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Copyright of Journal of Taibah University Medical Sciences is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Polyphenol oxidase (PPO) enzymes induce undesirable browning in fruits, vegetables, and juices like sugarcane and apple. Inactivation of PPO is crucial to mitigate this issue, achieved through methods like heat, radiation, ultrasound, p H adjustment, adsorbent addition, and inhibitors. Inhibitor selection is traditionally a time-consuming trial-and-error process. This study aimed to develop a homology model of sugarcane PPO and to streamline inhibitor selection using a rational approach, relying on knowledge of PPO's structure and active site. The research utilized homology modeling through SWISS-MODELER to predict the 3D structures of two types of sugarcane copper-based PPOs: met-PPO (Cu-Cu active site) and oxy-PPO (Cu-O-Cu active site), both composed of 235 amino acids. Model quality was assessed using Global Model Quality Estimation (GMQE) and Qualitative Model Energy Analysis (QMEAN), yielding favorable scores of 0.17 (GMQE), 0.44 ± 0.05 (QMEAN Co-Global) and z-score of –4.03. Ramachandran analysis indicated 78.8 % and 17.5 % of amino acid residues fell within the most favored and additional allowed regions, respectively. Docking analysis revealed strong affinities between m-hydroxybenzoic acid and p-hydroxybenzoic acid with binding energies of –4.40 Kcal/mol and –4.38 Kcal/mol, respectively, for met-PPO and oxy-PPO. Identified active site residues are ARG369, HIS325, GLU321, ALA361, and TRP313. This study enhances comprehension of sugarcane PPO and its active site, aiding rational inhibitor design to counteract undesired browning reactions. [Display omitted] • Sugarcane PPO homology model as developed using computational methods. • During MD analysis, m -hydroxybenzoic acid and p -hydroxybenzoic acid exhibited high binding energy. • Active site residues responsible for binding interactions are ARG369, HIS325, GLU321 and ALA361. • Comprehending the structure & function of Sugarcane PPO leads to ground breaking solutions to increase sugarcane's shelf life. [ABSTRACT FROM AUTHOR]

• Growth of cotton (Gossypium arboreum) plant and application of salt-stress. • Identification of salt stress responsive proteinase inhibitor (PI) gene at transcript level using differential display technique. • Characterizations and expression profiling under various abiotic stresses of PI gene. Cotton production in the world is constrained due to various abiotic stresses. Among these, salt-stress plays a key role in declining the cotton yield. The study of genetic makeup in cotton plants for salt-stress responsive factors may open a way to understand the molecular mechanism of the plant against salt-stress. The differentially expressed gene, proteinase inhibitor (gpi) was isolated at the transcript level from salt-tolerant Gossypium arboreum (local cultivar FDH-171) by differential display technique, which was made full-length using gene RACER kit and was characterized through expression profiling under salt, cold and drought stresses, and predicted 3-D structure of gpi protein. The size of full-length gpi was found 496 bps with one intronic region from 74 to 156 bases in sequence. The gpi showed maximum homology with pi of Macleaya cordata 73%, Lactuca sativa 72%, Daucus carota 71%, Corchorus olitorius 70%, Corchorus capsularis 70%, Artemisia annua 70%, Trema orientale 67%, and Ricinus communis 65%. The protein homology search in protein database revealed that gpi has 63% homology with Linum usitatissimum trypsin inhibitor (LUTI). When gpi was subjected to predictive secondary structure, sheets, beta turns, coils and helixes were evident but with the most solvent buried area rather than exposed area according to solvent accessibility standards. The expression analysis of gpi in different tissues of salt-stressed G. arboreum plant indicated that gpi has 31-fold higher expression in salt-stressed root tissue, 13-fold in leaf tissue and no expression in stem tissue compared to control; while gpi indicated 13-fold expression under salt, 7-fold in cold and 4-fold in drought stress compared to control. Subsequent analysis showed that gpi gene expression was up-regulated and its transcription might enhance salt tolerance in plants. Therefore, gpi gene would be helpful to develop salt-stress tolerant cotton plants. [ABSTRACT FROM AUTHOR]

• Full-length coding regions of the seven GA biosynthetic pathway genes (CPS, KS, KO, KAO, GA20ox, GA3ox and GA2ox)were cloned from coconut using a comparative genomics approach. • Expression profiling of theseven genes during germination of mature zygotic embryos under in vitro conditions in two phenotypically contrasting coconut accessions (West coast tall and chowghat green Dwarf) was carried out and in response to exogenously supplemented GA 3 and paclobutrazol (PBZ). • PBZ had an antagonistic effect on the GA biosynthesis pathway, GA 3 enhanced the overall GA production. • The results provide insights into GA biosynthesis in coconut, laying the foundation for future studies to decipher the genetics of dwarfism in coconut. Gibberellic acid (GA) is intricately associated with plant growth and developmental pathways. To elucidate GA metabolism in coconut, we cloned full-length coding regions of the seven GA biosynthetic pathway genes (CPS, KS, KO, KAO, GA20ox, GA3ox and GA2ox) using a comparative genomics approach, using sequences from oil palm and date palm. The predicted amino acid sequences of the seven coconut GA biosynthetic genes shared high identities with oil palm and date palm GA biosynthetic genes. In silico structural and functional analyses were performed, and secondary and tertiary structures were predicted. Compared to the other two palms, the evolutionary analysis of the seven genes in coconut revealed that these genes may not be evolving rapidly enough to keep pace with occurring mutations. Additionally, we performed expression profiling of these seven genes during germination of mature zygotic embryos under in vitro conditions in two phenotypically contrasting coconut accessions (West Coast Tall and Chowghat Green Dwarf) and in response to exogenously supplemented GA 3 and paclobutrazol (PBZ) in the embryo culture medium. While PBZ had an antagonistic effect on the GA biosynthesis pathway, GA 3 enhanced the overall GA production. These results provide the first insights into GA biosynthesis in coconut, laying the foundation for future studies to decipher the genetics of dwarfism in coconut. [ABSTRACT FROM AUTHOR]

Although plants don't have chitins, they produce chitinases to protect themselves from biotic and abiotic stressors. There are two forms of chitinases found in organisms: glycosyl hydrolase 18 (GH18) and 19 (GH19) families. Plant GH19 chitinases are well known for their role in protecting against pathogens, but the roles of GH18 chitinases have not been fully elucidated. This study aimed to produce and characterise two recombinant GH18 chitinases from Metroxylon sagu. Two GH18 chitinase genes, MsChi1 and MsChi2, were identified, with nucleotide sequences of 1009 and 1308 bp, respectively. The proteins encoded by MsChi1 and MsChi2 genes were single polypeptide chains of 310 and 300 amino acids with predicted molecular masses of 31.21 and 30.15 kDa, respectively. Both cDNAs were cloned and expressed in the GS115 strain of Pichia pastoris. Recombinant MsChi1 and MsChi2 exhibited optimal activity at 60 °C with acidic pH 4.0 and 5.0, respectively. Both recombinant enzymes could hydrolyze synthetic and natural substrates (colloidal chitin). rMsChi1 preferred 4-nitrophenol N , N′ -diacetyl-β-D chitobioside, while rMsChi2 preferred 4-nitrophenol N , N′ , N″ -triacetyl-β-D chitotriose, suggesting they might function as exochitinase and endochitinase, respectively. They also demonstrated antifungal activities against tested fungi. Homology modeling indicated ASP and GLU as essential residues for proton donation and acceptance. [ABSTRACT FROM AUTHOR]

• For the first time, we developed a novel prediction model to pre-assess the efficacy of IFX in patients with ulcerative colitis as the first step towards personalized treatment. • Next-step therapeutic targets, including drugs and non-coding RNAs, were provided for those predicted non-responders to IFX by the novel prediction model. • Deferasirox, an iron chelator targeting the key model-gene CYP24A1, was identified as the most promising adjuvant or alternative for IFX through Homology Modeling, Molecular Docking and cellular validation. Ulcerative colitis (UC) is a chronic immune-mediated inflammation of the colorectum, for which infliximab (IFX) is currently the mainstay of treatment. However, one-third of patients with UC still fail to benefit from the IFX therapy, and early exposure to IFX impairs the efficacy of other subsequent biologics. Therefore, personalized therapeutic system is urgently needed to assist in clinical decision-making and precision treatment. Four microarray datasets of colonic biopsies from UC patients treated with IFX were obtained from the GEO database to form the Training Cohort and Validation Cohort. Differentially expressed genes (DEGs) in Training Cohort were identified and enriched for GO, KEGG and immune cell infiltration analysis. A prediction model for IFX efficacy was developed based on the LASSO and Logistic regression. The predictive accuracy of the model was verified by the Validation Cohort, and the model-genes/proteins were validated by immunohistochemistry. Gene-drug, gene-ncRNA interaction analysis were performed to identify drugs or non-coding RNAs (ncRNAs) that potentially interacted with the model-genes. Homology Modeling and Molecular Docking were conducted to filter the optimal candidate as the subsequent adjuvant or alternative for IFX in predicted non-responders. At last, the down-regulation of the key model-gene/protein CYP24A1 by the drug candidate Deferasirox was verified by Western Blot and qRT-PCR Assay based on cellular experiments. A total of 113 DEGs were identified in the Training Cohort, mainly enriched in inflammatory cell chemotaxis, migration, and response to molecules derived from intestinal microbiota. Activated pro-inflammatory innate immune cells, including neutrophils, M1 macrophages, activated dendritic cells and mast cells, were significantly enriched in colons of non-responders. The prediction model based on three model-genes (IFI44L, CYP24A1, and RGS1) exhibited strong predictive efficacy, with AUC values of 0.901 and 0.80 in the Training and Validation Cohorts, respectively. Higher expression of the three model-genes/proteins in colons of non-responders to IFX was confirmed by clinical colonic mucosal biopsies. 4 Drugs (Calcitriol, Lunacalcipol, Deferasirox, Telaprevir), 15 miRNAs and 66 corresponding lnRNAs interacting with model-genes were identified. The protein 3D structure of the key model-gene/protein (human-derived CYP24A1) was developed. Through the Molecular Docking and cellular experimental validation, Deferasirox, which significantly down-regulated both the RNA and protein expression of CYP24A1, was identified as the optimal adjuvant or alternative for IFX in predicted non-responders with UC. This study developed a novel prediction model for pre-assessing the efficacy of IFX in patients with UC, as the first step towards personalized therapy. Meanwhile, drugs and non-coding RNAs were provided as potential candidates to develop the next-step precise treatment for the predicted non-responders. In particular, Defeasirox appears to hold promise as an adjuvant or alternative to IFX for the optimization of UC therapy. [ABSTRACT FROM AUTHOR]

