QMEANDisCo-distance constraints applied on model quality estimation

Pleiotropic signaling of single-chain thyrostimulin (GPB5-GPA2) on homologous glycoprotein hormone receptors (ScFSHR, ScLHR, ScTSHR) in the elasmobranch Scyliorhinus canicula reproduction

The pituitary glycoprotein hormones (GPHs) control several physiological processes in vertebrates such as reproduction and metabolism. They include the luteinizing hormone (LH), the follicle-stimulating hormone (FSH), and the thyroid-stimulating hormone (TSH), which activate their cognate leucine-rich repeat G protein-coupled receptors (LGRs), LHR, FSHR, and TSHR. Each GPH consists of a common α subunit and a specific βFSH, βLH or βTSH subunit. More recently, two supplementary GPH proteins, GPA and GPB, were identified in nearly all bilaterians and are the ancestors of the pituitary GPH α- and β-subunits, respectively. Chondrichthyans (holocephalans and elasmobranchs), the sister group of bony vertebrates, are the most ancient clade to possess diversified GPH subunits. In the present study, GPA2, GPB5, TSHβ2, but not TSHβ1, and TSHR sequences have been identified in several elasmobranch genomes, and their 3D models were analyzed. Functional hormone-receptor interactions were studied in the small-spotted catshark (Scyliorhinus canicula) and showed that conditioned media from cells expressing the recombinant single-chain ScGPB5-ScGPA2 were more effective than independent subunits in activating ScTSHR, ScFSHR, and ScLHR. Expression profiles were analyzed by real-time PCR, in situ hybridization, and immunohistochemistry along the male genital tract, other male and female tissues, and female tissues. A broader tissue distribution expression was observed for tshr and gpa2 than for gpb5, which was mainly observed in the testes. In testis, expression of tshr and gpb5 by Sertoli cells and of gpa2 by germ cells suggested paracrine/autocrine functions of GPA2/GPB5/GPHR signaling during spermatogenesis. This study complements the data on GPA2 and GPB5 by studying a chondrichthyan of phylogenetic interest for understanding the evolution of endocrine regulation in vertebrates.

RNA chaperone Hfq promotes the growth of Yersinia enterocolitica in refrigerated foods

Yersinia enterocolitica is a major foodborne pathogen causing yersiniosis, a significant zoonotic infection. Its unique cold tolerance makes it a potential threat to the safety of cold chain food. The RNA-binding protein Hfq is known to be involved in bacterial stress regulation, but its role in the cold tolerance of Y. enterocolitica remains unclear. Based on gene knockout and complementation, this study revealed that deleting the hfq gene disrupted the exponential growth phase of Y. enterocolitica under low-temperature conditions, leading to a biphasic growth phenomenon. Additionally, through the construction of point mutants, it was found that the critical amino acid sites for cold-tolerance regulation of Hfq in Y. enterocolitica are located on the distal and proximal surfaces. Further studies found that the biphasic growth process of the hfq deletion mutant was affected by the initial bacterial concentration and exogenous fatty acids. RT-qPCR results showed that Hfq regulation may affect the synthesis of branched-chain amino acids, and TCA cycle-related genes were significantly up-regulated during the second exponential growth. Studies based on milk and meat have shown that Hfq can promote the low-temperature growth of Y. enterocolitica in the food matrix. Our study provides evidence that Hfq-dependent regulation of energy metabolism is critical for cold tolerance in Y. enterocolitica. This study highlights the importance of Hfq in regulating cold tolerance in Y. enterocolitica and discusses its potential regulatory mechanism.

Biocontrol potential of Vibrio maritimus chitinase: Heterologous expression and insecticidal activity against Acanthoscelides obtectus

In this study, the chitinase gene from the marine bacterium Vibrio maritimus was heterologously expressed in Escherichia coli, purified via affinity chromatography and tested for its insecticidal activity against the storage pest Acanthoscelides obtectus. The recombinant VmChiA protein exhibited a molecular mass of ~60 kDa, with optimum activity observed at pH 6.0 and 40 °C. Enzyme kinetic analysis revealed a Km value of 0.042 mM, Vmax of 17.48 μmol min-1, kcat of 1.75 min-1 and catalytic efficiency of 41.61 mM-1 min-1, respectively. Furthermore, a dose of 40 U mL-1 of recombinant VmChiA showed similar efficacy to malathion insecticide against A. obtectus, with 100 % mortality in both treatments. LC50 and LC90 values of VmChiA were 13.95 U mL-1 and 27.66 U mL-1, respectively. Furthermore, the three-dimensional structure of the catalytic site of VmChiA was modeled. Molecular dynamics simulation technique was used to explore and analyze the dynamics and interactions. A salt bridge (GLU274-ARG296) in the α + β domain was observed as a critical feature facilitating substrate (GlcNAc)2 binding and enzymatic activity. These findings demonstrate that recombinant VmChiA possesses potent insecticidal properties, highlighting its potential as a bio-based, eco-friendly alternative for managing significant agricultural pests.

Phylogenetic and Structural Analyses of Vesicular Glutamate Transporters

Vesicular glutamate transporters are members of the solute carrier 17 (SLC17) family, and mammals express three closely related isoforms: vGluT1-3. While vGluT genes have been identified across various species in the Animalia kingdom, the evolutionary relationships and the natural history of vGluT members remain poorly understood. This study aimed to address these gaps by presenting a phylogenetic analysis of vGluTs across the animal kingdom. The study also included a detailed sequence analysis and structural modeling of vGluT isoforms among species. The phylogenetic tree revealed distinct clusters corresponding to the vGluts isoform 1, 2, and 3, with functional amino acid residues highly conserved among them. Invertebrate vGluTs emerged as the most divergent proteins, serving as the root of the tree. Sequence analysis confirmed the high conservation of vGluTs transmembrane core regions but identified high variations in the N and C-terminal ones. Structural analysis revealed that AlphaFold2-predicted models demonstrated high confidence quality in the transmembrane domains, but exhibited limited local similarity in the N-terminal, C-terminal, and loop regions. On the other hand, the expected topology of these helices was accurately captured and positioned in the Swiss-Model-generated structures, with the functionally relevant residues precisely positioned in three-dimensional space. In conclusion, we expect that our findings will contribute to a deeper understanding of vesicular glutamate transporter structure and function, as well as their roles across distinct species and biological contexts.

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.

Discovery of 1-phenyl-1,2,3-triazole ureas as dual VEGFR-2/JNK-1 type II kinase inhibitors targeting pancreatic cancer

In oncology, pancreatic cancer (PC) continues to be a problem that requires creative approaches to therapy. This research aims to create dual kinase inhibitors that target VEGFR-2 and JNK-1, two important factors in the angiogenesis and progression of PC. We found compounds with promising anticancer action using phenyltriazolyl piperazine/(piperidine) carboxamides (PTPCs) and phenyltriazolyl phenylureas (PTPUs). Compound 12b was the most effective in inhibiting VEGFR-2 (IC50: 46 nM) and JNK-1 (IC50: 35 nM) and showed the highest activity against PANC-1 cancer cells (IC50: 1.05 μM). Furthermore, 12b altered the caspase-3, Bcl-2, and Bax apoptotic markers. The binding interactions of 12b with target kinases were discovered by in silico investigations. This study emphasizes how dual kinase inhibitors may be a viable way to improve the effectiveness of cancer treatments and deal with resistance mechanisms.

Quaternary stabilization of a GH2 β-galactosidase from the psychrophile A. ikkensis, a flexible and unstable dimeric enzyme

Studies of cold-active enzymes may elucidate the basis for low-temperature activity and contribute to their wider application in energy-efficient processes. Here we investigate the cold-active GH2 β-galactosidase from the psychrophilic bacterium Alkalilactibacillus ikkensis (AiLac). AiLac has a specific activity twice as high as its closest structural homolog (the mesophilic Escherichia coli GH2 β-galactosidase) toward the lactose analog ONPG at room temperature and neutral pH, and shows biphasic behavior in Michaelis-Menten plots. AiLac is activated by Mg2+ and Na+ and is most effective at pH 7.0 and 30°C. However, early unfolding events are observed already at room temperature. Stability studies using intrinsic fluorescence, circular dichroism, and small-angle x-ray scattering (SAXS), combined with activity assays, showed AiLac to be highly sensitive to heat and urea and to be stabilized, but also inhibited, by loss of structural flexibility induced by the osmolyte trehalose. AlphaFold structure prediction combined with SAXS and flow-induced dispersion analysis support a reversible monomer-dimer model, suggesting structural adaptation to cold temperatures on a quaternary level. The low amount of dimeric buried surface area, high flexibility, and remarkably low chemical and thermal stability present an extreme example of cold adaptation promoted by high levels of solvent interactions. To investigate the relationship between evolution and oligomerization, we trained a generative deep learning model to successfully engineer functional variants that form stabilized dimers and tetramers by introducing high evolutionary fitness mutations at the interface, demonstrating an efficient way to explore the local sequence fitness landscape to modulate the equilibrium of oligomerization.

