FitDock: protein-ligand docking by template fitting.

Protein-ligand docking is an essential method in computer-aided drug design and structural bioinformatics. It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation sampling and scoring, which are computationally expensive and difficult. Recent studies demonstrated that it can be beneficial to docking with the guidance of existing similar co-crystal structures. In this work, we developed a protein-ligand docking method, named FitDock, which fits initial conformation to the given template using a hierarchical multi-feature alignment approach, subsequently explores the possible conformations and finally outputs refined docking poses. In our comprehensive benchmark tests, FitDock showed 40%-60% improvement in terms of docking success rate and an order of magnitude faster over popular docking methods, if template structures exist (> 0.5 ligand similarity). FitDock has been implemented in a user-friendly program, which could serve as a convenient tool for drug design and molecular mechanism exploration. It is now freely available for academic users at http://cao.labshare.cn/fitdock/.

CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting.

Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. The web server is freely available at https://cadd.labshare.cn/cb-dock2/.

Effect of molecular weight of chitosan on quercetin-loaded chitosan nanoparticles.

BACKGROUND: The widespread use of quercetin is limited by its instability, low solubility and poor oral bioavailability. Encapsulation of quercetin using a nanoparticle delivery system is an effective way to overcome these drawbacks. RESULTS: The effect of the molecular weight (Mw) of chitosan (CS) (100, 200, 500 and 1000 kDa) on quercetin-loaded chitosan nanoparticles (QCNPs) was investigated. The structure, stability, release properties and antioxidant activities of the nanoparticles (QCNP-10, QCNP-20, QCNP-50 and QCNP-100) were assessed. Particle size of QCNPs decreased and polydispersity index increased with the increasing Mw of CS. The main forces involved in the formation of QCNPs were hydrogen bonding and hydrophobic interaction. X-ray diffraction verified that quercetin was loaded into CS nanoparticles. The photostability and thermal stability of QCNPs increased with increasing Mw of CS. QCNP-100 exhibited the lowest release rate in a mixture of water and anhydrous ethanol. The antioxidant activities of QCNPs were enhanced with increasing Mw of CS, and QCNP-100 possessed the highest antioxidant activities, which might be relevant to its smallest particle size. CONCLUSION: Overall, these results revealed that the Mw of CS affected the properties of QCNPs, and QCNP-100 possessed the smallest particle, best stability, lowest release rate and highest antioxidant activities. © 2024 Society of Chemical Industry.

DrugRep: an automatic virtual screening server for drug repurposing.

Computationally identifying new targets for existing drugs has drawn much attention in drug repurposing due to its advantages over de novo drugs, including low risk, low costs, and rapid pace. To facilitate the drug repurposing computation, we constructed an automated and parameter-free virtual screening server, namely DrugRep, which performed molecular 3D structure construction, binding pocket prediction, docking, similarity comparison and binding affinity screening in a fully automatic manner. DrugRep repurposed drugs not only by receptor-based screening but also by ligand-based screening. The former automatically detected possible binding pockets of the receptor with our cavity detection approach, and then performed batch docking over drugs with a widespread docking program, AutoDock Vina. The latter explored drugs using seven well-established similarity measuring tools, including our recently developed ligand-similarity-based methods LigMate and FitDock. DrugRep utilized easy-to-use graphic interfaces for the user operation, and offered interactive predictions with state-of-the-art accuracy. We expect that this freely available online drug repurposing tool could be beneficial to the drug discovery community. The web site is http://cao.labshare.cn/drugrep/ .

Physicochemical and functional property of the Maillard reaction products of soy protein isolate with L-arabinose/D-galactose.

