ProMod3-A versatile homology modelling toolbox

The PA-X host shutoff site 100 V exerts a contrary effect on viral fitness of the highly pathogenic H7N9 influenza A virus in mice and chickens

Several viruses, including influenza A virus (IAV), encode viral factors to hijack cellular RNA biogenesis processes to direct the degradation of host mRNAs, termed "host shutoff." Host shutoff enables viruses to simultaneously reduce antiviral responses and provides preferential access for viral mRNAs to cellular translation machinery. IAV PA-X is one of these factors that selectively shuts off the global host genes. However, the specific role of PA-X host shutoff activity in viral fitness of IAV remains poorly understood. Herein, we successfully mapped PA-X 100 V as a novel site important for host shutoff of the H7N9 and H5N1 viruses. By analysing the polymorphism of this residue in various subtype viruses, we found that PA-X 100 was highly variable in H7N9 viruses. Structural analysis revealed that 100 V was generally close to the PA-X endonuclease active site, which may account for its host shutoff activity. By generating the corresponding mutant viruses derived from the parental H7N9 virus and the PA-X-deficient H7N9 virus, we determined that PA-X 100 V significantly enhanced viral fitness in mice while diminishing viral virulence in chickens. Mechanistically, PA-X 100 V significantly increased viral polymerase activity and viral replication in mammalian cells. Furthermore, PA-X 100 V highly blunted the global host response in 293T cells, particularly restraining genes involved in energy metabolism and inflammatory response. Collectively, our data provided information about the intricate role of the PA-X host shutoff site in regulating the viral fitness of the H7N9 influenza virus, which furthers our understanding of the complicated pathogenesis of the influenza A virus.

Modification of carbonyl reductase based on substrate pocket loop regions alteration: an application for synthesis of duloxetine chiral intermediate in high efficiency

Duloxetine, a prominent 5-hydroxytryptamine norepinephrine reuptake inhibitor, is deployed mainly in the management of adult depression, showcasing minimal side effects, swift therapeutic onset, and a robust safety profile. Ethyl (S)-3-hydroxy-3-(2-thienyl)propionate ((S)-HEES) is the crucial chiral intermediate for duloxetine production. Asymmetric synthesis of (S)-HEES using carbonyl reductase as the biocatalyst has exhibited advantages including mild reaction conditions, high catalytic efficiency and environmental friendliness. In the present study, a loop region alteration strategy was developed to screen for a carbonyl reductase for (S)-HEES synthesis and EaSDR6 from Exiguobacterium sp. s126 was identified with considerable catalytic performance and broad substrate adaptability. Site-directed mutagenesis was subsequently performed, Mut-R142A/N204A was identified with a 3.6-fold enhancement in activity relative to the wild-type EaSDR6. The mutant kcat value was 52.5 s-1, 2.9-fold compared to the wild type, and the total catalytic efficiency (kcat/KM) was 24.9 mM-1 s-1, 1.9-fold higher than the wild type. The n-butyl acetate-aqueous biphasic bioreaction system was established for the asymmetric synthesis of (S)-HEES with the conversion of ethyl 3-oxo-3-(2-thienyl)propionate (KEES) of 90.2%, the product e.e. of > 99% after 8 h reaction at a substrate concentration of 200 g/L. The spatiotemporal yield reached 22.5 g/(L·h), which was higher than the ever reports about (S)-HEES biosynthesis. The present research provides new knowledge and technology for the construction of stereoselective carbonyl reductase and the green biosynthesis of chiral alcohol pharmaceutical intermediates.

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.

Predicting estrogen receptor agonists from plastic additives across various aquatic-related species using machine learning and AlphaFold2

The absence of effective public databases greatly limits high-throughput prediction of hormonal effects mediated by nuclear receptors in aquatic organisms. In this study, we developed novel strategies for multi-species screening of estrogen receptor (ER) agonists in plastic additives using AlphaFold2. Firstly, Deep Forest (DF), artificial neural network (ANN) and conventional machine learning (ML) models were utilized to screen ERα agonists. The DF models using RDKit.Chem.Descriptors and MorganFingerprint achieved a sensitivity = 0.96, specificity > 0.99, and an F1 score > 0.95, identifying 42 plastic additives as ERα agonists. Subsequently, ERα structures for Danio rerio (Dr), Oryzias melastigma (Om), Delphinus delphis (Dd), Physeter catodon (Pc), Mytilus edulis (Me), Xenopus tropicalis (Xt), Nipponia nippon (Nn), and Aptenodytes forsteri (Af) were constructed using AlphaFold2. Except for Me ERα, most species shared two common key amino acid residues responsible for ERα activity: arginine 85 and glutamic acid 44 (aligned serial numbers in the LBD). However, aquatic-related species exhibited other three additional key residues: glycine 212, leucine 216 and phenylalanine 95 (aligned serial numbers in the LBD). The number of compounds with docking energy < -9 kcal/mol for Dr, Om, Dd, Pc, Me, Xt, Nn, and Af were 4, 8, 4, 12, 10, 13, 7, and 9, respectively. The docking energy of estrone in all species was < -9 kcal/mol, while that of bisphenol P varied greatly among different species. The combined application of ML and AlphaFold enables high-throughput evaluation of the ecotoxicity posed by emerging pollutants across multiple aquatic-related species.

AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools

Allostery refers to the activity regulation of biological macromolecules originating from the binding of an effector molecule at the allosteric site that is distant from the active site. The few existing allosteric data sets have not been updated with recent discoveries of allosteric proteins and are challenging to use for data-intensive tasks. Instead of providing another data set bound to become outdated, we present the AlloBench pipeline to create high-quality data sets of biomolecules with allosteric and active site information suitable for computational and data-driven studies of protein allostery. The pipeline produces a data set of 2141 allosteric sites from 2034 protein structures with 418 unique protein chains by integrating information from AlloSteric Database, UniProt, Mechanism and Catalytic Site Atlas, and Protein Data Bank. Furthermore, we use a subset of 100 proteins from the AlloBench data set to quantitatively compare the performance of currently available allosteric site prediction tools: APOP, PASSer, Ohm, ALLO, Allosite, STRESS, and AlloPred. Such a large-scale benchmarking of these programs has not been undertaken on a common test set. The results show a significant need for improvement, as the accuracy for all programs is well below 60%, with PASSer (Ensemble) outperforming the rest. The AlloBench pipeline will not only promote the development of improved allosteric site prediction tools but also serve as a reference for studying allostery in general.

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.

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.

The physics-AI dialogue in drug design

A long path has led from the determination of the first protein structure in 1960 to the recent breakthroughs in protein science. Protein structure prediction and design methodologies based on machine learning (ML) have been recognized with the 2024 Nobel prize in Chemistry, but they would not have been possible without previous work and the input of many domain scientists. Challenges remain in the application of ML tools for the prediction of structural ensembles and their usage within the software pipelines for structure determination by crystallography or cryogenic electron microscopy. In the drug discovery workflow, ML techniques are being used in diverse areas such as scoring of docked poses, or the generation of molecular descriptors. As the ML techniques become more widespread, novel applications emerge which can profit from the large amounts of data available. Nevertheless, it is essential to balance the potential advantages against the environmental costs of ML deployment to decide if and when it is best to apply it. For hit to lead optimization ML tools can efficiently interpolate between compounds in large chemical series but free energy calculations by molecular dynamics simulations seem to be superior for designing novel derivatives. Importantly, the potential complementarity and/or synergism of physics-based methods (e.g., force field-based simulation models) and data-hungry ML techniques is growing strongly. Current ML methods have evolved from decades of research. It is now necessary for biologists, physicists, and computer scientists to fully understand advantages and limitations of ML techniques to ensure that the complementarity of physics-based methods and ML tools can be fully exploited for drug design.

