Electrostatics of nanosystems: application to microtubules and the ribosome

Food-derived DPP4 inhibitors: Drug discovery based on high-throughput virtual screening and deep learning

Dipeptidyl peptidase-4 (DPP-4) is a critical target for the treatment of type 2 diabetes. This study outlines the development of six compounds derived from food sources and modified to create promising candidates for the treatment of diabetes. These compounds were identified through a combination of virtual screening, deep learning algorithms, ADMET characterization assessment, and molecular dynamics simulations. Furthermore, a taste prediction model was used to assess the flavor of these DPP-4 inhibiting compounds. After thorough evaluation, we concluded that the six food-derived DPP-4 inhibitors identified have significant potential for therapeutic success. This study has greatly contributed to the discovery of novel dietary supplements for the management of type 2 diabetes.

Diffusion properties of transfer RNAs in the yeast cytoplasm under normal and osmotic stress conditions

The mechanism by which aminoacyl-tRNAs are supplied to translating ribosomes for protein synthesis is likely to involve a process of diffusion within the cellular environment, which is inevitably impacted by macromolecular crowding. Osmotic stress leading to cell shrinkage increases the concentration of macromolecules in the cytoplasm, reducing protein diffusion. The impact of macromolecular crowding on the translation machinery in eukaryotes remains uncharacterised. In this study Brownian dynamics simulation were used for the first time to study the effect of macromolecular crowding on the microsecond-time scale diffusion properties of tRNAs and their ternary complexes within a model yeast cytoplasmic environment. Under normal cell-like conditions, the diffusion of tRNAs and ternary complexes was predicted to be reduced by up to 8-fold (compared with dilute conditions), whilst diffusion under severe osmotic stress conditions decreased by up to a remarkable 80-fold. All molecules exhibited sub-diffusive behaviour, which was stronger under osmotic stress. These findings may be readily used to predict protein translation dynamics, including the crucial process of tRNA delivery to the ribosome, under a variety of conditions.

Evaluation of mutations on O6-methylguanine methyl transferase structure and its interactions: molecular dynamics simulation study

O6-methylguanine DNA methyl transferase (MGMT) is a significant vehicle for the cellular clearance of alkyl lesions, particularly the methyl group of the O-6 and O-4 positions of guanine and thymine, respectively. Many publications have studied the correlation between polymorphisms in MGMT and susceptibility to various cancers. In the present study, we investigated the consequence of L84F, common single-nucleotide polymorphism, K125E, site-specific mutagenesis, and L84F/K125E on conformation, stability, and behavior of MGMT in the free form and interaction with proliferating cell nuclear antigen (PCNA) and DNA as partners in the biochemical network by using molecular dynamics simulation method. Our results showed that all free variants of MGMT differed from the native form. However, among all free variants of MGMT, the L84F/K125E variant exhibited similar properties compared with the wild-type. In contrast, in complex modes, only amino acid residues of the L84F variant are involved in the interactions with PCNA and DNA somewhat differently relative to the wild-type. Furthermore, L84F SNP showed the highest binding free energy compared to other variants and native forms. These alterations in the amino acids and binding free energy of L84F relative to the native are the reasons for changing its region connection compared to the native form. Therefore, we propose conducting further investigations into the impact of inhibitors or chemotherapeutic agents to assess their effectiveness on MGMT variants compared to the wild-type, aiming to reduce the cost of cancer treatment that will depend on inhibiting native MGMT protein.

NMR-Based Measurements of Site-Specific Electrostatic Potentials of Histone Tails in Nucleosome Core Particles

Electrostatics play a dominant role in guiding many biological processes. This is especially the case in the context of chromatin, where charge interactions modulate diverse activities such as DNA repair, transcription, replication, condensation, and phase separation. Using NMR experiments quantifying solvent paramagnetic relaxation enhancements of backbone amide and side chain methyl protons in the presence of paramagnetic cosolutes and focusing on the nucleosome core particle (NCP), we report near surface electrostatic potentials of tail residues of each of the four histone components of the NCP. These are all negative, despite sequences comprising a high density of positively charged amino acids, emphasizing the strong contribution of the negatively charged DNA with which the tails interact. Changes in electrostatic potentials of as much as 60 mV between isolated histone tails and tails in the context of the NCP are calculated. Notably, the tail potentials can vary significantly from each other, with enrichment in glycine residues correlating with less negative values, highlighting differences in the interactions with DNA.

A leigh syndrome mutation perturbs long-range energy coupling in respiratory complex I

Respiratory complex I is a central enzyme of cellular energy metabolism that couples electron transfer with proton translocation across a biological membrane. In doing so, it powers oxidative phosphorylation that drives energy consuming processes. Mutations in complex I lead to severe neurodegenerative diseases in humans. However, the biochemical consequences of these mutations remain largely unknown. Here, we use the Escherichia coli complex I as a model to biochemically characterize the F124LMT-ND5 mutation found in patients suffering from Leigh syndrome. We show that the mutation drastically perturbs proton translocation and electron transfer activities to the same extent, despite the remarkable 140 Å distance between the mutated position and the electron transfer domain. Our molecular dynamics simulations suggest that the disease-causing mutation induces conformational changes that hamper the propagation of an electric wave through an ion-paired network essential for proton translocation. Our findings imply that malfunction of the proton translocation domain is entirely transmitted to the electron transfer domain underlining the action-at-a-distance coupling in the proton-coupled electron transfer of respiratory complex I.

Molecular dynamics simulation and docking studies reveals inhibition of NF-kB signaling as a promising therapeutic drug target for reduction in cytokines storms

Nuclear factor-kappa B (NF-kB) plays a crucial role in numerous cellular processes, such as inflammation, immunological responses to infection, cell division, apoptosis, and the development of embryos and neurons. Cytokines, plays an important role in positive feedback loop and leads to inflammatory cell death through the release of pathogenic cytokine known to be cytokine storm which causes diseases like Acute Respiratory Disorder (ARD), multi-organ disorder, Hyperinflammation syndrome and may cause death. This cytochrome storm was identified in the people severely affected by covid-19. NF-kB presents a promising therapeutic opportunity to mitigate covid-19-induced cytokine storm and reduce the risk of severe morbidity and mortality resulting from the diseases. This paper therefore explores the modulation of the NF-kB pathway by inhibiting the binding of the transcription factor as a potential strategy to mitigate the morbidity and mortality caused by cytokine storms. To identify small molecule inhibitors of NF-kB signaling, we screened approximately 101 molecules in two identified pockets of NF-kB (p50/p65)-DNA complex. Each molecule was virtually screened in two pockets (A1 and A2). The focus library was developed starting from chemical structures obtained from the literature (Angelicin and Psolaren) which shows the inhibition of NF-kB signaling, as well as using artificial intelligence (WADDAICA) and rationally designed molecules. Among the 3 highest-scored ligands (NFAI64, NF30 and NF49) selected from the docking studies and further molecular dynamic investigations. The identified compound NF30 showed significantly higher binding affinity (ΔGbinding) in A2 pocket (60.92 ± 1.83 kJ/mol) as compared to the rest of the molecules, making it a promising molecule for the inhibition of NF-kB. The discovered novel compounds by computational studies could be of relevance to identify more potent inhibitors of NF-kB dependent biological functions beneficial to control the cytokine storm occurring in the patients affected with Covid-19.

Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning

Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN) trained to predict physicochemical and geometric properties including solvation-free energies, diffusion constants, and hydrodynamic radii, based on three-dimensional protein structures. By leveraging transfer learning, pretrained GSnet embeddings were adapted to predict solvent-accessible surface area (SASA) and residue-specific pKa values, achieving high accuracy and generalizability. Notably, GSnet outperformed existing protein embeddings for SASA prediction and a locally charge-aware variant, aLCnet, approached the accuracy of simulation-based and empirical methods for pKa prediction. Our GNN framework demonstrated robustness across diverse data sets, including intrinsically disordered peptides, and scalability for high-throughput applications. These results highlight the potential of GNN-based embeddings and transfer learning to advance protein structure analysis, providing a foundation for integrating predictive models into proteome-wide studies and structural biology pipelines.