We recently described the production of a detergent-biocompatible crude protease from Streptomyces mutabilis strain TN-X30. Here, we describe the purification, characterization, and immobilization of the serine alkaline protease (named SPSM), as well as the cloning, sequencing, and over-expression of its corresponding gene (spSM). Pure enzyme was obtained after ammonium sulphate precipitation followed by heat-treatment and Sephacryl® S-200 column purification. The sequence of the first 26 NH 2 -terminal residues of SPSM showed a high sequence identity to subtilisin-like serine proteases produced by actinobacteria. The spSM gene was heterologously expressed in Escherichia coli BL21(DE3)pLysS and E. coli BL21-AI™ strains using pTrc99A (rSPSM) and Gateway™ pDEST™ 17 [(His) 6 -tagged SPSM] vectors, respectively. Results obtained indicated that the (His) 6 -tagged SPSM showed the highest stability. The SPSM was immobilized using encapsulation and adsorption-encapsulation approaches and three different carriers. Features of SPSM in soluble and immobilized forms were analyzed by Fourier transform infrared (FTIR) spectroscopy in attenuated total reflection (ATR) mode, X-ray diffraction (XRD), zeta potential measurements, and field emission scanning electron microscopy (FE-SEM). The white clay and kaolin used in this study are eco-friendly binders to alginate-SPSM and show great potential for application of the immobilized SPSM in various industries. Molecular modeling and docking of N -succinyl- l -Phe- l -Ala- l -Ala- l -Phe- p -nitroanilide in the active site of SPSM revealed the involvement of 21 amino acids in substrate binding. [Display omitted] • Novel subtilisin-like serine protease (SPSM) from S. mutabilis TN-X30 was purified. • spSM gene was expressed in E. coli BL21(DE3)pLysS and BL21-AI™ cells using Gateway™. • SPSM immobilization was carried out by 2 different approaches onto 3 carriers. • Docking data make insight involvement of 21 amino acids in substrate selectivity. • This study can develop a reusable formulation of SPSM for commercial use. [ABSTRACT FROM AUTHOR]

Structural and conformational insights of a putative β-1,4-xylosidase (Ps GH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. Ps GH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of Ps GH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % β-strands. The homology modeled structure of Ps GH43F displayed a 5-bladed β-propeller fold for catalytic module at N-terminal and a β-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of Ps GH43F revealed the compactness and stability of the structure. Molecular docking studies of Ps GH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of Ps GH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of Ps GH43F by DLS was in the range, 0.25–0.28 μm. [Display omitted] • Ps GH43F has 5-bladed β-propeller for catalytic module and β-sandwich fold for CBM6. • Active site is composed of Asp33, Asp149 and Glu210 catalytic amino acid residues. • Secondary structure of Ps GH43F has 2.72 % α-helix, 36.06 % β-strands and 62.22 coils. • Molecular docking of Ps GH43F revealed maximum affinity with xylobiose. • MD simulation of Ps GH43F with xylobiose showed increased conformational stability. [ABSTRACT FROM AUTHOR]

The presence of textile dyes in wastewater of textile factories represents a major environmental problem, threatening aquatic life. The decolorisation and degradation of harmful textile-dyes therefore remains a key field of research. In this study, a novel extracellular heme-manganese-peroxidase (30 kDa-MnP AN30) produced by Aspergillus niger strain CTM10002, a strain which was isolated from contaminated-wastewater of a nitrogen-phosphate-potash (NPK) chemical company in Sfax (Tunisia), was evaluated for its efficiency in the decolorization of different textile-dyes. Purification yield reached 60%, with a specific activity of 372 U/mg and Reinheitzahl (RZ) value of 2.8 under the optimal conditions of 40 °C and pH 5. The MnP AN30 NH 2 -terminal sequence was characterized by a high degree of similarity with those of other fungal-peroxidases. The mnp AN30 gene was cloned, sequenced, and expressed in Escherichia coli strain BL21(DE3)pLysS. Biochemical properties of the recombinant enzyme (rMnP AN30) were similar to those of the native one. Interestingly, molecular modeling and docking of MnP AN30 heme binding site revealed the involvement of 19 amino acid residues in substrate binding. More interestingly, MnP AN30 is capable of decolorizing textile dyes with higher decolorization efficiency than MnP TC55 from Trametes pubescens strain i8. Accordingly, these properties showed the potential candidacy of MnP AN30 to be used in biological treatment and decolorization of synthetic textile dyes. [Display omitted] • New 30 kDa heme manganese peroxidase from A. niger CTM10002 was purified (MnP AN30). • Optimum pH and temperature values for activity were pH 5 and 40 °C, respectively. • The mnp AN30 gene was cloned, sequenced, and expressed in E. coli BL21(DE3)pLysS. • Docking data provided insight into the involvement of 19 amino acid residues in the substrate binding. • MnP AN30 is considered a promising candidate for textile dyes biological treatment and decolorization. [ABSTRACT FROM AUTHOR]

[Display omitted] • The model of lead molecule TeA binding to the QB site in Arabidopsis D1 protein was constructed. • A series of new derivatives were designed and docked to the Q B site of by molecular simulations. • Derivatives D6, D13 and D27 with better affinities than TeA were screened out and synthesized. • D6 and D13 are promising compounds to develop new PSII herbicides with superior performance. • Model-based ligand design is a valuable tool to find new PSII inhibitors based on lead molecule TeA. Computer-aided design has become an important tool to develop novel pesticides based on natural lead compounds. Tenuazonic acid (TeA), a typical representative of the natural tetramic acid family, was patented as a potential bioherbicide. However, its herbicidal efficacy is still not up to the ideal standard of commercial products. We aim to find new TeA's derivatives with improved potency. Molecular docking was used to build ligand-acceptor interaction models, design and screen new derivatives. Phytotoxicity, oxygen evolution rate, chlorophyll fluorescence and herbicidal efficacy were determined to estimate biological activity of compounds. With the aid of a constructed molecular model of natural lead molecule TeA binding to the Q B site in Arabidopsis D1 protein, a series of derivatives differing in the alkyl side chain were designed and ranked according to free energies. All compounds are stabilized by hydrogen bonding interactions between their carbonyl oxygen O2 and D1-Gly256 residue; moreover, hydrogen bond distance is the most important factor for maintaining high binding affinity. Among 54 newly designed derivatives, D6, D13 and D27 with better affinities than TeA were screened out and synthesized to evaluate their photosynthetic inhibitory activity and herbicidal efficacy. Analysis of structure-activity relationship indicated that D6 and D13 with sec -pentyl and sec -hexyl side chains, respectively, were about twice more inhibitory of PSII activity and effective as herbicide than TeA with a sec -butyl side chain. D6 and D13 are promising compounds to develop TeA-derived novel PSII herbicides with superior performance. [ABSTRACT FROM AUTHOR]

Researchers' attention has been greatly focused on the use of lignocellulosic wastes to produce bioethanol and biogas due to the depletion of non-renewable energy resources. In our effort to find a potent cellulase-producing fungal strain, the fungus NAS51 was isolated among eight isolates from a sponge collected from the Red Sea, Jeddah, and selected as it displayed the highest cellulase activity including (FP-ase, CMC-ase, and β-glucosidase enzymes) at levels of 3.13 U/ml, 2.52 U/ml, and 0.69 U/ml, respectively. The fungus was identified morphologically and genetically by sequencing its 18SrRNA gene as Aspergillus sp. NAS51. The cellulase activity of Aspergillus sp. NAS51 was optimized and maximum enzyme production was obtained at initial pH7, temp 30oC, incubation period 11 days, moisture content 70%, urea as a nitrogen source, and K2HPO4 (2 g/L). The crude cellulases from strain NAS51 were characterized, and results showed that the enzyme is stable over a wide pH range (6–10), with peak activity at pH 7.0 and 40 °C. The cellulase gene has been sequenced and the protein 3D structure was generated via in silico homology modeling. Determination of binding sites and biological annotations of the constructed protein was carried out via COACH and COFACTOR based on the I-TASSER structure prediction. To reach the maximum enzyme hydrolysis, the rice straw collected from Al-Ahsa, Kingdom of Saudi Arabia was pretreated with NaOH 1.5% to remove lignin and to enhance the saccharification process by Cellulase. The saccharified product was measured using HPLC, fermented by S. cerevisiae and the bioethanol yield produced from the fermentation was 0.454 mL ethanol/g fermentable sugars. This study indicates the potential application of fungal enzymes such as cellulase enzymes in biofuel generation and waste management. • Making bioethanol from lignocellulosic waste offers a viable option to diversify our energy sources and move away from non-renewable ones. • Identifying a cellulase-producing fungus is critical for improving bioethanol yield and efficiency. • In silico modeling of Aspergillus sp. NAS51 cellulose enzyme for bioethanol production from Hassawi rice straw. [ABSTRACT FROM AUTHOR]

