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Recent outbreaks of coronavirus have brought serious challenges to public health around the world, and it is essential to find effective treatments. In this study, the 3C-like proteinase (3CLpro) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been considered as an important drug target because of its role in viral replication. We initially optimized 251 compounds at the PM7 level of theory for docking with 3CLpro, and then we selected the top 12 compounds for further optimization with the B3LYP-D3/6-311G** method and obtained the top four compounds by further molecular docking. Quantum chemistry calculations were performed to predict molecular properties, such as the electrostatic potential and some CDFT descriptors. We also performed molecular dynamics simulations and free energy calculations to determine the relative stability of the selected four potential compounds. We have identified key residues controlling the 3CLpro/ligand binding from per-residue based decomposition of the binding free energy. Convincingly, the comprehensive results support the conclusion that the compounds have the potential to become a candidate for anti-coronavirus treatment.

Establish the quality control standard of rhubarb anti-trauma cataplasm. The qualitative analysis of rhubarb, angelica, and affective components of aloe-emodin, chrysophanol, and emodin has been done with thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC), respectively. The TLC spots of rhubarb and angelica in rhubarb antisurgery papu were clear, and the negative control had no interference. HPLC results demonstrate that high intense hydrophilic compound peaks are observed on the lower side; however, low intense peaks are towards the higher side of the scale. The intensity of these peaks is decreased from mixed reference solution to test solution and negative reference solution.

Since the main protease (Mpro) is crucial for the COVID-19 virus replication and transcription, searching for Mpro inhibitors is one possible treatment option. In our study, 258 small molecules were collected from lung-related herbal medicines, and their structures were optimized with the B3LYP-D3/6-31G* method. After the molecular docking with Mpro, we selected the top 20 compounds for the further geometry optimization with the larger basis sets. After the further molecular docking, the top eight compounds were screened out. Then we performed molecular dynamics simulations and binding free energy calculations to determine stability of the complexes. Our results show that mulberrofuran G, Xambioona, and kuwanon D can bind Mpro well. In quantum chemistry studies, such as ESP and CDFT analyses, the compounds properties are predicted. Additionally, the drug-likeness analyses and ADME studies on these three candidate compounds verified that all of them conform to Libinski’s rule and may be drug-like compounds. Communicated by Ramaswamy H. Sarma

In this paper, a fractional-order model for HIV with drug-resistance and CTL immune response is established. Two cases (subsystem with drug-sensitive and subsystem with drug-resistant) are considered. For both subsystems: firstly, the existence and uniqueness of the positive solution is proved; secondly, the sufficient conditions for the stability of the disease-free equilibrium are obtained; finally, some numerical simulations are performed to verify the theoretical results. After that, the main system is analyzed in a similar way. Calculation indicates that the basic reproduction number of the main system is the maximum value of the basic reproduction numbers of the corresponding subsystems. In addition, through numerical simulation, we know that the drug efficacy plays an important role in the treatment of HIV.

In order to investigate the influence of panel zone section size on the plastic damage distribution of H-shaped beam-column joints, a cruciform beam-column joint composed of common beams, columns a...

Plocabulin (PM060184) is a promising new anticancer drug as a microtubule inhibitor. The conformational structure and properties of plocabulin have been studied theoretically. The initial structure was screened by the B3LYP/3-21G* method, and then 32 unique conformations were further optimised with the B3LYP/6-311G* method. The single-point energies were determined at the M06-L/6-311G(2df,p) level. The UV excitation of the most stable plocabulin conformation in methanol was studied by the TD-CAM-B3LYP/6-311G(2df,p) method. High-quality human p-glycoprotein model was obtained through homology modelling. The binding interaction between p-glycoprotein and plocabulin was studied by docking and MD simulation. LEU65, TYR310, ILE340, THR945, PHE983, MET986, and GLN990 were found to be important amino acid residues in the interaction. From a certain perspective, the ‘reverse exclusion’ mechanism of plocabulin with p-glycoprotein was illustrated, and this mechanism provides theoretical guidance for the structural modification of plocabulin and for design of drug’s to avoid p-glycoprotein-mediated drug resistance.

