Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b.

ORF3b is one of the SARS-CoV-2 accessory proteins. Previous experimental study suggested that ORF3b prevents IRF3 translocating to nucleus. However, the biophysical mechanism of ORF3b-IRF3 interaction is elusive. Here, we explored the conformation ensemble of ORF3b using all-atom replica exchange molecular dynamics simulation. Disordered ORF3b has mixed α-helix, ß-turn and loop conformers. The potential ORF3b-IRF3 binding modes were searched by docking representative ORF3b conformers with IRF3, and 50 ORF3b-IRF3 complex poses were screened using molecular dynamics simulations ranging from 500 to 1000 ns. We found that ORF3b binds IRF3 predominantly on its CBP binding and phosphorylated pLxIS motifs, with CBP binding site has the highest binding affinity. The ORF3b-IRF3 binding residues are highly conserved in SARS-CoV-2. Our results provided biophysics insights into ORF3b-IRF3 interaction and explained its interferon antagonism mechanism.

Meteorological drought migration characteristics based on an improved spatiotemporal structure approach in the Loess Plateau of China.

The development of drought has spatial and temporal synchronization. Previous studies usually explore the spatial and temporal evolution of drought separately. Moreover, existing approaches are based on a fixed overlapping area and do not consider the variable drought cluster area during development. This study proposes an improved and simple approach to derive dynamic overlapping area threshold for 3-dimensional droughts extraction. Based on the one monthly Nonparametric Standardized Precipitation Index (NSPI), this improved approach was applied for investigating the migration characteristics of meteorological drought events in the Loess Plateau of China. Then, Random Forest and Extreme Gradient Boosting model with Shapley additive explanation values were used to quantify the importance of driving factors on the dynamics of drought characteristics. The results showed that: (1) the improved approach has a better performance on identifying prolonged droughts than the method using a fixed overlap area threshold; (2) spatially, meteorological drought events with high severity (DS), long duration (DD), large effected area (DA) and fast migration velocity (DV) mainly occur in the central region; (3) temporally, droughts are expected to aggravate with significantly increased DS and DA which are mainly caused by increased temperature and vegetation; and (4) meteorological droughts have a preferred westward migration direction and three dominant migration paths, which are crucial for local drought prevention and control. The findings of this study provide new perspectives on drought migration characteristics, which are important for the exploration of drought-driven mechanisms, risk assessment and future prediction.

Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies' Recognition of TRBC1 and TRBC2.

T cell receptor ß-chain constant (TRBC) is a promising class of cancer targets consisting of two highly homologous proteins, TRBC1 and TRBC2. Developing targeted antibody therapeutics against TRBC1 or TRBC2 is expected to eradicate the malignant T cells and preserve half of the normal T cells. Recently, several antibody engineering strategies have been used to modulate the TRBC1 and TRBC2 specificity of antibodies. Here, we used molecular simulation and artificial intelligence methods to quantify the affinity difference in antibodies with various mutations for TRBC1 and TRBC2. The affinity of the existing mutants was verified by FEP calculations aided by the AI. We also performed long-time molecular dynamics simulations to reveal the dynamical antigen recognition mechanisms of the TRBC antibodies.

Recent Progress in Antibody Epitope Prediction.

Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application significance, especially conformational epitope prediction. In this review, we examined the general features of antibody-antigen recognition, highlighting the conformation selection mechanism in flexible antibody-antigen binding. We recently highlighted the success and warning signs of antibody epitope predictions, including linear and conformation epitope predictions. While deep learning-based models gradually outperform traditional feature-based machine learning, sequence and structure features still provide insight into antibody-antigen recognition problems.

Accelerating antibody discovery and design with artificial intelligence: Recent advances and prospects.

Therapeutic antibodies are the largest class of biotherapeutics and have been successful in treating human diseases. However, the design and discovery of antibody drugs remains challenging and time-consuming. Recently, artificial intelligence technology has had an incredible impact on antibody design and discovery, resulting in significant advances in antibody discovery, optimization, and developability. This review summarizes major machine learning (ML) methods and their applications for computational predictors of antibody structure and antigen interface/interaction, as well as the evaluation of antibody developability. Additionally, this review addresses the current status of ML-based therapeutic antibodies under preclinical and clinical phases. While many challenges remain, ML may offer a new therapeutic option for the future direction of fully computational antibody design.

Computational Construction of a Single-Chain Bi-Paratopic Antibody Allosterically Inhibiting TCR-Staphylococcal Enterotoxin B Binding.