Ebola virus disease is a deadly pathogenic disease with a fatality rate of 25–90 % as recorded in previous outbreaks. The Ebola Virus glycoprotein (EBOV-GP) plays a crucial role in the entry of viruses into human cells, making it an interesting target for therapeutic discovery. Therefore, inhibiting this protein can directly limit the virus replication and disease progression at an early stage of infection. The present study focuses on the design of novel potent EBOV-GP inhibitors using multiple computational techniques. In this context, two QSAR models were built from a set of 86 amodiaquine derivatives as anti-EBOV-GP using Monte Carlo and genetic algorithm multiple linear regression methods. Both models confirmed their predictive performance with satisfactory statistical parameters of the validation (R2 = 0.9129; Q2 = 0.8848 for the CORAL model and R2 = 0.8848; Q2 = 0.8148 for the GA-MLR model). From the outputs of the CORAL model, the structural fragments responsible for increasing and decreasing the inhibition activity were extracted and interpreted. This molecular information was used to design 26 new potentially safe and active candidate drugs. Molecular docking and dynamics simulations have affirmed the efficacy of the designed compounds. Specifically, compounds D2 (pIC 50_coral = 7.12; pIC 50_GA-MLR = 7.07), D3 (pIC 50_coral = 7.83; pIC 50_GA-MLR = 7.10), and D5 (pIC 50_coral = 7.26; pIC 50_GA-MLR = 7.55) displayed notable predicted inhibitory activity , according to both models. These compounds also exhibited conformational and structural stability, as well as a favorable binding profile. Furthermore, these potential drug candidates were found to be non-toxicity and have acceptable pharmacological properties. [ABSTRACT FROM AUTHOR]

A paralytic shellfish toxin binding protein (PST-BP) was extracted and purified from the viscera of oyster (Crassostrea hongkongensis) that accumulates paralytic shellfish toxin (PST), and the amino acid sequence of the protein was detected via HPLC-MS-MS. The structure of the PST-BP was built by homology modeling, and the interaction between PST and PST-BP was studied using molecular docking. The results showed that the purity of PST-BP was more than 99.8% after the purification. The PST-BP carried a molecular weight of 33.5 kDa and sequence alignment revealed its high sequence similarities with glyceraldehyde-3-phosphate-dehydrogenase (GAPDH). It has been shown that 99.9% of the amino acid residues in the PST-BP homology model are within a reasonable range, which exceeds the 90% threshold requirement for residuals in high-quality model structures. The molecular docking results revealed that Arg, Asp, Lys, Ala, Ser, Gln, Gly, Trp, Asn, Met, and Pro were identified as the major interacting amino acids residues between PST-BP and PST. [Display omitted] • A novel paralytic shellfish toxin binding protein was identified in oysters (Crassostrea hongkongensis). • The binding protein had high homology with glyceraldehyde-3-phosphate-dehydrogenase. • Homology model of paralytic shellfish toxin binding protein was built and validated. • The key residues of paralytic shellfish toxin binding protein binding to toxins were identified. [ABSTRACT FROM AUTHOR]

• Grass carp Il-12 receptor beta 1 (gcIl-12rβ1) and gcIl-12rβ2 are isolated and identified. • In silico analysis shows three gcIl12 receptor candidates are single-copy gene. • The gcil12rβ1 has the binding ability with grass carp Il-12 (gcIl-12) isoforms. • Both gcIl-12rβ1 and gcIl-12rβ2a can mediate gcIl-12 isoforms signaling. • Another gcIl-12rβ2, gcil12rβ2b , should be the orthologue of mammalian IL-27Ra. Interleukin 12 (IL-12) binds its receptor complex of IL-12 receptor beta 1 (IL-12Rβ1) and IL-12Rβ2 to transduce cellular signaling in mammals. In teleosts, the function of Il-12 is drawing increasing attention, but molecular and functional features of Il-12 receptors remain obscure. Especially, the existence of multiple Il-12 isoforms in some fish species elicits the requirement to clarify their receptors. In this study, we isolated three cDNA sequences as Il-12 receptor candidates from grass carp, entitled as grass carp Il-12rβ1 (gcIl-12rβ1), gcIl-12rβ2a and gcIl-12rβ2b. In silico analysis showed that gcIl-12rβ1 and gcIl-12rβ2a shared the conserved gene locus and similar structure characteristics with their orthologues of zebrafish, frog, chicken, mouse and human, respectively. However, the Il-12rβ2b of grass carp and zebrafish was similar to IL-27Ra in non-fish species. Further locally installed BLAST and gene synteny analysis uncovered three gcIl-12 receptors being single copied genes. Tissue distribution assay revealed that gcil12rβ1 and gcil12rβ2a transcripts were predominantly expressed in head kidney, differing from the even distribution of gcil12rβ2b transcripts in all detected tissues. Subsequently, the binding ability and antagonistic effects of recombinant extracellular region of gcIl-12rβ1 with recombinant grass carp Il-12 (rgcIl-12) isoforms were explored, providing functional evidence of the newly cloned gcIl-12rβ1 being genuine orthologues of mammalian IL-12Rβ1. Moreover, our data showed that gcIl-12rβ1 and gcIl-12rβ2a but not gcIl-12rβ1 and gcIl-12rβ2b mediated the effects of rgcIl-12 isoforms on ifn-γ promoter activity, thereby revealing Il-12 receptor signaling in fish. These results identified grass carp Il-12 receptors, thereby advancing our understanding of Il-12 isoform signaling in fish. [ABSTRACT FROM AUTHOR]

[Display omitted] • A novel serine protease G3726 was expressed by Bacillus subtilis strain SCK6. • It exhibited excellent tolerance to nonionic surfactants and 0–200 g L−1 NaCl. • The 3D structure model of G3726 was built using the structure of 1dbi as template. • Docking data make insight the mechanism of G3726 in enzymatic dehairing. • It showed better dehairing efficacy than chemical Na 2 S and industrial enzyme AS1.398. The current study focused on the substitution of toxic Na 2 S with bio-enzyme G3726, a novel serine protease heterologously expressed by Bacillus subtilis strain SCK6. This protease was purified to electrophoretic homogeneity with 39.43 % recovery, 7.03-fold purification and an estimated molecular mass of 36 kDa. The maximal activity was achieved at pH 8, 75 °C and 40 g L−1 NaCl, and more than 70 % of the activity was retained across the broad salinity range of 0–200 g L−1. G3726 was activated by Sr2+ and Ca2+, displayed considerable stability to benzene and ethanediol, and exhibited excellent compatibility with Tweens (20 and 80) and Triton X-100. Simultaneously, the 3D structure of G3726 was constructed by homology modeling, and interacted well with the cementing substances glycoprotein and proteoglycan in the hair pores. Moreover, G3726 showed no collagenase activity, and could thoroughly dehair goatskin within 4 h without any damage, which was better than industrial enzyme AS1.398 and chemical Na 2 S. As compared to Na 2 S, G3726 enzymatic dehairing showed reduction in BOD 5 , COD and TSS by 53.81, 52.78 and 65.52 %, respectively, endowing the leather better physical properties. These outstanding findings indicate that protease G3726 may have application in dehairing for environment-friendly leather processing. [ABSTRACT FROM AUTHOR]

The venom of scorpions is a mixture of components that constitute a source of bioactive molecules. The venom of the scorpion Centruroides tecomanus contains peptides toxic to insects, however, to date no toxin responsible for this activity has yet been isolated and fully characterized. This communication describes two new peptides Ct-IT1 and Ct-IT2 purified from this scorpion. Both peptides contain 63 amino acids with molecular weight 6857.85 for Ct-IT1 and 6987.77 Da for Ct-IT2. The soluble venom was separated using chromatographic techniques of molecular size exclusion, cationic exchange, and reverse phase chromatography, allowing the identification of at least 99 components of which in 53 the insecticidal activity was evaluated. The LD 50 determined for Ct-IT1 is 3.81 μg/100 mg of cricket weight, but low amounts of peptides (0.8 μg of peptide) already cause paralysis in crickets. The relative abundance of these two peptides in the venom is 2.1% for Ct-IT1 and 1% for Ct-IT2. The molecular masses and N-terminal sequences of both insecticidal toxins were determined by mass spectrometry and Edman degradation. The primary structure of both toxins was compared with other known peptides isolated from other scorpion venoms. The analysis of the sequence alignments revealed the position of a highly conserved amino acid residue, Gly39, exclusively present in anti-insect selective depressant β-toxins (DBTXs), which in Ct-IT1 and Ct-IT2 is at position Gly40. Similarly, a three-dimensional structure of this toxins was obtained by homology modeling and compared to the structure of known insect toxins of scorpions. An important similarity of the cavity formed by the trapping apparatus region of the depressant toxin LqhIT2, isolated from the scorpion Leiurus quinquestriatus hebraeus , was found in the toxins described here. These results indicate that Ct-IT1 and Ct-IT2 toxins have a high potential to be evaluated on pests that affect economically important crops to eventually consider them as a potential biological control method. • Two new insecticides (Ct-IT1 and Ct-IT2) were purified from Centruroides tecomanus scorpion. • Ct-IT1 and CT2 contain 63 amino acids with an experimental molecular mass of 6857.85 and 6987.77 Da, respectively. • Ct-IT1 and Ct-IT2 are highly toxic in insects, causing paralysis and eventual death in crickets at low doses. • The residue Gly40, is present in Ct-IT1 and Ct-IT2 toxins, this amino acid may be key to toxicity in insects. [ABSTRACT FROM AUTHOR]