Eight novel fluorescent antifolates were designed and docked with folate receptors FRα and FRβ. The structures of the complexes were further calculated by molecular dynamic (MD) simulations. The binding energies were calculated by molecular docking and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) studies. The binding energy differences between FRα and FRβ (|E

Emphysematous phenotype is the most important phenotypic component of chronic obstructive pulmonary disease and is associated with substantial morbidity and mortality. The current pharmaceutical treatments and therapeutic procedures do not reduce pulmonary damage in patients with emphysematous phenotype. Therefore, it is important to identify effector molecules that can be used as interfering targets in such patients. Apoptosis of type II alveolar epithelial cells plays a key role in the phenotypic formation. This study aimed to further explore the molecular mechanisms involved in this process. The number of type II alveolar epithelial cells was significantly reduced due to increased apoptosis in patients with emphysematous phenotype compared to those with non-emphysematous phenotype. Pleckstrin homology like domain, family A, member 1 (PHLDA1) was mainly distributed in type II alveolar epithelial cells in both groups but was markedly reduced in patients with emphysematous phenotype. Overexpression of PHLDA1 prevented cigarette smoke extract-stimulated apoptosis of type II alveolar epithelial cells, whereas its knockdown worsened the apoptosis. PHLDA1 binding ability to tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon (YWHAE) was weakened after exposure to cigarette smoke extract, with decreased PHLDA1 level lowering the abundance of YWHAE and attenuating the binding ability of YWHAE to p-Bad. These results demonstrate that considerable apoptosis of type II alveolar epithelial cells occurs in patients with emphysematous phenotype, and PHLDA1 may act as an effective antiapoptotic factor via YWHAE. Moreover, PHLDA1 may serve as a potential interfering target, providing insights into therapeutic strategies for emphysematous phenotype.

Background: The aim of this study was to assess the differences in lower cranial nerve (LCN) complications predicted by the normal tissue complication probability (NTCP) model between Radiation Therapy Oncology Group (RTOG) and reduced-volume intensity-modulated radiotherapy (IMRT) planning for nasopharyngeal carcinoma (NPC) radiotherapy. Methods: A total of fifty patients with NPC were divided into two groups according to T-stages of T1-2 and T3-4, and the LCNs of each patient were contoured on CT simulation images. The targets were contoured based on the RTOG 0225 clinical trial and a working committee for clinical stage NPC in China in 2010. The NTCP differences in LCNs between the two plans were calculated. Results: The LCN volume of the 50 patients was 10.07 cc. The Dmax and Dmean of LCNs in RTOG plans were significantly larger than those in reduced-volume plans (7,453 vs . 7,401 cGy, 6,740 vs . 6,436 cGy, P=0.004, 0.000), and these values were lower in the T1-2 group than in the T3-4 group (7,390 vs . 7,464 cGy, 6,442 vs . 6,733 cGy, P=0.019, 0.000). NTCP in RTOG plans was significantly higher than that in reduced- volume plans (59.98% vs . 51.62%, P=0.000), among which NTCP was significantly lower in the T1-2 group than in the T3-4 group (51.72% vs . 59.88%, P=0.002). There were strong correlations of NTCP with Dmean and irradiation volume for more than 6,600 cGy (R=0.847, P=0.000; R=0.841, P=0.000). Conclusions: the clinical T-stage, a high Dmean and a large irradiation volume are important factors in predicting LCN complications. Of the two most common IMRT guidance plans in China, the LCN NTCP based on the reduced-volume plan is significantly lower than that based on the RTOG plan.