Discovery and In Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach

This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BANΔIT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 °C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 °C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 °C, respectively. BANΔIT analysis revealed that three xylanases exhibited lower B'-factor values in the β3-α1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B'-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the β9-η5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the η3 short-helix and the η3-α3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the β3-α1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the β9-η5 loop, η3 short-helix, and η3-α3 loop will also be focused on development of the catalytic efficiency.

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.

Harnessing Jasmonate Pathways: PgJAR1's Impact on Ginsenoside Accumulation in Ginseng

Ginsenosides, the most active components in Panax ginseng, exhibit pharmacological and therapeutic properties but are limited by their low abundance. Jasmonates (JAs), a class of stress-induced phytohormones, are integral in modulating plant defense responses and the biosynthesis of secondary metabolites, including ginsenosides. Jasmonoyl-isoleucine (JA-Ile), the primary bioactive JA compound, is biosynthesized by JA-Ile synthase 1 (JAR1). In this study, we cloned the 1555 bp PgJAR1 gene from ginseng roots and analyzed its structure, enzyme activity, and expression pattern. The PgJAR1 protein encompasses all the hallmark elements characteristic of the GH3 family. It exhibits N/C-terminal domains analogous to ANL, three ATP/AMP-binding motifs, and distinct secondary structures: an N-terminal beta-barrel with beta-sheets and alpha-helices, and a C-terminal beta-sheet surrounded by alpha-helices, similarly to AtGH3.11/AtJAR1. The recombinant PgJAR1 enzyme expressed in Escherichia coli BL21 specifically catalyzed jasmonic acid (JA) to JA-Ile. PgJAR1 is predominantly expressed in leaves and is upregulated by MeJA treatment. Moderate transient overexpression of PgJAR1 promoted the biosynthesis of both JA-Ile and ginsenosides, highlighting the crucial role of PgJAR1 in JA-Ile biosynthesis and its positive impact on ginsenoside accumulation. Nevertheless, elevated JA-Ile levels can impede cellular growth, reducing ginsenoside production. Consequently, balancing JA-Ile biosynthesis through PgJAR1 expression is essential for optimizing ginseng cultivation and enhancing its medicinal properties. Modulating endogenous JA-Ile levels offers a strategy for increasing ginsenoside production in ginseng plants.

Computational screening of coumarin derivatives as inhibitors of the NACHT domain of NLRP3 inflammasome for the treatment of Alzheimer's disease

The nucleotide-binding oligomerization domain (NOD)-like receptor (NLR), leucine-rich-repeat (LRR), and pyrin domain containing 3 (NLRP3) is one of the key players in neuroinflammation, which is a major pathological hallmark of Alzheimer's Disease (AD). Activated NLRP3 causes release of pro-inflammatory molecules that aggravate neurodegeneration. Thus, pharmacologically inhibiting the NLRP3 inflammasome has the potential to alleviate the inflammatory injury to the neurons. Coumarin is a multifunctional nucleus with potent anti-inflammatory properties and can be utilized to develop novel drugs for the treatment and management of AD. In the present study, we have explored the NLRP3-inhibitory activities of a library of coumarin derivatives through a computational drug discovery approach. Drug-like, PAINS free, and potentially BBB permeable compounds were screened out and subjected to molecular docking and in silico ADMET studies, resulting in three virtual hits, i.e. MolPort-050-872-358, MolPort-050-884-068, and MolPort-051-135-630. The hits exhibited better NLRP3-binding affinity than MCC950, a selective inhibitor of NLRP3. Further, molecular dynamics (MD) simulations, post-MD simulation analyses, and binding free energy calculations of the hits established their potential as promising virtual leads with a common coumarin scaffold for the inhibition of NLRP3 inflammasome.

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.

In-silico evaluation of potential plant-based tyrosinase inhibitors for cosmetic and pharmaceutical applications

Tyrosinase is involved in a critical step of melanin synthesis; therefore, tyrosinase inhibitors are gaining more importance in the medicinal and cosmetic industry for the treatment of different pigmentary disorders. In the last decades, mushroom tyrosinase was used as a standard enzyme for the identification and advancement of most tyrosinase inhibitors. Due to differences in structure and substrate specificity between mushroom and human tyrosinase, there is a need for a more specific study with human tyrosinase. Additionally, the tyrosinase inhibitors which are currently in use have various side effects, therefore, safer inhibitors from natural sources are required. Different tyrosinase inhibitors from natural sources (aloesin, norartocarpetin, hesperetin, morin and taxifolin) were evaluated for an effective eco-friendly whitening agent using different bioinformatics tools. To check the efficacy and safety of the selected compounds ADME analysis was performed which showed that all the selected compounds fulfilled most of the parameters of general drug discovery. Docking of selected ligands was performed against the predicted structure of human tyrosinase; and the binding affinity (in kcal/mol) of kojic acid, aloesin, norartocarpetin, hesperetin, morin and taxifolin were obtained to be - 5.6, - 7.2, - 7.6, - 7.5, - 7.3 and - 7.2 respectively. Among all the selected ligands, norartocarpetin had the lowest binding affinity, i.e., - 7.6 kcal/mol, which showed that norartocarpetin could be used as a potent tyrosinase inhibitor. This bioactive compound is widely distributed in Moraceae plants and therefore, poses as a natural solution to various melanin-based dermatological issues and it can have a potential application in pharmaceuticals and cosmetic industries for the treatment of pigmentary disorders.

Identification and prioritization of novel therapeutic candidates against glutamate racemase from Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae, a gram-negative bacterium in the Enterobacteriaceae family, is non-motile, encapsulated, and a major cause of nosocomial infections, particularly in intensive care units. The bacterium possesses a thick polysaccharide capsule and fimbriae, which contribute to its virulence, resistance to phagocytosis, and attachment to host cells. The bacterium has developed serious resistance to most antibiotics currently in use.

OBJECTIVE

This study aims to investigate the structural properties of MurI (glutamate racemase) from Klebsiella pneumoniae and to identify potential candidate inhibitors against the protein, which will help in the development of new strategies to combat the infections related to MDR strains of Klebsiella pneumoniae.

METHODS

The 3D structure of the protein was modelled using SWISS-MODEL, which utilizes the homology modelling technique. After refinement, the structure was subjected to virtual high throughput screening on the TACC server using Enamine AC collection. The obtained molecules were then put through various screening parameters to obtain promising lead candidates, and the selected molecules were then subjected to MD simulations. The data obtained from MD simulations was then assessed with the help of different global dynamics analyses. The protein-ligand complexes were also subjected to MM/PBSA-based binding free energy calculation using the g_mmpbsa program.

