Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

The roles of flaxseed gum and its oligosaccharides as stabilizers in zein nanoparticles for apigenin delivery: Stability, antioxidant activity, bioavailability, molecular simulations

Apigenin (Ap) is a bioactive compound, but its application is limited by poor solubility, stability, and bioavailability. This study developed flaxseed gum (FG) and its oligosaccharides (FGOS)-coated zein nanoparticles for Ap delivery (FG/Zein@Ap and FGOS/Zein@Ap). Compared to FG/Zein@Ap, FGOS/Zein@Ap exhibited smaller size, higher zeta potential, encapsulation efficiency (∼71.70 %), and loading capacity (∼7.66 %) as evidenced by dynamic light scattering, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), and transmission electron microscopy (TEM). FGOS/Zein@Ap also provided better stability of Ap under various conditions, thereby promoting stronger in vitro antioxidant activity, raising bioaccessibility and bioavailability. Molecular docking and molecular dynamics simulations revealed that FGOS interacted more strongly with zein, primarily through hydrogen bonding and van der Waals forces. This interaction provided greater binding stability throughout the simulation period, compared to FG. This study enhances the understanding of FG and FGOS, providing valuable insights for oligosaccharides-based delivery systems for hydrophobic bioactives.

Phenotypic and molecular insights into a cypovirus isolated from Antheraea assamensis Helfer (Lepidoptera: Saturniidae) and modelling of its polyhedrin protein structure

Antheraea assamensis Helfer (A. assamensis) or Muga silkworm is popularly known for producing golden silk and endemic to the region of Northeast India. The present work characterizes a cypovirus variant infecting A. assamensis larvae, exhibiting characteristic symptoms of flacherie disease. Scanning electron microscope and transmission electron microscope imaging revealed the presence of polyhedral occlusion bodies (OBs) and virion particles measuring 40-50 nm in size. The cypovirus strain comprised of 10 dsRNA genome segments, which were sequenced, assembled and annotated. The encoded viral proteins from different genomic fragments were studied. The phylogenetic analysis of the RNA-dependent RNA polymerase and polyhedrin revealed a close relationship with the previously classified Antheraea mylitta cypovirus 4. The strain was characterized as Antheraea assamensis cypovirus 4 (AaCPV4) with substantial genomic and proteomic evidence that was previously unexplored. The peptide fingerprints of the polyhedrin protein were analysed in the diseased and healthy silkworm lysate by using LC-MS/MS. The polyhedrin protein of AaCPV4 was modelled by different in silico methods and compared with the previously reported cypovirus strains. The multimeric models of polyhedrin were studied and demonstrated the mechanism of formation of OB geometry. Our study provides new insights into the complete genome of AaCPV4 and its viral proteins, which were previously unknown. The present work will help in understanding the differentiation of CPV4 variants infecting Antheraea species and different host adaptations.

An in silico vaccinomics strategy to develop multiepitope vaccine using essential hypothetical protein as a target against Brevundimonas subvibrioides: A combined subtractive proteomics and immunoinformatics approach

The genus Brevundimonas, responsible for a spectrum of diseases, encompasses opportunistic pathogens against diverse infections, with B. subvibrioides possessing the largest genome size. Presence of Brevundimonas genus has been found in clinical samples of patients with urinary tract infections (UTIs) and mastitis, specifically, B. subvibrioides. However, former treatment methods using antibiotics have rendered the bacteria resistant to the inhibitory effects of chloramphenicol, azithromycin, etc. as well as alternative chemical treatments. Reckoning with the present scenario, vaccination emerges as the safest and most effective treatment strategy to address the global issue of evolving microbial threats. The growing concern of antibiotic resistance necessitates a shift towards vaccination as the primary treatment strategy. For this study, a total of 15 essential hypothetical proteins (EsHPs) were retrieved from the database of essential genes (DEG) for further multi-server functional annotation, physicochemical characterization, and non-homology analysis. The target antigen for our peptide-based vaccine construct was localized in the extracellular space, exhibited virulence factor and non-homology against human host and gut microflora. The final screened candidate was detected to be antigenic, probable non-allergen, soluble, non-toxic with near absence of transmembrane helices. The linear B-cell lymphocyte (LBL), helper T lymphocyte (HTL), and cytotoxic T lymphocyte (CTL) epitopes present on this protein were predicted and further docked with their respective major histocompatibility complex (MHC) molecules to verify their affinities for favourable antigen presentation. The final vaccine construct was built with human beta-defensin 3 (HBD3) as the adjuvant, 2 LBL epitopes, 3 CTL epitopes, 1 HTL epitope, and the required linkers. The designed construct was found to be immune response-inducing and was therefore cloned into a suitable vector to assess the possibility of appropriate expression. The final construct, when docked with Toll-like receptor 4 (TLR4), followed by molecular dynamics (MD) simulation of unbound and bound complexes, demonstrated a strong generation of immunity, whose safety might be experimentally tested in the near future. This was corroborated by stabilizing root-mean-square deviation (RMSD) curves, increasing hydrogen bonds, and decreasing residual mobility.

Dynamic G-Quadruplexes in the Rous Sarcoma Virus Genome: Scaffolds for Protein Interaction and Potential Anti-Viral Targets

Summarising the study, RSV is an important pathogen that causes oncogenic transformation in its host via the action of a protein kinase that it expresses. The RSV genome is reverse-transcribed into its complementary DNA, which then integrates into the host genome. This DNA thereafter serves as a template for transcription to manufacture viral proteins. The viral life cycle can, therefore, be inhibited if the functional elements of this DNA are altered. In this aspect, G4s may play an important role due to their involvement in hijacking the host machinery. Interestingly, the RSV-DNA contains multiple probable G4 forming elements, among which the sequences with the highest G4 forming propensity are located within the GAG and POL genes. Additionally, a sequence within the SRC oncogene also has G4 forming potential. In this study, we verified the G4 formation in these sequences via various biophysical assays. Further, the structural topology of these G4s has also been studied using computational and biophysical methods. We have established that GG4 forms a parallel G4 structure while PG4 and SG4 form highly dynamic G4s, switching between various structural forms. Such molecular switching behaviour may also aid in the functional properties of these G4s in vivo. However, further studies are required to elucidate the functional properties of these elements. We have also analysed the binding of these G4s to specific small-molecule ligands and the structural changes induced by the binding of Braco-19 on the G4s. Finally, we have observed that the G4 forming sequences in the RSV-DNA are recognised and bound by human nucleolin, which is highly similar in structure to the chicken nucleolin. This suggests that the G4s in the RSV-DNA may be implicated in various biological functions. These studies conclude that G4s are formed in the RSV-DNA at multiple locations, and these G4s show molecular switching properties under physiological conditions. Further, these G4s are also bound by small-molecule ligands and proteins, which induce structural changes. Thus, these G4s may be targetable sites for the control of RSV infection.

Deciphering the Structural and Functional Effects of the R1150W Non-Synonymous Variant in SCN9A Linked to Altered Pain Perception

The SCN9A gene, a critical regulator of pain perception, encodes the voltage-gated sodium channel Nav1.7, a key mediator of pain signal transmission. This study conducts a multimodal assessment of SCN9A, integrating genetic variation, structural architecture, and molecular dynamics to elucidate its role in pain regulation. Using advanced computational methods, I-TASSER simulations generated structural decoys of the SCN9A homology domain, producing an ensemble of conformational states. SPICKER clustering identified five representative models with a C-score of -3.19 and TM-score of 0.36 ± 0.12, reflecting moderate structural similarity to experimental templates while highlighting deviations that may underpin functional divergence. Validation via ProSA-web supported model reliability, yielding a Z-score of -1.63, consistent with native-like structures. Central to the analysis was the R1150W non-synonymous variant, a potential pathogenic variant. Structural modeling revealed localized stability in the mutant conformation but disrupted hydrogen bonding and altered charge distribution. Its pathogenicity was underscored by a high MetaRNN score (0.7978498) and proximity to evolutionarily conserved regions, suggesting functional importance. Notably, the variant lies within the Sodium-Ion-Transport-Associated Domain, where perturbations could impair ion conductance and channel gating-mechanisms critical for neuronal excitability. These findings illuminate how SCN9A variants disrupt pain signaling, linking genetic anomalies to molecular dysfunction. While computational insights advance mechanistic understanding, experimental validation is essential to confirm the variant's impact on Nav1.7 dynamics and cellular physiology. By refining SCN9A's molecular blueprint and highlighting its therapeutic potential as a target for precision analgesics, this work provides a roadmap for mitigating pain-related disorders through channel-specific modulation. Integrating structural bioinformatics with functional genomics, this study deciphers SCN9A's role in pain biology, laying the groundwork for novel strategies to manage pathological pain.