BACKGROUND: Soy protein isolate (SPI) is widely used in the food industry because of its nutritional and functional properties. During food processing and storage, the interaction with co-existing sugars can cause changes in the structural and functional properties of SPI. In this study, SPI-l-arabinose conjugate (SPI:Ara) and SPI-d-galactose conjugate (SPI:Gal) were prepared using Maillard reaction (MR), and the effects of five-carbon/six-carbon sugars on the structural information and function of SPI were compared. RESULTS: MR unfolded and stretched the SPI, changing its ordered conformation into disorder. Lysine and arginine of SPI were bonded with the carbonyl group of sugar. The MR between SPI and l-arabinose has a higher degree of glycosylation compared to d-galactose. MR of SPI enhanced its solubility, emulsifying property and foaming property. Compared with SPI:Ara, SPI:Gal exhibited better aforementioned properties. The functionalities of amphiphilic SPI were enhanced by MR, SPI:Gal possessed better hypoglycemic effect, fat binding capacity and bile acid binding ability than SPI:Ara. MR endowed SPI with enhanced biological activities, SPI:Ara showed higher antioxidant activities, and SPI:Gal exhibited stronger antibacterial activities. CONCLUSION: Our work revealed that l-arabinose/d-galactose exhibited different effects on the structural information of SPI, and further affected its physicochemical and functional property. © 2023 Society of Chemical Industry.

The Impact of Food Processing on the Structure and Hypoglycemic Effect of Oat ß-glucan.

The impact of food processing including baking, steaming and bread making, on the structure and hypoglycemic effect of oat ß-glucan was studied. The structural analysis revealed the ß-D-glucopyranosyl units of ß-glucan was unchanged in aforementioned processing. The baking processing endowed ß-glucan with increased molecular weight (Mw) and viscosity, which enhanced the capacity of ß-glucan to delay starch digestion in vitro, such as the rapidly-digestible starch content decreased, the slowly-digestible and resistant starch content increased, and the glycemic index (GI) value decreased. Meanwhile, the inhibitory activity of ß-glucan against α-glucosidase and α-amylase was enhanced by baking processing. By contrast, during steaming and bread making processing, ß-glucan showed decreased Mw and viscosity, which accelerated starch digestion in vitro and reduced the inhibitory activity of ß-glucan against α-glucosidase and α-amylase. Apart from that, baking processing promoted the physiological and antioxidant properties of ß-glucan, but the properties decreased during steaming and bread making processing. The results suggest that oat raw materials can be treated with dry heat and high temperature, avoiding moist heat and fermentation treatments to maximize the hypoglycemic effect of ß-glucan.

DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design.

Since the outbreak of SARS-CoV-2, numerous compounds against COVID-19 have been derived by computer-aided drug design (CADD) studies. They are valuable resources for the development of COVID-19 therapeutics. In this work, we reviewed these studies and analyzed 779 compounds against 16 target proteins from 181 CADD publications. We performed unified docking simulations and neck-to-neck comparison with the solved co-crystal structures. We computed their chemical features and classified these compounds, aiming to provide insights for subsequent drug design. Through detailed analyses, we recommended a batch of compounds that are worth further study. Moreover, we organized all the abundant data and constructed a freely available database, DrugDevCovid19, to facilitate the development of COVID-19 therapeutics.

Leucandioxoles A and B, two 1,3-benzodioxole derivatives from the South China Sea sponge Leucandra sp.

Two new 1,3-benzodioxole derivatives, leucandioxoles A and B (1-2), together with two known related compounds (3-4), have been isolated from the South China Sea sponge Leucandra sp. The structures of all compounds were clearly elucidated on the basis of spectroscopic analyses and compared with the literatures. The cytotoxicity against A549, Hep G2, MDA-MB-231, and HeLa cell lines of 1-4 were evaluated. Only compound 1 exhibited moderate activity against MDA-MB-231 cells with the IC50 value of 7.98 ± 0.74 µM.

Cytotoxic Bryostatin Derivatives from the South China Sea Bryozoan Bugula neritina.

Four new macrocyclic lactones, bryostatin 21 (1) and 9-O-methylbryostatins 4, 16, and 17 (2-4), together with three known related compounds, bryostatins 4, 16, and 17 (5-7), have been isolated from an extract of the South China Sea bryozoan Bugula neritina. The structures of all compounds were unambiguously elucidated using detailed spectroscopic analysis. Structurally, the presence of a single methyl group at C-18 in compound 1 has not been observed before for known bryostatins. The isolated macrolides exhibited inhibitory effects against a small panel of human cancer cell lines.