β-ATPase of the Insect Panstrongylus megistus: Cloning, Bioinformatics Analysis, and Study of Its Interaction With Lipophorin

Lipophorin is the main lipoprotein of the insect's hemolymph. Although its role in lipid metabolism has been extensively analyzed, the mechanisms of lipid delivery to target tissues mediated by lipophorin are not completely understood. It has been reported that the β-chain of the ATP synthase complex (β-ATPase) acts as a nonendocytic receptor for lipophorin in the hematophagous insect Panstrongylus megistus, and this function is relevant for the transfer of lipids. The aim of this study was to gather new information regarding the β-ATPase, including its sequence and interaction with lipophorin. A β-ATPase cDNA encoding a 521-amino acid protein was cloned from P. megistus. β-ATPase is highly conserved, and molecular phylogenetic analyses grouped the deduced amino acid sequences according to their respective taxa. Structural modeling of β-ATPase revealed a conserved folding pattern and three-dimensional architecture that allows docking with a modeled lipophorin, suggesting potential interaction between the two proteins. Recombinant β-ATPase (rβ-ATPase) was expressed in Escherichia coli, and the rβ-ATPase was purified by affinity chromatography. rβ-ATPase was combined with lipophorin at various ratios, and the sedimentation properties of these mixtures were analyzed by analytical ultracentrifugation. The changes in sedimentation behavior of the protein mixture compared to that of the individual proteins are consistent with binding between rβ-ATPase and lipophorin. This finding, which confirms the interaction of β-ATPase and lipophorin, provides additional support for the role of β-ATPase in the uptake of lipids by tissues.

PPI networking, in-vitro expression analysis, virtual screening, DFT, and molecular dynamics for identifying natural TNF-α inhibitors for rheumatoid arthritis

In humans, rheumatoid arthritis (RA) is a deadly autoimmune disease that affects bone health. Although the specific etiology of RA is unknown, scientific evidence suggests that smoking, genetic abnormalities, and environmental factors may all contribute to the disease's progression. We employed protein-protein interaction (PPI) networking analysis to identify a possible therapeutic target for RA. The lead-like molecule for the selected target was then found via virtual screening in the Indian medicinal plants phytochemistry and therapeutics database. Molecular dynamics has confirmed the stability of drug target-lead-like molecule complexes. The networking analysis identifies TNF-α as a potential therapeutic target for RA. TNF-α expression was verified using in vitro studies. Cassamedine was identified as a possible lead molecule among 17,967 chemicals in the Indian Medicinal Plants Phytochemistry and Therapeutics database using virtual screening experiments. The molecular docking results of the lead compound interaction with TNF-α were clarified by the quantum mechanism (QM) technique, namely, density functional theory (DFT). The stability of the lead-like compound with TNF-α was confirmed using 200 ns of molecular dynamics simulations. Energy calculations using molecular mechanics Poisson-Boltzmann surface area (MMPBSA) confirm the free energy between TNF-α and lead-like molecules.

Structural and Biochemical Insights into Lignin-Oxidizing Activity of Bacterial Peroxidases against Soluble Substrates and Kraft Lignin

Great interest has recently been drawn to the production of value-added products from lignin; however, its recalcitrance and high chemical complexity have made this challenging. Dye-decolorizing peroxidases and catalase-peroxidases are among the enzymes that are recognized to play important roles in environmental lignin oxidation. However, bacterial lignin-oxidizing enzymes remain less characterized compared to related proteins from fungi. In this study, screening of 18 purified bacterial peroxidases against the general chromogenic substrate 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS) revealed the presence of peroxidase activity in all proteins. Agarose plate-based screens with kraft lignin identified detectable and high lignin oxidation activity in 15 purified proteins. Crystal structures were determined for the DyP-type peroxidases FC2591 from Frankia casuarinae, PF3257 from Pseudomonas fluorescens, and PR9465 from Pseudomonas rhizosphaerae. The structures revealed the presence of hemes with bound oxygens coordinated by conserved His, Arg, and Asp residues as well as three molecular tunnels connecting the heme with the protein surface. Structure-based site-directed mutagenesis of FC2591 identified at least five active site residues as essential for oxidase activity against both ABTS and lignin, whereas the S370A mutant protein showed a three- to 4-fold activity increase with both substrates. HPLC analysis of reaction products of the wild-type FC2591 and S370A mutant proteins with the model lignin dimer guaiacylglycerol-β-guaiacyl ether and kraft lignin revealed the formation of products consistent with the radical coupling of the reaction intermediates. Thus, this study identified novel bacterial heme peroxidases with lignin oxidation activity and provided further insights into our understanding of these enzymes.

The Photophysical Path to the Triplet State in Light-Oxygen-Voltage (LOV) Domains

Upon blue-light absorption, LOV domains efficiently undergo intersystem crossing (ISC) to the triplet state. Several factors potentially contribute to this efficiency. One often proposed in the literature is the heavy atom effect of the nearby (and eventually adduct-forming) cysteine. However, some LOV domain derivatives that lack the cysteine residue also undergo ISC efficiently. Using hybrid multireference quantum mechanical/molecular mechanical (QM / MM) models, we investigated the effect of the electrostatic environment in a prototypal LOV domain, Arabidopsis thaliana Phototropin 1 LOV2 (AtLOV2), compared to the effect of the dielectric of an aqueous solution. We find that the electrostatic environment of AtLOV2 is especially well tuned to stabilize a triplet( n N , π * ) ${(n_{\rm{N}}, \pi ^{\ast} )}$ state, which we posit is the state involved in the ISC step. Other low-lying triplet states that have( π , π * ) ${(\pi, \pi ^{\ast} )}$ and( n O , π * ) ${(n_{\rm{O}}, \pi ^{\ast} )}$ character are ruled out on the basis of energetics and/or their orbital character. The mechanistic picture that emerges from the calculations is one that involves the ISC of photoexcited flavin to a triplet( n N , π * ) ${(n_{\rm{N}}, \pi ^{\ast} )}$ state followed by rapid internal conversion to a triplet( π , π * ) ${(\pi, \pi ^{\ast} )}$ state, which is the state detected spectroscopically. This insight into the ISC mechanism can provide guidelines for tuning flavin's photophysics through mutations that alter the protein electrostatic environment and potentially helps to explain why ISC (and subsequent flavin photochemistry) does not occur readily in many classes of flavin-binding enzymes.

Effect of protein binding on the twist-stretch coupling of double-stranded RNA

The elasticities of RNAs are generally essential for their biological functions, and RNAs often become functional when interacting with their binding proteins. However, the effects of binding proteins on the elasticities of double-stranded (ds) RNAs, such as twist-stretch coupling, still remain little understood. Here, our extensive all-atom molecular dynamics simulations show that the twist-stretch coupling of dsRNAs can be reversed from positive to negative by their binding proteins. Our analyses revealed that such a reversing effect of binding proteins is attributed to the protein anchoring across the major groove of dsRNAs, which alters the dominating deformation pathway from a major-groove-mediated one to a helical-radius-mediated one through two base-pair parameters of slide and inclination. Meanwhile, the anchoring effect from binding proteins on dsRNAs is further ascribed to the strong electrostatic attractions between dsRNAs and the positively charged binding domain of the proteins.

Controlled and orthogonal partitioning of large particles into biomolecular condensates

Partitioning of client molecules into biomolecular condensates is critical for regulating the composition and function of condensates. Previous studies suggest that client size limits partitioning. Here, we ask whether large clients, such as macromolecular complexes and nanoparticles, can partition into condensates based on particle-condensate interactions. We seek to discover the fundamental biophysical principles that govern particle inclusion in or exclusion from condensates, using polymer nanoparticles surface-functionalized with biotin or oligonucleotides. Based on our experiments, coarse-grained molecular dynamics simulations, and theory, we conclude that arbitrarily large particles can controllably partition into condensates given sufficiently strong condensate-particle interactions. Remarkably, we also observe that beads with distinct surface chemistries partition orthogonally into immiscible condensates. These findings may provide insights into how various cellular processes are achieved based on partitioning of large clients into biomolecular condensates, and they offer design principles for drug delivery systems that selectively target disease-related condensates.