Identification and characterization of oncogenic KRAS G12V inhibitory peptides by phage display, molecular docking and molecular dynamic simulation

The KRAS G12V mutation is a critical oncogenic driver in aggressive cancers, yet developing effective inhibitors remains challenging due to its elusive structural features. In this study, we employed phage display technology using both linear and cyclic peptide libraries to identify inhibitory peptides against KRAS G12V. Through subtractive bio-panning against wild-type KRAS, we identified two 23-mer peptides (Pep I and Pep II) that demonstrated selective binding to KRAS G12V. Molecular dynamics simulations revealed distinct binding mechanisms - Pep II showed stronger selective binding to G12V (-35.96 kcal/mol) compared to wild-type KRAS (-18.06 kcal/mol), while Pep I exhibited similar binding energies but interacted with different regions. Notably, Pep I bound to functional regions in KRAS G12V but non-functional regions in wild-type KRAS. Both peptides demonstrated significant inhibition of KRAS G12V-carrying cancer cell lines (NCI-H2444 and SW620), reducing cell viability by 70-75 % at 400 μM after 48 h while showing minimal effects (20-30 % reduction) on wild-type KRAS-carrying Caco-2 cells, which is equal to DMSO diluent control. These findings provide new insights into peptide-based targeting of KRAS G12V and demonstrate the potential of using subtractive phage display for developing selective inhibitors against oncogenic mutations.

HDAC11 Inhibition as a Potential Therapeutic Strategy for AML: Target Identification, Lead Discovery, Antitumor Potency, and Mechanism Investigation

Herein, we identified that HDAC11 is involved in the pathogenesis of AML and is a potential therapeutic target for AML. Considering the scarcity of HDAC11 inhibitors, structurally novel HDAC11 inhibitors were developed, identifying A9 as the most potent one, which phenocopied the apoptosis induction, cell cycle arrest, and differentiation promotion effects of HDAC11 knockdown in AML cells. Moreover, A9 not only promoted iron uptake by upregulating TF and TFRC but also promoted iron release by upregulating HMOX1, which cooperatively led to iron homeostasis disruption and the consequent ferroptosis in AML cells. Mechanism investigation indicated that A9-induced HMOX1 upregulation was due to the activation of the p62-Keap1-Nrf2 pathway. Notably, the combination of A9 with chemotherapy drugs synergistically reduced AML cell viability in vitro. The robust in vivo anti-AML efficacy of A9, alone and combined with cytarabine, was also validated. Collectively, our study revealed pharmacological inhibition of HDAC11 as a potential therapeutic strategy for AML.

Structural Insights into Kainate Receptor Desensitization

Kainate receptors (KARs), along with AMPA and NMDA receptors, belong to the ionotropic glutamate receptor (iGluR) family and play critical roles in mediating excitatory neurotransmission throughout the central nervous system. KARs also regulate neurotransmitter release and modulate neuronal excitability and plasticity. Receptor desensitization plays a critical role in modulating the strength of synaptic transmission and synaptic plasticity. While KARs share overall structural similarity with AMPA receptors, the desensitized state of KARs differs strikingly from that of other iGluRs. Despite extensive studies on KARs, a fundamental question remains unsolved: why do KARs require large conformational changes upon desensitization, unlike other iGluRs? To address this, we present cryo-electron microscopy structures of GluK2 with double cysteine mutations in non-desensitized, shallow-desensitized and deep-desensitized conformations. In the shallow-desensitized conformation, two cysteine crosslinks stabilize the receptors in a conformation that resembles the desensitized state of AMPA receptors. However, unlike the tightly closed pore observed in the deep-desensitized KAR and desensitized AMPAR conformations, the channel pore in the shallow-desensitized state remains incompletely closed. Patch-clamp recordings and fluctuation analysis suggest that this state remains ion-permeable, indicating that the lateral rotational movement of KAR ligand-binding domains (LBDs) is critical for complete channel closure and stabilization of the receptor in desensitization states. Together with the multiple conformations representing different degree of desensitization, our results define the unique mechanism and conformational dynamics of KAR desensitization.

Highlights

We present cryo-EM structures of GluK2 kainate receptors with engineered cysteine crosslinks at the inter-dimer interface, which restrict subunit lateral rotation and attenuate receptor desensitization.The structure of GluK2 double cysteine mutant in complex with the allosteric potentiator BPAM344 and glutamate represents a non-desensitized state, highlighting the critical conformational changes required for ion channel gating.The glutamate-bound GluK2 mutant adopts multiple conformations, representing both shallow- and deep-desensitized states. Electrophysiological recordings indicate that the GluK2 kainate receptor mutant recovers from desensitization more rapidly, resembling AMPA receptors. Our structural and functional data suggest that shallow-desensitized KARs remain conductive, implying that the large lateral LBD rotation during KAR desensitization is essential for complete channel closure, distinguishing KARs from other iGluRs.

Clinicopathological correlation of PTPN3 expression in breast cancer and in silico drug screening against PTPN3 for therapeutics

PTPN3 regulates cellular signaling and is dysregulated in cancer. There has been less research about the oncogenic impact of PTPN3 in breast cancer patients. This study analyzed PTPN3 mRNA levels and their prognostic significance in breast cancer using TCGA datasets. qRT-PCR was used to assess PTPN3 expression in formalin-fixed, paraffin-embedded Indian breast cancer patient samples (tumor-74, control-36). PTPN3 protein levels (ER-positive 15; ER-negative: 15; distant normal breast tissues: 20) were also immunohistochemically assessed using the H-score method. The biomarker potential was examined using a receiver operating characteristic (ROC) analysis. Docking and molecular dynamics (MD) simulations were used to find PTPN3 inhibitors (PDB ID: 2B49) from 892 FDA-approved natural chemicals in the ZINC database. PTPN3 mRNA and protein expression were significantly higher in breast cancers and associated with clinicopathological variables such as age, ER status, tumor stage, grade, Ki-67 index, menopause, and lymph node metastasis (p < 0.05). ROC analysis revealed an AUC of 0.7654, indicating PTPN3's biomarker potential. Docking yielded three high-affinity inhibitors: Cyclocort (ZINC000003977777), Toposar (ZINC000003938684), and Tetracycline (ZINC000084441937), with binding energies of -9.3, -8.73, and -8.66 kcal/mol, respectively. MD simulations confirmed stable connections via hydrogen bonds and hydrophobic interactions under minimal constraints. In conclusion, PTPN3 overexpression supports its role as a prognostic biomarker, and Cyclocort, Toposar, and Tetracycline need further confirmation as potential PTPN3 inhibitors.

How to Tell an N from an O: Controlling the Chemoselectivity of Methyltransferases

S-Adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs) are important enzymes in numerous biological pathways. They share a common S N 2 mechanism but act on different nucleophilic substrates in vivo. Therefore, MTs have a specific chemoselectivity to transfer CH3 onto the correct atom type and substrate. Caffeate O-MT from Prunus persica (PpCaOMT) and anthranilate N-MT from Ruta graveolens (RgANMT) share a high similarity regarding their amino acid sequence (>74%). Nevertheless, the physiological substrates (caffeate vs anthranilate) and attacking nucleophiles (hydroxyl vs amino group) are strikingly different. We demonstrate that the differing chemoselectivity is governed by different conformational states of the two enzymes. O-Methylation catalyzed by CaOMTs requires a "closed" conformation, whereas ANMTs perform N-methylation in an "open" state. We rationally designed seven variants for both PpCaOMT and RgANMT, which changed their original nucleophile preference to different extents, up to a full inversion. Interestingly, the generated O-selective ANMT variant catalyzes O-methylation considerably faster than wildtype CaOMT. Molecular dynamics (MD) simulations and hydrogen/deuterium exchange mass spectrometry (HDX-MS) experiments showed that the mutations induced changes in the conformational dynamics of the enzyme variants and by modulating the open/closed transitions impact the corresponding chemoselectivity. Our data show that the selectivity of the methyl transfer reaction is not solely governed by the key residues directly involved in the methyl transfer but is rather synergistically modulated by the conformational dynamics of the enzyme and reaction conditions.

