Conformational Changes Research Articles

A carboxymethyl cellulase from the yeast Cryptococcus gattii WM276: Expression, purification and characterisation

Cryptococcus gattii and its medical implications have been extensively studied. There is, however, a significant knowledge gap regarding cryptococcal survival in its environmental niche, namely woody material, which is glaring given that infection is linked to environmental populations. A gene from C. gattii (WM276), the predominant global molecular type (VGI), has been sequenced and annotated as a putative cellulase. It is therefore, of both medical and industrial intertest to delineate the structure and function of this enzyme. A homology model of the enzyme was constructed as a fusion protein to a maltose binding protein (MBP). The CGB_E4160W gene was overexpressed as an MBP fusion enzyme in Escherichia coli T7 cells and purified to homogeneity using amylose affinity chromatography. The structural and functional character of the enzyme was investigated using fluorescence spectroscopy and enzyme activity assays, respectively. The optimal enzyme pH and temperature were found to be 6.0 and 50 °C, respectively, with an optimal salt concentration of 500 mM. Secondary structure analysis using Far-UV CD reveals that the MBP fusion protein is primarily α-helical with some β-sheets. Intrinsic tryptophan fluorescence illustrates that the MBP-cellulase undergoes a conformational change in the presence of its substrate, CMC-Na+. The thermotolerant and halotolerant nature of this particular cellulase, makes it useful for industrial applications, and adds to our understanding of the pathogen's environmental physiology.

Proline substitutions in the ASIC1 β11-12 linker slow desensitization

Desensitization is a prominent feature of nearly all ligand gated ion channels. Acid-sensing ion channels (ASIC) undergo desensitization within hundreds of milliseconds to seconds upon continual extracellular acidification. The ASIC mechanism of desensitization is primarily due to the isomerization or “flipping” of a short linker joining the 11th and 12th beta sheets in the extracellular domain. In the resting and active states this β11-12 linker adopts an “upward” conformation while in the desensitized conformation the linker assumes a “downward” state. It is unclear if a single linker adopting the “downward” state is sufficient to desensitize the entire channel, if all three are needed or some more complex scheme. To accommodate this “downward” state, specific peptide bonds within the linker adopt either trans-like or cis-like conformations. Since proline-containing peptide bonds undergo cis-trans isomerization very slowly, we hypothesized that introducing proline residues in the linker may slow or even abolish ASIC desensitization, potentially providing a tool valuable research tool. Proline substitutions in the chicken ASIC1 β11-12 linker (L414P and Y416P) slowed desensitization decays approximately 100 to 1000-fold as measured in excised patches. Both L414P and Y416P shifted the steady state desensitization curves to more acidic pHs while activation curves and ion selectivity were largely unaffected (except for a left shifted activation pH50 of L414P). To investigate the functional stoichiometry of desensitization in the trimeric ASIC, we created families of L414P and Y416P concatemers with zero, one, two or three proline substitutions in all possible configurations. Introducing one or two L414P or Y416P substitutions only slightly attenuated desensitization, suggesting that conformational changes in the single remaining faster wild type subunits were sufficient to desensitize the channel. These data highlight the unusual cis-trans isomerization mechanism of ASIC desensitization and support a model where ASIC desensitization requires only a single subunit.

Effects of anions on the electrospray ionization of proteins in strong acids.

The effect of anions on the positive electrospray ionization (ESI) of proteins in different strong acids with varying pH values from 3 to 1 is studied using high-pressure ESI. Reducing the pH from ∼2 to 1 caused a drastic shift in charge state from a high-charge-state distribution (HCSD) to a narrow low-charge-state distribution (LCSD). The shift in charge state was consistent with the circular dichroism result that showed a conformational change due to the "acid-induced folding" of proteins from an unfolding state to a compact molten globule state. Acids of different anions produced noticeable differences in the average charge for HCSD and LCSD. For HCSD, the average charge was lower than the value typically observed using formic and acetic acids. As for LCSD, the average charge was lower than the "native" charge. The high abundance of acid anion that induces the protein compaction was believed to play a role in charge reduction. The effectiveness of anions to "refold" a highly unfolded protein to a compact state and the propensity to reduce the charge of HCSD for proteins appeared to follow the selectivity series of anions towards the stationary phase in ion chromatography. However, the propensity of anions to reduce the charge for LCSD follows quite an opposite trend. The presence of ammonium salt in the acidic solution was found to increase the charge of LCSD. The simple mass spectrum with a narrow distribution of charge state obtained with perchloric acid at pH 1 was demonstrated to facilitate the counting of basic sites.

