM with an 81.5% accuracy. Our study shows that the use of these plasma denaturation profiles could answer the unmet neuro-oncology need for diagnostic predictive biomarker in combination with brain MRI and clinical data, in order to allow for a rapid orientation of patients for a definitive pathological diagnosis and then treatment. We complete this study by showing that discriminating another mutation, MGMT, seems harder, and that post-surgery monitoring using our approach is not conclusive in the 48 h that follow the surgery. [ABSTRACT FROM AUTHOR]

The p53 protein is a transcription factor that preserves the integrity of the genome. The TP53 gene has inactivating mutations in about 50% of all human cancers. Some missense mutations lead to decreased thermal stability in the p53 protein, its unfolding and aggregation under physiological conditions. A general understanding of the impact of point mutations on the stability and conformation of mutant p53 is essential for the design and development of small molecules that target specific p53 mutations. In this work, we determined the thermostability properties of some of the most common mutant forms of the p53 protein—p53(R273H), p53(R248Q), p53(R248W) and p53(Y220C)—that are often considered as attractive therapeutic targets. The results showed that these missense mutations lead to destabilization of the p53 protein and a decrease in its melting temperature. [ABSTRACT FROM AUTHOR]

The high‐temperature requirement A (HtrA) serine protease family presents an attractive target class for antibacterial therapeutics development. These proteins possess dual protease and chaperone functions and contain numerous binding sites and regulatory loops, displaying diverse oligomerization patterns dependent on substrate type and occupancy. HtrA proteins that are natively purified coelute with contaminating peptides and activating species, shifting oligomerization and protein structure to differently activated populations. Here, a redesigned HtrA production results in cleaner preparations with high yields by overexpressing and purifying target protein from inclusion bodies under denaturing conditions, followed by a high‐throughput screen for optimal refolding buffer composition using function‐agnostic biophysical techniques that do not rely on target‐specific measurements. We use Borrelia burgdorferi HtrA to demonstrate the effectiveness of our function‐agnostic approach, while characterization with both new and established biophysical methods shows the retention of proteolytic and chaperone activity of the refolded protein. This systematic workflow and toolset will translate to the production of HtrA‐family proteins in higher quantities of pure and monodisperse composition than the current literature standard, with applicability to a broad array of protein purification strategies. [ABSTRACT FROM AUTHOR]

The ubiquitin E2 variant domain of TSG101 (TSG101-UEV) plays a pivotal role in protein sorting and virus budding by recognizing PTAP motifs within ubiquitinated proteins. Disruption of TSG101-UEV/PTAP interactions has emerged as a promising strategy for the development of host-oriented broad-spectrum antivirals with low susceptibility to resistance. TSG101 is a challenging target characterized by an extended and flat binding interface, low affinity for PTAP ligands, and complex binding energetics. Here, we assess the druggability of the TSG101-UEV/PTAP binding interface by searching for drug-like inhibitors and evaluating their ability to block PTAP recognition, impair budding, and inhibit viral proliferation. A discovery workflow was established by combining in vitro miniaturized HTS assays and a set of cell-based activity assays including high-content bimolecular complementation, virus-like particle release measurement, and antiviral testing in live virus infection. This approach has allowed us to identify a set of chemically diverse molecules that block TSG101-UEV/PTAP binding with IC50s in the low μM range and are able to disrupt the interaction between full-length TSG101 and viral proteins in human cells and inhibit viral replication. State-of-the-art molecular docking studies reveal that the active compounds exploit binding hotspots at the PTAP binding site, unlocking the full binding potential of the TSG101-UEV binding pockets. These inhibitors represent promising hits for the development of novel broad-spectrum antivirals through targeted optimization and are also valuable tools for investigating the involvement of ESCRT in the proliferation of different virus families and study the secondary effects induced by the disruption of ESCRT/virus interactions., (© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Abstract The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows. Graphical Abstract