Three new aaptamine derivatives from the South China Sea sponge Aaptos aaptos.

Three new aaptamine derivatives (1-3), together with six known related compounds (4-9), have been isolated from the South China Sea sponge Aaptos aaptos. The structures of all compounds were unambiguously elucidated on the basis of spectroscopic analyses. Compounds 1, 4, 5, 7, and 9 showed cytotoxic activities against HeLa, K562, MCF-7, and U937 cell lines with IC50 values in the range of 0.90-12.32 µM.

Cytotoxic aaptamine derivatives from the South China Sea sponge Aaptos aaptos.

Nine new aaptamine derivatives (1-9), together with three known related compounds (10-12), have been isolated from the South China Sea sponge Aaptos aaptos. The structures of all compounds were unambiguously elucidated on the basis of spectroscopic analyses. Structurally, compound 1 possesses a piperidinyl group fused to a demethyl(oxy)aaptamine moiety, whereas compounds 3-6 share an imidazole-fused 1H-benzo[de][1,6]naphthyridin-2(4H)-one skeleton. The cytotoxic activities of the compounds were evaluated against various human cancer cell lines, and compounds 2, 8, 11, and 12 showed potent cytotoxicities against HL60, K562, MCF-7, KB, HepG2, and HT-29 cells, with IC50 values in the range of 0.03 to 8.5 µM.

Aaptamine derivatives with antifungal and anti-HIV-1 activities from the South China Sea sponge Aaptos aaptos.

Five new alkaloids of aaptamine family, compounds (1-5) and three known derivatives (6-8), have been isolated from the South China Sea sponge Aaptos aaptos. The structures of all compounds were unambiguously elucidated by spectroscopic analyses, as well as by comparison with the literature data. Compounds 1-2 are characterized with triazapyrene lactam skeleton, whereas compounds 4-5 share an imidazole-fused aaptamine moiety. These compounds were evaluated in antifungal and anti-HIV-1 assays. Compounds 3, 7, and 8 showed antifungal activity against six fungi, with MIC values in the range of 4 to 64 µg/mL. Compounds 7-8 exhibited anti-HIV-1 activity, with inhibitory rates of 88.0% and 72.3%, respectively, at a concentration of 10 µM.

[Present status and trend of heart fluid mechanics research based on medical image analysis].

With introduction of current main methods for heart fluid mechanics researches, we studied the characteristics and weakness for three primary analysis methods based on magnetic resonance imaging, color Doppler ultrasound and grayscale ultrasound image, respectively. It is pointed out that particle image velocity (PIV), speckle tracking and block match have the same nature, and three algorithms all adopt block correlation. The further analysis shows that, with the development of information technology and sensor, the research for cardiac function and fluid mechanics will focus on energy transfer process of heart fluid, characteristics of Chamber wall related to blood fluid and Fluid-structure interaction in the future heart fluid mechanics fields.

The Structural Framework and Opening Appearance of the VP1-Pocket of Enteroviruses Correlated with Viral Thermostability.

Enteroviruses (EVs and RVs) are prevalent worldwide and cause various diseases in humans, of which the VP1-pocket is a target of antivirals, with a lipid molecule as a pocket factor to stabilize the virion. However, the characterization of the structure of the VP1-pocket in EVs is poor. Here, we compared the published capsid crystals of EVs and RVs and proposed a structural framework for the VP1-pocket: Frame 1-4, which is located at the CD loop, GH loop, and C-terminus, presenting with an outward opening appearance or not. The non-outward viral strains-CVB3, Echo 11, RV-A81, and RV-B70-are more thermally stable, with a breakpoint temperature (B.T.) of 51~62 °C for genome releasing, which is 4~10 °C higher than its outward temperature of 41~47 °C, and infectivity preservation when treated at 50 °C for 3 min. Its outward versus non-outward opening is correlated significantly with the B.T. for genome release (r = -0.90; p = 0.0004) and infectivity (r = -0.82, p = 0.0039). The energy of Frames 1, 2, and 4, including Van der Waals attractive and repulsive interactions and hydrogen bonds, showed significant correlations with the B.T. (r = -0.67, 0.75, and -0.8; p = 0.034, 0.013, and 0.006, respectively). These characters of the VP1-pocket could be predictors for virion thermostability and aid in the development of vaccines or antivirals.