Let's Not Neglect Drug Discovery to Combat COVID-19: In Silico Study of the Anti-Cancer Compounds Flexible Heteroarotinoids as Candidate Inhibitors Against SARS-CoV-2 Proteins

The COVID-19 pandemic phase caused by the SARS-CoV-2 has ended, but the emergence of new variants continues to threaten public health. The public health toolbox for COVID-19 is in need of not only vaccines but also drug discovery against the SARS-CoV-2 virus, the causative agent for the ongoing COVID-19 infections. We report here an in silico molecular docking and dynamics study that uncovered the interactions of 26 flexible heteroarotinoids (FHT18), which are a class of anti-cancer compounds, as potential inhibitors against all 24 SARS-CoV-2 proteins. Of the 624 docked complexes, 69 displayed binding energies between -9.0 and -11.6 kcal/mol, indicating good to strong binding affinities. At least five of these compounds displayed excellent binding affinities against the nonstructural protein 2, papain-like protease, nonstructural protein 4 (Nsp4), proof-reading exoribonuclease, membrane protein, and nucleocapsid protein. Structure-activity relationship (SAR) analyses of these results revealed that a urea linker in place of a thiourea linker, enhanced the hydrophobic side chains attached to the chromane unit, and a CF3 or OCF3 functional group attached to the benzene ring contributed to increased binding affinities. Further, the molecular dynamics simulation study of the best-docked complex FHT18-6c with Nsp4 remained stable for at least 200 ns, leading to decreased structural fluctuations and increased compactness of the binding site. In conclusion, FHT18-6c deserves further translational research to explore its potential for repurposing as a potent drug candidate to combat COVID-19. We also call for continued drug discovery efforts to enrich the public health toolbox for COVID-19.

Genetic Diversity in the Fusion Gene of Respiratory Syncytial Virus (RSV) Isolated From Iraqi Patients: A First Report

Molecular evaluation of the respiratory syncytial virus (RSV) genome is one of the common strategies applied to understand the viral pathogenicity and control its spreading. In this study, we carried out molecular evaluation on the targeted fusion (F) gene region in the RSV-positive samples of Iraqi patients during the autumn and winter of 2022/2023. One hundred and fifty patients with lower respiratory tract infections were screened for RSV using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Sanger sequencing was performed on the RSV-positive samples targeting 1061 nucleotides (from nucleotide 6168 to 7228 within the RSV genome) and 1000 nucleotides (from nucleotide 6122 to 7121 within the RSV genome) of the F gene region for RSV-A and RSV-B, respectively. The results showed some nucleotide changes within the targeted F gene, which were grouped in distinct clade, closely related to isolates from Austria, Argentine, Finland, and France through phylogenetic analysis. In silico protein modeling using the SWISS-MODEL and I-TASSER web tools based on nonsynonymous changes of amino acid sequence showed some good-predicted models that can be utilized for antiviral screening. In summary, the identified nucleotide variations in the F gene could influence vaccine development as the F protein is the primary target for the major antigen of RSV. Molecular surveillance data of RSV local isolates are also essential for studying new genomic changes and enable the prediction of potential new antiviral agents.

Genome-wide identification and analysis of GH1-containing H1 histones among poplar species

Histone H1s are basic nuclear proteins, which played key role in the binding of DNA and nucleosome, eventually the stability of eukaryotic chromatin. In most species, H1s possess an evolutionarily conserved nucleosome-DNA binding globular domain (GH1), which is conserved between species, especially in mammals. However, there is limited information on the phylogeny, structure and function of H1s in poplar. In the present research, 21 GH1-containing proteins found in Populus trichocarpa were classified into three subgroups (H1s, Myb (SANK) GH1 and AT-hook GH1) based on their domains. The Populus H1 proteins contained lysine-rich N-, C-terminal tails and a conserved GH1 domain, particularly the characteristic amino acids in the helix and strand structures of the five H1 subtypes. The phylogenetic and structure diversity analysis of GH1 proteins across different Populus species and model plants revealed three conserved subgroups with characteristic amino acids. The variation in the number of members across the five subtypes was consistent with the evolutionary relationships among Populus species. The conserved characteristic amino acids among same Populus subtype can be served as markers for subtype identification. Furthermore, the abundance analysis of H1s in Populus indicated their unique functions in young tissues and stages, which may be related to DNA methylation. The consistent expression pattern of H1 across Populus species was in accordance with collinearity pairs. Present analyses provided valuable information on the diversity and evolution of H1s in Populus, advocating further research of H1s in plants.

Three Novel KIT Polymorphisms Found in Horses with White Coat Color Phenotypes

This paper reports three novel KIT variants likely responsible for previously unexplained white patterning phenotypes observed in three groups of horses. White spots and markings may have substantial consequences on the value and health of domesticated horses. This study aims to elucidate the genetic mechanisms underlying depigmented coat colors to aid in producing prosperous herds. Aligned whole genome sequences were manually screened to identify three polymorphisms in a family of Anglo-Arabian horses (N = 7), a family of Warmblood horses (N = 5), and a single stock-type mare with unexplained white markings. Sanger sequencing confirmed the presence of the variants, and in silico predictive programs were used to predict the functional impacts of each. We propose to term the novel variants W37, W38, and W39, respectively, per convention. The W37 polymorphism was always observed in the presence of one W35 allele, suggesting complete linkage. All three variants were predicted to alter or remove the KIT protein active domain, repressing typical protein folding and impacting pathways that upregulate pigmentation. The severe predicted impact on biological function suggests that these variants may cause increased white spotting, providing a possible explanation for the depigmentation phenotypes observed in affected individuals.

Determinants for Substoichiometric Inhibition of IAPP and Aβ Amyloid Aggregations by Bri2 BRICHOS

Bri2 BRICHOS, a folded domain of the transmembrane protein Bri2 expressed in both the brain and pancreas, is an experimentally known substoichiometric inhibitor of amyloid aggregation. The molecular chaperone effectively delays fibrillization at low molar ratios for both β-amyloid (Aβ) in Alzheimer's disease (AD) and islet amyloid polypeptide (IAPP) in type 2 diabetes (T2D). While discovering effective antiamyloid inhibitors that work at low doses is an appealing strategy to mitigate amyloid toxicity, the molecular mechanism underlying the broad and efficient antiamyloid activity of Bri2 BRICHOS remains unknown. Here, we computationally demonstrated that Bri2 BRICHOS exhibits a stronger binding affinity to fibril seeds than to monomers using atomistic discrete molecular dynamic simulations. By competing with monomers to bind the active elongation sites on newly nucleated, weakly populated fibril seeds, a small amount of Bri2 BRICHOS could block rapid fibril growth via monomer addition. The experimentally observed differential inhibition efficiency against IAPP and Aβ aggregation was found to depend on the relative fibril-binding affinities of the inhibitor compared to those of self-seeding monomers. Our computationally derived determinants for substoichiometric inhibition against amyloid aggregation by Bri2 BRICHOS may inform the future design of potent antiamyloid therapies for AD, T2D, and other amyloid diseases.

Decoding deception: the binding affinity of cuttlefish ink on shark smell receptors

Chemical signaling can play a crucial role in predator-prey dynamics. Here, we present evidence that ink from the common cuttlefish (Sepia officinalis) targets olfactory receptor proteins in sharks, potentially acting as a predator deterrent. We apply in silico 3D docking analysis to investigate the binding affinity of various odorant molecules to shark olfactory receptors of 2 shark species: cloudy catshark (Scyliorhinus torazame) and white shark (Carcharodon carcharias). Pavoninin-4 (a known shark repellent compound) displayed selectivity in binding to receptors in the white shark. In contrast, the primary component of cuttlefish ink, melanin, displayed the highest binding affinities to all shark olfactory receptor proteins in both species. Taurine, another important ink component, exhibited standard to strong bindings for both species. Trans-4,5-epoxy-(E)-2-decenal ("blood decenal"), an odorant associated with the smell of blood, displayed strong binding affinities to all shark olfactory receptors, similar to that of melanin. These findings provide new insights into the molecular interplay between cephalopod inking behavior and their shark predators, with cuttlefish ink likely exploiting the narrow band of the shark olfactory repertoire.

Conformational ensembles for protein structure prediction

Acquisition of conformational ensembles for a protein is a challenging task, which is actually involving to the solution for protein folding problem and the study of intrinsically disordered protein. Despite AlphaFold with artificial intelligence acquired unprecedented accuracy to predict structures, its result is limited to a single state of conformation and it cannot provide multiple conformations to display protein intrinsic disorder. To overcome the barrier, a FiveFold approach was developed with a single sequence method. It applied the protein folding shape code (PFSC) uniformly to expose local folds of five amino acid residues, formed the protein folding variation matrix (PFVM) to reveal local folding variations along sequence, obtained a massive number of folding conformations in PFSC strings, and then an ensemble of multiple conformational protein structures is constructed. The P53_HUMAN as a well-known protein and LEF1_HUMAN and Q8GT36_SPIOL as typical disordered proteins are token as the benchmark to evaluate the predicted outcomes. The results demonstrated an effective algorithm and biological meaningful process well to predict protein multiple conformation structures.