Most β-galactosidases reported are sensitive to the end product (galactose), making it the rate-limiting component for the efficient degradation of lactose through the enzymatic route. Therefore, there is ongoing interest in searching for galactose-tolerant β-galactosidases. In the present study, the predicted galactose-binding residues of β-galactosidase from Bacillus coagulans , which were determined by molecular docking, were selected for alanine substitution. The asparagine residue at position 148 (N148) is correlated with the reduction of galactose inhibition. Saturation mutations revealed that the N148C, N148D, N148S, and N148G mutants exhibited weaker galactose inhibition effects. The N148D mutant was used for lactose hydrolysis and exhibited a higher hydrolytic rate. Molecular dynamics revealed that the root mean square deviation and gyration radius of the N148D-galactose complex were higher than those of wild-type enzyme-galactose complex. In addition, the N148D mutant had a higher absolute binding free-energy value. All these factors may lead to a lower affinity between galactose and the mutant enzyme. The use of mutant enzyme may have potential value in lactose hydrolysis. [Display omitted] [ABSTRACT FROM AUTHOR]

• This review provides an overview on structural investigations of understudied CYPs. • We discuss the role of understudied CYPs as potential novel drug targets. • We highlight the value of homology models to structurally access understudied CYPs. • Molecular dynamics simulations help to mechanistically understand enzymatic activity. • Dynamic pharmacophores are a powerful novel tool for elucidating ligand recognition. Human cytochrome P450 (CYP) enzymes are widely known for their pivotal role in the metabolism of drugs and other xenobiotics as well as of endogenous chemicals. In addition, CYPs are involved in numerous pathophysiological pathways and, hence, are therapeutically relevant. Remarkably, a portion of promising CYP targets is still understudied and, as a consequence, untargeted, despite their huge therapeutic potential. An increasing number of X-ray and cryo-electron microscopy (EM) structures for CYPs have recently provided new insights into the structural basis of CYP function and potential ligand binding. This structural knowledge of CYP functionality is essential for both understanding metabolism and exploiting understudied CYPs as drug targets. In this review, we summarize and highlight structural knowledge about this enzyme class, with a focus on understudied CYPs and resulting opportunities for structure-based drug design. Teaser: This review summarizes recent structural insights into understudied cytochrome P450 enzymes. We highlight the impact of molecular modeling for mechanistically explaining pathophysiological effects establishing understudied CYPs as promising drug targets. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is one of the topmost causes of death in males in Saudi Arabia. In females, it was also within the top five cancer types. CRC is heterogeneous in terms of pathogenicity and molecular genetic pathways. It is very important to determine the genetic causes of CRC in the Saudi population. BRAF is one of the major genes involved in cancers, it participates in transmitting chemical signals from outside the cells into the nucleus of the cells and it is also shown to participate in cell growth. In this study, we mapped the spectrum of BRAF mutations in 100 Saudi patients with CRC. We collected tissue samples from colorectal cancer patients, sequenced the BRAF gene to identify gene alterations, and analyzed the data using different bioinformatics tools. We designed a three-dimensional (3D) homology model of the BRAF protein using the Swiss Model automated homology modeling platform to study the structural impact of these mutations using the Missense3D algorithm. We found six mutations in 14 patients with CRC. Four of these mutations are being reported for the first time. The novel frameshift mutations observed in CRC patients, such as c.1758delA (E586E), c.1826insT (Q609L), c.1860insA and c.1860insA/C (M620I), led to truncated proteins of 589, 610, and 629 amino acids, respectively, and potentially affected the structure and the normal functions of BRAF. These findings provide insights into the molecular etiology of CRC in general and to the Saudi population. BRAF genetic testing may also guide treatment modalities, and the treatment may be optimized based on personalized gene variations. [ABSTRACT FROM AUTHOR]

• Relative high flexibility of Mut-T1 lipase when binding with oleic acid. • Main driving force for the lipase-fatty acid complex formation was van der Waals. • Solvent accessible surface area of the complex was negatively related to acyl chain. A thermostable T1 lipase from Geobacillus zalihae exhibits broad substrate specificity and good potential application in fats and oils. However, structural insight into the enzyme against substrates is poorly understood at the molecular level. Herein, the study aimed to examine interactions between a mutant T1 lipase (Mut-T1 lipase) and selected fatty acids (caprylic, myristic, stearic, oleic, linoleic and linolenic acids) by performing molecular docking and molecular dynamics (MD) simulation. The structure of Mut-T1 lipase obtained by homology modeling was reliable for molecular docking and MD simulation. Molecular docking revealed that Mut-T1 lipase showed low binding affinity for caprylic acid (−4.97 kcal/mol) compared to the other fatty acids (−5.65 to −6.88 kcal/mol). However, the conformation of Mut-T1 lipase-caprylic acid complex was comparably stable during the simulation, in terms of less root-mean square fluctuation. Besides, solvent accessible surface area value of Mut-T1 lipase-fatty acid complexes decreased with increasing chain length of fatty acid. van der Waals interactions were requisite in maintaining complex stability during the binding process. This work provides structural insight into interactions between the lipase and the fatty acids, which will facilitate design and applications of new mutants of T1 lipase in modifying fats and oils. [ABSTRACT FROM AUTHOR]

The aim of this study was to improve the inhibitory resistance of xylanase Fg Xyn11C from Fusarium graminearum to XIP in cereal flour. Site saturation mutagenesis was performed using computer-aided redesign. Firstly, based on multiple primary structure alignments, the amino acid residues in the active site architecture were identified, and specific residue T144 in the thumb region of Fg Xyn11C was selected for site-saturation mutagenesis. After screening, Fg Xyn11CT144F was selected as the best mutant, as it displayed the highest enzymatic activity and resistance simultaneously compared to other mutants. The specific activity of Fg Xyn11CT144F was 208.8 U/mg and it exhibited complete resistance to SyXIP-I. Compared with the wild-type, Fg Xyn11CT144F displayed similar activity and the most resistant against SyXIP-I. The optimal temperature and pH of the wild-type and purified Fg Xyn11CT144F were similar at pH 5.0 and 30 °C. Our findings provided preliminary insight into how the specific residue at position 144 in the thumb region of Fg Xyn11C influenced the enzymatic properties and interacted with SyXIP-I. The inhibition sensitivity of Fg Xyn11C was reduced through directed evolution, leading to creation of the mutant enzyme Fg Xyn11CT144F. The Fg Xyn11CT144F resistance to SyXIP-I has potential application and can also provide references for engineering other resistant xylanases of the GHF11. [ABSTRACT FROM AUTHOR]

[Display omitted] • The synergistic effect of saltiness-enhancing peptides was demonstrated by S-curves. • The 3D model of TMC4 with ten transmembranes was constructed by homology modeling. • The binding mechanism of saltiness-enhancing peptides with TMC4 was explored. • The active sites of NEFGYSNR were calculated by frontier molecular orbitals analysis. The previously obtained chicken-derived umami peptides in the laboratory were evaluated for their saltiness-enhancing effect by sensory evaluation and S-curve, and the results revealed that peptides TPPKID, PKESEKPN, TEDWGR, LPLQDAH, NEFGYSNR, and LPLQD had significant saltiness-enhancing effects. In the binary solution system with salt, the ratio of the experimental detection threshold (129.17 mg/L) to the theoretical detection threshold (274.43 mg/L) of NEFGYSNR was 0.47, which had a synergistic saltiness-enhancing effect with salt. The model of transmembrane channel-like protein 4 (TMC4) channel protein was constructed by homology modeling, which had a 10-fold transmembrane structure and was well evaluated. Molecular docking and frontier molecular orbitals showed that the main active sites of TMC4 were Lys 471, Met 379, Cys 475, Gln 377, and Pro 380, and the main active sites of NEFGYSNR were Tyr, Ser and Asn. This study may provide a theoretical reference for low-sodium diets. [ABSTRACT FROM AUTHOR]