The presence of substrate warrants oxygen access tunnels toward the catalytic site of lipoxygenases

Ferroptosis is a regulated form of cell death driven by lipid peroxidation, with 15-lipoxygenase (15LOX) enzyme playing a critical role in catalyzing the oxygenation of polyunsaturated fatty acid-containing phospholipids, such as 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphoethanolamine (SAPE), to initiate this process. The molecular oxygen required for this catalytic reaction is subject to continuous competition among various oxygen-consuming enzymes, which influences the efficiency of lipid peroxidation. In this study, we utilized structure-based modeling and all-atom molecular dynamics simulations to explore the oxygen diffusion pathways in 15LOX-1 under varying oxygen concentrations and in the presence of key components, including a substrate, binding partner PE-binding protein 1 (PEBP1), and the membrane environment. Extensive computational experiments were performed on various system configurations, examining the role of substrate binding, membrane presence, and PEBP1 association in oxygen acquisition. Our computational results indicate that the substrate binding induces a conformational change in 15LOX-1, facilitating the simultaneous recruitment of one or two O2 molecules, which drive peroxidation, leading predominantly to monohydroperoxide products and, less frequently, to dihydroperoxide products. A similar trend was observed in our redox lipidomics analysis. Moreover, we noticed that the presence of the membrane significantly reduces irrelevant oxygen binding spots, directing oxygen molecules toward a primary tunnel essential for the catalytic activity. We identified two primary oxygen tunnels with sequentially and structurally conserved regions across the lipoxygenase family. These findings provide novel insights into the regulation of oxygen acquisition mechanism for LOX members, shedding light on the molecular basis of ferroptosis signaling.

Engineering IgG antibodies for intracellular targeting and drug delivery

Enabling immunoglobulin G (IgG)-format antibodies to autonomously internalize and localize in the cytosol of targeted cells-referred to as cytosol-penetrating antibodies (cytotransmab, CT)-is challenging yet highly promising. A primary barrier to cytosolic access for CT is limited endosomal escape. Herein, we developed a second-generation (2G) CT, named in2CT4.1, featuring an endosomal acidic pH-responsive endosomal escape motif (R-W/E motif) with Arg-Trp pairs and a Glu patch in the CH3 and CL domains of IgG1/κ antibody. This motif selectively destabilizes endosomal membranes at endosomal acidic pH to facilitate cytosolic access while remaining inactive at neutral pH. The 2G CT, in2CT4.1, achieves efficient cytosolic localization at nanomolar concentrations, demonstrating approximately 3-fold higher endosomal escape efficiency compared to the first-generation CT. The potential of 2G CT is validated by engineering a cytosolic α-tubulin-targeting CT via an α-tubulin-specific variable domain in in2CT4.1. Additionally, the 2G CT effectively delivers the catalytic domain of diphtheria toxin to the cytosol of epidermal growth factor receptor-overexpressing tumor cells, resulting in near-complete suppression of tumor growth in a xenograft mouse model. These results establish 2G CT as a versatile platform for targeting cytosolic proteins and delivering therapeutic payloads, with broad potential in targeted cancer therapy and other applications.

An Investigation of Physics Informed Neural Networks to Solve the Poisson-Boltzmann Equation in Molecular Electrostatics

Physics-informed neural networks (PINN) is a machine learning (ML)-based method to solve partial differential equations that has gained great popularity due to the fast development of ML libraries in the past few years. The Poisson-Boltzmann equation (PBE) is widely used to model mean-field electrostatics in molecular systems, and in this work we present a detailed investigation of the use of PINN to solve the linear PBE. Starting from a multidomain PINN for the linear PBE with an interface, we assess the importance of incorporating different features into the neural network architecture. Our findings indicate that the most accurate architecture utilizes input and output scaling layers, a random Fourier features layer, trainable activation functions, and a loss balancing algorithm. The accuracy of our implementation is on the order of 10-2-10-3, which is similar to previous work using PINN to solve other differential equations. We also explore the possibility of incorporating experimental information into the model, and discuss challenges and future work, especially regarding the nonlinear PBE. We are providing an open-source implementation to easily perform computations from a PDB file. We hope this work will motivate application scientists into using PINN to study molecular electrostatics, as ML technology continues to evolve at a high pace.

Electrochemical Biosensor Utilizing Low-Susceptibility Macrocyclic Stapled Peptide to Mitigate Biofouling for Reliable Protein Detection in Human Serum

Antifouling peptide surfaces have garnered increasing attention due to their immense potential across various biochemical fields. Cyclic peptides, in particular, demonstrate greater resistance to nonspecific substance adsorption compared to regular linear peptides. Herein, inspired by the macrocyclization method, we introduced two non-natural amino acids (R8 and S5) to cyclize the typical low-fouling sequence (EKEKEK) head-to-tail, thereby protecting terminal amino acids and reducing proteolytic susceptibility. This approach resulted in the formation of a novel stapled peptide (SP), which resisted protease hydrolysis and enhanced the antifouling capabilities of the SP-based biosensor compared to the conventional linear peptide (LP), demonstrated by electrochemical testing and fluorescence imaging experiments. Theoretically, molecular dynamics simulations were employed to calculate binding energies between the peptides and carboxypeptidase Y (CPY), and the results showcased a stronger binding affinity of LP with CPY, further confirming the lower proteolytic susceptibility of the engineered SP. Remarkably, the SP-based biosensor demonstrated high sensitivity in detecting the model target of carcinoembryonic antigen, with a limit of detection of 0.49 pg/mL. Moreover, clinical serum samples analyzed using the SP-based biosensor showed excellent concordance with hospital diagnostic methods, underscoring its exceptional accuracy and further highlighting the superiorities of the engineered SP structures.

The bacterial chaperone CsgC inhibits functional amyloid CsgA formation by promoting the intrinsically disordered pre-nuclear state

E. coli secretes a functional amyloid called curli during biofilm formation. Curli fibers are composed of polymers of the CsgA protein, which adopts a beta-sheet rich fold upon fibrillization. A chaperone-like protein called CsgC inhibits CsgA amyloid formation. Like other amyloidogenic proteins, CsgA undergoes a 3-stage aggregation process: an initial lag phase where a beta-rich nucleus forms, an exponential elongation phase, and a plateau phase. It is currently not known if CsgC inhibits amyloid formation by inhibiting formation of the pre-fibril nucleus, or rather, if CsgC inhibits a later stage of amyloid formation by blocking monomer addition to a growing fiber. Here, CsgC homologs from C. youngae , C. davisae , and H. alvei were purified and characterized for their ability to interrogate CsgA amyloid formation. Each of the CsgC homologs prolonged the lag phase of E. coli CsgA amyloid formation in a similar fashion as E. coli CsgC. Additionally, we found that E. coli CsgC interacted transiently and weakly with a monomeric, pre-nucleus species of CsgA and that this interaction delayed amyloid formation. A transient CsgC-CsgA heterodimer was observed using ion mobility-mass spectrometry. When CsgC was added to actively polymerizing CsgA, exponential growth commonly associated with nucleation-dependent amyloid formation was lost. However, the addition of preformed CsgA seeds did not rescue exponential growth indicating that CsgC also has inhibitory activity during fibril elongation. Indeed, CsgC interacted strongly with CsgA fibers, suggesting that the interaction between CsgC and CsgA fibers can slow new fiber growth. CsgC displays a unique inhibitory activity at multiple stages of amyloid formation. CsgC acts as an energy-independent chaperone that transiently interacts with prefibrillar CsgA as well as an amyloid fiber.

Structure of the CD33 Receptor and Implications for the Siglec Family

In the innate immune system, the CD33 receptor modulates microglial activity. Its downregulation promises to slow Alzheimer's disease, and it is already targeted in blood cancers. The mechanism underlying CD33 signaling is unresolved. Starting from the available crystal structure of its extracellular IgV-IgC1 domains, we have assembled a model of the human CD33 receptor by characterizing the oligomerization and structure of IgC1, transmembrane, and cytosolic domains in solution. IgC1 homodimerizes via intermolecular β-strand pairing and packing. In contrast, the 21-residue transmembrane helix of CD33 appears monomeric and straight, with a conserved thin neck and thick belly appearance followed by a positively charged cytosolic patch. The cytosolic domain is dynamically unstructured. Sequence alignment and AlphaFold models indicate that IgC domains in the family of human Siglecs, to which CD33 belongs, are surprisingly variable. Only Siglec-6 is identified to analogously dimerize via IgC1. Our CD33 structural model suggests that the receptor is not signaling via a monomer-dimer shift. Rather, we propose that, aided but also constrained by dimerization, multivalent ligands may concentrate the receptor transmembrane and cytosolic domains sufficiently to trigger colocalization with an activating kinase.