Evolution and pathogenicity of SARS-CoVs: A microcanonical analysis of receptor-binding motifs

The rapid evolution and global impact of coronaviruses, notably SARS-CoV-1 and SARS-CoV-2, underscore the importance of understanding their molecular mechanisms in detail. This study focuses on the receptor-binding motif (RBM) within the spike protein of these viruses, a critical element for viral entry through interaction with the ACE2 receptor. We investigate the sequence variations in the RBM across SARS-CoV-1, SARS-CoV-2, and its early variants of concern (VOCs). Utilizing multicanonical simulations and microcanonical analysis, we examine how these variations influence the folding dynamics, thermostability, and solubility of the RBMs. Our methodology includes calculating the density of states (DoS) to identify structural phase transitions and assess thermodynamic properties. Furthermore, we solve the Poisson-Boltzmann equation to model the solubility of the RBMs in aqueous environments. This methodology is expected to elucidate structural and functional differences in viral evolution and pathogenicity, likely improving targeted treatments and vaccines.

Bioinformatics analysis of the in silico engineered protein vaccine with and without Escherichia coli heat labile enterotoxin adjuvant on the model of Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumoniae) has been identified as a major cause of nosocomial infections with multidrug-resistant phenotypes. Vaccination is one of the most effective methods to prevent infectious diseases. We aim to design a vaccine candidate based on the epitope-rich domains of the OmpA, OMPK17, and fimb proteins of K. pneumoniae that could protect against this infection. A vaccine structure was constructed by selecting five epitope-rich domains from three proteins. We decided to add the heat-labile toxin (LT) of Escherichia coli as an adjuvant to the designed protein structure. The evaluation of the vaccine candidates' interaction with the immune system's receptors showed an appropriate interaction of the specially adjuvated protein with TLR2 and TLR4. The stability of the interactions was also studied by molecular dynamics (MD) for to 100 ns. All parameters showed that the structure of the candidate proteins alone and in complex with TLR2 and TLR4 are stable, especially the adjuvanted protein. Immune response simulations showed that both candidates induce acceptable protective immune responses. Overall, the LT-adjuvanted design protein may have the potential to induce more favorable protective immune responses. However, further in vitro and in vivo studies are required to obtain more definitive results.

Arabidopsis METHYLENETETRAHYDROFOLATE REDUCTASE 2 functions independently of PENETRATION 2 during primary immunity against rice blast

Non-host resistance (NHR) is the most durable and robust form of innate immunity, with a surge of interest in its role in crop improvement. Of the NHR genes identified against rice blast, a devastating disease caused by Magnaporthe oryzae, Arabidopsis PEN2 is indispensable for pre-penetration resistance to M. oryzae, while a consortium of genes orchestrates post-penetration resistance via lesser known mechanisms. We identified M. oryzae-susceptible mosA (mthfr2 pen2-3) from a randomly mutagenized Arabidopsis pen2-3 population using forward genetics. Analysis of T-DNA-inserted mthfr2 lines and pen2-3-complemented mosA lines revealed that MTHFR2-dependent resistance to M. oryzae is independent of PEN2. MTHFR2-defective plants exhibited higher accumulation of reactive oxygen species and expression of salicylic acid-dependent defense markers. MTHFR2-ligand docking revealed that A55V non-synonymous substitution in mosA altered ligand binding efficiency. This further affected the metabolomic profile of mosA, effectively allowing in vitro germination and development of M. oryzae conidia. Moreover, the loss-of-function mutation in mthfr2 (involved in the 1C metabolic pathway) potentiated mosA immunity against Pst DC3000. In conclusion, our findings showed that MTHFR2 is a positive modulator of NHR against M. oryzae. This work documents another layer of conserved yet divergent metabolomic defense in Arabidopsis regulated by folate-mediated 1C metabolism that has the potential to revolutionize crop improvement.

In-silico development of a novel TLR2-mediating multi-epitope vaccine against Mycobacterium tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still remains one of the leading causes of mortality worldwide. The elusive nature of this pathogen and its ability to develop drug resistance makes it a serious threat to global health. BCG, the only preventive vaccine for TB, has a limited efficacy and provides partial protection against the disease. A new effective recombinant vaccine capable of producing a stronger and more comprehensive immune response is required to address this global threat. In the present study, we adopted an in-silico approach to develop a multi-epitope vaccine by screening 198 "regulatory proteins" of Mtb H37Rv strain. Epitopes generated from these proteins were screened on the basis of antigenicity, cytokine profile, allergenicity, toxicity, conservancy and population coverage. Selected epitopes were docked with predominant MHC alleles that were used to develop a vaccine construct using suitable linkers and adjuvant. The construct was subjected to homology modelling, tertiary structure validation and refinement and was eventually docked with Toll-like receptor 2 receptor. Molecular dynamic simulation studies revealed stable interactions between the vaccine construct and TLR-2 receptor. The construct also displayed a high probability to elicit a protective immune response involving both humoral and cell-mediated components. In conclusion, the findings suggest that the constructed vaccine has the potential to induce a robust immune response against Mtb. However, further in-vitro and in-vivo studies are required to assess the safety, efficacy, and long-term protective effects of the vaccine construct.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00322-8.

Single Amino Acid Changes Impact the Ability of Drosophila melanogaster Cecropins to Inhibit Growth of Providencia Pathogens

As antibiotic-resistant bacteria spread worldwide, the need to develop novel antimicrobial agents is urgent. One rich source of potential antimicrobials is the insect immune system, as insects produce a wide range of antimicrobial peptides (AMPs) with diverse sequences and structures. Insects also encounter many bacterial pathogens, some of which are closely related to pathogens of clinical relevance. However, despite interest in AMPs as therapeutics, the relationships between the amino acid sequence, biophysical properties, antimicrobial activity, and specificity are still not generalizable. To improve our understanding of these relationships, we assessed how single amino acid changes in cecropin AMPs produced by the fruit fly, Drosophila melanogaster, impact both their structure and their ability to inhibit the growth of Providencia species isolated from wild-caught D. melanogaster. These pathogens are of particular interest as they have a range of virulence in fruit flies, and work in vivo suggests that differences in virulence could be partially attributable to differential susceptibility to AMPs. D. melanogaster cecropins are 40 amino acids long but vary at only 5 residues with largely conservative changes. We found that these changes could impact inhibitory concentrations by up to 8-fold against Providencia species. Our investigation focused on a single amino acid position due to the importance of a flexible "hinge" in cecropin function. We found that altering the identity of this amino acid alone greatly impacted antimicrobial activity, changing bacterial susceptibility up to 16-fold. Generally, Providencia species that are less virulent in vivo are more susceptible to cecropin AMPs in vitro. We also observed differences in the kinetics of permeabilization and bacterial killing between species, suggesting that peptide-membrane interactions were differently affected by single amino acid changes and that bacteria in this genus may vary in their membrane composition.

Afobazole: a potential drug candidate which can inhibit SARS CoV-2 and mimicry of the human respiratory pacemaker protein

In COVID-19 patients, respiratory failure was reported due to damage to the respiratory centers of the brainstem. Molecular mimicry of three brainstem pre-Botzinger complex proteins (DAB1, AIFM and SURF1) was regarded as the underlying reason for respiratory failure and the autoimmune neurological sequelae. Of the three brainstem proteins mimicked by SARS CoV-2, corresponding sequences to two of the mimicry peptides were located in the N-protein of SARS CoV-2. N-protein is important for viral RNA synthesis and genome packaging. Here, we have used molecular modeling, docking and MD simulations to discern potential drugs which can inhibit molecular mimicry of DAB1 by SARS CoV-2 and also eliminate it by interfering in genome packaging. The binding site (drug target) for molecular docking was defined as the amino acid sequence extending from position 168-185 of the N-protein which was a SLiM region and also included the mimicry hexapeptide. Molecular docking after MD simulations was used to discern probable inhibitors of the drug-target from FDA-approved neurological drugs in the Broad Institute's Drug Repurposing Hub. Our results revealed that an anti-anxiety drug afobazole qualified the ADMET parameters, formed a stable complex with the drug-target and exhibited the highest binding energy (-88.21 kJ/mol). This suggests that afobazole can be repurposed against SARS CoV-2 for disrupting molecular mimicry of human DAB1 protein and also eliminate the etiopathological agent by interfering in viral genome packaging.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00316-6.