L-asparaginase is a cardinal biotherapeutic drug for treating acute lymphoblastic leukemia, which is highly prevalent in children worldwide. In the current investigation, L-asparaginase producing marine bacterial isolate, Bacillus australimaris NJB19 (MG734654), was observed to be producing extracellular glutaminase free L-asparaginase (13.27 ± 0.4 IU mL−1). Production of L-asparaginase was enhanced by the Box-Behnken design approach that enumerated the significant variables affecting the enzyme production. The optimum levels of the derived variables resulted in 2.8-fold higher levels of the enzyme production (37.93 ± 1.06 IU mL−1). An 1146 bp L-asparaginase biosynthetic gene of Bacillus australimaris NJB19 was identified and cloned in E. coli DH5α , fused with a histidine tag. The in silico analysis of the protein sequence revealed the presence of a signal peptide and classified it as a type II L-asparaginase. Toxic peptide prediction disclosed no toxin domain in the protein sequence, hence suggesting it as a non-toxic protein. The secondary structure analysis of the enzyme displayed a comparable percentage of alpha-helical and random coil structure, while 14.39% and 6.57% of amino acid residues were composed of extended strands and beta-turns, respectively. The functional sites in the three-dimensional structural model of the protein were predicted and interestingly had a few less conserved residues. Bacillus australimaris NJB19 identified in this study produces type-II L-asparaginase, known for its high affinity for asparagine and effectiveness against leukemic cells. Hence, these observations indicate the L-asparaginase, thus obtained, as a potentially significant and novel therapeutic drug. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis HddA enzyme phosphorylates the M7P substrate and converts it to M7PP product in GDP-D-α-D-heptose biosynthetic pathway. For structural and functional studies on MtbHddA , we have purified the enzyme, which eluted as a monomer from size exclusion column. Purified MtbHddA had ATPase activity. The SAXS analysis supported globular monomeric scattering profile of MtbHddA in solution. The CD analysis showed that MtbHddA contains 45% α-helix, 18% β-stands, and 32% random coil structures and showed unfolding temperature (T M) ~ 47.5 °C. The unfolding temperature of MtbHddA is enhanced by 1.78±0.41 °C in ATP+Mg2+ bound state, 2.12±0.41 °C in Mannose bound state and 3.07±0.41 °C in Mannose+ ATP+Mg2+ bound state. The apo and M7P +ATP + Mg2+ complexed models of MtbHddA showed that enzyme adopts a classical GHMP sugar kinase fold with conserved ATP+Mg2+ and M7P binding sites. The dynamics simulation analysis on four MtbHddA models showed that ATP+Mg2+ and M7P binding enhanced the stability of active site conformation of MtbHddA. Our study provides important insights into MtbHddA structure and activity, which can be targeted for therapeutic development against M. tuberculosis. [ABSTRACT FROM AUTHOR]

• Domain III of EGFR was successfully expressed as the immunogen and had high affinity with anti-EGFR antibody H11. • A novel anti-EGFR nanobody (Nb AS32611) was screened through phage display and epitope binning. • The structure of AS32611 was built through homology modeling. • The epitope and paratope of AS32611 were predicted by molecular docking to provide the structural basis for multi-epitope therapy. Since EGFR is an important and effective target for tumor therapy in the clinic. Several monoclonal antibodies and nanobodies were proved to target domain III of EGFR. Regarding the increased attention on nanobodies, the present study aimed to generate nanobodies specifically against domain III. After camel immunization, a gene repertoire of sdAb fragments with a diversity of 3×109 clones was produced. Following the construction of two sdAb phage display libraries, the successful epitope binning was carried out to identify the nanobody with the designated epitope. Modelling of the identified nanobody and molecular docking studies illustrated the paratope and epitope. Docking analysis revealed that the paratope focused on CDR2 loop of the identified nanobody. The identified nanobody potently cover part of the epitope of Matuzumab and Nb 9G8, which indicated that it blocked EGFR by preventing dimerization of the receptors. [ABSTRACT FROM AUTHOR]

A new serine alkaline protease (designated as SAPGB) from Gracilibacillus boraciitolerans strain LO15, was produced (9000 U/mL), purified, and characterized. SAPGB has a monomer structure with a precise molecular weight of 30,285.03 kDa as learnt from matrix-assisted laser desorption/ionization-time of flight/mass spectroscopy (MALDI-TOF/MS) exploration. The NH 2 -terminal amino-acid succession revealed significant identity with Bacillus proteases. The SAPGB was irreversibly inhibited by diiodopropyl fluorophosphates (DFP) and phenylmethylsulfonyl fluoride (PMSF). The enzyme displayed optimum activity at 65 °C and pH 10. The maximal activity was achieved in the range 0.5–5 M NaCl and about 52% of the activity was preserved across the broad salinity range of 0–30%. SAPGB exhibited a considerable catalytic efficiency (ratio k cat / K m) and degree of hydrolysis (DH). In addition, SAPGB showed a high tolerance to several organic solvents and an excellent detergent compatibility than SAPV, SAPA, Thermolysin type X, and Esperase 8.0 L. These properties make SAPGB a potential candidate for detergent formulations. On the other hand, sapGB gene was cloned and expressed in E. coli BL21(DE3)pLysS and the biochemical properties of the purified extracellular recombinant protease (rSAPGB) were similar to those of SAPGB. Finally, a 3D structural model of SAPGB was constructed by homology modeling. Unlabelled Image • The protease SAPGB from Gracilibacillus boraciitolerans strain LO15 was purified and typified. • The optimum pH and temperature values for activity were pH 10 and 65 °C, respectively. • The sapGB gene encoding SAPGB, was cloned, sequenced, and expressed in E. coli BL21(DE3)pLysS. • Pro-SAPGB 3D-structure model was built using structure of Pro-subtilisin E (PDB ID: 3WHI). • The SAPGB enzyme is a potential candidate for peptide synthesis and detergent formulations. [ABSTRACT FROM AUTHOR]

Newcastle disease virus (NDV) has been explored to a great extent to understand the biology of negative-sense RNA viruses. Nucleoprotein (N) is the most abundant protein in the virus particles, and its primary function is to encapsidate the virus genome for its transcription, replication, and packaging. Here, we report the structural investigations of the N protein of NDV (NDV-N) in solution. The N gene of NDV was cloned and expressed in E. coli as a soluble protein of ~53 kDa in size. The FE-TEM imaging of the purified NDV-N displayed a nearly spherical shape with a diameter of 28 nm and the DLS analysis of the purified NDV-N displayed a monodispersed nature, with averaged hydrodynamic radius, 26.5 nm. The conformational behavior of the NDV-N in solution was studied by SAXS analysis, which suggested two ring structures of NDV-N formed by thirteen monomeric units each. Each ring interacts with RNA molecules and forms a large molecule with a size of ~1450 kDa and are stacked on each other in a spiral arrangement. More profound knowledge of the N protein structure will help us in deciphering the control of viral RNA synthesis at the early stage of NDV life-cycle. [ABSTRACT FROM AUTHOR]

• A reliable Glide docking-based virtual screening (VS) pipeline for P2Y 14 R was developed. • Several potent P2Y 14 R antagonists with novel scaffolds were identified utilizing the VS strategy. • P2Y 14 R inhibitory effect was evaluated by testing cAMP levels in HEK293 cells. • Anti-gout activity of screened compound was detected in MSU-treated THP-1 cells. • The mechanism of test compound in treating acute gouty arthritis was elucidated. P2Y 14 nucleotide receptor is a Gi protein-coupled receptor, which is widely involved in physiological and pathologic events. Although several P2Y 14 R antagonists have been developed thus far, few have successfully been developed into a therapeutic drug. In this study, on the basis of two P2Y 14 R homology models, Glide docking-based virtual screening (VS) strategy was employed for finding potent P2Y 14 R antagonists with novel chemical architectures. A total of 19 structurally diverse compounds identified by VS and drug-like properties testing were set to experimental testing. 10 of them showed good inhibitory effects against the P2Y 14 R (IC 50 < 50 nM), including four compounds (compounds 8 , 10 , 18 and 19) with IC 50 value below 10 nM. The best VS hit, compound 8 exhibited the best antagonistic activity, with IC 50 value of 2.46 nM. More importantly, compound 8 restrained monosodium uric acid (MSU)-induced pyroptosis of THP-1 cells through blocking the activation of Nod-like receptor 3 (NLRP3) inflammasome, which was attributed to its inhibitory effects on P2Y 14 R-cAMP pathways. The key favorable residues uncovered using MM/GBSA binding free energy calculations/decompositions were detected and discussed. These findings suggest that the compound 8 can be used as a good lead compound for further optimization to obtain more promising P2Y 14 R antagonists for the treatment of acute gouty arthritis. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 has caused tens of thousands of infections and more than one thousand deaths. There are currently no registered therapies for treating coronavirus infections. Because of time consuming process of new drug development, drug repositioning may be the only solution to the epidemic of sudden infectious diseases. We systematically analyzed all the proteins encoded by SARS-CoV-2 genes, compared them with proteins from other coronaviruses, predicted their structures, and built 19 structures that could be done by homology modeling. By performing target-based virtual ligand screening, a total of 21 targets (including two human targets) were screened against compound libraries including ZINC drug database and our own database of natural products. Structure and screening results of important targets such as 3-chymotrypsin-like protease (3CLpro), Spike, RNA-dependent RNA polymerase (RdRp), and papain like protease (PLpro) were discussed in detail. In addition, a database of 78 commonly used anti-viral drugs including those currently on the market and undergoing clinical trials for SARS-CoV-2 was constructed. Possible targets of these compounds and potential drugs acting on a certain target were predicted. This study will provide new lead compounds and targets for further in vitro and in vivo studies of SARS-CoV-2, new insights for those drugs currently ongoing clinical studies, and also possible new strategies for drug repositioning to treat SARS-CoV-2 infections. Twenty structures including 19 SARS-CoV-2 targets and one human target were built by homology modeling. Library of ZINC drug database, natural products, 78 anti-viral drugs were screened against these targets plus human ACE2. This study provides drug repositioning candidates and targets for further in vitro and in vivo studies of SARS-CoV-2. Image 1 [ABSTRACT FROM AUTHOR]