Influenza virus infections represent an ongoing public health threat as well as an economic burden. Although seasonal influenza vaccines have been available for some decades, efforts are being made to generate new efficient, flexible, and cost-effective technologies to be transferred into production. Our work describes the development of a model influenza hemagglutinin antigen that is capable of inducing protection against viral challenge in mice. High amounts of the H1 hemagglutinin ectodomain, HA18–528, were expressed in a bacterial system as insoluble inclusion bodies. Solubilization was followed by a thorough differential scanning fluorimetry (DSF)-guided optimization of refolding, which allows for fast and reliable screening of several refolding conditions, yielding tens of milligrams/L of folded protein. Structural and functional analysis revealed native-like folding as well as the presence of a mix of monomers and oligomers in solution. Mice immunized with HA18–528 were protected when exposed to influenza A virus as opposed to mice that received full-length denatured protein. Sera of mice immunized with HA18–528 showed both high titers of antigen-specific IgG1 and IgG2a isotypes as well as viral neutralization activity. These results prove the feasibility of the recombinant bacterial expression system coupled with DSF-guided refolding in providing influenza hemagglutinin for vaccine development.

Differential scanning fluorimetry is a rapid and economical biophysical technique used to monitor perturbations to protein structure during a thermal gradient, most often by detecting protein unfolding events through an environment-sensitive fluorophore. By employing an NTA-complexed fluorophore that is sensitive to nearby structural changes in histidine-tagged protein, a robust and sensitive differential scanning fluorimetry (DSF) assay is established with the specificity of an affinity tag-based system. We developed, optimized, and miniaturized this HIS-tag DSF assay (HIS-DSF) into a 1536-well high-throughput biophysical platform using the Borrelial high temperature requirement A protease (BbHtrA) as a proof of concept for the workflow. A production run of the BbHtrA HIS-DSF assay showed a tight negative control group distribution of Tm values with an average coefficient of variation of 0.51% and median coefficient of variation of compound Tm of 0.26%. The HIS-DSF platform will provide an additional assay platform for future drug discovery campaigns with applications in buffer screening and optimization, target engagement screening, and other biophysical assay efforts. [ABSTRACT FROM AUTHOR]

A comparative study was carried out on the thermal stability of ovotransferrins (OTrfs) from chicken, duck, guinea fowl, Japanese quail, ostrich and turkey by differential scanning calorimetry (DSC), differential scanning fluorimetry (DSF) and turbidimetry. The average temperature at the denaturation midpoint in DSC (TmDSC) was 42.8 ℃ at pH 4.0, 63.8 ℃ at pH 7.0 and 59.4 ℃ at pH 9.0, and the differences in the TmDSC values between chicken and the other poultry, except ostrich, were less than 3.5 ℃. The results of DSF were almost comparable to those of DSC. In an analysis of poultry OTrf solution turbidi ties, ostrich OTrf solution remained clear up to 95.0 ℃ at pH 4.0 and pH 8.0, while the others became turbid at around 40 ℃ at pH 4.0 and 60 ℃ at pH 8.0. Turkey, Japanese quail and duck OTrfs remained soluble at pH 9.0 up to 73.0 °C, 85.0 °C and 95.0 °C, respectively, though turbidity appeared up to 60 ℃ in the others. Such findings on the similarities and differences among poultry OTrfs should be significant for the utilization of poultry eggs other than chicken eggs since the thermal processes required for chicken egg products often depends on the behavior of heat-susceptible chicken OTrf. [ABSTRACT FROM AUTHOR]

Differential scanning fluorimetry is a rapid and economical biophysical technique used to monitor perturbations to protein structure during a thermal gradient, most often by detecting protein unfolding events through an environment-sensitive fluorophore. By employing an NTA-complexed fluorophore that is sensitive to nearby structural changes in histidine-tagged protein, a robust and sensitive differential scanning fluorimetry (DSF) assay is established with the specificity of an affinity tag-based system. We developed, optimized, and miniaturized this HIS-tag DSF assay (HIS-DSF) into a 1536-well high-throughput biophysical platform using the Borrelial high temperature requirement A protease (BbHtrA) as a proof of concept for the workflow. A production run of the BbHtrA HIS-DSF assay showed a tight negative control group distribution of Tm values with an average coefficient of variation of 0.51% and median coefficient of variation of compound Tm of 0.26%. The HIS-DSF platform will provide an additional assay platform for future drug discovery campaigns with applications in buffer screening and optimization, target engagement screening, and other biophysical assay efforts.