Background: The purpose was to investigate the prognosis of patients with synchronous and metachronous squamous cell carcinoma of head and neck (HNSCC) and esophagus (ESCC), and to evaluate the prognostic factors of these patients. Methods: A retrospective review was performed on 70 patients with synchronous and metachronous HNSCC and ESCC treated in our institution from January 2005 to December 2016. Kaplan-Meier method and Cox proportional hazard model were used to evaluate overall survival (OS) and determine the prognostic factors associated with survival outcomes. Results: The 1-, 2- and 3-year OS rates were 77.1%, 57.1% and 37.1% with the median survival time for 33.5 months. The univariate analysis results revealed that the patients with early-stage of ESCC, metachronous cancer, and receiving surgery for both cancer had better OS (P=0.003; P=0.035; P=0.002). The multivariate analysis showed that the clinical stage of ESCC and receiving surgery for both cancer or not were the independent prognostic factors for OS. Conclusions: The multidisciplinary treatment outcome is acceptable, especially for patients with early clinical stage ESCC and with chance to receiving surgery for both cancer.

Aims Acute exacerbation is a major event that alters the natural course of chronic obstructive pulmonary disease (COPD), and recurrent exacerbation results in worse clinical outcomes and greater economic consequences. While some patients suffer frequent exacerbations, others experience no exacerbations; this study was designed to detect proteins that were differentially abundant in COPD frequent exacerbators and assess whether those expression profiles are unique among COPD patients. Main methods Tandem mass tag labeled quantitative proteomics combined with two-dimensional liquid chromatography-tandem mass spectrometry was used to detect the changes in the lung proteome in COPD frequent exacerbators and infrequent exacerbators. A series of bioinformatics analyses were performed to screen potential signatures of COPD frequent exacerbations. The accuracy of proteomic results was further verified by western blot studies. Key findings Compared with infrequent exacerbators, 23 proteins in the lung tissues from frequent exacerbators showed significant degrees of differential expression; combined bioinformatics analyses of proteome indicated that the immune network for IgA production and the phenylalanine metabolism pathway were associated with frequent exacerbations. The Western blot analysis confirmed the expression pattern of three significantly regulated proteins (HLA-DQA1, pIgR and biglycan). Significance These findings indicate that immune response might play a key role in the pathophysiological mechanisms of COPD frequent exacerbations. Our results make a crucial contribution to the search for a comprehensive understanding of potential pathophysiological mechanisms associated with the frequent exacerbations of COPD, and might provide guidance for treating frequent exacerbations.

This paper is concerned with fundamental properties of a class of composite systems with fractional degree generalized frequency variables, including controllability, observability and stability. Firstly, some necessary and sufficient conditions are given to guarantee controllability and observability of such composite systems. Then we prove that the stability problem of such composite systems can be reduced to judging whether a fractional degree polynomial is stable. Finally, the stability analysis result is applied in the supervisory control of fractional-order multi-agent systems, and an example is provided to illustrate the effectiveness of the proposed methods.

Filamentous bacteria, particularly Microthrix parvicella, are mainly responsible for bulking or foaming of activated sludge. Based on the affinity of M. parvicella to the hydrophobic characteristics of long-chain fatty acids, a novel bisoctyl rhodamine B (BORB) and a novel fluorescence resonance energy transfer (FRET) complex probe were prepared herein to study their properties. When the FRET probe was used in in situ activated sludge, M. parvicella was clearly labeled at 20 nmol/L, which was a reduction of 50 times compared to that of the BORB (1 μmol/L) alone and 500 times compared to the carbazole–quinoline probe reported previously. Compared with fluorescence in situ hybridization, M. parvicella could be clearly labeled using BORB and the FRET probe in situ without requiring complicated pretreatments (i.e., shock and broken process, fixed sample, digestion, and lysozyme treatment). This study discusses the facile approach developed for labeling M. parvicella in early warning expansion, thereby inhibiting and controlling sludge bulking in situ.