• Three-dimensional structure of Zmays CALDH was modeled. • Daidzin was selected from a set of 20 putative inhibitors of the enzyme. • In silico and in vitro findings indicate that daidzin is a competitive inhibitor. • An alternative approach for studies on lignocellulose recalcitrance is suggested. Coniferyl aldehyde dehydrogenase (CALDH) catalyzes the oxidation of coniferyl aldehyde to ferulic acid. Because ferulic acid has a relevant role in the structure and recalcitrance of the cell wall, inhibition of CALDH can reduce its levels and increase the digestibility of lignocellulosic biomass. We prospected in silico a selective inhibitor of CALDH of Zea mays. The Zmays CALDH gene was identified by homology with the corresponding gene of Arabidopsis thaliana. The sequence was translated and analyzed, and the quaternary structure was modeled. A set of 20 putative inhibitors were screened from a virtual library and docked in the active site of Zmays CALDH, and daidzin (DZN) was selected as an enzyme inhibitor. The stability of the Zmays CALDH–DZN complex was evaluated by molecular dynamics simulations of the monomeric and tetrameric forms. For evaluation of kinetic analysis, Zmays CALDH activity was determined in vitro by high-performance liquid chromatography. In comparison to the DZN-free control, the data obtained indicated constant V max and enhanced K m. Altogether, in silico and in vitro findings indicated that DZN inhibited Zmays CALDH competitively. The DZN-induced inhibition of Zmays CALDH could be a valuable and promising approach to studies on ferulic acid biosynthesis and saccharification of lignocellulosic biomass. [ABSTRACT FROM AUTHOR]

The human taste experience is the result of five basic taste qualities, namely sweet, salty, bitter, sour and umami. Sweet, bitter, and umami are mediated by G protein-coupled receptors (GPCRs), whereas sour and salt are modulated by specialized membrane channels. Taste perception starts with the interaction between a taste-active molecule (substance) and a specialized receptor located on the taste buds at the level of the cell membrane. Once the interaction has occurred, taste receptor cells are able to transduce the information content of the chemical stimulus into nerve signals directly to the brain. Therefore, the receptor-mediated recognition of taste molecules is the first episode leading to taste perception. In this review, we provide a complete overview of in silico molecular modeling techniques applied to the study of umami, sweet, and bitter taste receptors. Structure-based computational tools, usually applied to investigate the binding mode of bioactive molecules into their targets and to rationally design new drug molecules, are proven equally useful in the field of chemical senses to shed light on the molecular acknowledgment of tastants. The recent computational advancements in the taste research field, and particularly the computation-driven investigations of the tastant-receptor binding, provided a better understanding of the molecular mechanisms underlying food tastants' sensing and could have an impressive contribution to the identification of new taste modulators in the future. • Structure prediction of sweet, umami, and bitter taste receptors. • Binding modes' predictions of sweet, umami, and bitter molecules into their respective receptors. • Contribution of computational approaches to the identification of new taste modulators. [ABSTRACT FROM AUTHOR]

[Display omitted] Mixed-lineage protein kinase 3 (MLK3) is implicated in several human cancers and neurodegenerative diseases. A series of 3 H -imidazo[4,5- b ]pyridine derivatives were designed, synthesized and evaluated as novel MLK3 inhibitors. A homology model of MLK3 was developed and all designed compounds were docked to assess their binding pattern and affinity toward the MLK3 active site. Based on this knowledge, we synthesized and experimentally evaluated the designed compounds. Majority of the compounds showed significant inhibition of MLK3 in the enzymatic assay. In particular, compounds 9a , 9e , 9j , 9 k , 12b and 12d exhibited IC 50 values of 6, 6, 8, 11, 14 and 14 nM, respectively. Furthermore, compounds 9a , 9e , 9 k and 12b exhibited favorable physicochemical properties among these compounds. [ABSTRACT FROM AUTHOR]

Though biodegradation is an important regulation pathway for microcystins (MCs) pollution, more consideration needs to be given to the potential risk associated with related biodegradation products (MC-BDPs). In this work, typical MCLR-BDPs were prepared and their toxicity was evaluated by protein phosphatases (PPs) inhibition assay. Results showed the initial ring opening of MCLR played a crucial role in detoxification. However, partial MCLR-BDPs still retained the critical structures and thus exhibited certain toxicity (2.8–43.5% of MCLR). With the aid of molecular simulation, the mechanism for the potential toxicity of BDPs targeting PP2A was elucidated. The initial ring opening made the loss of hydrogen bond Leu2←Arg 89 , and pi-H bond Adda5-His 191 , which was responsible for the significant reduction in the toxicity of MCLR-BDP. However, the key hydrogen bonds MeAsp3←Arg 89 , Glu6←Arg 89 , Adda5←Asn 117 , Adda5←His 118 , Arg4→Pro 213 , Arg4←Arg 214 , Ala1←Arg 268 , and Mdha7←Arg 268 , metal bond Glu6-Mn 1 2+, and ionic bonds Glu6-Arg 89 , and Glu6-Mn 2 2+ were preserved in varying degrees. Above preserved interactions maintained the interactions between PP2A and Mn2+ ions (reducing the exposure of Mn2+ ions). Above preserved interactions also hindered the combination of phosphate groups to Arg 214 residual and thus exhibited potential toxicity. [Display omitted] • PPs inhibition assay showed partial MCLR-BDPs exhibited residual toxicity. • The initial ring opening was highly efficient for the detoxification of MCs. • Residues Arg4 and Glu6 were crucial to the toxicity of MCLR-BDPs. • MCLR-BDP toxicity was attributed to the preserved key interactions. [ABSTRACT FROM AUTHOR]

GPR101 is a G protein-coupled receptor (GPCR) implicated in a rare form of genetic gigantism known as X-linked acrogigantism, or X-LAG. In particular, X-LAG patients harbor microduplications in the long arm of the X-chromosome that invariably include the GPR101 gene. Duplications of the GPR101 gene lead to the formation of a new chromatin domain that causes over-expression of the receptor in the pituitary tumors of the patients. Notably, GPR101 is a constitutively active receptor, which stimulates cells to produce the second messenger cyclic AMP (cAMP) in the absence of ligands. Moreover, GPR101 was recently reported to constitutively activate not only the cAMP pathway via G s , but also other G protein subunits (G q/11 and G 12/13). Hence, chemicals that block the constitutive activity of GPR101, known as inverse agonists, have the potential to be useful for the development of pharmacological tools for the treatment of X-LAG. In this study, we provide structural insights into the putative structure of GPR101 based on in-house built homology models, as well as third party models based on the machine learning methods AlphaFold and AlphaFold-Multistate. Moreover, we report a molecular dynamics study, meant to further probe the constitutive activity of GPR101. Finally, we provide a structural comparison with the closest GPCRs, which suggests that GPR101 does not share their natural ligands. While this manuscript was under review, cryo-electron microscopy structures of GPR101 were reported. These structures are expected to enable computer-aided ligand discovery efforts targeting GPR101. [Display omitted] • Compared homology and machine learning models of GPR101, a GPCR involved in X-linked acrogigantism. • The study suggests that GPR101 presents a bulge in TM5 analogous to the one seen in the adrenergic receptors. • Molecular dynamics suggests the inactive AlphaFold-Multistate model evolves towards an activated state. • Comparison of GPR101 and the α 1b adrenergic receptor suggests no shared natural ligands. [ABSTRACT FROM AUTHOR]

[Display omitted] • A method for identifying umami peptides was established with computer assistance. • Four novel umami peptides were discovered and validated. • Mechanism of umami peptide binding to T1R1/T1R3 was analyzed by computer simulation. • Amino acid types and residues in T1R1 that bind umami peptides were discovered. Umami peptides are an important component of food flavoring agents and have high nutritional value. This work aimed to identify umami peptides from tuna skeletal myosin using a new model method of computer simulation, explore their umami mechanism, and further validate the umami tastes with sensory evaluation. Umami peptides LADW, MEIDD, VAEQE, and EEAEGT were discovered, and all of them bound to taste type 1 receptor 1 and receptor 3 via hydrogen bonds and van der Waals forces to form stable complexes. LADW exhibited the best affinity energy and binding capability. Sensory evaluation and electronic tongue confirmed that all peptides possessed an umami taste, and LADW exhibited the strongest umami intensity. This study not only explored four novel umami peptides to improve the value of tuna skeletal myosin but also provided a new method for the rapid discovery of umami peptides. [ABSTRACT FROM AUTHOR]