Rab3A is a member of the Rab GTPase family involved in synaptic vesicle trafficking. Recent evidence has demonstrated that Rab3A is phosphorylated by leucine-rich repeat kinase 2 (LRRK2) that is implicated in both familial and sporadic forms of Parkinson's disease (PD), and an abnormal increase in Rab3A phosphorylation has been proposed as a cause of PD. Despite the potential importance of Rab3A in PD pathogenesis, its structural information is limited and the effects of bound nucleotides on its biophysical and biochemical properties remain unclear. Here, we show that GDP-bound Rab3A is preferentially phosphorylated by LRRK2 compared with GTP-bound Rab3A. The secondary structure of Rab3A, measured by circular dichroism (CD) spectroscopy, revealed that Rab3A is resistant to heat-induced denaturation at pH 7.4 or 9.0 regardless of the nucleotides bound. In contrast, Rab3A underwent heat-induced denaturation at pH 5.0 at a lower temperature in its GDP-bound form than in its GTP-bound form. The unfolding temperature of Rab3A was studied by differential scanning fluorimetry, which showed a significantly higher unfolding temperature in GTP-bound Rab3A than in GDP-bound Rab3A, with the highest at pH 7.4. These results suggest that Rab3A has unusual thermal stability under physiologically relevant conditions and that bound nucleotides influence both thermal stability and phosphorylation by LRRK2. • Rab3A is preferentially phosphorylated by LRRK2 in its GDP-bound form. • Rab3A is resistant to heat denaturation at pH 7.4 and 9.0 but not at pH 5.0. • GTP-bound Rab3A is thermally stable compared with GDP-bound Rab3A. [ABSTRACT FROM AUTHOR]

[Display omitted] • TPPU_DSF easily calculates thermodynamic parameters from a single DSF measurement. • Compatible with common real time PCR instruments used for DSF measurements and high-throughput compound screening campaigns. • For the Web application no installation is required. It is compatible with all operating systems, it is free and open source and generates publication-ready figures and tables. • Data security. Data never leaves the user's computer, thus ensuring confidentiality. Here we present TPPU_DSF (https://maciasnmr.net/tppu%5fdsf/). This is a free and open-source web application that opens, converts, fits, and calculates the thermodynamic parameters of protein unfolding from standard differential scanning fluorimetry (DSF) data in an automated manner. The software has several applications. In the context of screening compound libraries for protein binders, obtaining thermodynamic parameters provides a more robust approach to detecting hits than the changes in the melting temperature (T m) alone, thereby helping to increase the number of positive hits in screening campaigns. Moreover, changes in ΔG u o indicate protein response to binding at lower compound concentrations than those in the T m , thereby reducing the costs associated with the amounts of protein and compounds required for the assays. Also, by adding thermodynamic information to the T m comparison, the software can contribute to the optimization of protein constructs and buffer conditions, a common practice before structural and functional projects. [ABSTRACT FROM AUTHOR]

• A fluorescence-based DSF provides rapid assessment of adjuvant-adsorbed protein in a microplate format. • The effect of multi-factors in formulation development can be well-explored using smaller sample amount than DSC. • Good correlation of the results from well-established DSC and from high-throughput, automation amenable DSF is observed. Nano/microparticles are widely used as vaccine adjuvants to improve antigen stability and enhance immune response. Conformational stability of a given protein was normally assessed using differential scanning calorimetry (DSC) for the optimization of formulation and for ensuring antigen stability in vaccine products. Here, a higher throughput version, namely the microtiter plate-based differential scanning fluorimetry (DSF) method was developed and optimized for assessing the protein thermal stability in the particulate adjuvant-adsorbed form. Using recombinant human papillomavirus (HPV) vaccine antigens, along with several model proteins, enhanced sensitivity and correlation to the well-established differential scanning calorimetry were demonstrated. Higher throughput and much smaller sample consumption (1/10 ∼ 1/20 of the amount needed as compared to DSC) make the plate-based DSF a method of choice for formulation development, particularly during the early developmental phase of a project where the sample amount is usually quite limited. [ABSTRACT FROM AUTHOR]