Polyphenolic metacyclophane as a radical scavenger for therapeutic activation: a computational study

Modeling antioxidants for improved human health is a prime area of research. Inclusion complexes exhibit antioxidant activity. Supramolecular scaffolds like calixtyrosol are anticipated to have considerable antioxidant and therapeutic activity. In this study, we have designed 30 polyphenolic metacyclophanes and investigated their antioxidant properties. Exceptional O─H bond dissociation energy of 44 kcal/mol is reported for a metacyclophane with acyl urea linkage. This may be explained through a cooperative effect of localization of spin density distribution and an intramolecular hydrogen bonding of the corresponding radical. Further, the pharmacokinetics and toxicity analysis screened eight drug-like candidates. The interaction of the eight screened molecules with the Lysozyme transport protein and SOD protein has been studied using the molecular docking approach. Lastly, the MD simulations are performed to analyze the conformational changes of the transport protein after complexation with the proposed molecules. Comprehensive analyses including density functional studies of physiological parameters, favorable pharmacokinetics, toxicity, molecular docking, and MD simulations affirmed polyphenolic metacyclophane XXI as a radical scavenging and drug-like candidate.

Adaptability to the environment of protease by secondary structure changes and application to enzyme-selective hydrolysis

The reactions involving enzymes are significantly influenced by various environmental factors. Clarity of how the activity and structure of proteases impact their function is crucial for more efficient application of enzymes as a tool. The impact of temperature, pH, and ionic strength on changes in protease activity, secondary structure, and protein conformation during enzymatic hydrolysis were investigated in this study. The enzymatic activity and secondary structure of acid-base protease were found to undergo significant modifications under different physical conditions, as demonstrated by UV spectrophotometry and FTIR spectroscopy analysis. Specifically, variations in α-helix and β-fold content were observed to correlate with changes in enzyme activity. Molecular simulation analysis revealed that physical conditions have varying effects on the protease, particularly influencing enzyme activity and secondary structure. Evaluation of the proteases indicated alterations in both enzyme activity and structure. This treatment selectively hydrolyzed β-lactoglobulin and reduced sensitization. These findings offer novel perspectives on the functionalities and regulatory mechanisms of proteases, as well as potential industrial applications.

Deciphering the impact of F23L mutation on the aggregation propensity of human islet amyloid polypeptide using molecular simulations

The self-aggregation of 37-residue human islet amyloid polypeptide (hIAPP) into β-sheet rich oligomers and amyloid fibrils contributes to the loss of pancreatic β-cell mass in type 2 diabetes (T2D). A previous study highlighted that the F23L mutation in the amyloidogenic core (Ser20–Ser29) of hIAPP slows down its self-aggregation by a factor of 2.6. However, the underlying molecular mechanism behind slower aggregation and reduced cytotoxicity of hIAPP on F23L mutation remains obscure. Thus, the structural and conformational changes in F23L–hIAPP that lead to slower aggregation and lower cytotoxicity were examined by molecular dynamics (MD) simulations. The MD simulations depicted that F23L mutation marginally increases the helical content from 10.20 ± 1.94 to 11.50 ± 2.18 % accompanied by a noteworthy decrease in aggregation-prone β-sheet from 14.00 ± 1.58 to 0.80 ± 0.37 %. Notably, FEL conformations depicted a complete disappearance of β-sheet content in F23L–hIAPP as compared to 9–20 % in wt–hIAPP in agreement with the notably reduced toxicity of F23L–hIAPP aggregates against cultured INS-1 832/13 cells. Interestingly, dihedral principal component analysis (dPCA) depicted noteworthy compression in the conformational sub-space and a lower trace value of hIAPP on F23L mutation, which indicates lower conformational fluctuations in F23L–hIAPP. F23L mutation alters the conformational landscape of hIAPP dimer by lowering interchain contacts, and hydrogen bonds as well as reducing binding affinity between chains A-B of hIAPP dimer. Importantly, MD simulations illuminated the key role of Phe23 in mediating intramolecular interactions leading to aggregation-prone structures that promote hIAPP aggregation. The key insights regarding structural transitions and conformational preferences of hIAPP on F23L mutation illuminated from this work will benefit the design and optimization of potential inhibitors targeting Phe23-mediated interactions to block hIAPP aggregation in T2D.