Staphylococcal enterotoxin B (SEB) simultaneously crosslinks MHC class II antigen and TCR, promoting proliferation of T cells and releasing a large number of toxic cytokines. In this report, we computationally examined the possibility of using a single-chain biparatopic bispecific antibody to target SEB and prevent TCR binding. The design was inspired by the observation that mixing two anti-SEB antibodies 14G8 and 6D3 can block SEB-TCR activation, and we used 14G8-6D3-SEB tertiary crystal structure as a template. Twelve simulation systems were constructed to systematically examine the effects of the designed bispecific scFV MB102a, including isolated SEB, MB102a with different linkers, MB102a-SEB complex, MB102a-SEB-TCRß complex, MB102a-SEB-TCR-MHC II complex, and MB102a-SEB-MHC II. Our all atom molecular dynamics simulations (total 18,900 ns) confirmed that the designed single-chain bispecific antibody may allosterically prevent SEB-TCRß chain binding and inhibit SEB-TCR-MHC II formation. Subsequent analysis indicated that the binding of scFV to SEB correlates with SEB-TCR binding site motion and weakens SEB-TCR interactions.

Conformational Ensemble of TteAdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition.

Cobalamin riboswitch is a cis-regulatory element widely found in the 5'-UTRs of the vitamin B12-associated genes in bacteria, resulting in modulation and production of a particular protein. Thermoanaerobacter tengcongensis (Tte) AdoCbl riboswitches are the largest of the known riboswitches with 210 nucleotides, partially due to its long peripheral P6-extension, which enable high affinity of AdoCbl. Two structural elements, T-loop/T-looplike motif and kissing loop are key to the global folding of the RNA. While the structure of the TteAdoCbl riboswitch complex is known, we still do not understand the structure and conformation before AdoCbl ligand recognition. In order to delineate the conformational changes and the stabilities of long-range interactions, we have performed extensive all-atom replica-exchange molecular dynamics simulations of the TteAdoCbl riboswitch with a total simulation time of 2296 ns. We found that both the T-loop/T-looplike motif and kissing loop are very stable with ligand binding. The gating conformation changes of P6-extension allow the ligand to bind to the preorganized kissing loop binding pocket. The T-loop/T-looplike motif has much more hydrogen bonds than observed in TteAdoCbl riboswitch complex crystal structure, indicating an allosteric response of the T-loop/T-looplike motif. Our study demonstrated that the conformational ensemble of TteAdoCbl riboswitch provides stable structural elements for conformation selection and population shift in cobalamin recognition.

Annosquacin B induces mitochondrial apoptosis in multidrug resistant human breast cancer cell line MCF-7/ADR through selectively modulating MAPKs pathways.

CONTEXT: Multidrug resistance (MDR) is a major obstacle to efficient therapy of cancers. It is a prime concern for researchers to find compounds with anti-proliferative activity on MDR cell lines. In recent years, annonaceous acetogenins (ACGs) were reported to have anti-proliferative activity. However, the underlying mechanisms are still unknown. OBJECTIVE: This study determines the mechanisms of anti-proliferative activity induced by Annosquacin B (AB) against MCF-7/ADR cells. MATERIAL AND METHODS: The cytotoxicity of AB at varying concentrations (0.64, 1.6, 4, 10, 25, 62.5, 156.25 µM) on MCF-7/ADR cells was assessed using the MTT assay. Annexin V-FITC/propidium iodide staining and Acrinidine orange and ethidium bromide (AO/EB) staining were employed to investigate whether AB (14, 7, 3.5 µM) could induce apoptosis in MCF-7/ADR cells. Levels of caspase-3 and caspase-9, Bax, Bcl-2 and MAPKs kinases were evaluated by western blot assay following treatment with various concentrations of AB (3.5, 7, 14 µM) at different time points (0, 0.5, 1, 2, 4, 8, 12 h). RESULTS AND CONCLUSION: MTT assay showed that AB significantly decreased cell viability on MCF-7/ADR (IC50 of 14.69 µM). AB-induced apoptosis in MCF-7/ADR cells through mitochondrial apoptosis pathways. It induced typical apoptosis by morphologic changes; elevate levels of caspase-3, caspase-9 as well as the ratio of Bax/Bcl-2. In addition, AB increased the expression of p-p38 MAPK and decreased the expression of p-JNK, while whether ERK1/2 had an effect on the MCF-7/ADR apoptosis remains to be determined.