RESULTS

The screening parameters employed on the molecules obtained via virtual screening from the TACC server revealed that Z1542321346 and Z2356864560 out of four molecules have better potential to act as potential inhibitors for MurI protein. The binding free energy values, which came out to be -27.26±3.06 kcal/mol and -29.53±4.29 kcal/mol for Z1542321346 and Z2356864560 molecules, respectively, favoured these molecules in terms of inhibition potential towards targeted protein.

CONCLUSION

The investigation of MurI via computational approach and the subsequent analysis of potential inhibitors can pave the way for developing new therapeutic strategies to combat the infections and antibiotic resistance of Klebsiella pneumoniae. This study could significantly help the medical fraternity in the treatment of infections caused by this multidrug-resistant pathogen.

Strategies to enhance the hydrolytic activity of Escherichia coli BL21 penicillin G acylase based on heterologous expression and targeted mutagenesis

Penicillin G acylase (PGA) serves as a critical biocatalyst for the hydrolysis of penicillin G, yielding 6-aminopenicillanic acid, a vital precursor for β-lactam semi-synthetic antibiotics. The catalytic efficiency of PGA, however, remains suboptimal in native Escherichia coli strains. To improve this, E. coli BL21 was engineered as a microbial cell factory via heterologous expression and site-directed mutagenesis to enhance PGA activity. The heterologous pga gene from Providencia rettgeri was integrated into E. coli BL21 (DE3) for the biosynthesis of PGA, achieving a PGA activity of 253 ± 2 U/mL after 16 hours of fermentation. The N167 site underwent mutation, producing the sites N167A and N167I. Plasmids carrying these mutations were introduced into E. coli BL21(DE3), and the enzymatic activities were recorded as 293 ± 3 U/mL for the N167A mutant and 238 ± 2 U/mL for the N167I mutant. This study not only introduces a novel approach to enhancing PGA activity but also illustrates the potential for catalytic optimization through targeted modifications of the enzyme's active site.

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.

A homo-FRET assay for patatin-specific proteolytic activity

The potato protein patatin embeds bioactive peptides that require targeted hydrolysis to be released as promising food additives. This study presents a patatin-specific protease assay for assessing a wide range of protease activities in high-throughput format. Conjugating patatin to the amine reactive fluorogenic BODIPY FL dye provided a stable protease substrate with efficient homo-FRET quenching at a low degree (7-8) of labeling. Compared to commercial BODIPY-casein, BODIPY-patatin provided higher fluorescence enhancement (by de-quenching) at high protease concentrations, while the sensitivity was generally comparable for both highly specific (e.g. Trypsin) and industrial relevant proteases (e.g. Alcalase and Neutrase) at low doses. For Chymotrypsin, BODIPY-patatin provided a 39 % response improvement at 5 ng dose. A peptide-centric analysis of mass spectrometry-based bottom-up proteomics data identified several BODIPY-labeling sites with varying occupancies in patatin, indicating heterogenous labeling under the applied conjugation conditions. BODIPY-labeled patatin complements commercial BODIPY-labeled casein as a globular, plant-based alternative for screening of proteolytic activity.

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.

Structural Basis for Antagonist Binding to Vasopressin V1b Receptor Revealed by the Molecular Dynamics Simulations

The human V1b receptor (V1bR) is primarily expressed in the corticotropic cells of the anterior pituitary where it is involved in the regulation of the hypothalamic-pituitary-adrenal (HPA) axis. The activation of V1bR induces the secretion of adrenocorticotropin hormone (ACTH) from the anterior pituitary cells which, in turn, stimulates the production of cortisol via the adrenal cortex. Clinical studies have demonstrated the chronic dysfunction of the HPA axis in patients with several psychiatric disorders. Thus, the inhibition of the V1b receptor and normalizing the HPA axis hyperactivity is a promising approach to the treatment of many stress-related disorders such as anxiety and depression. Nelivaptan is a selective V1bR antagonist that can be used for this purpose and an excellent molecule to study how antagonists interact with V1bR, especially since in recent years the experimental structures of vasopressin V2 and oxytocin receptors were solved, providing high-similarity templates for homology modeling of V1bR. Therefore, in this work, six independent molecular dynamics simulations of a V1bR-nelivaptan complex in a fully hydrated lipid bilayer, yielding a total simulation time of 6.0 μs, have been conducted. In the lowest-energy complexes obtained in this work and proposed to be the most probable structure of the V1bR-nelivaptan complex, the location of the ligand inside the receptor pocket is very similar to that of the other ligands observed in the experimental structures of the vasopressin/oxytocin receptor family. The receptor-ligand interaction has been analyzed and described, revealing the details of the molecular mechanism of this antagonist binding to V1bR and a probable contribution of L2005×40 and T2035×43 to binding selectivity.

Identification of the linear Fc-binding epitope on the bovine IgG1 Fc receptor of (boFcγRI) using synthetic peptides

BACKGROUND

Bovine IgG1 Fc receptor (boFcγRI) is a homologue to human FcγRI (CD64) that has three extracellular Ig-like domains and can bind bovine IgG1 with high affinity. Identification of the linear epitope for Fc-binding on boFcγRI provides new insights for the IgG-Fcγ interaction and FcγR-targeting drugs development.

METHODS

The boFcγRI molecules were expressed on cell surface of the boFcγRI -transfected COS-7 cells. The extracellular domain of boFcγRI was expressed in Escherichia coli (E. coli) BL21, and the soluble boFcγRI was purified by Ni-chelation chromatography followed by refolding. To identify the Fc-binding epitope on the boFcγRI, peptides derived from the membrane-distal extracellular domain (EC2) of boFcγRI were synthesized and conjugated to a carrier protein of IgG-free bovine serum albumin (BSA). Binding of bovine IgG1 to the different peptides was tested by Dot-blot assay, and the peptide showing maximal IgG-binding was further modified by truncation and mutation. The inhibition effect of the Fc-binding peptide was determined by competitive ELISA and Fc-rosetting inhibition assay, respectively.

RESULTS

The minimal effective peptide TNLSHNGI corresponding to the sequence 142-149 of boFcγRI was found to bind bovine IgG1 specifically in Dot-blot suggesting it represents a linear ligand-binding epitope located in the putative E-F loop of the EC2 domain on the receptor. Mutation analysis of the peptide showed that the residues of Thr142, Asn143, Leu144, Gly148 and Ile149 within the linear epitope are critical for IgG1-binding. The Fc-binding peptide inhibited bovine IgG1 binding to the soluble recombinant protein of boFcγRII with IC50 of 20.27 μmol/L, and inhibited the rosette formation of bovine IgG1-sensitized RBCs on the boFcγRI transfected cells with IC50 of 86.75 μmol/L.

CONCLUSIONS

The linear epitope for Fc-binding as well as its crucial residues of EC2 domain on boFcγRI was identified using synthetic peptides. The Fc-binding peptide showed well capability of regulating boFcγRI-IgG1 interaction on cell surface.

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.