Predicting protein conformational motions using energetic frustration analysis and AlphaFold2

Proteins perform their biological functions through motion. Although high throughput prediction of the three-dimensional static structures of proteins has proved feasible using deep-learning-based methods, predicting the conformational motions remains a challenge. Purely data-driven machine learning methods encounter difficulty for addressing such motions because available laboratory data on conformational motions are still limited. In this work, we develop a method for generating protein allosteric motions by integrating physical energy landscape information into deep-learning-based methods. We show that local energetic frustration, which represents a quantification of the local features of the energy landscape governing protein allosteric dynamics, can be utilized to empower AlphaFold2 (AF2) to predict protein conformational motions. Starting from ground state static structures, this integrative method generates alternative structures as well as pathways of protein conformational motions, using a progressive enhancement of the energetic frustration features in the input multiple sequence alignment sequences. For a model protein adenylate kinase, we show that the generated conformational motions are consistent with available experimental and molecular dynamics simulation data. Applying the method to another two proteins KaiB and ribose-binding protein, which involve large-amplitude conformational changes, can also successfully generate the alternative conformations. We also show how to extract overall features of the AF2 energy landscape topography, which has been considered by many to be black box. Incorporating physical knowledge into deep-learning-based structure prediction algorithms provides a useful strategy to address the challenges of dynamic structure prediction of allosteric proteins.

Effects of ultrasound pretreatment on the structure, IgE binding capacity, functional properties and bioactivity of whey protein hydrolysates via multispectroscopy and peptidomics revealed

Whey protein is an important food ingredient, but it is also considered a major food allergen. The aim of this study was to investigate the effect of ultrasound pretreatment on the structure, IgE binding capacity, functional properties and biological activity of whey protein isolate (WPI) hydrolysates (WPH), including WPI hydrolyzed by a combination of enzymes from Bromelain and ProteAXH (BA-WPI) and WPI hydrolyzed by a combination of enzymes from Papain W-40 and ProteAXH (PA-WPI). The IgE binding capacity of BA-WPI and PA-WPI was reduced to 40.28% and 30.17%, respectively, due to disruption/exposure/shielding of conformational and linear epitopes. The IgE binding capacity of sonicated WPI was increased, but ultrasound pretreatment further reduced the IgE binding capacity of the hydrolysates to 32.89% and 28.04%. This is due to the fact that ultrasound pretreatment leads to conformational changes including increased α-helix and β-sheet structure, exposure of aromatic amino acids, surface hydrophobicity, and increased sulfhydryl content, which increases the accessibility of allergenic epitopes to WPI by the enzyme. Multispectral and LC-MS/MS results further indicated that ultrasound pretreatment altered the conformational and primary structural changes of the hydrolysates. The thermograms showed that ultrasound pretreatment mainly altered the epitope spectra of β-lactoglobulin hydrolysates, while it had less effect on the epitope spectra of α-lactalbumin hydrolysates. Additionally, ultrasound pretreatment significantly improved the foaming properties, antioxidant activity, and α-glucosidase inhibition of the hydrolysates without impairing the solubility and emulsification properties of the hydrolysates. Therefore, ultrasound pretreatment is a feasible method to reduce the allergenicity of WPH and to improve their functional properties and bioactivity. Notably, ultrasonic pretreatment improved the effectiveness and efficiency of WPI hydrolysis, which is a feasible method to produce high-quality protein feedstock in a green, efficient, and economical way.

Inhibition of α-amylase activity by quercetin via multi-spectroscopic and molecular docking approaches

The quercetin-induced inhibition of α-amylase activity was comprehensively studied using various spectroscopic methods, including UV–Visible, fluorescence, and Fourier-transform infrared spectroscopy. Quercetin acted as a mixed-type inhibitor, and its binding altered the kinetic properties of α-amylase. Quercetin exhibited static binding with α-amylase, as evidenced by a higher Stern-Volmer constant (KSV) at 298 K (9.56 ± 0.63 × 103 L/mol) compared to the KSV value at 318 K (5.56 ± 0.48 × 103 L/mol). Additionally, quercetin induced conformational changes in the hydrophobic micro-environment surrounding the tryptophan and tyrosine residues of α-amylase, as indicated by fluorescence spectroscopy. Hydrophobic interactions primarily drove the spontaneous binding between α-amylase and quercetin from thermodynamic data. Molecular docking studies supported the role of hydrogen bonds (Asp197 and Gln63) and hydrophobic interactions (with active site residues Ala198, Leu165, and Trp59) in the complex formation. These findings provide a detailed understanding of how quercetin inhibits α-amylase activity, reinforcing its potential as a glycemic controller in food formulations.