[Discussion of HPLC fingerprint of traditional Chinese medicine of Corydalis yanhusuo and its preparation].

Fingerprint of traditional Chinese medicine (TCM) is in the guidance of the basic theory of TCM, according to the variety and quality of TCM and using a variety of analytical methods and technology, to establish the objective, overall and multi index comprehensive evaluation system. The TCM fingerprint in one of the strategic subjects for TCM modernization. As more and more technologies have been applied to the fingerprint research of TCM, it is sure to play a much more important role in many aspects, such as the quality control of TCM, the researches of efficient components, and the mechanism in TCM, and so on. The fingerprint technology includes many modern technologies such as high-pressure liquid chromatography (HPLC). Corydalis yanhusuo is an ancient TCM, and recent years appears many researches about fingerprint of C. yanhusuo. This paper generalizes the research in progresses in research and analytical methods on fingerprint technology of C. yanhusuo, processed products (vinegar), and painkillers, to provide the scientific basis for fingerprint method and quality control of C. yanhusuo.

Lipophilic constituents from two processed products and three different parts of Changium smyrnioides Wolff.

This article reports the lipophilic chemical composition of different processed products (Changii Radix, Changii Radix Alba) and parts (root bark, leaf and fruit) of Changium smyrnioides Wolff.. The lipophilic constituents were extracted with petroleum ether in Soxhlet apparatus, subsequently identified and determined by gas chromatography-mass spectroscopy (GC-MS). Yield of lipophilic constituents from Changii Radix (3.65%) was about three times more than Changii Radix Alba's (1.07%), which indicated processing by boiling in water had an impact on the content of lipophilic constituents. Moreover, the major compounds in different processed products and parts were found to be fatty acids and sesquiterpenes. The results are a contribution for the lipophilic chemical composition and can serve as a reference for product development of Changium smyrnioides Wolff..

Structure-activity relationships of diverse ACGs against multidrug resistant human lung cancer cell line A549/Taxol.

Fifteen annonaceous acetogenins (ACGs) with different stereochemical structures and configuration, representing three main classes of bis-adjacent-tetrahydrofuran (THF), bis-nonadjacent-THF, and mono-THF ACGs, were selected to tested for their inhibition activity on A549/Taxol cell line, which is multidrug resistant (MDR). The present study showed that some tested compounds showed significant activity toward A549/Taxol cells, and were more potent than the positive control Verapamil. For example, squamostatin-D (14) (IC50 value=16.19µM) was 7.8 times more active than Verapamil (IC50 value=127.09µM). Those ACGs with more carbons between the THF ring and the γ-unsaturated lactone were more potent. Moreover, ACGs with stereochemical arrangement of erythro were more active than those of threo, the compounds with THF ring configuration of cis seemed to be superior to those of trans. However, if all other structural features were identical, the ACGs with more hydroxyls on the aliphatic chain were not more potent towards A549/Taxol, which was not in accordance with previous studies. Furthermore, bis-nonadjacent-THF ACGs whose molecular weight is 622, with three hydroxyl groups located at carbon 16, 19, 24 and stereochemical arrangement of erythro possibly produced notable cytotoxicity. Based on the above conclusions, we proposed a compound model that may be a promising anti-MDR cancer candidate drug in the future clinical trial.

[Low Polar Constituents from Annona squamosa Fruit Pericarp].

OBJECTIVE: To study the low polar constituents from Annona squamosa fruit pericarp. METHODS: The fruit pericarp was percolated with 95% EtOH at room temperature. The extract was subjected to Silica gel chromatography and eluted with gradually more polar and EtOAc-MeOH mixtures. The part eluted range Pet-EtOAc from 5:1 to 1:1 was subjected to repeated column chromatography. The constituents were identified by physicochemical property and NMR data. RESULTS: Eight constituents were isolated and identified as tricosane(1), ß-sitosterol(2), succinic acid (3), annosquamosin D(4), 4α-hydroxy-19-nor-(E)-kauran-17-oic acid(5), (E)-16ß, 17-dihydroxy-kauran-19-oic acid(6), (E)-16α, 17-dihydroxy-kauran-19-oic acid(7), and 16ß-hydroxy-17-acetoxy-(E)-kauran-19-oic acid(8). CONCLUSION: All constituents are firstly isolated from Annona squamosa fruit pericarp except compound 6.