Toxic Effects of Lead Exposure on Freshwater Climbing Perch, Anabas testudineus, and Bioremediation Using Ocimum sanctum Leaf Powder

The acute and chronic toxicity of lead to Anabas testudineus was determined in this study using static replacement bioassay testing. During the chronic toxicity studies, an experiment on the bioremediation of lead toxicity using Ocimum sanctum leaf powder was conducted. The 96 h LC50 values of lead for Anabas testudineus was 1.08 mg/L. Different biomarkers, such as the hepatosomatic index, gonadosomatic index, and fecundity, were significantly lower in fish subjected to 10% and 20% of the 96 h LC50 values of lead, compared to controls. The 45-day chronic exposure of fish to lead concentrations of 0.2 mg/L and above significantly lowered the number of total RBC, hemoglobin content, HCT (%), plasma protein, and cholesterol while decreasing the level of total WBC, plasma glucose, creatinine, serum AST and serum ALT. The leaf powder of Ocimum sanctum plays a significant role in ameliorating lead toxicity.

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.

Genomic signatures of sensory adaptation and evolution in pangolins

BACKGROUND

Pangolin is one of the most endangered mammals with many peculiar characteristics, yet the understanding of its sensory systems is still superficial. Studying the genomic basis of adaptation and evolution of pangolin's sensory system is expected to provide further potential assistance for their conservation in the future.

RESULTS

In this study, we performed a comprehensive comparative genomic analysis to explore the signature of sensory adaptation and evolution in pangolins. By comparing with the aardvark, Cape golden mole, and short-beaked echidna, 124 and 152 expanded gene families were detected in the genome of the Chinese and Malayan pangolins, respectively. The enrichment analyses showed olfactory-related genomic convergence among five concerned mammals. We found 769 and 733 intact OR genes, and 704 and 475 OR pseudogenes in the Chinese and Malayan pangolin species, respectively. Compared to other mammals, far more intact members of OR6 and OR14 were identified in pangolins, particularly for four genes with large copy numbers (OR6C2, OR14A2, OR14C36, and OR14L1). On the genome-wide scale, 1,523, 1,887, 1,110, and 2,732 genes were detected under positive selection (PSGs), intensified selection (ISGs), rapid evolution (REGs), and relaxed selection (RSGs) in pangolins. GO terms associated with visual perception were enriched in PSGs, ISGs, and REGs. Those related to rhythm and sound perception were enriched in both ISGs and REGs, ear development and morphogenesis were enriched in ISGs, and mechanical stimulus and temperature adaptation were enriched in RSGs. The convergence of two vision-related PSGs (OPN4 and ATXN7), with more than one parallel substituted site, was detected among five concerned mammals. Additionally, the absence of intact genes of PKD1L3, PKD2L1, and TAS1R2 and just six single-copy TAS2Rs (TAS2R1, TAS2R4, TAS2R7, TAS2R38, TAS2R40, and TAS2R46) were found in pangolins. Interestingly, we found two large insertions in TAS1R3, distributed in the N-terminal ectodomain, just in pangolins.

CONCLUSIONS

We found new features related to the adaptation and evolution of pangolin-specific sensory characteristics across the genome. These are expected to provide valuable and useful genome-wide genetic information for the future breeding and conservation of pangolins.

Implications of trinodal inhibitions and drug repurposing in MAPK pathway: A putative remedy for breast cancer

Breast cancer has been one of the supreme causes of cancer-related deaths among women worldwide. To make the case even more compounded, due to innate or acquired causes, cancer cells often develop resistance against the available chemotherapy or monotargeted treatments. This resistance is concomitant with increased activation of the MAPK (mitogen-activated protein kinase) signaling pathway. This study simultaneously targets three imperative intermediates in this pathway using molecular docking and real-time simulation. Docking was performed via the integrated AutoDock Vina 1.1.2 & 1.2.5 of the PyRx software, while the Discovery Studio (BIOVIA) v24.1.0.23298 was utilized to conduct the simulation. The aim is to investigate the therapeutic prospects of known potential inhibitors of the targeted intermediates and repurposable drugs to comprehend the effectiveness of targeting these trinodes simultaneously. The target points were deemed to be PDPK1 (3-phosphoinositide-dependent protein kinase 1), ERK1/2 (extracellular signal-related protein kinases 1/2), and mTOR (mammalian target of Rapamycin). Our study reveals that out of the candidate inhibitors chosen for each node, MP7 exhibited the most superior binding affinities for all three: -10.918 kcal/mol for PDPK1, -10.224 kcal/mol for ERK1, -10.134 kcal/mol for ERK2, and -9.2 kcal/mol for mTOR (via AutoDock Vina 1, .2.5). Some scores with MP7 were often higher than the available single-targeted drugs for different nodes in the MAPK pathway. Additionally, a total of 1867 repurposed analgesic, antibiotic, and antiparasitic drugs, including Zavegepant (-13.399 kcal/mol for PDPK1), Adozelesin (-11.74 kcal/mol for mTOR) and Modoflaner (-11.29 kcal/mol for PDPK1), showed promising binding energetics while targeting our triad points than other compounds used. This approach prompts for mitigating not only breast cancer but other elusive diseases as well, with state-of-the-art multitargeted therapies coupled with bioinformatic strategies.

Replacement of fish meal with full fat Hermetia illucens modulates hepatic FXR signaling in juvenile rainbow trout (Oncorhynchus mykiss): Exploring a potential role of ecdysteroids

The present study was conducted to investigate the effects of fish meal (FM) replacement with full fat Hermetia illucens (HI) on the molecular mechanisms regulating lipid and bile salt (BA) homeostasis in rainbow trout (Oncorhynchus mykiss) juveniles. We thus explore the presence of 20-hydroxyecdysone (20E) in an insect meal-based diet and evaluate its potential involvement in regulating the molecular mechanisms/basis of FXR:RXR axis signaling. Ecdysteroids are a category of steroid hormones which bind a nuclear-receptor complex composed of ecdysone receptor (EcR) and ultraspiracle protein (USP) and regulate insect molting and metamorphosis. In all vertebrates, including fish, EcR-USP homologs are the Farnesoid X receptors (FXR) and the Retinoid X receptors (RXR), which are known to regulate crucial physiological and metabolic aspects, including BA synthesis and cholesterol homeostasis. In silico prediction indicates that 20E binds the heterodimeric complex with a binding affinity constant Kd equals to 610 ± 60 nM and affects positively the dimerization process. Results also demonstrated the coordinated increased expression of FXR and RXR, as well as their downstream target genes (i.e. short heterodimer partner 1 and 2) in rainbow trout fed diets containing HI meal. This latter finding was paralleled by a significant down-regulation of CYP7a1 and CYP8b1 gene expression together with a decrease in hepatic total cholesterol, triglyceride, and BA levels. Overall, our study suggested that FXR is a potential target for 20E content in insect meal and provided preliminary data on the potential role of ecdysteroids in regulating the metabolic status of teleost fish through modulation of FXR signaling in the enterohepatic system.

Prostruc: an open-source tool for 3D structure prediction using homology modeling

Introduction

Homology modeling is a widely used computational technique for predicting the three-dimensional (3D) structures of proteins based on known templates,evolutionary relationships to provide structural insights critical for understanding protein function, interactions, and potential therapeutic targets. However, existing tools often require significant expertise and computational resources, presenting a barrier for many researchers.

Methods

Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. Integrating Biopython for sequence alignment, BLAST for template identification, and ProMod3 for structure generation, Prostruc streamlines complex workflows into a user-friendly interface. The tool enables researchers to input protein sequences, identify homologous templates from databases such as the Protein Data Bank (PDB), and generate high-quality 3D structures with minimal computational expertise. Prostruc implements a two-stage vSquarealidation process: first, it uses TM-align for structural comparison, assessing Root Mean Deviations (RMSD) and TM scores against reference models. Second, it evaluates model quality via QMEANDisCo to ensure high accuracy.