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL. By simulating these subunits with double-stranded DNA molecules, we predicted DNA binding patches on each subunit and quantified the affinities of these patches to DNA using their dissociation rate constants as a proxy. Then, we constructed the structural model of the whole cohesin complex and mapped the predicted high-affinity DNA binding patches on the structure. From the spatial relations of the predicted patches, we identified that multiple patches on the SMC1, SMC3, STAG1, and NIPBL subunits form a DNA clamping patch group. The simulations of the whole complex with double-stranded DNA molecules suggest that this patch group facilitates DNA bending and helps capture a DNA segment in the cohesin ring formed by the SMC1 and SMC3 subunits. In previous studies, these have been identified as critical steps in DNA loop extrusion. Therefore, this study provides experimentally testable predictions of DNA binding sites implicated in previously proposed DNA loop extrusion mechanisms and highlights the essential roles of the accessory subunits STAG1 and NIPBL in the mechanism.

Flavin-containing siderophore-interacting protein of Shewanella putrefaciens DSM 9451 reveals common structural and functional aspects of ferric-siderophore reduction

Shewanella are bacteria widespread in marine and brackish water environments and emergent opportunistic pathogens. Their environmental versatility depends on the ability to produce numerous iron-rich proteins, mainly multiheme c-type cytochromes. Although iron plays a vital role in the versatility of Shewanella species, very few studies exist regarding the strategies by which these bacteria scavenge iron from the environment. Siderophore-mediated iron transport is a commonly employed strategy for iron acquisition, and it was identified among Shewanella spp. over two decades ago. Shewanella species produce hydroxamate-type siderophores and iron removal from these compounds can occur in the cytoplasm via Fe(III)-siderophore reduction mediated by siderophore-interacting proteins (SIPs). The genome of Shewanella putrefaciens DSM 9451 isolated from an infected child contains representatives of the two different families of SIPs: the flavin-containing siderophore reductase (SbSIP) and the iron-sulfur cluster-containing ferric-siderophore reductase (SbFSR). Here, we report their expression, purification, and further biochemical characterization of SbSIP. The structural and functional characterization of SbSIP and comparison with the homologous SIP from Shewanella frigidimarina (SfSIP) revealed similarities between these proteins including a common binding pocket for NADH, NADPH, and siderophore substrates plus a pronounced redox-Bohr effect that ensures coupled transfer of electrons and protons in the physiological pH range. These mechanistic aspects open the door for further investigations on developing drugs that interfere with the iron metabolism of these bacteria and thereby prevent their spread.

Novel 1,2,4-triazole-derived Schiff base derivatives: Design, synthesis, and multi-enzyme targeting potential for therapeutic applications

This study synthesized a series of Schiff base derivatives featuring a 1,2,4-triazole framework and characterized through FT-IR, 1H NMR, 13C NMR, 19F NMR, MS, and elemental analysis. Subsequently, the inhibitory activities of these compounds were systematically evaluated in vitro against human carbonic anhydrase (hCA) isozymes I and II, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE). The results revealed that compounds 5a and 5c were particularly effective against cholinesterase enzymes, demonstrating their potential for neuroprotective applications. Meanwhile, compounds 5f and 5g exhibited remarkable inhibition of hCA I and II isozymes, suggesting their promise as selective inhibitors for therapeutic areas. Furthermore, molecular docking analyses revealed strong and specific interactions between the active compounds and enzyme binding sites, further supported by molecular dynamics simulations. Additionally, ADMET profiling of all compounds indicated favourable pharmacokinetic properties. The ADMET results suggest that these compounds hold significant potential for clinical applications in central nervous system and various disorders. These findings strongly suggest that the synthesized compounds are promising candidates for addressing unmet therapeutic needs in neurodegenerative and metabolic disorders, with potential applications in multi-enzyme targeting therapies.

Cholesterol Concentration in Cell Membranes and its Impact on Receptor-Ligand Interaction: A Computational Study of ATP-Sensitive Potassium Channels and ATP Binding

This work describes a computer study that looks at how different amounts of cholesterol (0%, 25%, and 50%) in cell membranes change the relationship between ATP and the KATP channel. This could explain why pancreatic beta-cells secrete insulin differently. We use computer simulations of molecular dynamics, calculations of binding free energy, and an integrated oscillator model to look at the electrical activity of beta-cells. There is a need for this kind of multiscale approach right now because cholesterol plays a part in metabolic syndrome and early type 2 diabetes. Our results showed that the increase in cholesterol concentration in the cell membrane affects the electrostatic interactions between ATP and the KATP channel, especially with charged residues in the binding site. Cholesterol can influence the properties of a membrane, including its local charge distribution near the channel. This affects the electrostatic environment around the ATP-binding site, increasing  the affinity of ATP for the channel as our results indicated from 0 to 25 and 50% cholesterol (- 141 to - 113 kJ/mol, respectively). Simulating this change in the affinity to ATP of the KATP channels in a model of the electrical activity of the pancreatic beta-cell indicates that even a minimal increase could produce hyperinsulism. The study answers an important research question about how the structure of the membrane affects the function of KATP and, in turn, insulin releases a common feature of metabolic syndrome and early stages of type 2 diabetes.

FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free-Energy Calculation Workflow for Drug Discovery

The binding affinity between a drug molecule and its target, measured by the absolute binding free energy (ABFE), is a crucial factor in the lead discovery phase of drug development. Recent research has highlighted the potential of in silico ABFE predictions to directly aid drug development by allowing for the ranking and prioritization of promising candidates. This work introduces an open-source Python workflow called FEP-SPell-ABFE, designed to automate ABFE calculations with minimal user involvement. The workflow requires only three key inputs: a receptor protein structure in PDB format, candidate ligands in SDF format, and a configuration file (config.yaml) that governs both the workflow and molecular dynamics simulation parameters. It produces a ranked list of ligands along with their binding free energies in the comma-separated values (CSV) format. The workflow leverages SLURM (Simple Linux Utility for Resource Management) for automating task execution and resource allocation across the modules. A usage example and several benchmark systems for validation are provided. The FEP-SPell-ABFE workflow, along with a practical example, is publicly accessible on GitHub at https://github.com/freeenergylab/FEP-SPell-ABFE, distributed under the MIT License.

Transport and InsP8 gating mechanisms of the human inorganic phosphate exporter XPR1

Inorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for cellular Pi homeostasis. When intercellular Pi is high, cells accumulate inositol pyrophosphate (1,5-InsP8), a signaling molecule required for XPR1 function. Inactivating XPR1 mutations lead to brain calcifications, causing neurological symptoms including movement disorders, psychosis, and dementia. Here, cryo-electron microscopy structures of dimeric XPR1 and functional characterization delineate the substrate translocation pathway and how InsP8 initiates Pi transport. Binding of InsP8 to XPR1, but not the related inositol polyphosphate InsP6, rigidifies the intracellular SPX domains, with InsP8 bridging the dimers and SPX and transmembrane domains. Locked in this state, the C-terminal tail is sequestered, revealing the entrance to the transport pathway, thus explaining the obligate roles of the SPX domain and InsP8. Together, these findings advance our understanding of XPR1 transport activity and expand opportunities for rationalizing disease mechanisms and therapeutic intervention.

Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL

Gallic acid (GA), a naturally occurring compound with antioxidant, anti-inflammatory, anti-apoptotic, and regenerative properties, has gained attention for its potential protective role against kidney dysfunction and diseases, though its therapeutic efficacy in this context remains underexplored. The primary objective of this study was to explore the therapeutic effects of GA in treating adenine-induced chronic kidney disease (CKD) in male Wistar rats. The study evaluated GA's therapeutic potential against CKD, along with its pharmacokinetic and drug-likeness properties through a comprehensive analysis. It also assessed GA's inhibitory effects on key kidney proteins, KIM-1 and NGAL, using gene expression analysis, molecular docking, and molecular dynamics simulations. The results demonstrated a range of positive effects, including significant improvement in adenine-induced kidney damage, as shown by changes in urine and serum markers, as well as oxidative stress biomarkers, following GA treatment. The study revealed that GA effectively suppresses the adenine-induced gene expression of KIM-1 and NGAL. Furthermore, GA adhered to Lipinski's Rule of Five, and molecular docking analysis indicated strong interactions and low binding energies between GA and the target proteins KIM-1 and NGAL, further supporting its efficacy in targeting these markers. Additionally, 100 ns molecular dynamics simulations showed that gallic acid has a stronger binding affinity for NGAL than for KIM-1, with higher binding energy, stability, and stronger hydrogen bonds, suggesting that it primarily influences NGAL interactions. This study underscores gallic acid's potential in reducing adenine-induced kidney damage and improving kidney function, with computational evidence supporting its promise as a treatment for CKD.

Regulation of NaCl on Bi-functionality of a chimeric enzyme for aromatic amino acid biosynthesis in Prevotella and Porphyromonas bacteria

3-Deoxy-D-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) are key enzymes in the shikimate pathway responsible for aromatic amino acid biosynthesis in bacteria. This study investigated the functional interplay between the DAH7PS and CM domains within the bifunctional enzyme PniDAH7PS-CM from Prevotella nigrescens, a representative of the chimeric enzyme group DAH7PS-CM that is primarily distributed in the Prevotella and Porphyromonas genera. Analysis of the surface polarity demonstrated that DAH7PS and CM domains rely on hetero-domain polar interactions for their catalytic functions, rather than hydrophobic contacts. We evaluated the effects of NaCl on the catalytic activity, conformation, thermal stability, and molecular aggregation of PniDAH7PS-CM at varying NaCl concentrations (0, 150, and 300 mM). Results demonstrated that increasing NaCl concentrations significantly reduced the enzymatic activities of both DAH7PS and CM, with a complete loss of DAH7PS function at 300 mM NaCl. Notably, high NaCl concentrations promoted a more extended conformation of PniDAH7PS-CM and interfere with enzyme aggregation, suggesting that NaCl modulates the inter-domain interactions. Our findings suggest that Na⁺ ions, as kosmotropic agents, likely via enhancing the hydration layer on the enzyme's surface, stabilizes PniDAH7PS-CM structure but disrupting essential polar interactions for catalysis. Conversely, Cl⁻ ions may act as chaotropic agents, further impairing these interactions. This study illuminates the balance between salt ion concentration and enzyme functionality, offering insights for developing therapeutic strategies targeting bacterial metabolism and growth in the context of periodontal diseases.

Binding mode between peptidyl-tRNA hydrolase and the peptidyl-A76 moiety of the substrate

Peptidyl-tRNA hydrolase (Pth) hydrolyzes the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of aborted translation, to prevent cell death by recycling tRNA. Numerous studies have attempted to elucidate the substrate recognition mechanism of Pth. However, the binding mode of the peptidyl-A76 (3'-terminal adenosine of tRNA) moiety of the substrate to Pth, especially the A76 moiety, remains unclear. Here, we present the crystal structure of Thermus thermophilus Pth (TtPth) in complex with adenosine 5'-monophosphate (AMP), a mimic of A76. In addition, we show the crystal structure of TtPth in which the active site cleft interacts with the C-terminal three amino acid residues of a crystallographically related neighboring TtPth molecule. Superimposition of these two crystal structures reveals that the C-terminal carboxyl group of the neighboring TtPth molecule and the 3'-hydroxyl group of AMP are located in positions favorable for ester bond formation, and we present a TtPth⋅peptidyl-A76 complex model. The complex model agrees with many previous NMR and kinetic studies, and our site-directed mutagenesis studies support its validity. Based on these facts, we conclude that the complex model properly represents the interaction between Pth and the substrate in the reaction. Furthermore, structural comparisons suggest that the substrate recognition mode is conserved among bacterial Pths. This study provides insights into the molecular mechanism of the reaction and useful information to design new drugs targeting Pth.

The Crystal Structure of the Domain of Unknown Function 1480 (DUF1480) From Klebsiella pneumoniae

Domains of unknown function (DUFs) continue to comprise a significant portion of bacterial proteomes, with more than 20% of bacterial proteins remaining annotated as DUFs. The characterization of their molecular structure can provide valuable insight that is not captured by the primary sequence analysis, thus providing a segue into the identification of the molecular function of DUF representatives. Here, we present the crystal structure of KPN_02352 from Klebsiella pneumoniae subsp. pneumoniae, a DUF1480 domain-containing protein, which was determined to be 1.75 Å resolution. Representatives of the DUF1480 family are found broadly across Enterobacterales and have been previously shown to contribute to the antibiotic response. Our structural analysis suggests that DUF1480 is comprised of a six-stranded split barrel fold featuring a small alpha helix that is positioned to cap one end of the split barrel. DUF1480 was found to be monomeric in solution, and harbors structural similarity to response regulators. The crystal structure of DUF1480 is the first experimental insight into the molecular structure of this conserved protein family, revealing several conserved features that may be functionally relevant.

Campesterol and dithymoquinone as a potent inhibitors of SARS cov-2 main proteases-promising drug candidates for targeting its novel variants

The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the global healthcare system. The discovery of the main protease structure of coronavirus (Mpro/Clpro) has resulted in the identification of compounds having antiviral potential, especially from the herbal system. In this study, the computer-associated drug design tools were utilised to analyze the reported phytoconstituents of Nigella sativa for their antiviral activity against the main protease. Fifty-eight compounds were subjected to pharmacological parameter analysis to determine their lead likeness in comparison to the standard drugs (chloroquine and nirmatrelvir) used in the treatment of SARS-CoV-2. Nearly 31 compounds were docked against five different SARS-CoV-2 main proteases, and all compounds showed better binding affinity and inhibition constant against the proteases. However, dithymoquinone and campesterol displayed the best binding scores and hence were further subjected to dynamics and MMPBSA study for 100 ns. The stability analysis shows that dithymoquinone and campesterol show less variation in fluctuation in residues compared to standard complexes. Moreover, dithymoquinone exhibited higher binding affinity and favorable interaction followed by campesterol as compared to the standard drug. The in silico computational analysis provides a promising hit for regulating the main proteases activity.

Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one

Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.

Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates

Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble and function within the cell remains unclear. Here we show that transcriptional condensates form in a stepwise manner to enable both graded and three-dimensional (3D) gene control in the yeast heat shock response. Molecular dissection revealed a condensate cascade. First, the transcription factor Hsf1 clusters upon partial dissociation from the chaperone Hsp70. Next, the coactivator Mediator partitions following further Hsp70 dissociation and Hsf1 phosphorylation. Finally, Pol II condenses, driving the emergent coalescence of HSR genes. Molecular analysis of a series of Hsf1 mutants revealed graded, rather than switch-like, transcriptional activity. Separation-of-function mutants showed that condensate formation can be decoupled from gene activation. Instead, fully assembled HSR condensates promote adaptive 3D genome reconfiguration, suggesting a role of transcriptional condensates beyond gene activation.

Molecular Principles of Proton-Coupled Quinone Reduction in the Membrane-Bound Superoxide Oxidase

Reactive oxygen species (ROS) are physiologically harmful radical species generated as byproducts of aerobic respiration. To detoxify ROS, most cells employ superoxide scavenging enzymes that disproportionate superoxide (O2·-) to oxygen (O2) and hydrogen peroxide (H2O2). In contrast, the membrane-bound superoxide oxidase (SOO) is a minimal 4-helical bundle protein that catalyzes the direct oxidation of O2·- to O2 and drives quinone reduction by mechanistic principles that remain unknown. Here, we combine multiscale hybrid quantum/classical (QM/MM) free energy calculations and microsecond molecular dynamics simulations with functional assays and site-directed mutagenesis experiments to probe the mechanistic principles underlying the charge transfer reactions of the superoxide-driven quinone reduction. We characterize a cluster of charged residues at the periplasmic side of the membrane that functions as a O2·- collecting antenna, initiating electron transfer via two b hemes to the active site for quinone reduction at the cytoplasmic side. Based on multidimensional QM/MM string simulations, we find that a proton-coupled electron transfer (PCET) reaction from the active site heme b and nearby histidine residues (H87, H158) results in quinol (QH2) formation, followed by proton uptake from the cytoplasmic side of the membrane. The functional relevance of the identified residues is supported by site-directed mutagenesis and activity assays, with mutations leading to inhibition of the O2·--driven quinone reduction activity. We suggest that the charge transfer reactions could build up a proton motive force that supports the bacterial energy transduction machinery, while the PCET machinery provides unique design principles of a minimal oxidoreductase.