The Identification and Characterization of a Novel Alginate Lyase from Mesonia hitae R32 Exhibiting High Thermal Stability and Potent Antioxidant Oligosaccharide Production

Alginate lyases are of great importance in biotechnological and industrial processes, yet research on these enzymes from Mesonia genus bacteria is still limited. In this study, a novel PL6 family alginate lyase, MhAly6, was cloned and characterized from the deep-sea bacterium Mesonia hitae R32. The enzyme, composed of 797 amino acids, contains both PL6 and GH28 catalytic domains. A phylogenetic analysis revealed its classification into subfamily 1 of the PL6 family. MhAly6 showed optimal activity at 45 °C and pH 9.0, retaining over 50% activity after 210 min of incubation at 40 °C, highlighting its remarkable thermal stability. The enzyme exhibited degradation activity toward sodium alginate, Poly M, and Poly G, with the highest affinity for its natural substrate, sodium alginate, producing alginate oligosaccharides (AOSs) with degrees of polymerization (DP) ranging from 2 to 7. Molecular docking identified conserved catalytic sites (Lys241/Arg262) and Ca2+ binding sites (Asn202/Glu234/Glu236), while the linker and GH28 domain played an auxiliary role in substrate binding. Antioxidant assays revealed that the MhAly6-derived AOSs showed potent radical-scavenging activity, achieving 80.64% and 95.39% inhibition rates against DPPH and ABTS radicals, respectively. This work not only expands our understanding of alginate lyases from the Mesonia genus but also highlights their biotechnological potential for producing functional AOSs with antioxidant properties, opening new avenues for their applications in food and pharmaceuticals.

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.

Two Avastrovirus Species Discovered in Psittaciformes Expand the Host Range of the Family Astroviridae

Metatranscriptomics has recently revealed greater species richness and host range of the Avastrovirus genus, quadrupling the number of avian orders known to host them in less than a decade. Despite this growing awareness of astrovirus presence in wild birds, limited attention has been paid to these viruses in the context of disease in Australian avifauna. Here we used unbiased RNA sequencing of intestinal samples from a galah (Eolophus roseicapilla) and an Australian king parrot (Alisterus scapularis) with a chronic diarrhoeal and wasting disease to detect the entire genomes of two novel astrovirus species. We propose naming these viruses Avastrovirus eolorosei (PQ893528) and Avastrovirus aliscap (PQ893527). The phylogenetic positions of these viruses highlight the importance of current and future metatranscriptomic virus screening in investigations of avian host landscapes beyond Galloanserae. This is also the first documentation of avastrovirus infections in Psittaciformes and the first to report their potential role as disease agents in them.

Association of VDR and TMPRSS2 gene polymorphisms with COVID-19 severity: a computational and clinical study

BACKGROUND

COVID-19 manifestations range from asymptomatic to severe, and are influenced by host genetic factors. This study examined the association between vitamin D receptor (VDR) polymorphisms (TaqI and FokI) and transmembrane serine protease 2 (TMPRSS2) gene polymorphisms (rs12329760) and COVID-19 severity.

METHODS AND RESULTS

242 COVID-19 patients underwent genotyping using PCR-RFLP. Statistical analysis were conducted using SPSS v.21 and SHesis software, and validated by Sanger sequencing. The association of the VDR TaqI, FokI, and TMPRSS2 rs12329760 polymorphisms with COVID-19 severity was investigated. Computational analysis of TMPRSS2 was used to determine the pathogenicity and structural effects of these SNPs. For VDR TaqI, the 'TC' genotype showed higher prevalence in severe cases (50.5%) compared to mild cases (41.4%); however, no statistically significant association was observed [OR: 1.545 (0.893-2.675), p > 0.05]. Similar patterns were noted for the 'CC' genotype and 'C' allele, without statistical significance. For VDR FokI, the 'Ff' genotype showed higher prevalence in severe cases (25.8%) compared to mild cases (20.0%) [OR: 0.766 (0.199-2.951), p = 0.69], with no significant association. In haplotype analysis, elevated frequencies of 'Tf' and 'ft' haplotypes were observed in severe cases, but without statistical significance. For TMPRSS2 rs12329760, the 'CT' genotype showed a marginally higher prevalence in severe cases (50.5%) than in mild cases (49.7%) [OR: 0.805 (0.276-2.345), p > 0.05], without significant association. Computational analysis indicated that the variant does not demonstrate pathogenic effects but may influence protein stability.

CONCLUSION

This study revealed no statistically significant association between VDR (TaqI and FokI) and TMPRSS2 (rs12329760) polymorphisms and COVID-19 severity. Large-scale investigations and functional analysis are required to delineate the impact of these genetic variations on COVID-19 susceptibility and severity.

Molecular dynamics of SARS-CoV-2 omicron variants from Philippine isolates against hesperidin as spike protein inhibitor

SARS-CoV-2 remains a global threat with new sublineages posing challenges, particularly in the Philippines. Hesperidin (HD) is being studied as a potential prophylactic for COVID-19. However, the virus's rapid evolution could alter how HD binds to it, affecting its effectiveness. Here, we study the mutation-induced variabilities of HD dynamics and their effects on molecular energetics in SARS-CoV-2 spike receptor complex systems. We considered eight different point mutations present in the Omicron variant. Root-mean-square deviation and binding energy analysis showed that S477N and Omicron did not eject HD throughout the simulation. Hydrogen bond distribution analysis highlighted the involvement of hydrogen bonding in mutant-HD stabilization, especially for S477N and Omicron. Root-mean-square fluctuation analysis revealed evidence of Y505H destabilization on complex systems, while distal-end loop mutations increased loop flexibility for all models bearing the three mutations. Per-residue energy decomposition demonstrated that Q493R substitution increased HD interaction. Free energy landscape and essential dynamics through principal component analysis provided insights into the conformational subspace distribution of mutant model molecular dynamics trajectories. In conclusion, significant mutations contributed to the HD interaction in different ways. S477N has shown significant binding contributions through favorable ligand interaction, while other mutations contribute via conformational modifications, increased affinity due to sidechain mutations, and increased loop flexibility.

Function analysis of RNase III in response to oxidative stress in Synechocystis sp. PCC 6803

RNase III, a ubiquitously distributed endonuclease, plays an important role in RNA processing and functions as a global regulator of gene expression. In this study, we explored the role of RNase III in mediating the oxidative stress response in Synechocystis sp. PCC 6803. Phenotypic analysis demonstrated that among the three RNase III-encoding genes (slr0346, slr1646, and slr0954), the deletional mutation of slr0346 significantly impaired the growth of cyanobacteria on BG11 agar plates. However, this growth effect was not observed in liquid culture. In contrast, the deletion of slr1646 and slr0954 did not affect the growth of cyanobacteria under the tested conditions. However, under methyl viologen (MV)-induced oxidative stress, the slr0346 deletion mutant exhibited a slower growth rate compared to the wild-type strain. Transcriptome analysis revealed that five pathways-nitrogen metabolism, ABC transporters, folate biosynthesis, ribosome biogenesis, and oxidative phosphorylation-were implicated in the oxidative stress response. The slr0346 gene suppressed global gene expression, with a particular impact on genes associated with energy metabolism, protein synthesis, and transport. Furthermore, we identified Ssl3432 as an interacting protein that may participate in the oxidative stress response in coordination with Slr0346. Overall, the deletion of slr0346 markedly weakened the ability of Synechocystis sp. PCC 6803 to respond to MV-induced oxidative stress. This study offers valuable insights into the oxidative stress response of Synechocystis sp. PCC 6803 and highlights the role of RNase III in adapting to environmental stress.

Brussonol and komaroviquinone as inhibitors of the SARS-CoV-2 Omicron BA.2 variant spike protein: A molecular docking, molecular dynamics, and quantum biochemistry approach

Since late 2019, humanity has faced the challenges posed by the COVID-19 pandemic, caused by the SARS-CoV-2 virus. The continuous evolution of SARS-CoV-2 has led to the emergence of multiple Variants of Concern (VOCs) and Variants of Interest (VOIs), posing significant risks to global health. SARS-CoV-2 infects host cells via the angiotensin-converting enzyme 2 (ACE2) receptors, facilitated by the spike (S) protein. Icetexane diterpenes, including brussonol and komaroviquinone, exhibit notable anti-inflammatory, antibacterial, antiviral, antiproliferative, and anticancer properties. Recent research has explored their potential as inhibitors of the SARS-CoV-2 3Clpro protease, showing promising efficacy comparable to Nirmatrelvir. This study investigates brussonol and komaroviquinone as potential inhibitors of the SARS-CoV-2 Omicron BA.2 variant spike protein using molecular docking, molecular dynamics simulations, and quantum biochemistry approaches. The stability and interaction energies of brussonol, komaroviquinone, and mefloquine with the SARS-CoV-2 Omicron BA.2 variant spike protein were evaluated. RMSD analysis demonstrated that komaroviquinone and mefloquine maintain more stable binding poses with the spike protein compared to various NAGs and glycans. Electrostatic potential maps revealed significant interactions with ASN603, a critical residue for ligand binding efficacy. Furthermore, this study addresses a gap in current research, as no studies were found that simulate the trimer of the SARS-CoV-2 BA.2 variant spike protein. Most existing studies focus on the monomer and often exclude the NAGs and glycans. This research underscores the importance of maintaining the NAGs and glycans in the trimer simulations, providing a more accurate representation of the protein's structure and its interactions with ligands. The findings indicate that both komaroviquinone and brussonol exhibit higher binding affinities compared to mefloquine. This study provides valuable insights into the molecular interactions of these compounds, highlighting their potential for further development as antiviral agents against SARS-CoV-2.