Results

The top five models are selected based on these metrics and provided to the user. Prostruc stands out by offering scalability, flexibility, and ease of use. It is accessible via a cloud-based web interface or as a Python package for local use, ensuring adaptability across research environments. Benchmarking against existing tools like SWISS-MODEL,I-TASSER and Phyre2 demonstrates Prostruc's competitive performance in terms of structural accuracy and job runtime, while its open-source nature encourages community-driven innovation.

Discussion

Prostruc is positioned as a significant advancement in homology modeling, making high-quality protein structure prediction more accessible to the scientific community.

Vaccination with OprB porin, and its epitopes offers protection against A. baumannii infections in mice

A. baumannii is a deadly antimicrobial resistance pathogen that acquires drug resistance through different mechanisms. Therefore, it is necessary to investigate all its virulence factors and design effective vaccines against it. For this purpose, OprB, an outer membrane porin, was investigated in this study, and its secondary and tertiary structures, physicochemical properties, and B-T epitopes were determined. The vaccine potential of this protein and its linear, non-continuous, and chimeric epitopes were also in-vivo analyzed. Based on the results, two surface epitopes and one non-continuous epitope were identified. Surface contiguous epitopes were produced recombinantly and non-continuous epitope sequences were synthesized and then produced. The chimeric epitope was also produced via the SOE-PCR technique. Active and passive immunization of mice with the whole OprB protein, non-continuous epitope, contiguous epitopes, two epitopes in chimeric form, as well as the mixture of two purified epitopes showed that the survival level and total IgG titer of the mice compared to non-vaccinated mice or mice that were vaccinated with an internal fragment increased significantly. The bacterial load in the immunized mice's lung, liver, kidney, and spleen was much lower than in the control groups, and the TNF-α, IFN-γ, and IL-6 cytokines levels were also lower in these groups and were similar to the naive mice. On the other hand, subunit vaccines showed acceptable safety and due to their minimal cross-activity, their use is much safer.

Drug Discovery in the Age of Artificial Intelligence: Transformative Target-Based Approaches

The complexities inherent in drug development are multi-faceted and often hamper accuracy, speed and efficiency, thereby limiting success. This review explores how recent developments in machine learning (ML) are significantly impacting target-based drug discovery, particularly in small-molecule approaches. The Simplified Molecular Input Line Entry System (SMILES), which translates a chemical compound's three-dimensional structure into a string of symbols, is now widely used in drug design, mining, and repurposing. Utilizing ML and natural language processing techniques, SMILES has revolutionized lead identification, high-throughput screening and virtual screening. ML models enhance the accuracy of predicting binding affinity and selectivity, reducing the need for extensive experimental screening. Additionally, deep learning, with its strengths in analyzing spatial and sequential data through convolutional neural networks (CNNs) and recurrent neural networks (RNNs), shows promise for virtual screening, target identification, and de novo drug design. Fragment-based approaches also benefit from ML algorithms and techniques like generative adversarial networks (GANs), which predict fragment properties and binding affinities, aiding in hit selection and design optimization. Structure-based drug design, which relies on high-resolution protein structures, leverages ML models for accurate predictions of binding interactions. While challenges such as interpretability and data quality remain, ML's transformative impact accelerates target-based drug discovery, increasing efficiency and innovation. Its potential to deliver new and improved treatments for various diseases is significant.

Detectability of cytokine and chemokine using ELISA, following sample-inactivation using Triton X-100 or heat

Clinical samples are routinely inactivated before molecular assays to prevent pathogen transmission. Antibody-based assays are sensitive to changes in analyte conformation, but the impact of inactivation on the analyte detectability has been overlooked. This study assessed the effects of commonly used inactivation-methods, Triton X-100 (0.5%) and heat (60 °C, 1 h), on cytokine/chemokine detection in plasma, lung aspirates, and nasopharyngeal samples. Heat significantly reduced analyte detectability in plasma (IL-12p40, IL-15, IL-16, VEGF, IL-7, TNF-β) by 33-99% (p ≤ 0.02), while Triton X-100 minimally affected analytes in plasma and nasopharyngeal samples (11-37%, p ≤ 0.04) and had no significant impact on lung aspirates. Structural analysis revealed that cytokines affected by heat had more hydrophobic residues and higher instability-indices. As the protein-detectability was affected differently in different sample types, the sample environment could also influence protein stability. This underscores the importance of selecting the most suitable inactivation methods for clinical samples to ensure accurate cytokine/chemokine analysis in both clinical and research settings.

Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an α/β folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity.

Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering

Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.

Dynamic formation of the protein-lipid prefusion complex

Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) to release neuronal transmitters. The SV protein synaptotagmin 1 (Syt1) serves as a Ca2+ sensor for evoked fusion. Syt1 is thought to trigger fusion by penetrating the PM upon Ca2+ binding; however, the mechanistic detail of this process is still debated. Syt1 interacts with the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) complex, a coiled-coil four-helical bundle that enables the SV-PM attachment. The SNARE-associated protein complexin (Cpx) promotes Ca2+-dependent fusion, possibly interacting with Syt1. We employed all-atom molecular dynamics to investigate the formation of the Syt1-SNARE-Cpx complex interacting with the lipid bilayers of the PM and SVs. Our simulations demonstrated that the PM-Syt1-SNARE-Cpx complex can transition to a "dead-end" state, wherein Syt1 attaches tightly to the PM but does not immerse into it, as opposed to a prefusion state, which has the tips of the Ca2+-bound C2 domains of Syt1 inserted into the PM. Our simulations unraveled the sequence of Syt1 conformational transitions, including the simultaneous docking of Syt1 to the SNARE-Cpx bundle and the PM, followed by Ca2+ chelation and the penetration of the tips of Syt1 domains into the PM, leading to the prefusion state of the protein-lipid complex. Importantly, we found that direct Syt1-Cpx interactions are required to promote these transitions. Thus, we developed the all-atom dynamic model of the conformational transitions that lead to the formation of the prefusion PM-Syt1-SNARE-Cpx complex. Our simulations also revealed an alternative dead-end state of the protein-lipid complex that can be formed if this pathway is disrupted.

Identifying Rab2 Protein as a Key Interactor of Centrin1 Essential for Leishmania donovani Growth

Previously, we have demonstrated that deletion of a growth-regulating gene (LdCen1) in the Leishmania donovani parasite (LdCen1-/-) attenuated the parasite's intracellular amastigote growth but not the growth of extracellular promastigotes. LdCen1-/- parasites were found to be safe and efficacious against homologous and heterologous Leishmania species as a vaccine candidate in animal models. The reason for the differential growth of LdCen1-/- between the two stages of the parasite needed investigation. Here, we report that LdCen1 interacts with a novel Ras-associated binding protein in L. donovani (LdRab2) to compensate for the growth of LdCen1-/- promastigotes. LdRab2 was isolated by protein pull-down from the parasite lysate, followed by nano-LC-MS/MS identification. The RAB domain sequence and the functional binding partners of the LdRab2 protein were predicted via Search Tool for the Retrieval of Interacting Proteins (STRING) analysis. The closeness of the LdRab2 protein to other reported centrin-binding proteins with different functions in other organisms was analyzed via phylogenetic analysis. Furthermore, in vitro and in silico analyses revealed that LdRab2 also interacts with other L. donovani centrins 3-5. Since centrin is a calcium-binding protein, we further investigated calcium-based interactions and found that the binding of LdRab2 to LdCen1 and LdCen4 is calcium-independent, whereas the interactions with LdCen3 and LdCen5 are calcium-dependent. The colocalization of LdCen1 and LdRab2 at the cellular basal-body region by immunofluorescence supports their possible functional association. The elevated expression of the LdRab2 protein in the mutant promastigotes suggested a probable role in compensating for the promastigote growth of this mutant strain, probably in association with other parasite centrins.