The cytochrome P450 enzymes of the CYP4G subfamily are some of the most intriguing insect P450s in terms of structure and function. In Drosophila , CYP4G1 is highly expressed in the oenocytes and is the last enzyme in the biosynthesis of cuticular hydrocarbons, while CYP4G15 is expressed in the brain and is of unknown function. Both proteins have a CYP4G-specific and characteristic amino acid sequence insertion corresponding to a loop between the G and H helices whose function is unclear. Here we address these enigmatic structural and functional features of Drosophila CYP4Gs. First, we used reverse genetics to generate D. melanogaster strains in which all or part of the CYP4G-specific loop was removed from CYP4G1. We showed that the full loop was not needed for proper folding of the P450, but it is essential for function, and that just a short stretch of six amino acids is required for the enzyme's ability to make hydrocarbons. Second, we confirmed by immunocytochemistry that CYP4G15 is expressed in the brain and showed that it is specifically associated with the cortex glia cell subtype. We then expressed CYP4G15 ectopically in oenocytes, revealing that it can produce of a blend of hydrocarbons, albeit to quantitatively lower levels resulting in only a partial rescue of CYP4G1 knockdown flies. The CYP4G1 structural variants studied here should facilitate the biochemical characterization of CYP4G enzymes. Our results also raise the question of the putative role of hydrocarbons and their synthesis by cortex glial cells. [Display omitted] • D. melanogaster CYP4G15 is a functional P450 localized in CNS cortex glial cells. • CYP4G15 oenocyte ectopic expression reveals its decarbonylase activity. • Ablation of CYP4G1-specific loop revealed it is essential for CHC production. • A 6-aa stretch into the CYP4G1-specific loop is critical for CHC production. [ABSTRACT FROM AUTHOR]

• A total of 30 candidate UGT genes were identified from the antennal transcriptome of X. quadripes. • X. quadripes UGTs were phylogenetically classified into ten sub-families. • Coleopteran UGT50 sub-family showed a strict single copy, intron gains and losses. • Most X. quadripes UGT genes were highly expressed in antennae associated with olfactory functions. The antenna of Xylotrechus quadripes is the principle olfactory organ that is subjected to a large number of endogenous and exogenous compounds. The gene families associated with the detoxification of these compounds are essential for the adaptive evolution of insect defensive strategies. However, knowledge on uridine diphosphate (UDP)-glycosyltransferases (UGTs) of X. quadripes is unavailable. Here, we characterized 30 UGT genes identified from an antennal transcriptome of X. quadripes. Among them, 16 UGT genes encoding 508–527 amino acids shared the full-length sequences and signal peptides in N-terminus. Multiple sequence alignment revealed that X. quadripes UGTs had a variable N-terminus and a conserved C-terminus. Phylogenetic analysis showed that X. quadripes UGTs were classified into ten sub-families with the largest UGT one of UGT352 (nine genes) and a strict single copy of UGT50 within coleopteran species. Gene structural analysis indicated that coleopteran UGT50s underwent intron gains or losses. Expression profile revealed that all studied X. quadripes UGTs were transcribed in the antennae of both sexes, some of which exhibited sex-biased expression including UGT2 , UGT6 , UGT20 and UGT27 in females as well as UGT3 , UGT11 and UGT12 in males. In addition, most of UGTs were widely expressed in other tissues, indicating their functional diversities in this beetle. Together, these findings provide valuable information for further functional studies of UGTs in X. quadripes , especially their roles in olfaction. [ABSTRACT FROM AUTHOR]

Organic pesticides are one of the main environmental pollutants, and how to reduce their environmental risks is an important issue. In this contribution, we disclose the molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides using site-directed mutagenesis and molecular modeling and then construct an effective screening model. The results indicated that the target-site mutation (Trp-1999-Leu) in acetyl-coenzyme A carboxylase (ACCase) can affect the effectiveness of the pesticides (clodinafop, fenoxaprop, cyhalofop, and metamifop), and the plant resistance to fenoxaprop, clodinafop, cyhalofop, and metamifop was found to be 564, 19.5, 10, and 0.19 times, respectively. The established computational models (i.e. wild-type/mutant ACCase models) could be used for rational screening and evaluation of the resistance to pesticides. The resistance induced by target gene mutation can markedly reduce the bioreactivity of the ACCase-clodinafop/fenoxaprop adducts, and the magnitudes are 10 and 102, respectively. Such event will seriously aggravate environmental pollution. However, the biological issue has no distinct effect on cyhalofop (RI＝10), and meanwhile it may markedly increase the bioefficacy of metamifop (RI＝0.19). We could selectively adopt the two chemicals so as to decrease the residual pesticides in the environment. Significantly, research findings from the computational screening models were found to be negatively correlated with the resistance level derived from the bioassay testing, suggesting that the screening models can be used to guide the usage of pesticides. Obviously, this story may shed novel insight on the reduction of environmental risks of pesticides and other organic pollutants. Image 1 • Target-site mutation in American sloughgrass will aggravate pesticide pollution. • The changes in enzyme bioaffinity can greatly affect the pesticides usage. • Computational findings are negatively related to the results of bioassay testing. • Computational screening models could be used for reducing environmental stress. [ABSTRACT FROM AUTHOR]

The SPX gene family, ubiquitous in all vascular plants, plays a critical role in plant development and growth as well as in response to phosphorus stress. Based on genomic census, 46 TaSPX genes were identified in the wheat genome. All of them are evenly distributed on 13 of the 21 wheat chromosomes and chromosome 7A contains the largest members. As many as 57 gene specific SSRs were discovered among genomic sequences of identified TaSPX s. MicroRNA target analysis revealed that TaSPX genes were targeted by 9 different miRNAs including tae-miR1120a, tae-miR1120b-3p, tae-miR1120c-5p, tae-miR1122b-3p, tae-miR1122c-3p, tae-miR1130a, tae-miR1130b-3p, tae-miR1137a, and tae-miR1137b-5p. Expression profiles derived from transcriptome data and real-time quantitative PCR revealed that TaSPX genes were significantly induced by Pi starvation. The modeled 3D structure of wheat SPX proteins shared high level of homology with template structures, providing information to understand their functions at proteomic level. We have also refined the modeled 3D structures on 10 ns using molecular dynamics simulations for conformational stability. The discovered members of SPX gene family and their targeting miRNAs may provide resource for genetic improvement and promote P use efficiency in cereals. [ABSTRACT FROM AUTHOR]

Cytochrome P450 enzymes (CYPs) of the equine CYP3A subfamily are predominantly involved in drug metabolism. In this study, genetic variants of the equine CYP3A94, CYP3A95, and CYP3A97 were identified and characterized using in silico modeling and in vitro enzyme kinetics. The genomes of 81 horses were sequenced to obtain the genetic variants. Structural CYP modifications of the most frequent variants were analyzed in silico using the 3D-structures predicted by homology modeling. Enzyme kinetic analyses were performed using testosterone as substrate. Twenty genetic variants were found including five missense variants (CYP3A94:p.Asp217Asn, CYP3A95:p.Asp214His, CYP3A95:p.Ser392Thr, CYP3A97:p.Ile119Thr, CYP3A97:p.Met500Val) with a higher percentage of minor allele frequency (MAF) (range 0.2–0.4). A splice-site variant (c.798 + 1G > A) in CYP3A94, likely to generate a truncated protein, was found in 50% of the horses. CYP3A94:p.Asp217Asn and CYP3A95:p.Asp214His were localized on the CYP F-α-helix, an important region for the substrate interactions in the human CYP3A4. Testosterone 2β-hydroxylation was diminished in CYP3A94217Asn and CYP3A95392Thr. Ketoconazole inhibited 2β-hydroxylation differently in the five variants with the most pronounced inhibition obtained for CYP3A95392Thr. In vitro and in silico analyses of genetic variants allow unraveling structural features in equine CYPs that correlate with changes in the CYP activity. • Twenty genetic variants were found in the equine CYP3A94, CYP3A95 and CYP3A97. • Testosterone 2β-hydroxylation differed between these equine CYPs. • Five missense variants with a minor allele frequency (MAF) between 0.2 and 0.4 were obtained. • A common splice site variant with a MAF between 0.2 and 0.4 was found for CYP3A94. • CYP3A94217Asn, CYP3A95214His and CYP3A95392Thr modulated 2β-hydroxylation. [ABSTRACT FROM AUTHOR]

• Conformation of linked scFvs cause multipeak elution of bispecific antibodies. • Balance of interdomain and protein surface interactions is critical. • A single linked scFv causes two elution peaks, a pair causes three peaks. • Interdomain crosslinking eliminates multipeak elution behavior. • CEX base matrix hydrophobicity promotes extended BiSAb configurations. In Part I of this work we determined the experimental cation exchange behavior of bivalent bispecific antibodies (BiSAb) comprising a pair of single chain variable fragment (scFv) domains flexibly linked to a framework immunoglobulin G (IgG), which exhibit a complex, three-peak elution pattern dependent on the residence time. A phenomenological model was developed assuming that the BiSAb molecules exist in multiple configurations that interact differently with the resin surface and interconvert at finite rates. In Part II of this work we provide relevant biomolecular perspectives that shed light on the underlying mechanisms. Firstly, we show that crosslinking the BiSAb molecules with a bifunctional reagent, which limits conformational flexibility, suppresses multiple peak elution. Secondly, we show that of the fragments obtained by enzymatic digestion of the BiSAb molecules only those that exhibit a pair of scFv domains show three-peak elution, while only two peaks are observed if a single scFv is present. Thirdly, we analyze the roles of electrostatic and hydrophobic surface properties of the BiSAb domains, identifying regions that are likely responsible for inter-domain and protein-surface interactions. The results demonstrate that the complex elution behavior catalyzed by the combination of surface charge and hydrophobicity of the stationary phase is associated with outstretched and collapsed configurations of the scFv domains relative to the framework IgG. [ABSTRACT FROM AUTHOR]