Preclinical evaluation of the RBD-Trimeric vaccine: A novel approach to strengthening biotechnological sovereignty in developing countries against SARS-CoV-2 variants

New immunogens against emerging new virus variants are essential for controlling new variants.

METHODS

A preclinical study in which a receptor-binding domain (RBD) trimer was designed in silico with information from the Beta (B.1.351), Omicron (BA.5), and Wuhan 1 variant. A three-dimensional model of the RBD-trimer was made, and the synthesis of the trimer was based on the RBD domain of the S protein of Beta and Omicron. For the experimental trials, 63 BALB/c mice were immunized and divided into three groups: control (n = 15), adjuvant (n = 15), and RBD-trimer (n = 33).

RESULTS

81 % (13/16), 90 % (9/10), and 85 % (6/7) of BALB/c mice that received one dose, two doses, and three doses, respectively, seroconverted. Significant statistical differences (p < 0.001) were found between the experimental group vaccinated with the RBD-trimer, the group with adjuvant, and the control group. The booster did not show significant differences (p > 0.05. No inflammatory or cellular changes were observed, highlighting the safety of the RBD vaccine candidate. Kinetics and seroconversion of 75 % were obtained in the mice with two doses of tri-RBD. (P < 0.0001).

CONCLUSIONS

Applying two doses of the RBD vaccine candidate in BALB/c mice was safe and immunogenic against SARS-CoV-2. This study provides support for the country's biotechnological sovereignty and its potential contribution to public health in Colombia.

Improving the hydrophilic microenvironment surrounding the catalytic site of fructosyltransferase enhances its catalytic ability

The hydrophilic microenvironment surrounding an enzyme's active site can influence its catalytic activity. This study examines the effect of enhancing this environment in the Aspergillus niger fructosyltransferase, SucC. Bioinformatics analysis identified a cysteine residue (C66) near the catalytic triad (D64, D194, E271) as vital for maintaining the active site's structure and facilitating substrate transport. Simulated mutagenesis suggested that mutating cysteine to serine (C66S) could increase hydrophilicity without altering the structure significantly. This mutation was predicted to enhance substrate affinity, with binding energy changing from -3.65 to -4.14 kcal mol-1. The C66S mutant, expressed in Pichia pastoris GS115, showed a 61.3% increase in specific activity, a 13.5% decrease in Km (82.20/71.14 mM), and a 21.6% increase in kcat (112.23/136.48 min-1), resulting in a 40.1% increase in catalytic efficiency (1.37/1.92 min-1 mM-1). For fructooligosaccharides (FOS) production, C66S demonstrated enhanced transfructosylation, particularly in the initial stages of the reaction, achieving higher overall FOS yields. These findings highlight that modifying the active site hydrophilicity, without causing major structural changes, is a promising strategy for improving an enzyme's catalytic efficiency.

A genetically encoded fluorescent biosensor for visualization of acetyl-CoA in live cells

Acetyl-coenzyme A is a central metabolite that participates in many cellular pathways. Evidence suggests that acetyl-CoA metabolism is highly compartmentalized in mammalian cells. Yet methods to measure acetyl-CoA in living cells are lacking. Herein, we engineered an acetyl-CoA biosensor from the bacterial protein PanZ and circularly permuted green fluorescent protein (cpGFP). The sensor, "PancACe," has a maximum change of ∼2-fold and a response range of ∼10 μM-2 mM acetyl-CoA. We demonstrated that the sensor has a greater than 7-fold selectivity over coenzyme A, butyryl-CoA, malonyl-CoA, and succinyl-CoA, and a 2.3-fold selectivity over propionyl-CoA. We expressed the sensor in E. coli and showed that it enables detection of rapid changes in acetyl-CoA levels. By localizing the sensor to either the cytoplasm, nucleus, or mitochondria in human cells, we showed that it enables subcellular detection of changes in acetyl-CoA levels, the magnitudes of which agreed with an orthogonal PicoProbe assay.

Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses an ongoing threat to the efficacy of vaccines and therapeutic antibodies. Mutations predominantly affect the receptor-binding domain (RBD) of the spike protein, which mediates viral entry. The RBD is also a major target of monoclonal antibodies that were authorised for use during the pandemic. In this study, an in silico approach was used to investigate the mutational landscape of SARS-CoV-2 RBD variants, including currently circulating Omicron subvariants. A total of 40 single-point mutations were assessed for their potential effect on protein stability and dynamics. Destabilising effects were predicted for mutations such as L455S and F456L, while stabilising effects were predicted for mutations such as R346T. Conformational B-cell epitope predictions were subsequently performed for wild-type (WT) and variant RBDs. Mutations from SARS-CoV-2 variants were located within the predicted epitope residues and the epitope regions were found to correspond to the sites targeted by therapeutic antibodies. Furthermore, homology models of the RBD of SARS-CoV-2 variants were generated and were utilised for protein-antibody docking. The binding characteristics of 10 monoclonal antibodies against WT and 14 SARS-CoV-2 variants were evaluated. Through evaluating the binding affinities, interactions, and energy contributions of RBD residues, mutations that were contributing to viral evasion were identified. The findings from this study provide insight into the structural and molecular mechanisms underlying neutralising antibody evasion. Future antibody development could focus on broadly neutralising antibodies, engineering antibodies with enhanced binding affinity, and targeting spike protein regions beyond the RBD.

MY, Barbosa BF, Ferro EAV, Ávila VDMR. Insights into the Role of Proteolytic and Adhesive Domains of Snake Venom Metalloproteinases from Bothrops spp. in the Control of Toxoplasma gondii Infection

Toxoplasmosis is an alarming public health problem that affects more than one-third of the world's population. In our work, we investigated the antiparasitic effects of catalytically active [BpMP-I and Jararhagin (Jar)] and catalytically inactive [Jararhagin-C (Jar-C)] snake venom metalloproteinases (SVMPs) in human HeLa cells. These toxins impaired the parasite invasion and intracellular growth, and modulated IL-6, IL-8, and MIF cytokines that control the cell susceptibility and response against T. gondii. Furthermore, we verified that the antiprotozoal activities are not restricted to the presence of the proteolytic domain, and the adhesive domains participate in the control of T. gondii infection. Also, by analyzing the structures of Jar and Jar-C through molecular modeling and dynamics, we observed that the adhesive domains in Jar-C are more exposed due to the absence of the proteolytic domain, which could favor the interaction with different targets. Our investigation on the role of SVMP domains in combating T. gondii infection highlights their potential application as biotechnological tools for creating more effective treatments for toxoplasmosis.

Apoptotic proteins in Leishmania donovani: in silico screening, modeling, and validation by knock-out and gene expression analysis

Visceral leishmaniasis, a life-threatening vector-borne illness that disproportionately affects children and elderly immunocompromised people, is a primary tropical neglected disease. No apoptotic partner proteins have yet been reported in Leishmania donovani, while their identification could contribute to knowledge on parasite cell death and the establishment of alternative therapeutics. We searched for mammalian Bcl-2 family protein orthologs and found one anti-apoptotic and two pro-apoptotic orthologs in L. donovani. A pro-death aquaporin protein, due to its characteristic BH3 domain known to interact with pro-apoptotic proteins in mammalian Bcl-2 family proteins, was also included in this study. Molecular docking and molecular dynamics simulations were conducted to assess protein-protein interactions between the identified apoptotic proteins and mimic mammalian intrinsic apoptotic pathways. The results showed that both pro-apoptotic proteins interacted with the hydrophobic pocket of the anti-apoptotic ortholog, forming a stable complex. This interaction may represent a critical event in an apoptotic pathway in L. donovani. To further characterise it, we used CRISPR-Cas9 approaches to target the identified proteins. Pure knocked population mutants, and episomal over-expressing mutant cells were exposed to apoptotic stimuli. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and quantitative expression profiling suggested that these proteins are involved in the parasite's apoptosis and could play a role in its survival.

Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350

Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with malignancies in humans. Viral infection of B cells is initiated by the viral glycoprotein 350 (gp350) binding to complement receptor 2 (CR2). Despite decades of effort, no vaccines or curative agents have been developed, partly due to lack of atomic-level understanding of the virus-host interface. Here, we determined the 1.7 Å structure of gp350 in complex with CR2. CR2 binding of gp350 utilized the same set of Arg residues required for recognition of its natural ligand, complement C3d. We further determined the structures of gp350 in complex with three potently neutralizing antibodies (nAbs) obtained from vaccinated macaques and EBV-infected individuals. Like the CR2 interaction, these nAbs targeted the acidic pocket within the CR2-binding site on gp350 using Arg residues. Our results illustrate two axes of molecular mimicry-gp350 versus C3d and CR2 versus EBV nAbs-offering insights for EBV vaccines and therapeutics development.

The unique activity of the bone morphogenetic protein TGH4 affects the embryonic development of Trichinella spiralis and the establishment of vaccine protection

In recent years, animal outbreaks of trichinellosis have been reported in Mexico, China, Algeria, Croatia and others, which is a challenge to meat safety and public health. Vaccination is an important means to control trichinellosis, but one of the main challenges in vaccine development is screening for protective candidate antigens. Bone morphogenetic proteins (BMP)), which are potential vaccine research targets, play key roles in the growth and development of metazoans. The BMP homologue TGH4 was identified from Trichinella spiralis (T. spiralis), and recombinant C-terminal mature rTGH4-m had BMP activity and exerted regulatory effects on both mouse fibroblast and T. spiralis embryonic development. The construction of a protein mutant without activation potential confirmed that BMP activity had a negative regulatory effect on the establishment of immune protection by affecting the innate, adaptive, and humoral immunity of mice. Stripping protein activity can enhance immune protection and host resistance to T. spiralis. Our findings demonstrate that the TGH4 mutant is an important vaccine candidate antigen that blocks embryonic development, kills larvae, and provides insight into parasite vaccine research.

Design of the Inhibitors for Pseudorabies Virus Replication by Reinforcement Learning from HSV-1 DNA Polymerase Inhibitors

The reintroduction of the pseudorabies virus (PRV) has led to the emergence of epidemics in some pig farms in China, resulting in significant economic losses. Moreover, the number of human infections with PRV has increased. Therefore, research into the prevention and treatment of PRV strains is imperative. In this work, the PRV DNA polymerase (DNA pol) was found to exhibit a high degree of sequence and structural similarity to the herpes simplex virus 1 (HSV-1) DNA pol. Consequently, we provided the first experimental evidence that PNU-183792, a non-nucleoside inhibitor of HSV-1, inhibited PRV replication in cell assay, with an EC50 of 100 pM, providing the basis for further studies on PRV inhibitors. Then, with the great help of reinforcement learning, some new potential hits were discovered based on the HSV-1 DNA pol inhibitors. One of the compounds, c14, which showed significant anti-PRV potency and safety, with an EC50 of 14 pM and a CC50 of 343.7 μM, can be considered as a highly promising lead compound to support drug discovery and development for anti-PRV.

Elucidating specific interactions for designing novel pyrrolamide derivatives as potential GyrB inhibitors based on ab initio fragment molecular orbital calculations

Tuberculosis (TB), the second leading infectious killer, causes serious public health problems worldwide. To develop novel anti-TB agents, many biochemical studies have targeted the subunit B of DNA gyrase (GyrB), which captures a second DNA segment and responses for ATP hydrolysis. Here, we investigated specific interactions between GyrB residues and existing pyrrolamide derivatives at an electronic level using ab initio fragment molecular orbital (FMO) calculations and designed potent inhibitors against GyrB. The evaluated binding affinities between GyrB and pyrrolamides were confirmed to be consistent with the IC50 values obtained from previous experiments. Thus, we employed the most potent pyrrolamide (compound 1) as a lead compound and proposed novel pyrrolamide derivatives. The specific interactions between GyrB and these derivatives were investigated using molecular mechanic optimizations and FMO calculations. The results revealed that our proposed derivatives had strong hydrogen bonds with Asp79 and Arg141 and exhibited electrostatic interactions with Glu56 and Ile84 of GyrB. In addition, the binding affinity between GyrB and compound 1 was enhanced significantly by the replacement at the R3 site of compound 1. The present results may provide structural concepts for the rational design of potent GyrB inhibitors as anti-TB agents.Communicated by Ramaswamy H. Sarma.

Enzymatic and structural properties of a novel oxalate decarboxylase BsOxdC from Bacillus safensis and its potential pH-dependent catalytic mechanism

Oxalate decarboxylase converts oxalate to formate and CO2 without requiring organic cofactors, making it biotechnologically relevant for applications in food, agriculture, and diagnostics. Its activity is highly dependent on pH; however, the pH-dependent catalytic mechanism remains poorly understood. This study identified a novel oxalate decarboxylase, BsOxdC, from Bacillus safensis and investigated its catalytic properties through heterologous expression and enzymatic assays. The purified BsOxdC efficiently degrades oxalate at an optimum temperature of 50 °C and a pH of 4.0, achieving a Vmax of 8.54 μmol/(min·mg). The apparent values of kcat, Km, and kcat/Km were 85.35 s-1, 4.67 μM, and 18.28 μM/s, respectively. The predicted structure of BsOxdC features two conserved cupin barrel folds at the N-terminal and C-terminal. Additionally, the docking model of the oxalate-BsOxdC complex is more stable than those of the formate-BsOxdC or acetate-BsOxdC complexes due to its lowest binding energy. In the open conformation of BsOxdC, the carboxyl group of the catalytic residue E181, located in the active loop S180E181N182S183T184, points away from both the oxalate and the active-site Mn ion. Simulations suggest that S180 and E181 interact with the substrate via ionic bonds and/or water bridges only at low pH (4.0), not at pH 8.0. Additionally, THR184 forms more molecular interactions with oxalate at pH 4.0 than at pH 8.0.

Dataset of SARS-CoV-2 spike protein receptor binding domain variants in complex with antigen-binding fragments targeting COVID-19 vaccine-referenced variants

In this paper, we present a dataset of homology-modeled structures of SARS-CoV-2 Spike protein Receptor Binding Domain (RBD) variants complexed with antigen-binding fragments (Fab) derived from the PDB structures 8GPY (Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv), 8H7Z (BA.2 RBD in complex with BA7535 Fab), and 8XE9 (XBB.1.5 RBD in complex with BD55-1205). The dataset consists of six sets of complex structures generated by combining 14 RBD variants with three different Fab pairs. The SARS-CoV-2 Spike protein sequence variants included in the dataset are Wild Type, BETA, EPSILON, IOTA, ETA, GAMMA, LAMBDA, KAPPA, BA.2, BA.4, XBB.1.5, EG.5.1, and KP.2. Notably, the KP.2 variant, which has gained attention due to its inclusion in recent vaccine updates (https://www.ema.europa.eu/), is also part of this dataset. The models were refined using the Schrödinger Bioluminate suite of software. For each variant, the homology-modeled RBDs were complexed with the Fab fragments from 8GPY, 8H7Z, and 8XE9 by grafting them onto the RBDs, followed by energy minimization, both individually and in combination. This process resulted in a comprehensive dataset of RBD-Fab complexes, suitable for comparative analysis and further investigations. Binding affinities between the RBD-Fab pairs were calculated using the Prime MM-GBSA tool (VSGB solvation model and OPLS4 force field), enabling the ranking of antigen-antibody interactions. Structural minimizations were performed to accurately estimate interaction energies, providing insights into the efficacy of antibody binding across different variants. This dataset provides high-quality structural data that can be reused for in-depth studies of antibody-antigen interactions, particularly in the context of vaccine efficacy and viral immune evasion strategies. The inclusion of the KP.2 variant, which is central to the latest COVID-19 vaccine updates, makes these homology models especially relevant. Supplementary files include the homology-modeled structures, computed binding affinities, and quality assessments (QMEANDisCo) for each model, ensuring reproducibility and reliability for further analyses.

Mechanism of low molecular weight impurity formation in an IgG1 monoclonal antibody formulation

Formulation robustness study was performed for a biosimilar monoclonal antibody (IgG1) manufactured at Dr. Reddy's Laboratory, where the pH and concentration level of excipients in the drug product formulation were systematically varied from the target formulation. It was observed that the IgG1 formulation having relatively low pH and high citrate (buffer salt) concentration were predisposed to the formation of low molecular weight impurities. Mass spectrometry analysis of the mAb1 fragments detected the pyroglutamate species from LC-LC dimer and fragmentation in the -DKTH- amino acid sequence of the heavy chain. Blind docking indicated binding of citrate with Lysine 222 residue in the proximity of Cys224 could have potentially fragmented IgG1.

Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBE) is a neurotrophic disease that has spread more rapidly throughout Europe and Asia in the past few years. At the same time, no cure or specific therapy is known to battle the illness apart from vaccination. To find a pharmacologically relevant drug, a computer-aided drug screening was initiated. Such a procedure probes a possible binding of a drug to the RNA Polymerase of TBE. The crystal structure of the receptor, however, includes missing and partially modeled regions, which rendered the structure incomplete and of questionable use for a thorough drug screening procedure. The quality of the receptor model was addressed by studying three putative structures created. We show that the choice of receptor models greatly influences the binding affinity of potential drug molecules and that the binding location could also be significantly impacted. We demonstrate that some drug candidates are unsuitable for one model but show decent results for another. Without any prejudice on the three employed receptor models, the study reveals the imperative need to investigate the receptor structure before drug binding is probed whether experimentally or computationally.

Conformation and binding of 12 Microcystin (MC) congeners to PPP1 using molecular dynamics simulations: A potential approach in support of an improved MC risk assessment

Microcystins (MCs) occur frequently during cyanobacterial blooms worldwide, representing a group of currently about 300 known MC congeners, which are structurally highly similar. Human exposure to MCs via contaminated water, food or dietary supplements can lead to severe intoxications with ensuing high morbidity and in some cases mortality. Currently, one MC congener (MC-LR) is almost exclusively considered for risk assessment (RA) by the WHO. Many MC congeners co-occur during bloom events, of which MC-LR is not the most toxic. Indeed, MC congeners differ dramatically in their inherent toxicity, consequently raising question about the reliability of the WHO RA and the derived guidance values. Molecular dynamics (MD) simulation can aid in understanding differences in toxicity, as experimental validation for all known MC congeners is not feasible. Therefore, we present MD simulations of a total of twelve MC congeners, of which eight MC congeners were simulated for the first time. We show that depending on their structure and toxicity class, MCs adapt to different backbone conformations. These backbone conformations are specific to certain MC congeners and can change or shift to other conformations upon binding to PPP1, affecting the stability of the binding. Analysis of the interactions with PPP1 demonstrated that there are frequently occurring patterns for individual MC congeners, and that published PPP interactions could be reproduced. In addition, common but also unique patterns were found for individual MC congeners, suggesting differences in binding behaviour. The MD simulations presented here therefore enhance our understanding of MC congener-specific differences and demonstrated that congener-specific investigations are prerequisite for allowing characterisation of yet untested or even unknown MC congeners, thereby allowing for a novel potential approach in support of an improved RA of microcystins in humans.

Novel biallelic nonsense mutation in IGHMBP2 gene linked to neuropathy (CMT2S): A comprehensive clinical, genetic and bioinformatic analysis of a Turkish patient with literature review

BACKGROUND

Spinal muscular atrophy with respiratory distress type 1 (SMARD1) and Charcot-Marie-Tooth type 2S (CMT2S) typically present before age 10. Genetic factors account for up to 50 % of neuropathies, which often display varied symptoms. Mutations in the IGHMBP2 gene are associated with both CMT2S and SMARD1, resulting in a rare clinical condition marked by axonal neuropathy, spinal muscular atrophy, respiratory distress, and muscle weakness.

METHOD

Detailed family histories and medical data were collected. Segregation analysis was performed using Sanger sequencing and whole exome sequencing. Additionally, a review of molecularly confirmed patients was conducted. Protein tertiary structures expressed in the IGHMBP2 gene were tested for topological and conformational changes using modeling programs and in-silico tools.

RESULTS

We identified a novel homozygous nonsense mutation (c.2568_2569del p.Gly857Alafs*27) in a family with a member showing neuropathy. This report details the clinical and genetic findings of the affected individuals, including a Turkish patient with neuropathy, and compares them with literature cases.

CONCLUSION

Understanding the clinical impact of the (c.2568_2569del p.Gly857Alafs*27) mutation will enhance our knowledge of IGHMBP2 gene defects role in neuropathy. This study aims to highlight this severe recessive disease caused by pathogenic IGHMBP2 gene mutations and to examine the mutation spectrum and phenotype differences.

The mutational spectrum of NRAS gene discovers a novel frameshift mutation (E49R) in Saudi colorectal cancer patients

Colorectal cancer (CRC) is a major health problem the world face currently and one of the leading causes of death worldwide. CRC is genetically heterogeneous and multiple genetic aberrations may appear on course of the disease throughout patient's lifetime. Genetic biomarkers such as BRAF, KRAS, and NRAS may provide early precision treatment options that are crucial for patient survival and well-being. The aim of this study was to identify pathogenic mutations in the NRAS gene causing colorectal cancer in the Saudi population. We enrolled 80 CRC tumor tissue samples and performed molecular analyses to establish the mutation spectrum status in the western region of Saudi Arabia. We identified 5 different mutations in 10 patients, 4 of whom were reported previously (G10R, E37K, Q61K, and Q61*) in the literature while we discovered one novel lethal insertion mutation (E49R). A novel identified insertion mutation was present in the third codon of the NRAS gene [c.145 insA (p.Glu49ArgTer85)], causing a frameshift in the amino acid sequence of the protein, and leading to an aberrant and truncated protein of 85 amino acids. Subsequent bioinformatics analysis showed that the mutation was highly deleterious and affected protein function to a greater extent. This identification may further improve the prognosis of CRC and benefit subsequent treatment choices.

Fluopyram analogues containing an indole moiety: synthesis, biological activity and molecular docking study

Succinate dehydrogenase (SDH) has been identified as one of the ideal targets for the development of novel nematicides. However, the resistance of nematodes to fluopyram, one of the commercialized SDH inhibitors, is becoming a growing concern. Since expanding the structural diversity around an active scaffold is a useful strategy for drug development, herein a series of fluopyram analogues with a broad, biologically relevant indole moiety were synthesized and evaluated for nematicidal activity against C. elegans. Fifty-six novel target compounds were synthesized and characterized by 1H NMR, 13C NMR, and HRMS. The bioscreen results revealed that a few compounds such as C16 and D21 with LC50/72 h values of 8.65 mg/L and 6.83 mg/L, respectively, showed compatible activity to that of the commercial nematicide tioxazafen (LC50/72 h = 5.98 mg/L). Molecular docking indicated that these compounds could effectively bind to the active site of SDH by forming hydrogen bonds with Trp215 and Tyr96, and causing a cation-π interaction with Arg74. The work suggests that indole-containing derivatives may represent a promising template for the development of new nematicides.

Activity of an anaerobic Thermoanaerobacterales hydrolase on aliphatic and aromatic polyesters

This study focuses on the biochemical characterization of a new hydrolase (Thb) expressed from anaerobic Thermoanaerobacterales, which could be used to improve biogas plant efficiency for plastic waste treatment. The specificity of Thb for various polyesters, including polyethylene terephthalate (PET), polybutylene adipate terephthalate (PBAT), polybutylene succinate (PBS), and polylactic acid (PLA), was compared to the well-studied cutinase HiC from Humicola insolens. Based on gravimetric analysis and quantification (high-performance liquid chromatography (HPLC)) of monomers solubilized upon enzymatic hydrolysis, Thb was found to be more active on aromatic polyesters, while HiC led to a higher amount of hydrolysis products on aliphatic polyesters (PBS and PLA). Polyester hydrolysis was further investigated by scanning electron microscopy and infrared spectroscopy. A comparison of the two enzyme structures indicated the higher aromatic character of specific regions of the Thb surface as a possible reason for these differences in specificity.

In-silico screening and analysis of missense SNPs in human CYP3A4/5 affecting drug-enzyme interactions of FDA-approved COVID-19 antiviral drugs

Single nucleotide polymorphisms (SNPs) represent the prevailing form of genetic variations observed in the human population. Such variations could alter the encoded enzymes' activities. CYP3A4/5 enzymes are involved in metabolizing drugs, notably antivirals against SARS-CoV-2. In this work, we computationally investigated antiviral-enzyme interactions of CYP3A4/5 genetic variants. We also examined the deleterious impact of 751 missense single nucleotide polymorphisms (SNPs) within the CYP3A4/5 genes. An ensemble of bioinformatics tools, [SIFT, PolyPhen-2, cadd, revel, metaLr, mutation assessor, Panther, SNP&GO, PhD-SNP, SNAP, Meta-SNP, FATHMM, I-Mutant, MuPro, INPS, CONSURF, GPS 5.0, MusiteDeep and NetPhos], identified a total of 94 variants (47 SNPs in CYP3A4, 47 SNPs in CYP3A5) to potentially impact the structural integrity as well as the activity of the CYP3A4/5 enzymes. Molecular docking was done to recognize the structural stability and binding properties of the CYP3A4/5 protein isoforms with 3 FDA-approved antiviral drugs. Our findings indicated that the CYP3A4 gene variants; R418T, I335T and R130P and the CYP3A5 gene variants; I335T, L133P and R130Q are considered the most deleterious missense SNPs. These mutants potentially affect drug-enzyme binding and hence may alter therapeutic response. Cataloguing deleterious SNPs is essential for personalized gene-based pharmacotherapy.