Functional analysis of AtTX11/12 TIR-domain proteins identifies key residues for basal and temperature-insensitive growth inhibition

Plant Toll/interleukin-1 receptor (TIR) domains function as NADases and ribosyl-transferases generating second messengers that trigger hypersensitive responses. TIR-X (TX) proteins contain a TIR domain with or without various C-terminal domains and lack the canonical nucleotide-binding site and leucine-rich repeat domain. In a previous study, we identified an Arabidopsis thaliana activation-tagging line with severe growth defects caused by the overexpression of the AtTX12 gene. Here, we investigated the domains and specific amino acid residues required for the growth inhibition activity of AtTX12 and its homolog AtTX11. C-terminal truncation analysis revealed that the AtTX12C173Δ mutant, lacking 30 C-terminal amino acids, retained partial activity, whereas the C163Δ, lacking 40 amino acids, lost activity entirely indicating that the fifth α-helix within the TIR domain is critical for activity, while the sixth α-helix in the extra domain is dispensable. The substitution mutagenesis revealed that residues essential for enzymatic activities (E79 for NADase, C76 for 2',3'-cAMP/cGMP synthetase), self-association (H25, E43, K142/G144, K150), and undefined roles (I97) were crucial for growth inhibition activity with varying effects. Temperature sensitivity tests revealed that the AtTX12 N36D mutant, which exhibited moderately strong growth inhibition activity at normal temperatures, became inactive under high-temperature conditions in which Enhanced Disease Susceptibility 1 (EDS1) is almost non-functional. In contrast, wild-type AtTX12 retained activity under elevated temperatures, implicating N36 in maintaining temperature-insensitive functionality. Furthermore, a slightly reduced growth inhibition phenotype induced by AtTX12 overexpression in the eds1 mutant was consistently observed under both normal and high temperatures. These results suggest that AtTX12-mediated growth inhibition integrates EDS1-dependent (temperature-sensitive) and EDS1-independent (temperature-insensitive) pathways. Our findings suggest that attenuated AtTX11/12 mutants could be used to optimize the growth-defense trade-off, enhancing plant defense with minimal growth penalties.

Biosynthesis of a Novel Ginsenoside with High Anticancer Activity by Recombinant UDP-Glycosyltransferase and Characterization of Its Biological Properties

UDP-glycosyltransferases (UGTs) contribute to catalyzing the glycosylation of numerous functional natural products and novel derivatives with improved bioactivities. UDP-glucose sterol glucosyltransferase (SGT) is normally involved in the synthesis of sterol glycosides in a variety of organisms. SGT was derived from Salinispora tropica CNB-440 and heterologously expressed in Escherichia coli BL21 (DE3). Novel 12-O-glucosylginsenoside Rh2 was identified using HPLC, high-resolution MS (HR-MS), and NMR analysis. The cell viability assay was performed on 12-O-glucosylginsenoside-treated AGS stomach cancer, HeLa cervical cancer, U87MG glioma, and B16F10 melanoma cell lines. Protein structure modeling, molecular docking, and dynamics simulations were performed using AutoDock 4.2 and GROMACS 2020.1 software. The SGT gene is comprised of 1284 nucleotides and codes for 427 amino acids. The 12-O-glucosylginsenoside Rh2 may be a potential anticancer agent due to its potent viability inhibition of cancer cells. Structural analysis showed critical perspectives into the intermolecular interactions, stability, and binding energetics of the enzyme-ligand complex, with outcomes complementing the experimental data, thereby deepening our understanding of the structural basis of SGT-mediated glycosylation and its functional implications. This report presents a novel ginsenoside, 12-O-glucosylginsenoside Rh2, utilizing reshuffled SGT derived from S. tropica, and provides a promising candidate for anticancer drug research and development.

Yaravirus brasiliense genomic structure analysis and its possible influence on the metabolism

Here we analyze the Yaravirus brasiliense, an amoeba-infecting 80-nm-sized virus with a 45-kbp dsDNA, using structural molecular modeling. Almost all of its 74 genes were previously identified as ORFans. Considering its unprecedented genetic content, we analyzed Yaravirus genome to understand its genetic organization, its proteome, and how it interacts with its host. We reported possible functions for all Yaravirus proteins. Our results suggest the first ever report of a fragment proteome, in which the proteins are separated in modules and joined together at a protein level. Given the structural resemblance between some Yaravirus proteins and proteins related to tricarboxylic acid cycle (TCA), glyoxylate cycle, and the respiratory complexes, our work also allows us to hypothesize that these viral proteins could be modulating cell metabolism by upregulation. The presence of these TCA cycle-related enzymes specifically could be trying to overcome the cycle's control points, since they are strategic proteins that maintain malate and oxaloacetate levels. Therefore, we propose that Yaravirus proteins are redirecting energy and resources towards viral production, and avoiding TCA cycle control points, "unlocking" the cycle. Altogether, our data helped understand a previously almost completely unknown virus, and a little bit more of the incredible diversity of viruses.

The molecular features of non-peptidic nucleophilic substrates and acceptor proteins determine the efficiency of sortagging

Sortase A-mediated ligation (SML) or "sortagging" has become a popular technology to selectively introduce structurally diverse protein modifications. Despite the great progress in the optimization of the reaction conditions and design of miscellaneous C- or N-terminal protein modification strategies, the reported yields of conjugates are highly variable. In this study, we have systematically investigated C-terminal protein sortagging efficiency using a combination of several rationally selected and modified acceptor proteins and a panel of incoming surrogate non-peptidic amine nucleophile substrates varying in the structural features of their amino linker parts and cargo molecules. Our data suggest that the sortagging efficiency is modulated by the combination of molecular features of the incoming nucleophilic substrate, including the ionization properties of the reactive amino group, structural recognition of the nucleophilic amino linker by the enzyme, as well as the molecular nature of the attached payload moiety. Previous reports have confirmed that the steric accessibility of the C-terminal SrtA recognition site in the acceptor protein is also the critical determinant of sortase reaction efficiency. We suggest a computational procedure for simplifying a priori predictions of sortagging outcomes through the structural assessment of the acceptor protein and introduction of a peptide linker, if deemed necessary.

Molecular Insights into the Heme-Binding Potential of Plant NCR247-Derived Peptides

Heme is involved in many critical processes in pathogenic bacteria as iron acquisition by these microorganisms is achieved by either direct uptake of heme or use of heme-binding proteins called hemophores. Exploring the underlying mechanisms on a molecular level can open new avenues in understanding the host-pathogen interactions. Any imbalance of the heme concentration has a direct impact on the bacterial growth and survival. Thus, heme-regulated proteins that are involved in heme homeostasis poise to be promising targets for research. Similarly, naturally occurring compounds, including cysteine-rich peptides from either plant secondary metabolites or venom toxins from vertebrates and invertebrates, have been studied for their therapeutic potential. NCR247 is such a cysteine-rich peptide, known to be crucial for nitrogenase activity in M. truncatula and its symbiotic relation with S. meliloti. NCR247-derived peptides were suggested to serve as high-affinity heme-binding molecules with remarkable heme-capturing properties. A comprehensive biochemical and computational analysis of NCR247-derived peptides, however, redefines their heme-binding capacity and consequently their potential therapeutic role.

Structure-function relationships between the human bitter taste receptor TAS2R38 and propylthiouracil: An in-silico investigation

Taster categorisation uses bitter thiourea compounds like propylthiouracil (PROP) and phenylthiocarbamide (PTC), which are frequently associated with amino acid alterations at positions 49, 262 and 296 in human taste 2 receptor member 38 (hTAS2R38). Since the hTAS2R38 protein lacked a crystallographic structure, it was modelled using contact-guided iterative threading assembly refinement, its residues were mutated and refined, and the binding pocket area and volume were assessed using CASTp. Bitter thiourea molecules were docked using the ligand extra precision module and the receptor-ligand complex was manually positioned in a fully hydrated, equilibrated 1-palmitoyl-2-oleoylphosphatidylcholine bilayer using the CHARMM GUI membrane constructor, a 100 ns simulation was carried out using the Desmond program. Analysis revealed that the PROP binds to the allosteric hydrophobic pocket of hTAS2R38 and forms a hydrogen bond with ASN190. The native structure (hTAS2R38PAV) has a higher glide energy (-24.164 kcal/mol) and docking score (-7.212 kcal/mol) than mutants, corroborating our taste preference study. In contrast, PTC lacks hydrogen bonds in the binding pocket but exhibits pi-pi stacking interactions with the native structure. Structures with mutations at the 49th or 296th position showed the largest root mean square deviations and fluctuations. A triple mutation increases surface area and volume, making the 262nd position critical to the binding pocket. These results highlight the functional roles of these three residues in hTAS2R38.

Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics

The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein-ligand interactions in seven inactive cyclin-dependent kinase 2-ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.95). In addition, the EFP pairwise interaction energy decomposition analysis identifies critical interactions between the ligands and protein residues and provides insight into their nature. Overall, this study indicates the potential applications of the EFP method in structure-based drug design.