Neuronal calcium sensors (NCSs) are the family of EF-hand proteins mediating Ca2+-dependent signaling pathways in healthy neurons and neurodegenerative diseases. It was hypothesized that the calcium sensor activity of NCSs can be complemented by sensing fluctuation of intracellular zinc, which could further diversify their function. Here, using a set of biophysical techniques, we analyzed the Zn2+-binding properties of five proteins belonging to three different subgroups of the NCS family, namely, VILIP1 and neurocalcin-δ/NCLD (subgroup B), recoverin (subgroup C), as well as GCAP1 and GCAP2 (subgroup D). We demonstrate that each of these proteins is capable of coordinating Zn2+ with a different affinity, stoichiometry, and structural outcome. In the absence of calcium, recoverin and VILIP1 bind two zinc ions with submicromolar affinity, and the binding induces pronounced conformational changes and regulates the dimeric state of these proteins without significant destabilization of their structure. In the presence of calcium, recoverin binds zinc with slightly decreased affinity and moderate conformational outcome, whereas VILIP1 becomes insensitive to Zn2+. NCALD binds Zn2+ with micromolar affinity, but the binding induces dramatic destabilization and aggregation of the protein. In contrast, both GCAPs demonstrate low-affinity binding of zinc independent of calcium, remaining relatively stable even at submillimolar Zn2+ concentrations. Based on these data, and the results of structural bioinformatics analysis, NCSs can be divided into three categories: (1) physiological Ca2+/Zn2+ sensor proteins capable of binding exchangeable (signaling) zinc (recoverin and VILIP1), (2) pathological Ca2+/Zn2+ sensors responding only to aberrantly high free zinc concentrations by denaturation and aggregation (NCALD), and (3) Zn2+-resistant, Ca2+ sensor proteins (GCAP1, GCAP2). We suggest that NCS proteins may therefore govern the interconnection between Ca2+-dependent and Zn2+-dependent signaling pathways in healthy neurons and zinc cytotoxicity-related neurodegenerative diseases, such as Alzheimer's disease and glaucoma. [ABSTRACT FROM AUTHOR]

The covalent attachment of a bacterial-derived capsular polysaccharide to protein is of critical importance in transforming the polysaccharide from an antigen with limited immunogenicity in infants and older adults to an antigen that can prevent potentially fatal disease. For a polysaccharide-protein conjugate vaccine (PCV) candidate to be successful, it must be sufficiently stable. Chemical breakage of carbohydrate bonds in the polysaccharide may result in the reduction of "conjugate dose" and could negatively impact immunogenicity and the ability of the vaccine to prime for memory responses. Therefore, development of analytical tools to monitor the integrity of a polysaccharide-protein conjugate (glycoconjugate) vaccine is of practical significance. In this work, reducing SDS-PAGE, Intrinsic Protein Fluorescence Spectroscopy (IPFS), Differential Scanning Fluorimetry (DSF) were evaluated methods to study the impact of time, temperature, and formulation composition on the stability of a glycoconjugate vaccine prepared by multisite coupling of polysaccharide to a carrier protein. In addition, an automated capillary Western system was also evaluated to study the impact of storage on glycoconjugate vaccine stability. Two streptococcus pneumoniae polysaccharide-protein conjugates (serotype 3 and serotype 19A) were chosen to examine their physicochemical stability when formulated as a single antigen vaccine. While all methods require only a small amount of test article and can test multiple samples per assay run, automated capillary Western has the additional advantage of being highly sensitive even at low concentrations in complex vaccine formulations that contain aluminum adjuvant and multiple antigens. Results suggest that automated capillary Western is stability-indicating and may be an effective analytical technology tool for the formulation development of a multivalent glycoconjugate vaccine. [ABSTRACT FROM AUTHOR]

Objective: Uncoupling protein 1 (UCP1) catalyses mitochondrial proton leak in brown adipose tissue to facilitate nutrient oxidation for heat production, and may combat metabolic disease if activated in humans. During the adrenergic stimulation of brown adipocytes, free fatty acids generated from lipolysis activate UCP1 via an unclear interaction. Here, we set out to characterise activator binding to purified UCP1 to clarify the activation process, discern novel activators and the potential to target UCP1. Methods: We assessed ligand binding to purified UCP1 by protein thermostability shift analysis, which unlike many conventional approaches can inform on the binding of hydrophobic ligands to membrane proteins. A detailed activator interaction analysis and screening approach was carried out, supported by investigations of UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1 expression-controlled cell lines. Results: We reveal that fatty acids and other activators influence UCP1 through a specific destabilising interaction, behaving as transport substrates that shift the protein to a less stable conformation of a transport cycle. Through the detection of specific stability shifts in screens, we identify novel activators, including the over-the-counter drug ibuprofen, where ligand analysis indicates that UCP1 has a relatively wide structural specificity for interacting molecules. Ibuprofen successfully induced UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1-expressing HEK293 cells but not in cultured brown adipocytes, suggesting drug delivery differs in each cell type. Conclusions: These findings clarify the nature of the activator-UCP1 interaction and demonstrate that the targeting of UCP1 in cells by approved drugs is in principle achievable as a therapeutic avenue, but requires variants with more effective delivery in brown adipocytes.