Characterization of the oxygen-tolerant formate dehydrogenase from Clostridium carboxidivorans

Fixation of CO2 into the organic compound formate by formate dehydrogenases (FDHs) is regarded as the oldest autotrophic process on Earth. It has been proposed that an FDH-dependent CO2 fixation module could support CO2 assimilation even in photoautotrophic organisms. In the present study, we characterized FDH from Clostridium carboxidivorans (ccFDH) due to its ability to reduce CO2 under aerobic conditions. During the production of recombinant ccFDH, in which the selenocysteine codon was replaced by Cys, we were able to replace the W with Mo as the transition metal in the ccFDH metal cofactor, resulting in a two-fold increase of 6 μmol formate min-1 in enzyme activity. Then, we generated ccFDH variants in which the strict NADH preference of the enzyme was changed to NADPH, as this reducing agent is produced in high amounts during the photosynthetic light process. Finally, we showed that the native ccFDH can also directly use ferredoxin as a reducing agent, which is produced by the photosynthetic light reactions at photosystem I. These data collectively suggest that ccFDH and, particularly, its optimized variants can be regarded as suitable enzymes to couple formate production to photosynthesis in photoautotroph organisms, which could potentially support CO2 assimilation via the Calvin-Benson-Bassham (CBB) cycle and minimize CO2 losses due to photorespiration.

Differential Inhibition by Cenobamate of Canonical Human Nav1.5 Ion Channels and Several Point Mutants

Cenobamate is a new and highly effective antiseizure compound used for the treatment of adults with focal onset seizures and particularly for epilepsy resistant to other antiepileptic drugs. It acts on multiple targets, as it is a positive allosteric activator of γ-aminobutyric acid type A (GABAA) receptors and an inhibitor of neuronal sodium channels, particularly of the late or persistent Na+ current. We recently evidenced the inhibitory effects of cenobamate on the peak and late current component of the human cardiac isoform hNav1.5. The determined apparent IC50 values of 87.6 µM (peak) and 46.5 µM (late current) are within a clinically relevant range of concentrations (the maximal plasma therapeutic effective concentration for a daily dose of 400 mg in humans is 170 µM). In this study, we built a 3D model of the canonical hNav1.5 channel (UniProt Q14524-1) in open conformation using AlphaFold2, embedded it in a DPPC lipid bilayer, corrected the residue protonation state (pH 7.2) with H++, and added 2 Na+ ions in the selectivity filter. By molecular docking, we found the cenobamate binding site in the central cavity. We identified 10-point mutant variants in the binding site region and explored them via docking and MD. Mutants N1462K/Y (rs1064795922, rs199473614) and M1765R (rs752476527) (by docking) and N932S (rs2061582195) (by MD) featured higher predicted affinity than wild-type.

The receptor binding mechanism of mouse sPLA2 group IIE

Secreted phospholipase A2s (sPLA2s) participate in physiological function by their enzyme and receptor binding activity. Muscle-type phospholipase A2 receptor (M-type PLA2R) is the sPLA2 binding protein with the highest affinity so far, and also inhibits the enzyme activity of sPLA2. There is species specificity and pH dependence for the binding of M-type PLA2R to sPLA2. Mouse sPLA2 Group IIE (mGIIE) has been verified to have a high affinity for mouse M-type PLA2R (M-type mPLA2R) at the nanomolar scale. For further exploration of the receptor binding mechanism of GIIE, in this study, we use Alphafold Multimer to generate complex models of mGIIE with the M-type mPLA2R ectodomain, wild-type CTLD5 domain of mPLA2R, and three CTLD5 mutants, respectively. mPLA2R-mGIIE models exhibit heterogeneous extended mPLA2R conformations with uncovered sPLA2-binding surface of CTLD5 domain. Complexed models of mGIIE with wild-type and mutated mCTLD5 further confirm that helix α1 of mCTLD5, especially essential residues F838 and W842, interact with the substrate pocket of mGIIE and thus inhibit its enzyme activity. Peptides from helix α1 of mCTLD5 are verified to inhibit the enzymatic activity of mGIIE. This AI-guided research would substantially accelerate our understanding of the functional study of GIIE, and provide the lead-peptide for the further inhibitor design of sPLA2.

Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module

The NAD+-reducing soluble [NiFe] hydrogenase (SH) is the key enzyme for production and consumption of molecular hydrogen (H2) in Synechocystis sp. PCC6803. In this study, we focused on the reductase module of the SynSH and investigated the structural and functional aspects of its subunits, particularly the so far elusive role of HoxE. We demonstrated the importance of HoxE for enzyme functionality, suggesting a regulatory role in maintaining enzyme activity and electron supply. Spectroscopic analysis confirmed that HoxE and HoxF each contain one [2Fe2S] cluster with an almost identical electronic structure. Structure predictions, alongside experimental evidence for ferredoxin interactions, revealed a remarkable similarity between SynSH and bifurcating hydrogenases, suggesting a related functional mechanism. Our study unveiled the subunit arrangement and cofactor composition essential for biological electron transfer. These findings enhance our understanding of NAD+-reducing [NiFe] hydrogenases in terms of their physiological function and structural requirements for biotechnologically relevant modifications.

Screening and Identification of Natural Compounds as Potential Inhibitors of Glutamate Racemase, an Emerging Drug Target of Food Pathogen E. coli O157:H7: An In-silico Approach to Combat Increasing Drug Resistance

BACKGROUND

Shiga Toxin-Producing Escherichia coli (E. coli) O157:H7, capable of causing serious food-borne illnesses, is extensively studied and is known to be transmitted through animal reservoirs or person-to-person contact, leading to severe disease outbreaks. The emergence of antibiotic resistance in these strains, coupled with increased adverse effects of existing therapeutics, underscores the urgent need for alternative therapeutic strategies.

OBJECTIVE

This study aims to evaluate Glutamate Racemase (MurI protein) of the food-pathogenic E. coli O157:H7 (EC MurI) as a novel drug target. Furthermore, the study seeks to identify new compounds with potential inhibitory effects against this protein.

METHODS

Using computational tools, the study identified inhibitor binding sites on EC MurI and identified relevant inhibitors capable of binding to these sites. Molecular docking techniques were employed to assess potential hits, and selected compounds were further analyzed for their structural activity and binding affinity to the protein.

RESULTS

The results of the study revealed that Frigocyclinone and Deslanoside, exhibited the best binding affinity with EC-MurI. Subsequent molecular dynamic (MD) simulations of the selected complexes indicated that both compounds were stable. This suggests that Frigocyclinone and Deslanoside have the potential to serve as potent inhibitors of EC-MurI.

CONCLUSION

In summary, this study highlights the urgent need for alternative therapies against food-pathogenic E. coli, focusing on E. coli O157:H7. Evaluation of Glutamate Racemase as a drug target identified Frigocyclinone and Deslanoside as promising inhibitors. MD simulations indicated their stability, suggesting their potential as lead molecules for further research and treatment development.

β-Triketones from Leptospermum scoparium (mānuka) oil show potential as scabicides

BACKGROUND

Scabies is a debilitating and neglected infectious disease with limited effective treatment options and affecting millions of people worldwide, mainly in poor and overcrowded settings. Essential oils from Australasian Myrtaceae are known to have parasiticidal properties, often attributed to the presence of β-triketones, which are known inhibitors of the tyrosine catabolism pathway through inhibition of hydroxyphenylpyruvate dioxygenase (HPPD).

PURPOSE

In this study, essential oils from mānuka (Leptospermum scoparium) were evaluated in vitro for miticidal and ovicidal activities and their active β-triketone constituents (flavesone, leptospermone, and isoleptospermone) were identified.

METHODS

Mite survival and egg hatching bioassays were performed to assess the scabicidal (miticidal and ovicidal) properties of Australasian Myrtaceae essential oils (mānuka, tea tree, and kunzea), mānuka oil fractions and three β-triketones (leptospermone, isoleptospermone, flavesone). Scabicidal constituents of mānuka oil were determined and quantified by 1H NMR spectroscopy and gas chromatography. To investigate HPPD as a potential target of β-triketones in scabies, tyrosine and fumarate levels were measured in mites following exposure to flavesone, and in silico docking of β-triketones in homology models of scabies HPPD structures was performed.