Woodylides A-C, new cytotoxic linear polyketides from the South China Sea sponge Plakortis simplex.

Three new polyketides, woodylides A-C (1-3), were isolated from the ethanol extract of the South China Sea sponge Plakortis simplex. The structures were elucidated by spectroscopic data (IR, 1D and 2D NMR, and HRESIMS). The absolute configurations at C-3 of 1 and 3 were determined by the modified Mosher's method. Antifungal, cytotoxic, and PTP1B inhibitory activities of these polyketides were evaluated. Compounds 1 and 3 showed antifungal activity against fungi Cryptococcus neoformans with IC50 values of 3.67 and 10.85 µg/mL, respectively. In the cytotoxicity test, compound 1 exhibited a moderate effect against the HeLa cell line with an IC50 value of 11.2 µg/mL, and compound 3 showed cytotoxic activity against the HCT-116 human colon tumor cell line and PTP1B inhibitory activity with IC50 values of 9.4 and 4.7 µg/mL, respectively.

Physical, Mechanical and Biological Properties of Phenolic Acid-Grafted Soluble Soybean Polysaccharide Films.

Three kinds of phenolic acid-grafted soluble soybean polysaccharide (SSPS) with similar grafting ratios were prepared, and their structure was characterized by FT-IR, UV-vis and 1 H NMR. The impact of phenolic acid on the antioxidant activity of SSPS was evaluated. Then, films were prepared by using phenolic acid-grafted SSPS. The physical, mechanical and biological performances of phenolic acid-grafted SSPS films were further investigated. The results indicated that an ester linkage was formed between the SSPS and phenolic acid. The grafting ratio of para-hydroxybenzoic acid, protocatechuic acid and gallic acid-grafted SSPS was 29.45, 31.76 and 30.74 mg/g, respectively. Phenolic acid endowed SSPS with improved antioxidant properties. Gallic acid (GA)-grafted SSPS possessed the best DPPH radical scavenging ability and reducing power, which may be related to the three phenolic hydroxyl groups in GA. Phenolic acid-grafted SSPS films showed increased moisture content and decreased water solubility compared to SSPS film. The phenolic acid-g-SSPS decreased the mechanical properties but enhanced the water vapor barrier property, and antioxidant and antibacterial properties of SSPS film. Meanwhile, the para-hydroxybenzoic acid-grafted SSPS film showed the lowest water vapor permeability (3.70 × 10-7 g mm/h cm2 Pa), and the GA-grafted SSPS film exhibited the best antioxidant and antibacterial activities.

Taste compounds generation and variation of broth in pork meat braised processing by chemical analysis and an electronic tongue system.

The aim was to unveil the generation and variation rule of the main taste components in braised broth for 10 quantitative repeated braising cycles. The major taste compounds of three groups (MS, broth cooked with meat and spices; M, broth cooked with meat; and S, broth cooked with spices) were systematically analyzed by the state-of-art chromatography and electronic sensory technology. As braising cycles progressed, contents of free 5'-nucleotides and amino acids were increased in MS and M, while those nucleotides were not detected in S. A significant discrimination of taste in MS and M was revealed by electronic tongue evaluation during the process. As the formation rates (FR) of taste compounds and the transformation rates (TR) of taste compounds to volatile compounds were mainly accounting for the generation and variation of flavor in broth, a hypothesis was proposed to illustrate the whole variation of taste compounds in the process integrally that the ratio of FR/TR dividing the process into three stages, Degradation, Balance, and Accumulation. PRACTICAL APPLICATIONS: The traditional braising process and formula are empirical and extensive, which impede the increase in meat products output. Nowadays, the industry of braising products is facing a problem of standardization and quality control, and needs to carry out scientific and quantitative process improvement efficiently. Therefore, the developed comprehensive approach demonstrates great potential for braised meat broth flavor monitoring and quality control in an objective and holistic manner. It provides data support and new ideas of technology development for quality control in the process of meat braising.