Tetranitromethane was used to selectively modify tyrosine residues of a humanized anti-cocaine mAb (h2E2), under development for the treatment of cocaine use disorders. The effect of mild tyrosine nitration on the affinity of cocaine and two high affinity cocaine metabolites, cocaethylene and benzoylecgonine, was assessed using differential scanning fluorimetry to measure ligand affinities via ligand-induced thermal stabilization of the mAb antigen binding region. Nitrated tyrosine residues were identified by mass spectral analysis of thermolysin peptides. One objective was to understand the binding affinity differences observed for these three ligands, which are not explained by the published crystal structure of the h2E2 mAb Fab fragment co-crystalized with benzoylecgonine, since the carboxylic acid of benzoylecgonine that is esterified to form cocaine and cocaethylene is not in contact with the mAb. Importantly, the binding affinity of the cocaine metabolite benzoylecgonine was not decreased by mild nitration, whereas the binding affinities of cocaine and cocaethylene were decreased about two-fold. These ligands differ only in the substituent attached to the carboxylate moiety of the compound, with benzoylecgonine having an unesterified carboxylate, and cocaine and cocaethylene having methyl and ethyl esters, respectively, at this position. The results are consistent with nitration of light chain tyrosine residue 34, resulting in a less favorable interaction with cocaine and cocaethylene carboxylate esters, while not affecting binding of benzoylecgonine. Thus, light chain Tyr34 residue may have molecular interactions with cocaine and cocaethylene not present for benzoylecgonine, leading to the observed affinity differences for these three ligands.

Differential scanning fluorimetry (DSF) is used to assess protein stability, transition states, or the Kd values of various ligands, drug molecules, and antibodies. All fluorescent probes published to date either are incompatible with hydrophobic proteins/ligands, precluding analyses of transmembrane or membrane-associated proteins, or have excitation and detection wavelengths outside the range of real-time polymerase chain reaction (RT-PCR) machines, necessitating the use of dedicated devices. Here, we describe a thiol-reactive probe, BODIPY FL L-cystine (BFC), to overcome both of these shortcomings. The probe supports an inexpensive application of DSF measurements suitable for detection with standard RT-PCR machines in a hydrophilic or hydrophobic environment.

A new interest in the study of small molecules arises with the development of science and technology and consideration to the accumulated knowledge in genomics, proteomics and metabolomics. Now it appears no less important to explore the functional activity and roles of individual metabolites, as well as to elucidate the pathways of biological processes, their cascade reactions, in norm and pathology. We turned our attention to lactate, which is no longer considered as a "dead end" of anaerobic metabolism, produced in tissues with accelerated glycolysis. In recent years, lactate has been predominantly viewed as a metabolite that plays an important role in regulating the function of many cells (adipocytes, endothelial cells, neurons) and is involved in tissue remodeling, angiogenesis, proliferation and differentiation. The study of the effect of lactate on isolated catalytic proteins is able to reveal important and as yet unexplored roles of small molecules in intermolecular processes. We chose the enzyme glycerol-3-phosphate dehydrogenase (G3PDH), which is responsible for the switching of carbohydrate and lipid metabolism, as a potential target of its action. The study aimed to assess lactate affinity for G3PDH in order to find out the functional ability of the intermediate. The range of lactate biological activities was revealed and its protein partners were characterized by computer modeling. Using differential scanning fluorimetry and microcapillary thermophoresis, we found the G3PDH–lactate interaction and demonstrated changes in the conformational stability of the enzyme. [ABSTRACT FROM AUTHOR]