Herein, we report four series of mutual prodrugs of epalrestat by combining it with different antioxidants using glycine, beta-alanine, and phenylalanine as a linker and by directly linking them through an ester linkage. The designed prodrugs were subjected to pharmacophore and docking-based virtual screening to determine the susceptibility of these prodrugs to be hydrolyzed by human carboxylesterases (hCES1 and hCES2). Five best prodrugs from each series were further submitted to detailed mechanistic study of hCES1 and hCES2 based hydrolytic activation using quantum mechanics and molecular dynamics approach. Additionally, Verloop'ssterimol parameters (B1-B5, L) were calculated in order to investigate the steric constraint of prodrugs to the catalytic sites of hCES1 and hCES2 enzymes. Our results indicated that, among these prodrugs, EP-D4, EP-E13, EP-F5, and EP-F14 are best substrates for hCES1 while EP-G3 and EP-G15 are potential substrates for hCES2. On the other hand, EP-D19 serves as good substrates for both enzymes. Image 1 • Epalrestat-antioxidant mutual prodrugs were designed. • Homology model was built for hCES2. • Pharmacophore models were generated for both hCES1 and hCES2. • Molecular docking and dynamics simulations were performed. • Quantum mechanical and sterimol parameters were calculated to determine the catalytic efficiency of hCES1 and hCES2. [ABSTRACT FROM AUTHOR]

• Immunoblotting analysis and ELISA yielded 5 of 5 positive reactions to recombinant Der f 32. • Eight B-cell epitopes and four T-cell epitopes of Der f 32 were determined ultimately via different bioinformatic tools. • A typical structure of T-cell epitopes being surrounded by B-cell epitopes in Der f 32 was elucidated. • Our present results are beneficial for the diagnosis and treatment of dust-mite allergic disorders. Dermatophagoides farinae is a common indoor allergen source that produces more than 30 allergens, which induces diverse allergic diseases such as allergic rhinitis, allergic asthma and atopic dermatitis. Der f 32 is an inorganic pyrophosphatase and an important allergen from Dermatophagoides farinae. In the present study, Der f 32 was cloned, expressed and purified in order to better understand its structure and immunogenicity. Immunoblotting analysis and ELISA showed 5 of 5 positive reactions to recombinant Der f 32 using serum from house dust mite (HDM)-allergic patients. We constructed homology modeling and predicted epitopes of Der f 32 via bioinformatic tools. The sequence and structural analysis indicated that Der f 32 belonged to the pyrophosphatase family and represented a special structure of external α-helices and internal antiparallel closed β-sheets. In addition, eight B-cell epitopes and four T-cell epitopes were predicted. B-cell epitopes were 24–31, 111–121, 135–140, 168–172, 200–207, 214–220, 237–243, and 268–274 and T-cell epitopes were 47–55, 78–90, 127–135 and 143–151. The B-cell epitopes were distributed completely on the surface of Der f 32 and were located largely in random coils of secondary structures. Hydrophobic and charged amino acids comprised more than 80% of the residues of B-cell epitopes and may participate in IgE binding. The T-cell epitopes were located primarily in the interior of Der f 32 and, to a certain extent avoided degradation by proteases. The structures of T-cell epitopes were surrounded by B-cell epitopes, and this arrangement may have important biological significance for maintaining the immunogenicity of allergens. [ABSTRACT FROM AUTHOR]

Docking pose of compound 1x into the crystal structure of NPP3. A new series of sulfonate derivatives 1a – zk were synthesized and evaluated as inhibitors of nucleotide pyrophosphatases. Most of the compounds exhibited good to moderate inhibition towards NPP1, NPP2, and NPP3 isozymes. Compound 1m was a potent and selective inhibitor of NPP1 with an IC 50 value of 0.387 ± 0.007 µM. However, the most potent inhibitor of NPP3 was found as 1x with an IC 50 value of 0.214 ± 0.012 µM. In addition, compound 1e was the most active inhibitor of NPP2 with an IC 50 value of 0.659 ± 0.007 µM. Docking studies of the most potent compounds were carried out, and the computational results supported the in vitro results. [ABSTRACT FROM AUTHOR]

The global production of plastics increases every year, because these materials are widely used in several segments of modern life. Polyurethanes are a very important class of polymers, used in many areas of everyday life, from automotive equipments to mattresses. The waste management usually involves accumulation in landfills, incineration, and reuse processes. However, bioremediation processes are being increasingly tested, due to the efficiency of enzymes in the degradation, besides adding value to the generated waste. Several experimental tests indicate that hydrolases, such as proteases, ureases, and esterases, are able to degrade polyurethanes. In this work, the three-dimensional structure of enzymes that are experimentally know to degrade polyurethanes were obtained for the first time, by the technique of homology modeling. The theoretical models showed good stereochemical quality and through molecular dynamics simulations analysis it was observed the stability of the structures. The molecular docking results indicated that all ligands, monomers of polyurethane, showed favorable interactions with the modeled enzymes. Image 1 • Polyurethanases are enzymes that degrade polyurethanes. • Theoretical models of polyurethanases showed good stereochemical quality. • Monomers of polyurethane showed favorable interactions with the polyurethanases. • Molecular dynamics simulations provide insights about stability of polyurethanases. [ABSTRACT FROM AUTHOR]

In the metabolic glycosylation grid of steviol glycosides, UGT76G1 was shown to catalyze at least eight different glucosylation steps, including the formation of rebaudioside B (Reb B) and rebaudioside A (Reb A) (Olsson et al., 2016). In this study, the accumulation of steviolbioside, Reb B, stevioside (ST) and Reb A in more than 140 samples of stevia leaves collected from different regions in China were analyzed by high-performance liquid chromatography (HPLC), and five genotypes, 'N01-N05', with significantly different levels of the abovementioned glycosides were discovered. Mutations in the UGT76G1 gene cloned from cDNAs from these five genotypes were identified, and the functions of the recombinant UGT76G1 variants were ascertained by adding steviolbioside and ST substrates. In addition, homology modeling and molecular docking were used to elucidate the functional differences between variants and UGT76G1. Comparing the sequences of the five variants ' N01-N05 ' with UGT76G1 (AY345974.1) revealed that base substitutions were not observed in ' N01 '. By contrast, ' N02 ' exhibited 9 single nucleotide polymorphisms (SNPs) and 9 associated amino acid substitutions or insertions with notable variations in the protein structure; however, an enzyme assay showed similar functionalities between the variant and UGT76G1. In ' N03 ', 49 SNPs and 29 associated amino acid substitutions or insertions were identified and shown to induce significant variations in the protein structure, especially in the binding pocket, resulting in the lack of functionality of this variant in the enzyme assay. These results were in agreement with the docking profiles. Moreover, a nonsense mutation of p.1090T > G in ' N04 ' and an insertion of a 68 base fragment in ' N05 ' were found, and both produced a premature protein without any catalytic activity. Therefore, UGT76G1 , which is vital to the content of main steviol glycosides, should be a key gene marker for the molecular breeding of Stevia rebaudiana. Our investigations also revealed the location and orientation of active groups of the receptors and donors in the UGT76G1 enzyme, which play key roles in determining whether the enzyme has any enzymatic activity. Image 1 • Five stevia genotypes with significantly different concentration of steviol glycosides were found by a broad screening. • Five variants of UGT76G1 were finally detected and three of them were discovered for the first time. • Insertion of a fragment containing 68 bases in the UGT76G1 leds to production of premature protein. • UGT76G1 should be a key marker gene for molecular breeding of S. rebaudiana. • The location and orientation of active groups of receptor and donor play a key role to the enzyme activity of UGT76G1. [ABSTRACT FROM AUTHOR]

Abstract Noroviruses are the primary cause of non-bacterial acute gastroenteritis worldwide, and GII.8 belongs to a non-epidemic genotype with a limited understanding currently. In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the "4+1+1" application strategy with newly designed primer sets, the genome of one GII.8 strain GZ2017-L601 from China was firstly sequenced that comprised 7476 nucleotides. The homology of the new genome and the previous only GII.8 genome reached 93.8% identity at the nucleotide level, but only 10, 6, 7 amino acid mutations occurred in three ORFs. When compared the new strain with other GII reference strains, p22 and P2 were calculated as the variable encoding regions, and NTPase, VPg, 3CL, RdRp and S were shown as the conserved ones. We then reconstructed the evolutionary process of the GII.8 genotype using other available sequences in GenBank. Based on the partial N/C region, all GII.8 strains could be subdivided chronologically into four clusters, which spans 1967–1994, 1997–2005, 2003–2009, and 2007–2017, respectively. Moreover, differences of capsid P proteins between GII.8 strains and the epidemic GII.4 strain VA387 were also compared. There existed 147/310 distinct amino acid sites in the alignment, including two insertion and three deletion mutations. Distribution of antigen epitopes of two GII.8 variants was comparable, but the numbers of antigenic sites of GII.8 strains were less than that of VA387. In summary, the first GII.8 genome from China was assembled and extensively characterized, and a time-order evolutionary process of this genotype was identified with a static pattern of antigenic variations. Highlights • The first GII.8 norovirus genome sequence from China was obtained and analyzed. • GII.8 could be chronologically divided into four clusters based on the N/C region. • The numbers of antigenic sites of GII.8 strains were less than that of GII.4 VA387. • No obvious changes in epitope distribution were found between different GII.8 strains. [ABSTRACT FROM AUTHOR]