Micro-nano particle formation and transformation mechanisms of broth in meat braised processing.

The formation and transformation mechanisms of micro-nano particles (MNPs) in broth during meat braising were systematically investigated through a sophisticated controlled process. Dynamic changes in the morphology, composition and spatial distribution of MNPs were comprehensively characterized, and subsequently the mechanisms were visually uncovered from microcosmic-spatial perspectives. MNPs formed as circular-shape colloidal systems with an aggrandizing tendency for particle number and size and gradually stabilize eventually. Specifically, the major MNPs gradually increased the size from <400 nm to ~1500 nm and accumulated triglycerides and glycoconjugates resulting from lipid oxidation, Maillard reaction, etc. Continuous formation of MNPs in broth progressively facilitated the spatial coalescence and self-assembly of free substances driven by intermolecular interactions, and consequently principal nutrients and flavor compounds further accumulated in the MNPs by the braising process. Hence, this work not only revealed the MNP formation and transformation mechanisms but offered a foundation for investigating MNP-dependent effect on broth flavor.

Functional properties and preservative effect on Penaeus vannamei of chitosan films with conjugated or incorporated chlorogenic acid.

The chlorogenic acid-grafted-chitosan conjugates (CA-g-CS) with three grafting ratios were synthesized. Then the CA-g-CS conjugated films (CA-g-CS I, CA-g-CS II, and CA-g-CS III) and the CA-CS incorporated films (CA-CS I, CA-CS II, and CA-CS III) with equivalent chlorogenic acid content were prepared, respectively. The physical, mechanical, and biological properties of CA-g-CS conjugated and CA-CS incorporated films were evaluated. Further, the CA-g-CS III and CA-CS III were chosen to evaluate their preservative effect on shrimp. Compared with CS film, CA-g-CS conjugated and CA-CS incorporated films showed enhanced opacity and water solubility, changed thickness and water vapor permeability, and reduced moisture content, tensile strength and elongation at break. Conjugation or incorporation of CA enhanced antioxidant and antibacterial activities of CS films, and these activities increased with the increasing of CA content. CA-g-CS III showed better preservative effect on shrimp than CA-CS III in terms of weight loss, pH value, total volatile basic nitrogen, total bacterial count and sensory score of shrimp during storage. Therefore, CA-g-CS conjugated films exhibited better bioactivities and preservative effect on shrimp than CA-CS incorporated films. Compared with incorporation, conjugation of CA with CS is a more efficient way to improve properties of CS film.

Integrated recognition and quantitative detection of starch in surimi by infrared spectroscopy and spectroscopic imaging.

Surimi products have become increasingly-consumed food with prominent characteristics of high nutrition and convenience and its supply falls short of demand. However, due to exhausted fishery resource in recent years, surimi adulteration, such as addition of plant proteins, starch and other animal origin meat, is becoming serious, so recognition of these exogenous substances has become an urgent issue. In this study, Fourier transform infrared spectroscopy (FT-IR) combined with infrared spectroscopic imaging could distinguish heterogeneity in surimi qualitatively and quantitatively and obtain integral chemical images so that spatial distribution of each component in surimi could be visually displayed, thus a rapid recognition method and a prediction model were developed. The different starch contents in surimi had been primarily identified through intensity change of infrared absorption peaks at 1045cm-1 and 988cm-1, specifically with peak shifts to 1041cm-1 and to 992cm-1, respectively. In infrared imaging analysis, principal components (PCs) were separated and one key PC was confirmed as starch by characteristic peaks comparison at 1147cm-1, 1075cm-1, 997cm-1 and 930cm-1. Meanwhile, an established statistic model could predict starch content in surimi correctly with a reliable correlation coefficient (R=0.9856) and root mean square error of prediction (RMSEP=5.64). Therefore, FT-IR combined with infrared spectroscopic imaging could be applicable to integrally recognize and quantitatively detect starch in surimi.