Impact of pH on the structure, interfacial and foaming properties of pea protein isolate: Investigation of the structure – Function relationship

This study explored the relationship between pea protein foaming properties and their structure and physicochemical properties under neutral and acidic pH. Results showed that pH modified the zeta potential, particle size and surface tension due to electrostatic changes. FT-MIR and fluorescence spectra revealed pH-induced conformational changes, exposing hydrophobic groups and increasing sulfhydryl content, promoting protein aggregation. At pH 3, the highest foaming capacity (1.273) and lowest foam expansion (6.967) were observed, associated with increased surface hydrophobicity and net charges, ideal for creating light foams with high liquid incorporation for acidic beverages or fruit-based mousses. Pea protein isolate generated stable foams with foam volume stability between 86.662 % and 94.255 %. Although neutral pH conditions showed the highest foam volume stability, their air bubbles increased in size and transitioned from spherical to polyhedral shape, suitable for visual-centric applications, like cappuccino foam and beer-head retention. Foams at pH 5 exhibited the smallest bubbles and maintained their spherical shape, enhancing drainage resistance, beneficial for whipped toppings. Strong correlations (Pearson correlation coefficient higher than 0.600) were noted between the structure, surface and foaming properties, providing crucial insights into optimizing pea protein functionality across various pH conditions, enabling the development of plant-based foamed products with tailored properties.

Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair

Ribonucleotides in DNA cause several types of genome instability and can be removed by ribonucleotide excision repair (RER) that is finalized by DNA ligase 1 (LIG1). However, the mechanism by which LIG1 discriminates the RER intermediate containing a 5'-RNA–DNA lesion generated by RNase H2-mediated cleavage of ribonucleotides remains unknown. Here, we determine X-ray structures of LIG1/5'-rG:C at the initial step of ligation where AMP is bound to the active site of the ligase, and uncover a large conformational change downstream the nick resulting in a shift at Arg(R)871 residue in the Adenylation domain of the ligase. Furthermore, we demonstrate a diminished ligation of the nick DNA substrate with a 5'-ribonucleotide in comparison to an efficient end joining of the nick substrate with a 3'-ribonucleotide by LIG1. Finally, our results demonstrate that mutations at the active site residues of the ligase and LIG1 disease-associated variants significantly impact the ligation efficiency of RNA–DNA heteroduplexes harboring “wrong” sugar at 3'- or 5'-end of nick. Collectively, our findings provide a novel atomic insight into proficient sugar discrimination by LIG1 during processing of the most abundant form of DNA damage in cells, genomic ribonucleotides, during initial step of the RER pathway.

Characterization of metal-binding behavior of DOM component structure in biochar: Analysis of binding sites, binding sequences and impact pathways

The binding of biochar-derived dissolved organic matter (BDOM) to heavy metals is a complex and dynamic process, with potentially different impact pathways. The outer electrons of various heavy metals can also affect their binding ability. This study comprehensively investigated the binding sites, sequences, constants, and influencing pathways of each component structure in BDOM through modern spectroscopic methods and multidimensional chemometrics. Here, the dominance of carboxyl and phenolic groups in the interaction of chromogenic dissolved organic matter (CDOM) with metal ions, which complex with BDOM, leads to an increase in the size of the BDOM molecule. In addition, Cu and Zn primarily bound to humic acids fluorophore, while Pb and Ni preferentially bound to protein-like fluorophore, likely due to the varying affinities of nitrogen- and carbon-based functional groups for different metals. Significant differences were observed in the interactions between different metal ions and fluorophores, involving both direct and indirect effects. Molecular perspectives and pathways suggested that the binding of BDOM to Zn was notably intricate, involving multiple conformational changes and impact pathways. These findings offer a crucial scientific foundation for a comprehensive comprehension of the interaction mechanisms between various metal ions and BDOM components.