The ATPase activity of yeast chromosome axis protein Hop1 affects the frequency of meiotic crossovers

Saccharomyces cerevisiae meiosis-specific Hop1, a structural constituent of the synaptonemal complex, also facilitates the formation of programmed DNA double-strand breaks and the pairing of homologous chromosomes. Here, we reveal a serendipitous discovery that Hop1 possesses robust DNA-independent ATPase activity, although it lacks recognizable sequence motifs required for ATP binding and hydrolysis. By leveraging molecular docking combined with molecular dynamics simulations and biochemical assays, we identified an ensemble of five amino acid residues in Hop1 that could potentially participate in ATP-binding and hydrolysis. Consistent with this premise, we found that Hop1 binds to ATP and that substitution of amino acid residues in the putative ATP-binding site significantly impaired its ATPase activity, suggesting that this activity is intrinsic to Hop1. Notably, K65A and N67Q substitutions in the Hop1 N-terminal HORMA domain synergistically abolished its ATPase activity, noticeably impaired its DNA-binding affinity and reduced its association with meiotic chromosomes, while enhancing the frequency of meiotic crossovers (COs). Overall, our study establishes Hop1 as a DNA-independent ATPase and reveals a potential biological function for its ATPase activity in the regulation of meiotic CO frequency.

Transcriptome analysis of Colletotrichum nymphaeae-Strawberry interaction reveals in planta expressed genes associated with virulence

Colletotrichum nymphaeae, the causal agent of anthracnose fruit rot, is globally recognized as a major pathogen of strawberries due to its economic impact. Fungal pathogens utilize secreted proteins to facilitate infection by acquiring host nutrients and suppressing plant immunity. Understanding the transcriptomic responses of C. nymphaeae during infection can provide critical insights into its pathogenic mechanisms. In this study, RNA sequencing (RNA-seq) was performed to profile the transcriptome of C. nymphaeae strain 02-179 during infection of leaf and fruit tissues of the susceptible strawberry (Fragaria x ananassa) cultivar Florida Beauty. Differential gene expression analysis identified fungal genes upregulated during these interactions. Transcriptomic profiling revealed a set of genes encoding secreted effector proteins, including NUDIX hydrolase and LysM domain-containing proteins. Additionally, genes associated with Carbohydrate-Active enzymes (CAZymes), such as multicopper oxidase, pectinesterase, pectate lyase, glycosyl hydrolase family 7, and endochitinase, were significantly upregulated. Notably, two novel tannase genes were identified among the top upregulated genes in strawberry-infected leaves and fruits. Tannase enzymes are hypothesized to degrade tannins, a group of plant secondary metabolites abundant in strawberries, known for their defensive roles against pests and pathogens. The identification of tannase genes and the other genes associated with virulence underscores the complex molecular strategies employed by C. nymphaeae to infect and colonize strawberry tissues. Genes involved in degrading plant cell walls, suppressing host defenses, and potentially overcoming chemical barriers such as tannins play critical roles in the pathogenesis of anthracnose. Further functional characterization of these genes will enhance our understanding of the disease mechanisms and could inform the development of improved management strategies for C. nymphaeae infections in strawberries.

Treponema denticola major surface protein (Msp): a key player in periodontal pathogenicity and immune evasion

Treponema denticola, a bacterium that forms a "red complex" with Porphyromonas gingivalis and Tannerella forsythia, is associated with periodontitis, pulpitis, and other oral infections. The major surface protein (Msp) is a surface glycoprotein with a relatively well-established overall domain structure (N-terminal, central and C-terminal regions) and a controversial tertiary structure. As one of the key virulence factors of T. denticola, Msp is associated with adherence, immune response, and pore formation by the microorganism. It also mediates several pathological changes in histocytes, such as cytoskeleton disruption, neutrophil phagocytosis, and phosphoinositide balance interruption. In addition, the Msp of T. denticola is also an ortholog of the Treponema pallidum repeat (Tpr) proteins and Msp or Msp-like proteins that have been detected in other oral treponeme species. This review will discuss the structure, pathogenicity and homologs of Msp produced by T. denticola, illuminate the controversy regarding the structure and membrane topology of native Msp, explore the potential roles of Msp in the mechanism of T. denticola immune escape and provide an overview of the cytotoxicity and adherence ability of Msp. Further understanding of the structure and functions of Msp will offer new insights that will help promote further investigations of the pathogenic mechanisms of T. denticola and other treponemes, leading to more effective prophylactic or therapeutic treatments for relevant diseases.

A novel antimicrobial peptide WBp-1 from wheat bran: Purification, characterization and antibacterial potential against Listeria monocytogenes

This study introduces a novel antimicrobial peptide (AMP), WBp-1, isolated from wheat bran and purified via reversed-phase high-performance liquid chromatography. The amino acid sequence, determined as IITGASSGIGKAIAKHFI by LC-MS/MS, was composed predominantly of alkaline and hydrophobic residues. WBp-1 was predicted to be a stable, hydrophobic, cationic peptide with an α-helical structure. Moreover, it displayed significant antibacterial efficacy against Listeria monocytogenes, with a minimum inhibitory concentration of 150 μg/mL. Further mechanistic studies suggest that WBp-1 exerts its bactericidal activity by disrupting cell membrane integrity, impeding peptidoglycan synthesis by binding to penicillin-binding protein 4 via hydrogen bonding, increasing cell permeability, altering membrane potential and fluidity, and altering surface hydrophobicity. Interestingly, WBp-1 showed minimal hemolytic activity and cytotoxicity against LO2 cells, even at 16× MIC. These findings highlight the strong potential of WBp-1 as a novel antibacterial agent and food preservative against Listeria monocytogenes.

Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models

True three-dimensional (3D) data are prevalent in domains such as molecular science or computer vision. In these data, machine learning models are often asked to identify objects subject to intrinsic flexibility. Our study introduces two datasets from molecular science to assess the classification robustness of common model/feature combinations. Molecules are flexible, and shapes alone offer intra-class heterogeneities that yield a high risk for confusions. By blocking training and test sets to reduce overlap, we establish a baseline requiring the trained models to abstract from shape. As training data coverage grows, all tested architectures perform better on unseen data with reduced overfitting. Empirically, 2D embeddings of voxelized data produced the best-performing models. Evidently, both featurization and task-appropriate model design are of continued importance, the latter point reinforced by comparisons to recent, more specialized models. Finally, we show that the shape abstraction learned from database samples extends to samples that are evolving explicitly in time.

Developing an Effective Therapeutic HPV Vaccine to Eradicate Large Tumors by Genetically Fusing Xcl1 and Incorporating IL-9 as Molecular Adjuvants

BACKGROUND

Human papillomavirus (HPV) is a prevalent infection affecting both men and women, leading to various cytological lesions. Therapeutic vaccines mount a HPV-specific CD8+ cytotoxic T lymphocyte response, thus clearing HPV-infected cells. However, no therapeutic vaccines targeting HPV are currently approved for clinical treatment due to limited efficacy. Our goal is to develop a vaccine that can effectively eliminate tumors caused by HPV.

METHODS

We genetically fused the chemokine XCL1 with the E6 and E7 proteins of HPV16 to target cDC1 and enhance the vaccine-induced cytotoxic T cell response, ultimately developing a DNA vaccine. Additionally, we screened various interleukins and identified IL-9 as an effective molecular adjuvant for our DNA vaccine.

RESULTS

The fusion of Xcl1 significantly improved the quantity and quality of the specific CD8+ T cells. The fusion of Xcl1 also increased immune cell infiltration into the tumor microenvironment. The inclusion of IL-9 significantly elevated the vaccine-induced specific T cell response and enhanced anti-tumor efficacy. IL-9 promotes the formation of central memory T cells.

CONCLUSIONS

the fusion of Xcl1 and the use of IL-9 as a molecular adjuvant represent promising strategies for vaccine development.

In silico drug repurposing at the cytoplasmic surface of human aquaporin 1

Aquaporin 1 (AQP1) is a key channel for water transport in peritoneal dialysis. Inhibition of AQP1 could therefore impair water transport during peritoneal dialysis. It is not known whether inhibition of AQP1 occurs unintentionally due to off-target interactions of administered medications. A high-throughput virtual screening study has been performed to investigate the possible binding of licensed medications to the water pore of human AQP1. A complete model of human AQP1 based on its canonical sequence was assembled using I-TASSER and MODELLER. The model was refined via the incorporation of pore water molecules from a high-resolution yeast aquaporin structure. Docking studies were conducted for the cytoplasmic domain of the AQP1 monomer against a library of all compounds listed in the British National Formulary (BNF), using the PLANTS software with the ChemPLP scoring function. The stability of the best docked conformations within the intrinsic water pore was assessed via short 15 nanosecond molecular dynamics (MD) simulations using the GROMACS-on-Colab utility. Of the 1512 compounds tested, 1002 docking results were obtained, and 198 of these conformations occupied a position within the intrinsic water pore. 30 compounds with promising docking scores were assessed by MD. The docked conformations for dopamine, gabapentin, pregabalin, and methyldopa were stable in these short MD studies. For furosemide and pravastatin, the MD trajectory suggested a binding mode different to the docking result. A small set of compounds which could impede water transport through human AQP1 have been identified in this computational screening study.

Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks

Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.

Genome-wide identification, characterization, and functional analysis of the CHX, SOS, and RLK genes in Solanum lycopersicum under salt stress

The cation/proton exchanger (CHX), salt overly sensitive (SOS), and receptor-like kinase (RLK) genes play significant roles in the response to salt stress in plants. This study is the first to identify the SOS gene in Solanum lycopersicum (tomato) through genome-wide analysis under salt stress conditions. Quantitative reverse transcription PCR (qRT-PCR) results indicated that the expression levels of CHX, SOS, and RLK genes were upregulated, with fold changes of 1.83, 1.49, and 1.55, respectively, after 12 h of exposure to salt stress. Genome-wide analysis revealed 21 CHX, 5 SOS, and 86 RLK genes in S. lycopersicum. CHX genes were found on chromosomes 2, 3, 4, 5, 6, 7, 8, 9, 11, and 12 of S. lycopersicum. SOS genes were found on chromosomes 1, 4, 6, and 10. RLK genes were found on all chromosomes of S. lycopersicum. The Ka/Ks ratios indicate that the CHX, SOS, and RLK genes have been primarily influenced by purifying selection. This suggests that these genes have faced strong environmental pressures throughout their evolution. Purifying selection typically results in a decrease in genetic diversity. The estimated duplication time for CHX paralogous gene pairs ranged from approximately 26.965 to 245.413 million years ago (Mya), while the duplication time for SOS paralogous gene pairs ranged from around 116.682 to 275.631 Mya. For RLK paralogous gene pairs, the duplication time varied from approximately 27.689 to 239.376 Mya. Synteny analysis of the CHX, SOS, and RLK genes demonstrated collinear relationships with orthologous genes in Arabidopsis thaliana, but no collinearity orthologous relationships in Oryza sativa (rice). Furthermore, the analysis revealed that there were 6 orthologous SlCHX genes, 2 orthologous SlSOS genes, and 44 orthologous SlRLK genes paired with those in A. thaliana. The results of the present study may help to elucidate the role of the CHX, SOS, and RLK genes in salt stress in S. lycopersicum.

Characterization of the ligand-binding properties of odorant-binding protein 38 from Riptortus pedestris when interacting with soybean volatiles

Background

Riptortus pedestris (Fabricius) (Hemiptera: Alydidae) is a major soybean pest throughout East Asia that relies on its advanced olfactory system for the perception of plant-derived volatile compounds and aggregation pheromones for conspecific and host plant localization. Odorant binding proteins (OBPs) facilitate the transport of odorant compounds across the sensillum lymph within the insect olfactory system, enabling their interaction with odorant receptors (ORs).

Methods

Real-time quantitative PCR (qRT-PCR) analyses, fluorescence-based competitive binding assays, and molecular docking analyses were applied to assess the expression and ligand-binding properties of OBP38 from R. peddestris.

Results

The qRT-PCR analyses revealed high levels of RpedOBP38 expression in the antennae without any apparent sex bias, and it was also highly expressed in the adult stage. Recombinant RpedOBP38 was prepared by expressing it in E. coli BL21 (DE3) followed by its purification with a Ni-chelating affinity column. RpedOBP38 was found to bind most strongly to trans-2-decenal (Ki = 7.440) and trans-2-nonenal (Ki = 10.973), followed by β-pinene, (+) -4-terpineol, carvacrol, methyl salicylate, and (-)-carvone. The 3D structure of RpedOBP38 contains six α-helices and three interlocked disulfide bridges comprising a stable hydrophobic binding pocket. In a final series of molecular docking analyses, several polar (e.g., His 94, Glu97) and nonpolar (e.g., Leu29, Ile59) residues were found to be involved in RpedOBP38-ligand binding.

Conclusion

These data support a role for RpedOBP38 in the perception of volatiles derived from host plants, providing important insight into the mechanisms that govern olfactory recognition in R. pedestris, thereby informing the development of ecologically friendly approaches to managing R. pedestris infestations.

Characterization of a novel cold-active β-Xylosidase from Parabacteroides distasonis and its synergistic hydrolysis of beechwood xylan

Although β-xylosidases have broad applications in fields such as food and medicine, there is limited research on cold-active β-xylosidases. This study cloned a novel cold-active β-xylosidase XYL13 from Parabacteroides distasonis. The purified XYL13 exhibited the highest activity at 40 °C, with 42 % and 25 % of its maximum activity at 4 °C and 0 °C, respectively. Meanwhile, XYL13 predominantly produces X1 while degrading X2-X6. Additionally, XYL13 showed a significant synergistic effect (18.5-fold) with endo-xylanase for degrading beechwood xylan at low temperatures. Moreover, the site-directed mutagenesis assay indicated that Ile269 and Glu621 are essential catalytic sites of XYL13. Finally, molecular docking showed that XYL13 has an excellent binding effect with X2-X6, verifying that XYL13 can effectively cut X2-X6 to produce xylose. These results highlight the potential of cold-adapted XYL13 from P. distasonis for application in the food industry.

Novel Dolutegravir and Lenacapavir Resistance Patterns in Human Immunodeficiency Virus Type 2 Infection: A Case Report

Background

The treatment management of human immunodeficiency virus (HIV)-2 infection presents greater challenges compared to HIV-1 infection, primarily because of inherent resistance against non-nucleoside reverse transcriptase inhibitors. Integrase strand transfer inhibitors, particularly dolutegravir, have improved treatment outcomes for people with HIV-2. Lenacapavir, a novel and potent antiretroviral capsid inhibitor, offers additional therapeutic options. However, limited knowledge exists regarding HIV-2 resistance against dolutegravir and lenacapavir.

Methods

We report the case of a treatment-experienced individual who did not achieve virological suppression with regimens containing dolutegravir and lenacapavir. Clinical monitoring, genotypic and phenotypic resistance assays, and in silico structural modeling were performed.

Results

Lenacapavir was added to a failing regimen of boosted darunavir, twice daily dolutegravir, and 2 nucleoside reverse transcriptase inhibitors. Initially, this addition led to a decline in the viral load and increase in CD4+ T-cell count, despite the identification of a previously unreported combination of integrase resistance mutations. However, virological suppression was not achieved and viral load, although reduced, resumed increasing. This rebound was associated with the development of an N73D capsid substitution in HIV-2, which conferred resistance against lenacapavir. Based on cell-based assays predicting hypersusceptibility to bictegravir, the regimen was adjusted to oral lenacapavir plus bictegravir/emtricitabine/tenofovir alafenamide, resulting in a resumption in viral load decline.

Conclusions

Although lenacapavir demonstrated therapeutic potential, our case underscores the critical need to combine it with other fully active antiretroviral agents to prevent the rapid emergence of resistance and achieve long-term virological control in treatment-experienced individuals with HIV-2.

Comprehensive computational analysis of deleterious nsSNPs in PTEN gene for structural and functional insights

Single nucleotide polymorphisms (SNPs) are pivotal in understanding the genetic basis of complex disorders. Among them, nonsynonymous SNPs (nsSNPs) that alter amino acid sequences can significantly impact protein structure and function. This study focuses on analyzing deleterious nsSNPs in the tumor suppressor gene PTEN (Phosphatase and TENsin Homolog), which plays a central role in regulating the PI3K/Akt signaling pathway and tumorigenesis. Out of 43,855 SNPs in PTEN, 17 deleterious nsSNPs were identified using six computational tools. Protein stability analysis revealed that 15 variants reduce stability, potentially leading to functional impairment. Structural evaluations using HOPE and ConSurf classified mutations into buried structural residues disrupting protein integrity and exposed functional residues affecting molecular interactions. STRING database analysis highlighted PTEN as a central node in an intricate protein network, with deleterious mutations impairing critical interactions with partners such as PIK3CA, AKT1, and TP53. Secondary structure analysis revealed distinct structural deviations, particularly for G129E, which exhibited the most pronounced destabilization. Molecular dynamics simulations confirmed stability variations across mutants, with G129E exhibiting greater instability. This comprehensive analysis enhances understanding of PTEN nsSNP impacts, offering insights for therapeutic interventions and future experimental validation.