RESULTS

Mānuka oil had superior scabicidal activity compared to conventional treatments, ivermectin and permethrin, as well as kunzea and tea tree oils. The analysis of the chemical composition of mānuka oil revealed a high abundance of sesquiterpenes (42 %), and three β-triketones, flavesone (4.7 %), leptospermone (17.2 %), and isoleptospermone (5.1 %). Miticidal and ovicidal activity was strongly correlated with the presence of these β-triketones, but not the sesquiterpenes. The β-triketones had similar miticidal activity (LC50 58.6-61.7 mM at 4 h; LT50 1.3-1.4 h at 150 mM) to each other and to mānuka oil, and showed high ovicidal activity in young and mature eggs, with leptospermone being the most potent (LC50 33.6-75.9 mM). Significantly altered tyrosine and fumarate levels in mites after exposure to flavesone compared to untreated mites indicate a possible interference of flavesone with the tyrosine catabolism pathway. Molecular docking experiments indicate that this activity is likely underpinned by their inhibition of the Sarcoptes scabiei hydroxyphenylpyruvate dioxygenase (SsHPPD).

CONCLUSIONS

Our results demonstrated that mānuka oil and the β-triketones flavesone, leptospermone, and isoleptospermone can effectively kill scabies mites and eggs at early and late developmental stages, likely through their inhibition of tyrosine catabolism. This work has revealed SsHPPD as a potential new target for the development of novel topical scabies drugs that target all life-stages of the parasite.

A Computational Approach Using α-Carbonic Anhydrase to Find Anti-Trypanosoma cruzi Agents

BACKGROUND

Chagas disease has an ineffective drug treatment despite efforts made over the last four decades. The carbonic anhydrase of Trypanosoma cruzi (α-TcCA) has emerged as an interesting target for the design of new antiparasitic compounds due to its crucial role in parasite processes.

OBJECTIVE

The aim in this study was identify potential α-TcCA inhibitors with trypanocidal activity.

METHODS

A maximum common substructure (MCS) and molecular docking were used to carried out a ligand- and structure-based virtual screening of ZINC20 and MolPort databases. The compounds selected were evaluated in an in vitro model against the NINOA strain of Trypanosoma cruzi, and cytotoxicity was determined in a murine model of macrophage cells J774.2.

RESULTS

Five sulfonamide derivatives (C7, C9, C14, C19, and C21) had the highest docking scores (-6.94 to -8.31 kcal/mol). They showed key residue interactions on the active site of the α-TcCA and good biopharmaceutical and pharmacokinetic properties. C7, C9, and C21 had half-maximal inhibitory concentration (IC50) values of 26, 61.6, and 49 μM, respectively, against NINOA strain epimastigotes of Trypanosoma cruzi.

CONCLUSION

Compounds C7, C9, and C21 showed trypanocidal activity; therefore, these results encourage the development of new trypanocidal agents based in their scaffold.

Molecular mechanism of interactions of SPIN1 with novel inhibitors through molecular docking and molecular dynamics simulations

Methyllysine reading protein Spindlin 1 (SPIN1) plays a crucial role in histone post-translational modifications and serves as an effective target for the treatment of various malignant tumours. Although several inhibitors targeting SPIN1 expression have been identified, the atomic-level interactions between SPIN1 and inhibitors remain unclear. In this study, six potential SPIN1 inhibitors A366, EML631, MS31, MS8535, vinspinln, and XY49-92B were selected for molecular docking with SPIN1. Conformational changes in SPIN1 induced by these inhibitors, as well as their interactions, were investigated using molecular dynamics simulation (MD) and energy prediction methods including molecular mechanics generalized Born surface area (MM-GBSA) and solvation interaction energy (SIE). The findings indicate that the binding pockets within domain II, specifically Phe141, Trp151, Tyr170, and Tyr177, engage in cation-π interactions with these inhibitors, while also contributing to van der Waals hydrophobic interactions of varying strengths. These van der Waals hydrophobic interactions are critical for their binding affinity, while electrostatic interactions are significantly counterbalanced by polar solvation effects. In addition, through virtual screening and molecular docking, a new lead compound CXY49 was found presenting an effective binding to SPIN1. The structural and energetic changes identified in this study provide valuable insights for the development of new SPIN1 inhibitors.

Elucidating the potential of bioactive of Trichoderma sp.. in combating pathogenesis by Fusarium sp.. by targeting pectin lyases: a bioinformatics approach

Pectin lyase is an industrially important enzyme, predominately used in fruit juice clarification and retting of fibers. It also promotes pathogenesis via the degradation of the pectin. The phytopathogen, Fusarium infects various crops and causes several diseases. Trichoderma sp. is a promising biocontrol agent that is vital in maintaining plant health and disease prevention. In the current study, a computational approach utilizing structure prediction, molecular docking, molecular dynamics, and MM-PBSA analysis was used to analyze the potential role of bioactive compounds secreted by Trichoderma sp. in inhibiting the pectin lyase enzyme from Fusarium proliferatum, F. fujikuroi, F. graminearum, F. oxysporum and F. verticillioides. Molecular docking with secondary metabolites revealed that Viridiofungin A secreted by Trichoderma harzianum and Virone secreted by T. virens are bioactive compounds with immense potential to inhibit PNLs of Fusarium species. Further, the rigidity of the structure and stability of the docked complex were confirmed via Molecular dynamic simulations assessed through multiple parameters from the simulation trajectory data. Dual culture assay of T. harzianum and T. virens with F. proliferatum, F. fujikuroi, F. graminearum, F. oxysporum, and F. verticillioides showed variable mycelial inhibition. The research provides insight into the potential of the bioactive compounds secreted by Trichoderma species as an effective agent for the inhibition of pectin lyases produced by phytopathogens, especially Fusarium species. The proposed research can be used to develop bioformulations that function as biopesticides, offering a sustainable replacement for chemical products.

Exploring the Structure-Function Relationships in a 5-Aminolevulinic Acid Synthase and the Use of Protein Engineering to Expand its Substrate Range

5-Aminolevulinate synthase (ALAS) is a PLP-dependent enzyme that catalyzes the production of 5-aminolevulinate from succinyl-CoA and glycine. Its ability to catalyze the essentially irreversible C-C bond formation has significant potential in chemoenzymatic synthesis of α-amino ketones. Native ALAS, unfortunately, is extremely substrate-selective, and this seriously limits its synthetic utility. Here, we have used three different protein engineering strategies to overcome this problem for the acyl-CoA substrate. By combining previously reported mutation results and structural analysis, a series of site-saturation mutagenesis/screening efforts were focused on R21, T82, N84, and T362 of Rhodopseudomonas palustris ALAS. These yielded single, double, and triple mutants with significantly improved substrate ranges. The steady-state kinetic parameters of several key variants were determined. These data were analyzed in the framework of the ALAS catalytic mechanism to identify the steps that may have been impacted. The most active variant was used in a larger-scale reaction to demonstrate its synthetic potential. Taken together, our results show how ALAS might become a useful biocatalyst for α-amino ketone synthesis and have also allowed us to comment on the relative merits of each the three protein engineering strategies utilized.

In silico design of a novel hybrid epitope-based antigen harboring highly exposed immunogenic peptides of BamA, OmpA, and Omp34 against Acinetobacter baumannii

Acinetobacter baumannii, is among the highest priority bacteria according to the WHO categorization which necessitate the exploration of alternative strategies such as vaccination. OmpA, BamA, and Omp34 are assigned as appropriate antigens to serve in vaccine development against this pathogen. Experimentally validated exposed epitopes of OmpA and Omp34 along with selected exposed epitopes predicted by an integrative in silico approach were represented by the barrel domain of BamA as a scaffold. Among the 8 external loops of BamA, 5 loops were replaced with selected loops of OmpA and Omp34. The designed antigen was analyzed regarding the physicochemical properties, antigenicity, epitope retrieval, topology, structure, and safety. BamA is a two-domain OMP with a 16-stranded barrel in which L4, L6, and L7 were the longest loops of BamA in order. The designed antigen consisted of 478 amino acids with antigen probability of 0.7793. The novel antigen was a 16-stranded barrel. No identical 8-meric peptides were found in the human proteome against the designed antigen sequence. The designed construct was safe regarding the allergenicity, toxicity, and human proteome reactivity. The designed antigen could develop higher protection against A. baumannii in comparison to either OmpA, BamA, or Omp34 alone.