Structure of the human K2P13.1 channel reveals a hydrophilic pore restriction and lipid cofactor site

Polyunsaturated fatty acid (PUFA) lipids modulate the neuronal and microglial leak potassium channel K2P13.1 (THIK1) and other voltage-gated ion channel (VGIC) superfamily members through poorly understood mechanisms. Here we present cryo-electron microscopy structures of human THIK1 and mutants, revealing a unique two-chamber aqueous inner cavity obstructed by a hydrophilic barrier important for gating, the flow restrictor, and a P1-M4 intersubunit interface lipid at a site, the PUFA site, corresponding to the K2P small-molecule modulator pocket. This overlap, together with functional studies, indicates that PUFA site lipids are THIK1 cofactors. Comparison with a PUFA-responsive VGIC, Kv7.1, reveals a shared modulatory role for the pore domain intersubunit interface, providing a framework for understanding PUFA action on the VGIC superfamily. Our findings reveal the distinct THIK1 architecture, highlight the importance of the P1-M4 interface for K2P control by natural and synthetic ligands and should aid in the development of THIK subfamily modulators for neuroinflammation and autism.

Absolute and Relative Binding Free Energy Calculations of Nucleotides to Multiple Protein Classes

Polyphosphate nucleotides, such as ATP, ADP, GTP, and GDP, play a crucial role in modulating protein functions through binding and/or catalytically activating proteins (enzymes). However, accurately calculating the binding free energies for these charged and flexible ligands poses challenges due to slow conformational relaxation and the limitations of force fields. In this study, we examine the accuracy and reliability of alchemical free energy simulations with fixed-charge force fields for the binding of four nucleotides to nine proteins of various classes, including kinases, ATPases, and GTPases. Our results indicate that the alchemical simulations effectively reproduce experimental binding free energies for all proteins that do not undergo significant conformational changes between their triphosphate nucleotide-bound and diphosphate nucleotide-bound states, with 87.5% (7 out of 8) of the absolute binding free energy results for 4 proteins within ±2 kcal/mol of experimental values and 88.9% (8 out of 9) of the relative binding free energy results for 9 proteins within ±3 kcal/mol of experimental values. However, our calculations show significant inaccuracies when divalent ions are included, suggesting that nonpolarizable force fields may not accurately capture interactions involving these ions. Additionally, the presence of highly charged and flexible ligands necessitates extensive conformational sampling to account for the long relaxation times associated with long-range electrostatic interactions. The simulation strategy presented here, along with its demonstrated accuracy across multiple protein classes, will be valuable for predicting the binding of nucleotides or their analogs to protein targets.

Combined immunoinformatic approaches with computational biochemistry for development of subunit-based vaccine against Lawsonia intracellularis

Lawsonia intracellularis (LI) are obligate intracellular bacteria and the causative agent of proliferative hemorrhagic enteropathy that significantly impacts the health of piglets and the profitability of the swine industry. In this study, we used immunoinformatic and computational methodologies such as homology modelling, molecular docking, molecular dynamic (MD) simulation, and free energy calculations in a novel three stage approach to identify strong T and B cell epitopes in the LI proteome. From ∼ 1342 LI proteins, we narrowed our focus to 256 proteins that were either not well-identified (unknown role) or were expressed at a higher frequency in pathogenic strains relative to non-pathogenic strains. At stage 1, these proteins were analyzed for predicted virulence, antigenicity, solubility, and probability of residing within a membrane. At stage 2, we used NetMHCPan4-1 to identify over ten thousand cytotoxic T lymphocyte epitopes (CTLEs) and 286 CTLEs were ranked as having high predicted binding affinity for the SLA-1 and SLA-2 complexes. At stage 3, we used homology modeling to predict the structures of the top ranked CTLEs and we subjected each of them to molecular docking analysis with SLA-1*0401 and SLA-2*0402. The top ranked 25 SLA-CTLE complexes were selected to be an input for subsequent MD simulations to fully investigate the atomic-level dynamics of proteins under the natural thermal fluctuation of water and thus potentially provide deep insight into the CTLE-SLA interaction. We also performed free energy evaluation by Molecular Mechanics/Poisson-Boltzmann Surface Area to predict epitope interactions and binding affinities to the SLA-1 and SLA-2. We identified the top five CTLEs having the strongest binding energy to the indicated SLAs (-305.6 kJ/mol, -219.5 kJ/mol, -214.8 kJ/mol, -139.5 kJ/mol and -92.6 kJ/mol, respectively.) W also performed B-cell epitope prediction and the top-ranked 5 CTLEs and 3 B-cell epitopes were organized into a multi-epitope subunit antigen vaccine construct joined using EAAAK, AAY, KK, and GGGGG linkers with 40 residues of the LI DnaK protein attached to the N-terminus to further enhance the antigenicity of the vaccine construct. Blind docking studies showed strong interactions between our vaccine construct with swine Toll-like receptor 5. Collectively, these molecular modeling and immunoinformatic analyses present a useful in silico protocol for the discovery of candidate antigen in many viral and bacterial pathogens.

Systemic HER3 ligand-mimicking nanobioparticles enter the brain and reduce intracranial tumour growth

Crossing the blood-brain barrier (BBB) and reaching intracranial tumours is a clinical challenge for current targeted interventions including antibody-based therapies, contributing to poor patient outcomes. Increased cell surface density of human epidermal growth factor receptor 3 (HER3) is associated with a growing number of metastatic tumour types and is observed on tumour cells that acquire resistance to a growing number of clinical targeted therapies. Here we describe the evaluation of HER3-homing nanobiological particles (nanobioparticles (NBPs)) on such tumours in preclinical models and our discovery that systemic NBPs could be found in the brain even in the absence of such tumours. Our subsequent studies described here show that HER3 is prominently associated with both mouse and human brain endothelium and with extravasation of systemic NBPs in mice and in human-derived BBB chips in contrast to non-targeted agents. In mice, systemically delivered NBPs carrying tumoricidal agents reduced the growth of intracranial triple-negative breast cancer cells, which also express HER3, with improved therapeutic profile compared to current therapies and compared to agents using traditional BBB transport routes. As HER3 associates with a growing number of metastatic tumours, the NBPs described here may offer targeted efficacy especially when such tumours localize to the brain.

In Vitro Evaluation of the Antiviral Activity of Polyphenol (-)-Epigallocatechin-3-Gallate (EGCG) Against Mayaro Virus

The Mayaro virus (MAYV), Togaviridae family, genus Alphavirus, has caused several sporadic outbreaks, affecting countries in the Americas. Currently, there are no licensed drugs against MAYV, requiring the search for effective antiviral compounds. Thus, this study aimed to evaluate the antiviral potential of polyphenol (-)-epigallocatechin-3-gallate (EGCG) against MAYV infection, in vitro. Antiviral assays against MAYV were performed in BHK-21 and Vero E6 cells. In addition, molecular docking was performed with EGCG and the MAYV non-structural and structural proteins. EGCG showed a significant protective effect against MAYV infection in both cell lines. The virucidal assay showed an effect on extracellular viral particles at the entry stage into BHK-21 cells. Finally, it also showed significant inhibition in the post-entry stages of the MAYV replication cycle, acting on the replication of the genetic material and late stages, such as assembly and release. In addition, the MAYV proteins E1 and nsP1 were significantly inhibited by the EGCG treatment in BHK-21 cells. Molecular docking analysis also showed that EGCG could interact with MAYV Capsid and Envelope proteins (E1 and E2). Therefore, this study shows the potential of EGCG as a promising antiviral against MAYV, as it acts on different stages of the MAYV replication cycle.