Design and evaluation of a multi-epitope DNA vaccine against HPV16

Cervical cancer, among the deadliest cancers affecting women globally, primarily arises from persistent infection with high-risk human papillomavirus (HPV). To effectively combat persistent infection and prevent the progression of precancerous lesions into malignancy, a therapeutic HPV vaccine is under development. This study utilized an immunoinformatics approach to predict epitopes of cytotoxic T lymphocytes (CTLs) and helper T lymphocytes (HTLs) using the E6 and E7 oncoproteins of the HPV16 strain as target antigens. Subsequently, through meticulous selection of T-cell epitopes and other necessary elements, a multi-epitope vaccine was constructed, exhibiting good immunogenic, physicochemical, and structural characteristics. Furthermore, in silico simulations showed that the vaccine not only interacted well with toll-like receptors (TLR2/TLR3/TLR4), but also induced a strong innate and adaptive immune response characterized by elevated Th1-type cytokines, such as interferon-gamma (IFN-γ) and interleukin-2 (IL2). Additionally, our study investigated the effects of different immunization intervals on immune responses, aiming to optimize a time-efficient immunization program. In animal model experiments, the vaccine exhibited robust immunogenic, therapeutic, and prophylactic effects. Administered thrice, it consistently induced the expansion of specific CD4 and CD8 T cells, resulting in substantial cytokines release and increased proliferation of memory T cell subsets in splenic cells. Overall, our findings support the potential of this multi-epitope vaccine in combating HPV16 infection and signify its candidacy for future HPV vaccine development.

Investigation of bioremediation for glyphosate and its metabolite in soil using arbuscular mycorrhizal GmHsp60 protein: a molecular docking and molecular dynamics simulations approach

The widespread use of glyphosate and the high dependence of the agricultural industry on this herbicide cause environmental pollution and pose a threat to living organisms. One of the appropriate solutions in sustainable agriculture to deal with pollution caused by glyphosate and its metabolites is creating a symbiotic relationship between plants and mycorrhizal fungi. Glomalin-related soil protein is a key protein for the bioremediation of glyphosate and its metabolite aminomethyl phosphonic acid in soil. This study uses homology modeling, molecular docking, and molecular dynamic simulation approaches to investigate the binding mechanism of glomalin-related soil protein from arbuscular mycorrhiza (GmHsp60) with glyphosate and its metabolite and the role of soil protein in the removal and sequestering of common agricultural soil pollutants. GmHsp60 protein structure was predicted by homology modeling, and the quality of the generated model was assessed. Then, the interaction between glyphosate and aminomethyl phosphonic acid and the modeled GmHsp60 protein was explored by molecular docking. Based on docking results, GmHsp60 has an efficient role in the bioremediation of glyphosate and aminomethyl phosphonic acid (-6.03 and -5.34 kcal/mol). Glyphosate forms three hydrogen bonds with Lys258, Gly262, and Glu58 of GmHsp60, and aminomethyl phosphonic acid forms three hydrogen bonds with Lys258, Gly261, and Gly262 of GmHsp60. In addition, the glyphosate's and its metabolite's stability was confirmed by molecular docking simulations and binding free energy calculations using MM/PBSA analysis. This study provides a molecular-level understanding of GmHsp60 expression and function for glyphosate bioremediation.

Antimicrobial Peptides from Porcine Blood Cruor Hydrolysates as a Promising Source of Antifungal Activity

Porcine blood, a significant byproduct of the pork industry, represents a potential source of antimicrobial peptides (AMPs). AMPs offer a promising alternative to chemical antimicrobials, which can be used as natural preservatives in the food industry. AMPs can exhibit both antibacterial and/or antifungal properties, thus improving food safety and addressing the growing concern of antibiotic and antifungal resistance. The objective of this study was to evaluate the antimicrobial activity of potential AMPs previously identified from porcine cruor hydrolysates. To this end, a total of sixteen peptides were chemically synthesized and their antimicrobial activities (antibacterial, anti-mold, and anti-yeast) were evaluated using microtitration and agar well diffusion methods against a wide range of microorganisms. Five new peptide sequences demonstrated antifungal activity, with Pep5 (FQKVVAGVANALAHKYH), an alpha-helix peptide, exhibiting the most promising results. Pep5 demonstrated efficacy against nine of the eleven fungal isolates, exhibiting low minimum inhibitory concentrations (MICs) and a fungicidal effect against key spoilage fungi (Rhodotorula mucilaginosa, Debaryomyces hansenii, Candida guilliermondii, Paecilomyces spp., Eurotium rubrum, Mucor racemosus, Aspergillus versicolor, Penicillium commune, and P. chrysogenum). These findings illustrate the potential of porcine blood hydrolysates as a source of AMPs, particularly antifungal peptides, which are less known and less studied than the antibacterial ones. Among the tested sequences, Pep5 exhibited the most promising characteristics, including broad-spectrum activity, low MICs, and a fungicidal effect. It is, therefore, a promising candidate for further research and for potential applications in the porcine industry and beyond.

The sequence 581Ser-610Val in the fibrinogen Aα chain is responsible for the formation of complexes between plasminogen and αC-regions of fibrin(ogen)

Objective

This study aimed to identify the binding sites for plasminogen (Pg) and its kringle-containing fragments within the αC-region of fibrin(ogen). This investigation is crucial while the conversion of fibrinogen into fibrin induces conformational changes that expose binding sites for Pg and tissue-type Pg activator (tPA), facilitating effective zymogen activation on the fibrin surface.

Methods

Two C-terminal fragments of the Aα chain ‒ 45 kDa (225Val-610Val) and 40 kDa (225Val-580Lys), were obtained through plasmin hydrolysis of human fibrinogen and subsequently characterized using MALDI TOF mass spectrometry. The interactions of Glu-Pg and Lys-Pg, as well as Pg kringle fragments (K1-3, K4, and K5), with the obtained αC truncated polypeptides were analyzed using ELISA and Western blot techniques with the use of specific antibodies.

Results

It was demonstrated that Pg and its fragments K1-3, K4, and K5 interact exclusively with the 45-kDa fragment (225Val-610Val) of the αC region of fibrinogen with high affinity in a concentration-dependent manner (Kd values for Glu-Pg = 7.10 × 10-9 M, Lys-Pg = 6.01 × 10-9 M, K1-3 = 1.08 × 10-7 M, K4 = 5.06 × 10-7 M, and K5 = 2.50 × 10-7 M). This fragment, unlike the 40-kDa polypeptide (225Val-580Lys), contains the α581Ser-610Val sequence.

Conclusions

It was shown that the sequence 581Ser-610Val of fibrinogen Aα-chain, which becomes exposed during the conversion of fibrinogen to fibrin, is essential for the formation of complexes between Pg and αC regions of fibrin(ogen), thereby contributing to the initiation and regulation of fibrinolysis.

Design and computational analysis of a novel Azurin-BR2 chimeric protein against breast cancer

Cancer is one of most lethal diseases worldwide. Chemotherapeutics and surgeries are among the treatment facilities available for curing cancer. However due to their negative impact on normal cells and drug resistance development, new treatment strategies have yet to be developed. Some microbial products exhibit therapeutic potential for treating cancer. Pseudomonas aeruginosa Azurins have shown anticancer effects against breast cancer without affecting normal cells. To enhance its cytotoxic effect and targeted delivery, we fused Azurin with a cell-penetrating peptide (BR2) through a rigid linker and evaluated its anticancer potential via in silico analysis. The prediction of the secondary and the tertiary structures and analysis of physiochemical properties of chimeric proteins were computationally performed. The Azurin-BR2 chimeric protein has a basic nature with a molecular weight of 16.8 kDa. The quality indices and validation of chimeric proteins were performed with ERRAT2 and Ramachandran plot values, respectively. The quality index of the chimeric protein was predicted to be 81% to 84.6%, and residues residing in the most favoured region were identified. The HDOCK bioinformatics tool was used for docking a chimeric protein with a cancer suppressor protein p53. The results of the current study support that an Azurin-BR2 fusion protein has a high binding affinity for p53 can induce apoptosis in cancerous cells, and can be used in tumor-targeting therapy.