Molecular and biochemical characterization of a plant-like iota-class glutathione S-transferase from the halotolerant cyanobacterium Halothece sp. PCC7418

AIMS

This study identifies a unique glutathione S-transferase (GST) in extremophiles using genome, phylogeny, bioinformatics, functional characterization, and RNA sequencing analysis.

METHODS AND RESULTS

Five putative GSTs (H0647, H0729, H1478, H3557, and H3594) were identified in Halothece sp. PCC7418. Phylogenetic analysis suggested that H0647, H1478, H0729, H3557, and H3594 are distinct GST classes. Of these, H0729 was classified as an iota-class GST, encoding a high molecular mass GST protein with remarkable features. The protein secondary structure of H0729 revealed the presence of a glutaredoxin (Grx) Cys-Pro-Tyr-Cys (C-P-Y-C) motif that overlaps with the N-terminal domain and harbors a topology similar to the thioredoxin (Trx) fold. Interestingly, recombinant H0729 exhibited a high catalytic efficiency for both glutathione (GSH) and 1-chloro-2, 4-dinitrobenzene (CDNB), with catalytic efficiencies that were 155- and 32-fold higher, respectively, compared to recombinant H3557. Lastly, the Halothece gene expression profiles suggested that antioxidant and phase II detoxification encoding genes are crucial in response to salt stress.

CONCLUSION

Iota-class GST was identified in cyanobacteria. This GST exhibited a high catalytic efficiency toward xenobiotic substrates. Our findings shed light on a diversified evolution of GST in cyanobacteria and provide functional dynamics of the genes encoding the enzymatic antioxidant and detoxification systems under abiotic stresses.

Structure-based virtual screening approach reveals natural multi-target compounds for the development of antimalarial drugs to combat drug resistance

Compared to the previous year, there has been an increase of nearly 2 million malaria cases in 2021. The emergence of drug-resistant strains of Plasmodium falciparum, the most deadly malaria parasite, has led to a decline in the effectiveness of existing antimalarial drugs. To address this problem, the present study aimed to identify natural compounds with the potential to inhibit multiple validated antimalarial drug targets. The natural compounds from the Natural Product Activity and Species Source (NPASS) database were screened against ten validated drug targets of Plasmodium falciparum using a structure-based molecular docking method. Twenty compounds, with targets ranging from three to five, were determined as the top hits. The molecular dynamics simulations of the top six complexes (NPC246162 in complex with PfAdSS, PfGDH, and PfNMT; NPC271270 in complex with PfCK, PfGDH, and PfdUTPase) confirmed their stable binding affinity in the dynamic environment. The Tanimoto coefficient and distance matrix score analysis show the structural divergence of all the hit compounds from known antimalarials, indicating minimum chances of cross-resistance. Thus, we propose further investigating these compounds in biochemical and parasite inhibition studies to reveal the real therapeutic potential. If found successful, these compounds may be a new avenue for future drug discovery efforts to combat existing antimalarial drug resistance.Communicated by Ramaswamy H. Sarma.

Ion-combination specific effects driving the enzymatic activity of halophilic alcohol dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures

Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme alcohol dehydrogenase 2 from the halophilic archaeon Haloferax volcanii in thirteen different ion combinations for relative activity and analyse the results against molecular dynamics (MD) simulations of the same IL systems. We probe the ionic liquid property space based on ion polarizability and molecular electrostatic potential. Using the radial distribution functions, survival probabilities and spatial distribution functions of ions, we show that cooperative ion-ion interactions determine ion-protein interactions, and specifically, strong ion-ion interactions equate to higher enzymatic activity if neither of the ions interact strongly with the protein surface. We further demonstrate a tendency for cations interacting with the protein surface to be least detrimental to enzymatic activity if they show a low polarizability when combined with small hydrophilic anions. We also find that the IL ion influence is not mitigated by the surplus of negatively charged residues of the halophilic enzyme. This is shown by free energy landscape analysis in root mean square deviation and distance variation plots of active site gating residues (Trp43 and His273) demonstrating no protection of specific structural elements relevant to preserving enzymatic activity. On the other hand, we observe a general effect across all IL systems that a tight binding of water at acidic residues is preferentially interrupted at these residues through the increased presence of potassium ions. Overall, this study demonstrates a co-ion interaction dependent influence on allosteric surface residues controlling the active/inactive conformation of halophilic alcohol dehydrogenase 2 and the necessity to engineer ionic liquid systems for enzymes that rely on the integrity of functional surface residues regardless of their halophilicity or thermophilicity for use in bioprocessing.

Development of New Multi-Glycosylation Routes to Facilitate the Biosynthesis of Sweetener Mogrosides from Bitter Immature Siraitia Grosvenorii Using Engineered Escherichia coli

Mogrosides, which have various pharmacological activities, are mainly extracted from Siraitia grosvenorii (Luo Han Guo) and are widely used as natural zero-calorie sweeteners. Unfortunately, the difficult cultivation and long maturation time of Luo Han Guo have contributed to a shortage of mogrosides. To overcome this obstacle, we developed a highly efficient biosynthetic method using engineered Escherichia coli to synthesize sweet mogrosides from bitter mogrosides. Three UDP-glycosyltransferase (UGT) genes with primary/branched glycosylation catalytic activity at the C3/C24 sites of mogrosides were screened and tested. Mutant M3, which could catalyze the glycosylation of nine types of mogrosides, was obtained through enhanced catalytic activity. This improvement in β-(1,6)-glycosidic bond formation was achieved through single nucleotide polymorphisms and direct evolution, guided by 3D structural analysis. A new multienzyme system combining three UGTs and UDP-glucose (UDPG) regeneration was developed to avoid the use of expensive UDPG. Finally, the content of sweet mogrosides in the immature Luo Han Guo extract increased significantly from 57% to 95%. This study not only established a new multienzyme system for the highly efficient production of sweet mogrosides from immature Luo Han Guo but also provided a guideline for the high-value utilization of rich bitter mogrosides from agricultural waste and residues.