An Insight into the Mechanism of DNA Cleavage by DNA Endonuclease from the Hyperthermophilic Archaeon Pyrococcus furiosus.

Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N6-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme-substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature.

Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway

Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD+-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus Thermochaetoides thermophila. By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications.

Unraveling the mechanism of aroma loss during prolonged hot air drying of non-smoked bacon: Insights into aroma compounds generation and retention

In this study, the potential mechanism of aroma loss in non-smoked bacon due to excessive hot air drying (beyond 24 h) was investigated, focusing on protein conformational changes and the inhibition of heme protein-mediated lipid oxidation by oleic acid. The results showed that prolonged hot-air drying caused a stretching of the myofibrillar protein (MP) conformation in bacon before 36 h, leading to an increase in reactive sulfhydryl groups, surface hydrophobicity, and the exposure of additional hydrophobic sites. Consequently, the binding ability of MP to the eight key aroma compounds (hexanal, 1-octen-3-ol, (E)-2-nonenal, 3-methyl-butanoic acid, 2-undecenal, (E, E)-2,4-decadienal, 2,3-octanedione, and dihydro-5-pentyl-2(3H)-furanone) was enhanced, resulting in their retention. On the other hand, a sustained increase in oleic acid levels has been demonstrated to effectively inhibit heme protein-mediated lipid oxidation and the formation of these key aroma compounds. Using lipidomic techniques, 30 lipid molecules were identified as potential precursors of oleic acid during the bacon drying process. Among these precursors, triglycerides (16:0/18:0/18:1) may be the most significant.

Structural analysis of the human C5a-C5aR1 complex using cryo-electron microscopy

The complement system is a complex network of proteins that plays a crucial role in the innate immune response. One important component of this system is the C5a-C5aR1 complex, which is critical in the recruitment and activation of immune cells. In-depth investigation of the activation mechanism as well as biased signaling of the C5a-C5aR1 system will facilitate the elucidation of C5a-mediated pathophysiology. In this study, we determined the structure of C5a-C5aR1-Gi complex at a high resolution of 3 Å using cryo-electron microscopy (Cryo-EM). Our results revealed the binding site of C5a, which consists of a polar recognition region on the extracellular side and an amphipathic pocket within the transmembrane domain. Furthermore, we found that C5a binding induces conformational changes of C5aR1, which subsequently leads to the activation of G protein signaling pathways. Notably, a key residue (M265) located on transmembrane helix 6 (TM6) was identified to play a crucial role in regulating the recruitment of β-arrestin driven by C5a. This study provides more information about the structure and function of the human C5a-C5aR1 complex, which is essential for the proper functioning of the complement system. The findings of this study can also provide a foundation for the design of new pharmaceuticals targeting this receptor with bias or specificity.

Interaction between Halogenated Phenols and Thyroxine‐Binding Protein: A Multispectral and Computational Approach

AbstractThe aim of this study was to understand the interaction between transthyretin (TTR) and halogenated phenols (HPs) including 2,4‐dichlorophenol (DCP), 2,4,6‐trichlorophenol (TCP), pentachlorophenol (PCP), 2‐bromophenol (2‐BP), 2,4‐dibromophenol (DBP) and 2,4,6‐tribromophenol (TBP). Computer simulation and multi‐spectroscopy techniques were used to investigate the interaction. The fluorescence of TTR was found to be quenched through static quenching and non‐radiative energy transfer by HPs, suggesting that the binding process between HPs and TTR was primarily influenced by van der Waals forces and hydrogen bonds. ANS substitution experiments indicated that HPs interacted with TTR at the T4 binding site. Three‐dimensional fluorescence spectra and Fourier transform infrared spectroscopy were used to investigate the conformational and microenvironmental changes of TTR resulting from the interactions with HPs. Additionally, molecular docking and reduced density gradient analysis were used to identify the specific residues and binding forces involved in the interaction between HPs and TTR binding sites. The findings were subsequently validated through quantum chemical analysis. This research integrates state‐of‐the‐art multispectral analytical methodologies with sophisticated computational modeling to introduce an innovative approach for dissecting the interactions between halogenated phenols (HPs) and transthyretin (TTR). This methodology offers a novel avenue for investigating the molecular interplay between HPs and TTR, thereby providing critical insights that are instrumental in assessing the latent toxicity of these compounds.