Differential scanning fluorimetry (DSF) is a widely used biophysical technique with applications to drug discovery and protein biochemistry. DSF experiments are commonly performed in commercial real-time polymerase chain reaction (qPCR) thermal cyclers or nanoDSF instruments. Here, we report the construction, validation, and example applications of an open-source DSF system for 176 €, which, in addition to protein-DSF experiments, also proved to be a versatile biophysical instrument for less conventional RNA-DSF experiments. Using 3D-printed parts made of polyoxymethylene, we were able to fabricate a thermostable machine chassis for protein-melting experiments. The combination of blue high-power LEDs as the light source and stage light foil as filter components was proven to be a reliable and affordable alternative to conventional optics equipment for the detection of SYPRO Orange or Sybr Gold fluorescence. The ESP32 microcontroller is the core piece of this openDSF instrument, while the in-built I2S interface was found to be a powerful analog-to-digital converter for fast acquisition of fluorescence and temperature data. Airflow heating and inline temperature control by thermistors enabled high-accuracy temperature management in PCR tubes (±0.1 °C) allowing us to perform high-resolution thermal shift assays (TSA) from exemplary biological applications.

The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows. [ABSTRACT FROM AUTHOR]

All biological processes rely on the formation of protein–ligand, protein–peptide and protein–protein complexes. Studying the affinity, kinetics and thermodynamics of binding between these pairs is critical for understanding basic cellular mechanisms. Many different technologies have been designed for probing interactions between biomolecules, each based on measuring different signals (fluorescence, heat, thermophoresis, scattering and interference, among others). Evaluation of the data from binding experiments and their fitting is an essential step towards the quantification of binding affinities. Here, user‐friendly online tools to analyze biophysical data from steady‐state fluorescence spectroscopy, microscale thermophoresis and differential scanning fluorimetry experiments are presented. The modules of the data‐analysis platform (https://spc.embl‐hamburg.de/) contain classical thermodynamic models and clear user guidelines for the determination of equilibrium dissociation constants (Kd) and thermal unfolding parameters such as melting temperatures (Tm). [ABSTRACT FROM AUTHOR]

Purification of recombinant proteins for biochemical assays and structural studies is time-consuming and presents inherent difficulties that depend on the optimization of protein stability. The use of dyes to monitor thermal denaturation of proteins with sensitive fluorescence detection enables rapid and inexpensive determination of protein stability using real-time PCR instruments. By screening a wide range of solution conditions and additives in a 96-well format, the thermal shift assay easily identifies conditions that significantly enhance the stability of recombinant proteins. The same approach can be used as an initial low-cost screen to discover new protein-ligand interactions by capitalizing on increases in protein stability that typically occur upon ligand binding. This unit presents a methodological workflow for small-scale, high-throughput thermal denaturation of recombinant proteins in the presence of SYPRO Orange dye.

Differential Scanning Fluorimetry (DSF) is a valuable and versatile tool in the field of protein and antibody stability studies, providing valuable insights into their thermal stability, and aiding in the optimization of experimental conditions for various applications. Antibody fragments provide armamentarium for researchers and practitioners across various fields, enabling advancements in medicine, diagnostics, research, and industrial applications. In the present study, single-chain antibodies derived from mAb 4B7 and mAb 1245 were expressed in E. coli , refolded, and checked for their binding with the antigen - Pfs25 (transmission-blocking malaria vaccine candidate). We used nano-DSF as a valuable tool to assess thermal stability, consequently aiding in predicting the correct folding of single-chain antibodies.. Employing nano-DSF as a checkpoint enables the determination of whether to proceed with functional and binding studies on the refolded single-chain antibodies. • Refolded single chain antibodies showed differential nano-DSF profiles. • Nano-DSF profiles correlated with antibody binding efficiency. • Nano-DSF profile can serve as a checkpoint to shortlist refolded scFvs. [ABSTRACT FROM AUTHOR]

Testing of an expanded, 800-compound set of analogues of the earlier described Strecker-type α-aminonitriles (selected from publicly available Enamine Ltd. Screening Collection) in thermal shift assay against bovine carbonic anhydrase (bCA) led to further validation of this new class of inhibitors and identification a new, refined chemotype represented by inhibitors with 10-improved potency.

The differential scanning fluorimetry (DSF) screening of 5.692 fragments in combination with benzenesulfonamide (BSA) against bovine carbonic anhydrase (bCA) delivered >100 hits that either caused, on their own, a significant thermal shift (ΔTm, °C) in the protein melting temperature or significantly influenced the thermal shift observed for BSA alone. Three hits based on 1,2,3-triazole moiety represent the periphery of the recently reported potent inhibitors of hCA II, IX and XII which were efficacious in vivo. Such a re-discovery of suitable BSA periphery essentially validates the new fragment-based approach to the discovery of future CAIs. Structures of other validated fragment hits are reported.