Elucidation of the CadA Protein 3D Structure and Affinity for Metals

The mitigation of cadmium (Cd) pollution, a significant ecological threat, is of paramount importance. Pseudomonas aeruginosa harbors 2 Cd resistance genes, namely, cadR and cadA. Presently, our focus is on the identification and characterization of the cation-transporting P-type ATPase (cadA) in Pseudomonas aeruginosa BC15 through in silico methods. The CadA protein and its binding capacities remain poorly understood, with no available structural elucidation. The presence of the cadA gene in P aeruginosa was confirmed, showing a striking 99% sequence similarity with both P aeruginosa and P putida. Phylogenetic analysis unveiled the evolutionary relationship between CadA protein sequences from various Pseudomonas species. Physicochemical analysis demonstrated the stability of CadA, revealing a composition of 690 amino acids, a molecular weight of 73 352.85, and a predicted isoelectric point (PI) of 5.39. Swiss-Model homology modelling unveiled a 33.73% sequence homology with CopA (3J09), and the projected structure indicated that 89.3% of amino acid residues were situated favourably within the Ramachandran plot, signifying energetic stability. Notably, the study identified metal-binding sites in CadA, namely, H3, C30, C32, C35, H48, C89, and C106. Docking studies revealed a higher efficiency of Cd binding with CadA compared to other heavy metals. This underscores the crucial role of N-terminal cysteine residues in Cd removal. It is evident that CadA of P aeruginosa BC15 plays a crucial role in Cd tolerance, rendering it a potential microorganism for Cd toxicity bioremediation. The structural and functional elucidation of CadA, facilitated by this study, holds promise for advancing cost-effective strategies in the remediation of cadmium-contaminated environments.

Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes

Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through -1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the -1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.

Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective

Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three-dimensional (3D) structures of fusion proteins remains a difficult task because the current AI-based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template-based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi-level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta and D-I-TASSER for modelling the 3D structures. HIGHLIGHTS: This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein. This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step. This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models. This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures.

The Dynamic Plasticity of P. aeruginosa CueR Copper Transcription Factor upon Cofactor and DNA Binding

Bacteria use specialized proteins, like transcription factors, to rapidly control metal ion balance. CueR is a Gram-negative bacterial copper regulator. The structure of E. coli CueR complexed with Cu(I) and DNA was published, since then many studies have shed light on its function. However, P. aeruginosa CueR, which shows high sequence similarity to E. coli CueR, has been less studied. Here, we applied room-temperature electron paramagnetic resonance (EPR) measurements to explore changes in dynamics of P. aeruginosa CueR in dependency of copper concentrations and interaction with two different DNA promoter regions. We showed that P. aeruginosa CueR is less dynamic than the E. coli CueR protein and exhibits much higher sensitivity to DNA binding as compared to its E. coli CueR homolog. Moreover, a difference in dynamical behavior was observed when P. aeruginosa CueR binds to the copZ2 DNA promoter sequence compared to the mexPQ-opmE promoter sequence. Such dynamical differences may affect the expression levels of CopZ2 and MexPQ-OpmE proteins in P. aeruginosa. Overall, such comparative measurements of protein-DNA complexes derived from different bacterial systems reveal insights about how structural and dynamical differences between two highly homologous proteins lead to quite different DNA sequence-recognition and mechanistic properties.

Exploring the Structural Insights of Thermostable Geobacillus esterases by Computational Characterization

This study conducted an in silico analysis of two biochemically characterized thermostable esterases, Est2 and Est3, from Geobacillus strains. To achieve this, the amino acid sequences of Est2 and Est3 were examined to assess their biophysicochemical properties, evolutionary connections, and sequence similarities. Three-dimensional models were constructed and validated through diverse bioinformatics tools. Molecular dynamics (MD) simulation was employed on a pNP-C2 ligand to explore interactions between enzymes and ligand. Biophysicochemical property analysis indicated that aliphatic indices and theoretical T m values of enzymes were between 82-83 and 55-65 °C, respectively. Molecular phylogeny placed Est2 and Est3 within Family XIII, alongside other Geobacillus esterases. DeepMSA2 revealed that Est2, Est3, and homologous sequences shared 12 conserved residues in their core domain (L39, D50, G53, G55, S57, G92, S94, G96, P108, P184, D193, and H223). BANΔIT analysis indicated that Est2 and Est3 had a significantly more rigid cap domain compared to Est30. Salt bridge analysis revealed that E150-R136, E124-K165, E137-R141, and E154-K157 salt bridges made Est2 and Est3 more stable compared to Est30. MD simulation indicated that Est3 exhibited greater fluctuations in the N-terminal region including conserved F25, cap domain, and C-terminal region, notably including H223, suggesting that these regions might influence esterase catalysis. The common residues in the ligand-binding sites of Est2-Est3 were determined as F25 and L167. The analysis of root mean square fluctuation (RMSF) revealed that region 1, encompassing F25 within the β2-α1 loop of Est3, exhibited higher fluctuations compared to those of Est2. Overall, this study might provide valuable insights for future investigations aimed at improving esterase thermostability and catalytic efficiency, critical industrial traits, through targeted amino acid modifications within the N-terminal region, cap domain, and C-terminal region using rational protein engineering techniques.

Mushroom Tyrosinase: Six Isoenzymes Catalyzing Distinct Reactions

"Mushroom tyrosinase" from the common button mushroom is the most frequently used source of tyrosinase activity, both for basic and applied research. Here, the complete tyrosinase family from Agaricus bisporus var. bisporus (abPPO1-6) was cloned from mRNA and expressed heterologously using a single protocol. All six isoenzymes accept a wide range of phenolic and catecholic substrates, but display pronounced differences in their specificity and enzymatic reaction rate. AbPPO3 ignores γ-l-glutaminyl-4-hydroxybenzene (GHB), a natural phenol present in mM concentrations in A. bisporus, while AbPPO4 processes 100 μM GHB at 4-times the rate of the catechol l-DOPA. All six AbPPOs are biochemically distinct enzymes fit for different roles in the fungal life cycle, which challenges the traditional concept of isoenzymes as catalyzing the same physiological reaction and varying only in secondary properties. Transferring this approach to other enzymes and organisms will greatly stimulate both the study of the in vivo function(s) of enzymes and the application of these highly efficient catalysts.

Unraveling the potential of uninvestigated thermoalkaliphilic lipases by molecular docking and molecular dynamic simulation: an in silico characterization study

Thermoalkaliphilic lipase enzymes are mostly favored for use in the detergent industry. While there has been considerable research on Geobacillus lipases, a significant portion of these enzymes remains unexplored or undocumented in the scientific literature. This work performed in silico phylogeny, sequence alignment, structural and enzyme-substrate interaction analyses of the five thermoalkaliphilic lipases belonging to different Geobacillus species (Geobacillus stearothermophilus lipase = GsLip, Geobacillus sp. B4113_201601 lipase = Gb4Lip, Geobacillus kaustophilus HTA426 lipase = GkLip, Geobacillus sp. SP22 lipase = GspLip, Geobacillus sp. NTU 03 lipase = GntLip). For this purpose, unreviewed enzyme sequences of five Geobacillus thermoalkaliphilic lipases were analyzed at sequence and phylogeny levels. 3D homology enzyme models were built, validated, and investigated by different bioinformatics tools. The ligand interactions screening using seven para-nitrophenyl (pNP) esters and enzyme-ligand interactions were analyzed on Gb4Lip:pNP-C12 and BTL2:pNP-C12 by MD simulation. Biophysicochemical characteristic analysis showed that Gb4Lip had a theoretical T m value of above 65 ºC, and a higher aliphatic index indicating greater thermal stability. Sequence alignment showed a hydrophilic threonine in the α6 helix of Gb4Lip, indicating high enzymatic activity. A normalized temperature factor B (B'-factor) analysis showed that the lid domains of five lipases significantly possessed lower B'-factor values, compared to G. thermocatenulatus lipase 2 (BTL2), indicating that they had higher rigidity. Molecular docking results indicated that the five lipases had the highest binding affinity toward pNP-C12. The RMSF investigation revealed that the thermostability of Gb4Lip is influenced by specific molecular elements: D202-S203 within the αB region of the lid domain, and E274-Q275 within the b3 strand, as well as W278 in the b3-b4 loop, and H282 in the b4 strand of the Ca2+-binding region. MD simulation analysis showed that catalytic residue S114 and at least one oxyanion hole residue (F17 and/or Q114) in Gb4Lip frequently formed hydrogen bonds with the pNP-C12 ligand at 343 K and 348 K throughout the simulation process, indicating that Gb4Lip might catalyze relatively long-chain ligand pNP-C12 with high performance. In conclusion, Gb4Lip might be a more suitable candidate as the detergent additive. In addition, this investigation can offer valuable perspectives on Family I.5 lipases such as Gb4Lip for future exploration in the field of protein engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04023-5.