Design and synthesis of novel 3,7-dihydro-1H-purine-2,6-diones as DPP-4 inhibitors: An in silico, in vitro and in vivo approach

The inhibition of enzyme DPP-4 is pivotal for targeting type 2 diabetes mellitus (DM). The study introduces two series of novel 1,3-dimethyl-3,7-dihydro-1H-purine-2,6-diones derivatives (PB01-PB10) and 3,7-dihydro-1H-purine-2,6-diones compounds (PB11-PB16) were developed using linagliptin scaffold. Sixteen derivatives were synthesized and screened in vitro against DPP-4, revealing IC50 ranging from 15.66 ± 2.546 to 28.45 ± 4.441 nM. Compounds PB01 and PB11 demonstrated high potency comparable to reference standard linagliptin (IC50 = 15.66 ± 2.546, 16.16 ± 1.214, 15.37 ± 2.481 nM, respectively). Further studies showed that the compound possesses negligible cytotoxicity up to 100 μM concentration. A high glucose-induced DPP-4 upregulation model was further utilized to assess the protective effect of PB01 and PB11, and their efficacy was compared with linagliptin. PB01 and PB11 showed comparable protective effects against high glucose-induced ROS generation and mitochondrial superoxide production, and the compounds also effectively reduced the DPP-4 cellular expression. The in vivo anti-diabetic efficacy, effect on change in body weight, and OGTT due to PB01 and PB11 treatments were evaluated using the STZ-Nicotinamide-induced experimental model of diabetes in mice. Post induction of diabetes, the periodic estimation of blood serum glucose levels reveals that treatment with PB01 and PB11 decreased the high blood serum glucose levels in both acute and chronic studies. The expressions of DPP-4 were observed by IHC, Flowcytometry, and RT-qPCR. The docked complexes of both compounds, along with the standard drug linagliptin, were subjected to molecular dynamics simulation for 140ns to evaluate the complexes' stability and binding affinity.

Phytocompounds from Phyllanthus acidus (L.) Skeels in the management of Monkeypox Virus infections

Monkeypox is a communicable disease similar to smallpox, primarily occurring in African countries. However, recently it has spread to countries outside Africa and may arise as the next threat after COVID-pandemic. The causative organism, i.e. Monkeypox Virus (MPV) spreads from one individual to another primarily through inhalation of respiratory droplets or through contact with skin lesions of infected individuals. No known drugs are available specifically for MPV. Due to its similarity with smallpox, treatment of monkeypox is being attempted through the administration of the smallpox vaccine. Therefore, we evaluated the efficacy of the plant Phyllanthus acidus against MPV since it is traditionally used in the treatment of chickenpox and smallpox. Through functional annotation, PASS prediction and Network pharmacology analysis, the effectiveness of these chosen P. acidus-derived phytocompounds against MPV was confirmed. Target prediction of the phytocompounds identified in GC-MS analysis of the plant extract showed them to be associated with 76 human proteins. The compounds also show good binding affinity with selected viral proteins: DNA polymerase (DNApol), Putative Virulence Factor (vPVF) and Cytokine Binding Protein. Prediction of Activity Spectra for Substances (PASS) and functional annotation of the target proteins further support their antiviral nature through interaction with these proteins. The compounds were found to modulate pathways related to symptoms of viral infection and this may help in maintaining homeostasis. Our study demonstrates antiviral activity as well as the therapeutic potential of the plant against MPV infection.Communicated by Ramaswamy H. Sarma.

Nucleosome fibre topology guides transcription factor binding to enhancers

Cellular identity requires the concerted action of multiple transcription factors (TFs) bound together to enhancers of cell-type-specific genes. Despite TFs recognizing specific DNA motifs within accessible chromatin, this information is insufficient to explain how TFs select enhancers1. Here we compared four different TF combinations that induce different cell states, analysing TF genome occupancy, chromatin accessibility, nucleosome positioning and 3D genome organization at the nucleosome resolution. We show that motif recognition on mononucleosomes can decipher only the individual binding of TFs. When bound together, TFs act cooperatively or competitively to target nucleosome arrays with defined 3D organization, displaying motifs in particular patterns. In one combination, motif directionality funnels TF combinatorial binding along chromatin loops, before infiltrating laterally to adjacent enhancers. In other combinations, TFs assemble on motif-dense and highly interconnected loop junctions, and subsequently translocate to nearby lineage-specific sites. We propose a guided-search model in which motif grammar on nucleosome fibres acts as signpost elements, directing TF combinatorial binding to enhancers.

Some Challenges of Diffused Interfaces in Implicit-Solvent Models

The standard Poisson-Boltzmann (PB) model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult numerically, but also are not a realistic physical picture, as it forces the dielectric constant and ionic strength of bulk in the near-solute region. An alternative to alleviate some of these issues is to represent the molecular surface as a diffuse interface, however, this also presents challenges. In this work we analyzed the impact of the shape of the interfacial variation of the field parameters in solvation and binding energy. However we used a hyperbolic tangent functiontanh k p x $$ \left(\tanh \left({k}_px\right)\right) $$ to couple the internal and external regions, our analysis is valid for other definitions. Our methodology, restricted to the linear PB, was based on a coupled finite element (FEM) and boundary element (BEM) scheme that allowed us to have a special treatment of the permittivity and ionic strength in a bounded FEM region near the interface, while maintaining BEM elsewhere. Our results suggest that the shape of the function (represented byk p $$ {k}_p $$ ) has a large impact on solvation and binding energy. We saw that high values ofk p $$ {k}_p $$ induce a high gradient on the interface, to the limit of recovering the sharp jump whenk p → ∞ $$ {k}_p\to \infty $$ , presenting a numerical challenge where careful meshing is key. Using the FreeSolv database to compare with molecular dynamics, our calculations indicate that an optimal value ofk p $$ {k}_p $$ for solvation energies was around 3. However, more challenging binding free energy tests make this conclusion more difficult, as binding showed to be very sensitive to small variations ofk p $$ {k}_p $$ . In that case, optimal values ofk p $$ {k}_p $$ ranged from 2 to 20.

Investigating Pb2 CAP-binding domain inhibitors from marine bacteria for targeting the influenza A H5N1

The ongoing increase in the prevalence and mutation rate of the influenza virus remains a critical global health issue. A promising strategy for antiviral drug development involves targeting the RNA-dependent RNA polymerase, specifically the PB2-cap binding domain of Influenza A H5N1. This study employs an in-silico approach to inhibit this domain, crucial for viral replication, using potential inhibitors derived from marine bacterial compounds. Utilizing the MTi-OpenScreen web server, we screened a library of compounds to assess their molecular interactions with the target. This process identified four potential inhibitors: CMNPD25830, CMNPD18675, CMNPD18676, and CMNPD27216. Subsequent molecular dynamics simulations, conducted using the Amber software suite, evaluated their binding affinities and dynamic interactions with the PB2 protein. Notably, CMNPD25830 and CMNPD27216 emerged as the most promising candidates, exhibiting higher binding affinities and more favourable interaction profiles compared to the control molecule. Additional analyses, including post-simulation free energy calculations and free energy landscape analysis, strengthened the potential of these compounds as effective PB2-cap binding domain inhibitors. This comprehensive computational investigation identifies CMNPD27216 and CMNPD25830 as standout candidates due to their superior binding energies and dynamic stability, suggesting their strong potential as therapeutic agents against influenza. This research sets the stage for further in vitro validation and optimization of these lead compounds, potentially supporting the development of more effective influenza treatments.

Identification of DDR1 Inhibitors from Marine Compound Library Based on Pharmacophore Model and Scaffold Hopping

Ulcerative colitis (UC) is a chronic inflammatory condition that affects the intestines. Research has shown that reducing the activity of DDR1 can help maintain intestinal barrier function in UC, making DDR1 a promising target for treatment. However, the development of DDR1 inhibitors as drugs has been hindered by issues such as toxicity and poor binding stability. As a result, there are currently no DDR1-targeting drugs available for clinical use, highlighting the need for new inhibitors. In a recent study, a dataset of 85 DDR1 inhibitors was analyzed to identify key characteristics for effective inhibition. A pharmacophore model was constructed and validated to screen a library of marine natural products for potential DDR1 inhibitors. Through high-throughput virtual screening and precise docking, 17 promising compounds were identified from a pool of over 52,000 molecules in the marine database. To improve binding affinity and reduce potential toxicity, scaffold hopping was employed to modify the 17 compounds, resulting in the generation of 1070 new compounds. These new compounds were further evaluated through docking and ADMET analysis, leading to the identification of three compounds-39713a, 34346a, and 34419a-with superior predicted activity and drug-like properties compared to the original 17 compounds. Further analysis showed that the binding free energy values of the three candidate compounds were less than -12.200 kcal/mol, which was similar to or better than -12.377 kcal/mol of the known positive compound VU6015929, and the drug-like properties were better than those of the positive compounds. Molecular dynamics simulations were then conducted on these three candidate compounds, confirming their stable interactions with the target protein. In conclusion, compounds 39713a, 34346a, and 34419a show promise as potential DDR1 inhibitors for the treatment of ulcerative colitis.

Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small DNA-binding protein that specifically targets AT-rich DNA sequences. Structurally, HMGA2 is an intrinsically disordered protein (IDP), comprising three positively charged 'AT-hooks' and a negatively charged C-terminus. HMGA2 can form homodimers through electrostatic interactions between its 'AT-hooks' and C-terminus. This suggests that the negatively charged C-terminus may inhibit DNA binding by interacting with the positively charged 'AT-hooks.' In this paper, we demonstrate that the C-terminus significantly influences HMGA2's DNA-binding properties. For example, the C-terminal deletion mutant HMGA2Δ95-108 binds more tightly to the AT-rich DNA oligomer FL814 than wild-type HMGA2. Additionally, a synthetic peptide derived from the C-terminus (the C-terminal motif peptide or CTMP) strongly inhibits HMGA2's binding to FL814, likely by interacting with the 'AT-hooks,' as shown by various biochemical and biophysical assays. Molecular modeling demonstrates that electrostatic interactions and hydrogen bonding are the primary forces driving CTMP's binding to the 'AT-hooks.' Intriguingly, we found that hydration does not play a role in HMGA2-DNA binding. These results suggest that the highly negatively charged C-terminus of HMGA2 plays a critical role in regulating its DNA-binding capacity through autoinhibition, likely facilitating the target search process for AT-rich DNA sequences.

Influence of aqueous solutions of 2-(tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol) on the stabilization of the secondary structure of melittin: comparison with aqueous trifluoroethanol using molecular dynamics simulations and circular dichroism experiments

The influence of aqueous solutions of 2-(tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol) and 2,2,2-trifluoroethanol (TFE) on the secondary structure of melittin was studied using circular dichroism (CD) and molecular dynamics (MD) simulations. In water, melittin transitions into a random coil. However, upon addition of even as little as 1% by volume of CF3SF4-ethanol, the secondary structure of melittin stabilizes as a helix. Contrarily, the addition of 40% by volume of TFE is required for the greatest helicity. Fluoroalcohols stabilize melittin's hydrophobic side chain residues, thereby enhancing the helical structure. Locally alcohol concentrations approach nearly 70-90% in the near vicinity of the hydrophobic side chains increasing hydrophobic interactions and reducing water-peptide hydrogen bonding. Using the molecular mechanics-Poisson Boltzmann surface area method (MMPBSA), the free energy of binding between the peptide and fluoroalcohols highlighted the role of nonpolar residues in stabilizing the secondary structure. Secondary structure content analysis (SESCA) validated the simulation results, confirming CF3SF4-ethanol as an effective, eco-friendly enhancer of helicity at low concentrations. The far UV circular dichroism (CD) spectrum of melittin in solutions containing TFE corroborates previous findings and likewise affirms that the addition of CF3SF4-ethanol to an aqueous solution can enhance helicity. The agreement between the experimental and calculated helicities highlights the potential of CF3SF4-ethanol. This study offers insights into peptide stabilization by fluoroalcohols, with implications for peptide-based therapeutic design.

The molecular basis of Human FN3K mediated phosphorylation of glycated substrates

Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of the target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However, the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in the apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rational small molecule design targeting FN3K.

Toll-like receptor 4 pathway evolutionary trajectory and functional emergence

Introduction

Toll-like receptors 4 (TLR4) recognize lipopolysaccharides (LPS) from bacteria as their conventional ligands and undergo downstream signaling to produce cytokines. They mediate the signaling either by the TIRAP-MyD88 complex or by the TRAM-TRIF complex. The MyD88 pathway is common to all other TLRs, whereas the TRAM-TRIF complex is largely exclusive to TLR4. Here we study the TIR domain of TRAM and TRIF ortholog proteins that are crucial for downstream signaling. Our previous work on pan-genome-wide survey, indicates Callorhincus milli to be the ancestral organism with both TRAM and TRIF proteins.

Methods

To gain a deeper insight into the protein function and to compare them with Homo sapiens adaptor proteins, we modeled the docking of the TRAM-TRIF complex of representative organisms across various taxa. These modeling experiments provide insights to ascertain a possible interaction surface and calculate the energetics and electrostatic potential of the complex. Furthermore, this enables us to employ normal mode analysis (NMA) to examine fluctuating, interacting, and other specific residue clusters that could have a role in protein functioning in both C. milli and H. sapiens. We also performed molecular dynamics simulations of these complexes and cross-validated the functionally important residues using network parameters.

Results

We compared the stoichiometry of TRAM-TRIF complexes and found that the tetrameric models (TRAM and TRIF dimer) were more stable than the trimeric model (TRAM dimer and TRIF monomer). While the critical residues of TIRAP, TRIF, and MyD88 were preserved, we also found that the important residues of TRAM signaling were not conserved in C. milli.

Discussion

This suggests the presence of functional TIRAP-MyD88-mediated TLR4 signaling and TRIF-mediated TLR3 signaling in the ancestral species. The overall biological function of this signaling domain appears to be gradually acquired through the orchestration of several motifs through an evolutionary scale.

Molecular interactions driving the complexation of rose bengal by triazine-carbosilane dendrons

Amphiphilic dendrons or Janus dendrimers self-assembling into nanoscale vesicles offer promising avenues for drug delivery. Triazine-carbosilane dendrons have shown great potential for the intracellular delivery of rose bengal, additionally enhancing its phototoxic activity through non-covalent interactions. Thus, understanding the complexation dynamics between dendrons and photosensitizers is crucial for the development of efficient drug carriers. To address this issue, we employed computational modelling and experimental approaches to investigate the formation of stable complexes between triazine-carbosilane dendrons and rose bengal. Molecular dynamics simulations revealed rapid and stable complex formation, primarily driven by electrostatic interactions, particularly under acidic conditions. Conformational dynamics of dendrons significantly influenced complex stability and configurational entropy. Experimental validation confirmed dendron-rose bengal complexation, with pH influencing stoichiometry and thermodynamics of complexes. Overall, our study underscores the critical role of electrostatic interactions in mediating dendron-drug complexation and highlights the importance of pH in modulating complex formation dynamics.

APE1 active site residue Asn174 stabilizes the AP-site and is essential for catalysis

Apurinic/Apyrimidinic (AP)-sites are common and highly mutagenic DNA lesions that can arise spontaneously or as intermediates during Base Excision Repair (BER). The enzyme apurinic/apyrimidinic endonuclease 1 (APE1) initiates repair of AP-sites by cleaving the DNA backbone at the AP-site via its endonuclease activity. Here, we investigated the functional role of the APE1 active site residue N174 that contacts the AP-site during catalysis. We analyzed the effects of three rationally designed APE1 mutations that alter the hydrogen bonding potential, size, and charge of N174: N174A, N174D, and N174Q. We found impaired catalysis of the APE1 N174A and APE1 N174D mutants due to disruption of hydrogen bonding and electrostatic interactions between residue 174 and the AP-site. In comparison, the APE1 N174Q mutant was less impaired due to retaining similar hydrogen bonding and electrostatic characteristics as N174 in wild-type APE1. Structures and computational simulations further revealed that the AP-site was destabilized within the active sites of the APE1 N174A and APE1 N174D mutants due to loss of hydrogen bonding between residue 174 and the AP-site. Cumulatively, we show that N174 stabilizes the AP-site within the APE1 active site through hydrogen bonding and electrostatic interactions to enable effective catalysis. These findings highlight the importance of N174 in APE1's function and provide new insights into the molecular mechanism by which APE1 processes AP-sites during DNA repair.