Twenty novel compounds with different functional groups (-COOH, -OH, -NH2 and -CH3) were designed to study the interaction mechanism of ligands with folate receptors (FRs). The optimized structure and the dipole moment of the novel compounds were calculated by a density functional tight-binding method (DFTB). The binding mechanism of the compounds with FRs was studied by molecular docking, molecular dynamic (MD) simulations and MM/PBSA free energy calculations. The binding energies, root mean square displacement and root mean square fluctuation of the complexes were analyzed to further illustrate the effect of the functional groups. The functional groups play important roles in stabilizing the bound complexes. Compared to other groups, -OH is more stably linked with the compound. These data provide a theoretical basis for the design of novel compounds targeted with FRs.

Unlike a general integer-order linear system, the L 1 and L 2 norms of its state and output variables may not be convergent in an infinite time interval even if the concerned fractional-order linear system is asymptotically stable or even Mittag-Leffler stable. Therefore, this study mainly investigates the analysis and synthesis of L 1 and L 2 performances in a finite time interval for a class of fractional-order positive systems. The L ∞ performance problem in the infinite time interval is also concerned since the boundness of the L ∞ norm of the state and output variables can be guaranteed in the infinite time interval if the concerned fractional-order positive system is asymptotical stable. The L 1 and L ∞ performance characterisations are expressed by linear programming and L 2 performance characterisation is expressed in terms of linear matrix inequality with a diagonal positive definite solution. Based on these performance conditions, the problems of stabilisation by a state feedback controller with L p (p ∈ {1, 2, ∞})-gain guaranteed are solved for fractional-order positive systems. An example is presented to show the effectiveness of the proposed methods in this study.

Objective To analyse the clinical characteristics of miliary tuberculosis (TB) in pregnant women after in vitro fertilisation and embryo transfer (IVF-ET). Methods Six pregnant women with miliary TB after IVF-ET between October 2010 and July 2015 were retrospectively analysed. Results The patients were aged between 29 and 39 years. Fever, cough and dyspnoea were the main symptoms, and started during the first and second trimesters of pregnancy. Erythrocyte sedimentation rate and C-reactive protein were increased. White blood cell count was normal or slightly increased. Tuberculin purified protein derivative and acid-fast smear of sputum tests were negative. T-SPOT®.TB was performed in two cases and the results were positive. Chest computed tomography showed typical miliary nodules. One patient had tuberculous meningitis. Although all patients were cured, the foetuses died. Conclusions The principal symptoms of miliary TB in pregnant women after IVF-ET were fever and dyspnoea. Physicians should consider the occurrence of miliary TB, particularly in the case of fever of long duration, respiratory symptoms and no response to antibiotic treatment.

Chronic obstructive pulmonary disease (COPD) is a highly heterogeneous disease. Emphysematous phenotype is the most common and critical phenotype, which is characterized by progressive lung destruction and poor prognosis. However, the underlying mechanism of this structural damage has not been completely elucidated. A total of 12 patients with COPD emphysematous phenotype (COPD-E) and nine patients with COPD non-emphysematous phenotype (COPD-NE) were enrolled to determine differences in differential abundant protein (DAP) expression between both groups. Quantitative tandem mass tag–based proteomics was performed on lung tissue samples of all patients. A total of 29 and 15 lung tissue samples from patients in COPD-E and COPD-NE groups, respectively, were used as the validation cohort to verify the proteomic analysis results using western blotting. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted for DAPs. A total of 4,343 proteins were identified, of which 25 were upregulated and 11 were downregulated in the COPD-E group. GO and KEGG analyses showed that wound repair and retinol metabolism–related pathways play an essential role in the molecular mechanism of COPD emphysematous phenotype. Three proteins, namely, KRT17, DHRS9, and FMO3, were selected for validation. While KRT17 and DHRS9 were highly expressed in the lung tissue samples of the COPD-E group, FMO3 expression was not significantly different between both groups. In conclusion, KRT17 and DHRS9 are highly expressed in the lung tissue of patients with COPD emphysematous phenotype. Therefore, these proteins might involve in wound healing and retinol metabolism in patients with emphysematous phenotype and can be used as phenotype-specific markers.