The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate

During infection viruses hijack host cell metabolism to promote their replication. Here, analysis of metabolite alterations in macrophages exposed to poly I:C recognises that the antiviral effector Protein Kinase RNA-activated (PKR) suppresses glucose breakdown within the pentose phosphate pathway (PPP). This pathway runs parallel to central glycolysis and is critical to producing NADPH and pentose precursors for nucleotides. Changes in metabolite levels between wild-type and PKR-ablated macrophages show that PKR controls the generation of ribose 5-phosphate, in a manner distinct from its established function in gene expression but dependent on its kinase activity. PKR phosphorylates and inhibits the Ribose 5-Phosphate Isomerase A (RPIA), thereby preventing interconversion of ribulose- to ribose 5-phosphate. This activity preserves redox control but decreases production of ribose 5-phosphate for nucleotide biosynthesis. Accordingly, the PKR-mediated immune response to RNA suppresses nucleic acid production. In line, pharmacological targeting of the PPP during infection decreases the replication of the Herpes simplex virus. These results identify an immune response-mediated control of host cell metabolism and suggest targeting the RPIA as a potential innovative antiviral treatment.

Temperature effect in the inhibition of PLA2 activity of Bothrops brazili venom by Rosmarinic and Chlorogenic acids, experimental and computational approaches

Myotoxicity caused by snakebite envenoming emerges as one of the main problems of ophidic accidents as it is not well neutralized by the current serum therapy. A promising alternative is to search for efficient small molecule inhibitors that can act against multiple venom components. Phospholipase A2 (PLA2) is frequently found in snake venom and is usually associated with myotoxicity. Thus it represents an excellent target for the search of new treatments. This work reports the effect of temperature in the inhibition of catalytic properties of PLA2 from Bothrops brazili venom by Rosmarinic (RSM) and Chlorogenic (CHL) acids through experimental and computational approaches. Three temperatures were evaluated (25, 37 and 50 °C). In the experimental section, enzymatic assays showed that RSM is a better inhibitor in all three temperatures. At 50 °C, the inhibition efficiency decayed significantly for both acids. Docking studies revealed that both ligands bind to the hydrophobic channel of the protein dimer where the phospholipid binds in the catalytic process, interacting with several functional residues. In this context, RSM presents better interaction energies due to stronger interactions with chain B of the dimer. Molecular dynamics simulations showed that RSM can establish selective interactions with ARG112B of PLA2, which is located next to residues of the putative Membrane Disruption Site in PLA2-like structures. The affinity of RSM and CHL acids towards PLA2 is mainly driven by electrostatic interactions, especially salt bridge interactions established with residues ARG33B (for CHL) and ARG112B (RSM) and hydrogen bonds with residue ASP89A. The inability of CHL to establish a stable interaction with ARG112B was identified as the reason for its lower inhibition efficiency compared to RSM at the three temperatures. Furthermore, extensive structural analysis was performed to explain the lower inhibition efficiency at 50 °C for both ligands. The analysis performed in this work provides important information for the future design of new inhibitors.Communicated by Ramaswamy H. Sarma.

Molecular characterization and phylogenetic analyses of MetAP2 gene and protein of Nosema bombycis isolated from Guangdong, China

Background

Pebrine, caused by microsporidium Nosema bombycis, is a devastating disease that causes serious economic damages to the sericulture industry. Studies on development of therapeutic and diagnostic options for managing pebrine in silkworms are very limited. Methionine aminopeptidase type 2 (MetAP2) of microsporidia is an essential gene for their survival and has been exploited as the cellular target of drugs such as fumagillin and its analogues in several microsporidia spp., including Nosema of honeybees.

Methods

In the present study, using molecular and bioinformatics tools, we performed in-depth characterization and phylogenetic analyses of MetAP2 of Nosema bombycis isolated from Guangdong province of China.

Results

The full length of MetAP2 gene sequence of Nosema bombycis (Guangdong isolate) was found to be 1278 base pairs (bp), including an open reading frame of 1,077 bp, encoding a total of 358 amino acids. The bioinformatics analyses predicted the presence of typical alpha-helix structural elements, and absence of transmembrane domains and signal peptides. Additionally, other characteristics of a stable protein were also predicted. The homology-based 3D models of MetAP2 of Nosema bombycis (Guangdong isolate) with high accuracy and reliability were developed. The MetAP2 protein was expressed and purified. The observed molecular weight of MetAP2 protein was found to be ~43-45 kDa. The phylogenetic analyses showed that MetAP2 gene and amino acids sequences of Nosema bombycis (Guangdong isolate) shared a close evolutionary relationship with Nosema spp. of wild silkworms, but it was divergent from microsporidian spp. of other insects, Aspergillus spp., Saccharomyces cerevisiae, and higher animals including humans. These analyses indicated that the conservation and evolutionary relationships of MetAP2 are closely linked to the species relationships.

Conclusion

This study provides solid foundational information that could be helpful in optimization and development of diagnostic and treatment options for managing the threat of Nosema bombycis infection in sericulture industry of China.

Two novel TMEM67 variations in a Chinese family with recurrent pregnancy loss: a case report

BACKGROUND

Recurrent pregnancy loss (RPL) is a common pregnancy complication that brings great pain to pregnant women and their families. Genetic factors are an important cause reason of RPL. However, clinical research on monogenic diseases with recurrent miscarriage is insufficient.

CASE PRESENTATION

Here we reported a Chinese family with RPL and genetic analysis of the abortion and parents. A paternally inherited heterozygous missense variant c.1415T > G (p.V472G) and a maternally inherited heterozygous nonsense variant c.2314del (p.M772*) in TMEM67 gene were identified by trio-exome sequencing. c.2314del (p.M772*) generated a premature stop codon and truncated protein, was classified as "pathogenic". c.1415T > G (p.V472G) located in extra-cellular region, was classified as "likely pathogenic". Biallelic variants in TMEM67 gene cause lethal Meckel syndrome 3, consistent with the proband's prenatal phenotype.

CONCLUSION

The current study of the Chinese family expands the pathogenic variant spectrum of TMEM67 and emphasizes the necessity of exome sequencing in RPL condition.