Exploring the Potential of Biomimetic Peptides in Targeting Fibrillar and Filamentous Alpha-Synuclein-An In Silico and Experimental Approach to Parkinson's Disease

Alpha-synuclein (ASyn) is a protein that is known to play a critical role in Parkinson's disease (PD) due to its propensity for misfolding and aggregation. Furthermore, this process leads to oxidative stress and the formation of free radicals that cause neuronal damage. In this study, we have utilized a biomimetic approach to design new peptides derived from marine natural resources. The peptides were designed using a peptide scrambling approach where antioxidant moieties were combined with fibrillary inhibition motifs in order to design peptides that would have a dual targeting effect on ASyn misfolding. Of the 20 designed peptides, 12 were selected for examining binding interactions through molecular docking and molecular dynamics approaches, which revealed that the peptides were binding to the pre-NAC and NAC (non-amyloid component) domain residues such as Tyr39, Asn65, Gly86, and Ala85, among others. Because ASyn filaments derived from Lewy body dementia (LBD) have a different secondary structure compared to pathogenic ASyn fibrils, both forms were tested computationally. Five of those peptides were utilized for laboratory validation based on those results. The binding interactions with fibrils were confirmed using surface plasmon resonance studies, where EQALMPWIWYWKDPNGS, PYYYWKDPNGS, and PYYYWKELAQM showed higher binding. Secondary structural analyses revealed their ability to induce conformational changes in ASyn fibrils. Additionally, PYYYWKDPNGS and PYYYWKELAQM also demonstrated antioxidant properties. This study provides insight into the binding interactions of varying forms of ASyn implicated in PD. The peptides may be further investigated for mitigating fibrillation at the cellular level and may have the potential to target ASyn.

Co-Regulation Mechanism of Host p53 and Fos in Transcriptional Activation of ILTV Immediate-Early Gene ICP4

Infectious laryngotracheitis virus (ILTV) exhibits a cascade expression pattern of encoded genes, and ICP4 is the only immediate-early gene of ILTV, which plays a crucial role in initiating the subsequent viral genes. Therefore, studying the transcriptional regulation mechanism of ICP4 holds promise for effectively blocking ILTV infection and spread. Host transcriptional factors p53 and Fos are proven to regulate a variety of viral infections, and our previous studies have demonstrated their synergistic effects in regulating ILTV infection. In this study, we constructed eukaryotic expression vectors for p53 and Fos as well as their specific siRNAs and transfected them into a chicken hepatoma cell line. The results showed that knocking down p53 or Fos significantly inhibited ICP4 transcription, while overexpressing p53 or Fos had an opposite effect. A further CoIP and ChIP-qPCR assay suggested p53 and Fos physically interacted with each other, and jointly bound to the upstream transcriptional regulatory region of ICP4. To elucidate the specific mechanisms of p53 and Fos in regulating ICP4 transcription, we designed p53 and Fos protein mutants by mutating their DNA binding domains, which significantly reduced their binding ability to DNA without affecting their interaction. The results showed that Fos directly bound to the promoter region of ICP4 as a binding target of p53, and the p53-Fos protein complex acted as a transcriptional co-regulator of ICP4. Studying the transcriptional process and regulatory pattern of ICP4 is of great significance for understanding the molecular mechanism of ILTV infection, and thus for finding effective methods to control and prevent it.

Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic

Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein, AdfB, as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinical V. cholerae isolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance of V. cholerae and its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.IMPORTANCEThe global bacterial pathogen Vibrio cholerae causes an estimated 1 to 4 million cases of cholera each year. Thus, studying the factors that influence its persistence as a pathogen is of great importance. One such influence is the lytic phage ICP1, as once infected by ICP1, V. cholerae is destroyed. To date, we have observed that the phage ICP1 shapes V. cholerae evolution through the flux of anti-phage bacterial immune systems. Here, we probe clinical V. cholerae isolates for novel anti-phage immune systems that can inhibit ICP1 and discover the toxin-antitoxin system DarTG as a potent inhibitor. Our results underscore the importance of V. cholerae and ICP1 surveillance to elaborate novel means by which V. cholerae can persist in both the human host and aquatic reservoir in the face of ICP1.

Unlocking Hope: Paving the Way for a Cutting-Edge Multi-Epitope Dengue Virus Vaccine

Dengue fever is a significant health issue in Pakistan, demanding a vaccine effective against all the viral strains. This study employs reverse vaccinology to develop potential dengue vaccine candidates (DVAX I-III). The study thoroughly examined conserved areas of dengue virus serotypes 1-4's structural and non-structural proteins. Key viral proteins were analyzed to find antigenic peptides, which were incorporated into vaccine candidates and potentiated with adjuvants. Computational methods predicted peptide structures and evaluated their binding to immune receptors TLR 2, TLR 4, HLA *A1101, and DRB*401. A molecular dynamics simulation lasting 100 ns of the DVAX II-TLR4 complex at different time intervals clearly indicated that the ligand is attached to the receptor. Normal mode analysis assessed the stability and flexibility of these interactions. Encouragingly, all three vaccine candidates demonstrated favorable interactions with these immune receptors and the potential to induce a robust immune response. These findings suggest their safety and warrant further in vivo studies to evaluate their efficacy for clinical development.

Mechanistic and structural insights into vitamin B2 metabolizing enzyme riboflavin kinase from Leishmania donovani

Leishmania donovani relies on specific vitamins and cofactors crucial for its survival and pathogenesis. Tailoring therapies to disrupt these pathways offers a promising strategy for the treatment of Visceral Leishmaniasis. Current treatment regimens are limited due to drug resistance and high costs. The dependency of Leishmania parasites on Vitamin B2 and its metabolic products is not known. In this study, we have biochemically and biophysically characterized a Vitamin B2 metabolism enzyme, riboflavin kinase from L. donovani (LdRFK) which converts riboflavin (vitamin B2) into flavin mononucleotide (FMN). Sequence comparison with human counterpart reflects 31.58 % identity only, thus opening up the possibility of exploring it as drug target. The rfk gene was cloned, expressed and the recombinant protein was purified. Kinetic parameters of LdRFK were evaluated with riboflavin and ATP as substrates which showed differential binding affinity when compared with the human RFK enzyme. Thermal and denaturant stability of the enzyme was evaluated. The rfk gene was overexpressed in the parasites and its role in growth and cell cycle was evaluated. In the absence of crystal structure, homology modelling and molecular dynamic simulation studies were performed to predict LdRFK structure. The data shows differences in substrate binding between human and parasite enzyme. This raises the possibility of exploring LdRFK for specific designing of antileishmanial molecules. Gene disruption studies can further validate its candidature as antileishmanial target.

In Silico Design of a Trans-Amplifying RNA-Based Vaccine against SARS-CoV-2 Structural Proteins

Nucleic acid-based vaccines allow scalable, rapid, and cell-free vaccine production in response to an emerging disease such as the current COVID-19 pandemic. Here, we objected to the design of a multiepitope mRNA vaccine against the structural proteins of SARS-CoV-2. Through an immunoinformatic approach, promising epitopes were predicted for the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Fragments rich in overlapping epitopes were selected based on binding affinities with HLA classes I and II for the specific presentation to B and T lymphocytes. Two constructs were designed by fusing the fragments in different arrangements via GG linkers. Construct 1 showed better structural properties and interactions with toll-like receptor 2 (TLR-2), TLR-3, and TLR-4 during molecular docking and dynamic simulation. A 50S ribosomal L7/L12 adjuvant was added to its N-terminus to improve stability and immunogenicity. The final RNA sequence was used to design a trans-amplifying RNA (taRNA) vaccine in a split-vector system. It consists of two molecules: a nonreplicating RNA encoding a trans-acting replicase to amplify the second one, a trans-replicon (TR) RNA encoding the vaccine protein. Overall, the immune response simulation detected that activated B and T lymphocytes and increased memory cell formation. Macrophages and dendritic cells proliferated continuously, and IFN-γ and cytokines like IL-2 were released highly.

Metabolite Profiling and Identification of Sweet/Bitter Taste Compounds in the Growth of Cyclocarya Paliurus Leaves Using Multiplatform Metabolomics

Cyclocarya paliurus tea, also known as "sweet tea", an herbal tea with Cyclocarya paliurus leaves as raw material, is famous for its unique nutritional benefits and flavor. However, due to the unique "bittersweet" of Cyclocarya paliurus tea, it is still unable to fully satisfy consumers' high-quality taste experience and satisfaction. Therefore, this study aimed to explore metabolites in Cyclocarya paliurus leaves during their growth period, particularly composition and variation of sweet and bitter taste compounds, by combining multi-platform metabolomics analysis with an electronic tongue system and molecular docking simulation technology. The results indicated that there were significant differences in the contents of total phenols, flavonoids, polysaccharides, and saponins in C. paliurus leaves in different growing months. A total of 575 secondary metabolites were identified as potential active metabolites related to sweet/bitter taste using nontargeted metabolomics based on UHPLC-MS/MS analysis. Moreover, molecular docking technology was utilized to study interactions between the candidate metabolites and the sweet receptors T1R2/T1R3 and the bitter receptors T2R4/T2R14. Six key compounds with high sweetness and low bitterness were successfully identified by using computational simulation analysis, including cis-anethole, gluconic acid, beta-D-Sedoheptulose, asparagine, proline, and citrulline, which may serve as candidates for taste modification in Cyclocarya paliurus leaves. These findings provide a new perspective for understanding the sweet and bitter taste characteristics that contribute to the distinctive sensory quality of Cyclocarya paliurus leaves.