Introduction to the concept of effective albumin concentration.

In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. The purpose of this article is to discuss how the structural and presumably functional integrity of albumin, as described by the concept of effective albumin concentration (eAlb), has potentially important clinical implications beyond the total albumin concentration (tAlb) routinely reported by clinical laboratories. Albumin has several functions beyond its oncotic effects, including molecule binding, substance transport, detoxification actions, and serving as an antioxidant. However, there are conformational changes that occur during or following the manufacture of albumin and during its administration to patients with various disease states, such as decompensated liver disease, that often impair these functions. Such impairments are not reflected in tAlb values reported by clinical laboratories and might explain the disconnect often seen between albumin's proposed beneficial mechanistic functions and its less-than-predicted clinical effectiveness as noted in published studies. The concept of eAlb has been introduced to describe albumin with structural and functional integrity. Limited studies have found associations between eAlb values and patient prognostic indicators, but the techniques used to decide these effective concentrations to date are complicated and require specialized equipment and experienced researchers for proper interpretation. Estimation of eAlb may provide valuable information on the functional ability of albumin beyond the tAlb reported by clinical laboratories, but more research is needed to decide how this information is best used in the clinical setting.

Computational investigation of remdesivir, favipiravir, ribavirin, and their phosphate derivatives against Nipah virus RNA-dependent RNA polymerase

ABSTRACT Outbreaks of human Nipah virus (NiV) cases have recently been reported in several countries. With a mortality rate of around 80% and no known therapy, there is an urgent need to test existing antivirals repurposed for it. Due to its central role in virus replication, the RNA-dependent RNA polymerase (RdRp) of NiV-L protein is a potential target for such antiviral therapies. In this study, Favipiravir, Remdesivir, Ribavirin, and their metabolites, including monophosphate (MP), diphosphate (DP), and triphosphate (TP), were virtually screened against RdRp. Using molecular dynamics (MD) simulations, lead hits from the docking study were examined for conformational changes. Additional analyses, including MM-PBSA, residual decomposition energy, and principal component analysis, were performed on the MD trajectory. Remdesivir-TP, Favipiravir-TP, and Ribavirin-TP exhibited the lowest binding energies of –7.8, −7.4, and −6.9 kcal/mol, respectively, and displayed an affinity for pocket 1, forming interactions with active site residues Asp726 and Asn727. During the 100 ns MD simulation, Remdesivir-TP demonstrated a more stable binding mode compared to Favipiravir-TP and Ribavirin-TP. The relative binding energies were −94.709 kJ/mol, −68.882 kJ/mol, and −46.98 kJ/mol for Remdesivir-TP, Favipiravir-TP, and Ribavirin-TP, respectively. This research anticipates Remdesivir-TP to be a potential candidate for an antiviral drug against NiV infection.

Live Cell Monitoring of Phosphodiesterase Inhibition by Sulfonylurea Drugs.

Sulfonylureas (SUs) are a class of antidiabetic drugs widely used in the management of diabetes mellitus type 2. They promote insulin secretion by inhibiting the ATP-sensitive potassium channel in pancreatic β-cells. Recently, the exchange protein directly activated by cAMP (Epac) was identified as a new class of target proteins of SUs that might contribute to their antidiabetic effect, through the activation of the Ras-like guanosine triphosphatase Rap1, which has been controversially discussed. We used human embryonic kidney (HEK) 293 cells expressing genetic constructs of various Förster resonance energy transfer (FRET)-based biosensors containing different versions of Epac1 and Epac2 isoforms, alone or fused to different phosphodiesterases (PDEs), to monitor SU-induced conformational changes in Epac or direct PDE inhibition in real time. We show that SUs can both induce conformational changes in the Epac2 protein but not in Epac1, and directly inhibit the PDE3 and PDE4 families, thereby increasing cAMP levels in the direct vicinity of these PDEs. Furthermore, we demonstrate that the binding site of SUs in Epac2 is distinct from that of cAMP and is located between the amino acids E443 and E460. Using biochemical assays, we could also show that tolbutamide can inhibit PDE activity through an allosteric mechanism. Therefore, the cAMP-elevating capacity due to allosteric PDE inhibition in addition to direct Epac activation may contribute to the therapeutic effects of SU drugs.