Biophysical methods such as mass spectrometry, surface plasmon resonance, nuclear magnetic resonance, and both differential scanning isothermal titration calorimetry are now well established as key components of the early drug discovery process. These approaches are used successfully for a range of activities, including assay development, primary screening, hit confirmation and detailed mechanistic characterisation of compound binding. Matching the speed, sensitivity and information content of the various techniques to the generation of critical data and information required at each phase of the drug discovery process has been key. This review describes the framework by which these methods have been applied in the drug discovery process and provides case studies to exemplify the impact.

Fibroblast growth factors (FGFs) regulate embryonic development and homeostasis, including tissue and organ repair and specific aspects of metabolism. The basic FGF and acidic FGF, now known as FGF2 and FGF1, are widely used protein drugs for tissue repair. However, they are susceptible to denaturation at ambient temperatures and during long‐time storage, which will reduce their biological activity. The interaction of FGFs with the sulfated domains of heparan sulfate and heparin is essential for their cellular signaling and stability. Therefore, we analyzed the interactions of FGF1 and FGF2 with four sulfated polysaccharides: heparin, dextran sulfate (DXS), λ‐carrageenan, and chondroitin sulfate. The results of thermal stability and cell proliferation assays demonstrate that heparin, DXS, and λ‐carrageenan bound to both FGFs and protected them from denaturation. Our results suggest heparin, DXS, and λ‐carrageenan are potential formulation materials that bind and stabilize FGFs, and which may also potentiate their activity and control their delivery.

• Study on rpMHC-I thermostability shows a two-step mechanism of thermal denaturation. • High-affinity rpMHC-I are pH-stable, but buffer substances influence Tm. • NanoDSF is a robust and sensitive method for measuring stability and folding energies of rpMHC-I. • NanoDSF allows buffer formula optimization and quality control of rpMHC-I. • NanoDSF is suitable for estimating the binding affinity of peptides to MHC-I. Recombinant major histocompatibility complex class I molecules are used in diagnostic and therapeutic approaches in cancer immunotherapy, with many studies exploring their binding to antigenic peptides. Current techniques for kinetic peptide binding studies are hampered by high sample consumption, low throughput, interference with protein stability, and/or high background signal. Here, we validate nanoscale differential scanning fluorimetry (nanoDSF), a method using the tryptophan fluorescence of class I molecules, for class I/peptide binding, and we use it to determine the molecular mechanism of the thermal denaturation of HLA-A*02:01. [ABSTRACT FROM AUTHOR]

The stability and aggregation of NIST monoclonal antibody (NISTmAb) were investigated by hydrogen/deuterium exchange mass spectrometry (HDX‐MS), differential scanning calorimetry (DSC), and nano‐differential scanning fluorimetry (nanoDSF). NISTmAb was prepared in eight formulations at four different pHs (pH 5, 6, 7, and 8) in the presence and absence of 150 mM NaCl and analyzed by the three methods. The HDX‐MS results showed that NISTmAb is more conformationally stable at a pH near its isoelectric point (pI) in the presence of NaCl than a pH far from its pI in the absence of NaCl. The stabilization effects were global and not localized. The midpoint temperature of protein thermal unfolding transition results also showed the CH2 domain of the protein is more conformationally stable at a pH near its pI. On the other hand, the onset of aggregation temperature results showed that NISTmAb is less prone to aggregate at a pH far from its pI, particularly in the absence of NaCl. These seemingly contradicting results, higher conformational stability yet higher aggregation propensity near the pI than far away from the pI, can be explained by intramolecular and intermolecular electrostatic repulsion using Lumry‐Eyring model, which separates folding/unfolding equilibrium and aggregation event. The further a pH from the pI, the higher the net charge of the protein. The higher net charge leads to greater intramolecular and intermolecular electrostatic repulsions. The greater intramolecular electrostatic repulsion destabilizes the protein and the greater intermolecular electrostatic repulsion prevents aggregation of the protein molecules at pH far from the pI. [ABSTRACT FROM AUTHOR]