Pathogenesis of Secondary Pulmonary Tuberculosis and Role of Cord Factor in Secondary Infection / 中国医学科学院学报

The primary and secondary tuberculosis features two completely different pathogenesis.At present,the pathogenesis of primary tuberculosis has been clear,whereas that of secondary tuberculosis remains unclear.In order to decipher the mechanism of secondary infection of

Homologous modeling and binding ability analysis of Spike protein after point mutation of severe acute respiratory syndrome coronavirus 2 to receptor proteins and potential antiviral drugs / 北京大学学报(医学版)

OBJECTIVE@#To explore the natural mutations in Spike protein (S protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the changes of affinity between virus and associated receptors or drug molecules before and after the mutation based on whole length sequencing results.@*METHODS@#In the study, the bioinformatics analysis of all the published sequences of SARS-CoV-2 was conducted and thus the high frequency mutation sites were affirmed. Taking advantages of PolyPhen-2, the functional influence of each mutation in S protein was prospected. The 3D homologous modelling was performed by SWISS-MODEL to establish mutated S protein structural model, in which the protein-docking was then implemented with angiotensin-converting enzyme 2 (ACE2), dipeptidyl peptidase-4 (DPP4) and aminopeptidase N (APN) by ZDOCK, and the combining capacity of each mutated S protein evaluated by FiPD. Finally, the binding ability between mutated S proteins and anti-virus drugs were prospected and evaluated through AutoDock-Chimera 1.14.@*RESULTS@#The mutations in specific region of S protein had greater tendency to destroy the S protein function by analysis of mutated S protein structure. Protein-receptor docking analysis between naturally mutated S protein and host receptors showed that, in the case of spontaneous mutation, the binding ability of S protein to ACE2 tended to be weakened, while the binding ability of DPP4 tended to be enhanced, and there was no significant change in the binding ability of APN. According to the computational simulation results of affinity binding between small molecular drugs and S protein, the affinity of aplaviroc with S protein was significantly higher than that of other small molecule drug candidates.@*CONCLUSION@#The region from 400-1 100 amino acid in S protein of SARS-CoV-2 is the mutation sensitive part during natural state, which was more potential to mutate than other part in S protein during natural state. The mutated SARS-CoV-2 might tend to target human cells with DPP4 as a new receptor rather than keep ACE2 as its unique receptor for human infection. At the same time, aplaviroc, which was used for the treatment of human immunodeficiency virus (HIV) infection, may become a new promising treatment for SARS-CoV-2 and could be a potential choice for the development of SARS-CoV-2 drugs.

A retrieval method of drug molecules based on graph collapsing / 北京大学学报(医学版)

OBJECTIVE@#To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval.@*METHODS@#Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced. This system accepted the photos taken from smartphones and the sketches drawn on tablet personal computers as CSF inputs, and formalized the CSFs with the corresponding graphs. Then this paper proposed a compact and efficient hypergraph representation for molecules on the basis of analyzing factors that directly affected the efficiency of graph matching. According to the characteristics of CSFs, a hierarchical collapsing method combining graph isomorphism and frequent subgraph mining was adopted. There was yet a fundamental challenge, subgraph overlapping during the collapsing procedure, which hindered the method from establishing the correct compact hypergraph of an original CSF graph. Therefore, a graph-isomorphism-based algorithm was proposed to select dominant acyclic subgraphs on the basis of overlapping analysis. Finally, the spatial similarity among graphical CSFs was evaluated by multi-dimensional measures of similarity.@*RESULTS@#To evaluate the performance of the proposed method, the proposed system was firstly compared with Wikipedia Chemical Structure Explorer (WCSE), the state-of-the-art system that allowed CSF similarity searching within Wikipedia molecules dataset, on retrieval accuracy. The system achieved higher values on mean average precision, discounted cumulative gain, rank-biased precision, and expected reciprocal rank than WCSE from the top-2 to the top-10 retrieved results. Specifically, the system achieved 10%, 1.41, 6.42%, and 1.32% higher than WCSE on these metrics for top-10 retrieval results, respectively. Moreover, several retrieval cases were presented to intuitively compare with WCSE. The results of the above comparative study demonstrated that the proposed method outperformed the existing method with regard to accuracy and effectiveness.@*CONCLUSION@#This paper proposes a graph-similarity-based retrieval approach for medicine information. To obtain satisfactory retrieval results, an isomorphism-based algorithm is proposed for dominant subgraph selection based on the subgraph overlapping analysis, as well as an effective and efficient hypergraph representation of molecules. Experiment results demonstrate the effectiveness of the proposed approach.

Construction of chemical information database based on optical structure recognition technique / 北京大学学报(医学版)

OBJECTIVE@#To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically.@*METHODS@#Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database.@*RESULTS@#A reasonable construction protocol of chemical information database was created successfully. A total of 174 research articles and 25 reviews published in Marine Drugs from January 2015 to June 2016 collected as essential data source, and an elementary marine natural product database named PKU-MNPD was built in accordance with this protocol, which contained 3 262 molecules and 19 821 records.@*CONCLUSION@#This data aggregation protocol is of great help for the chemical information database construction in accuracy, comprehensiveness and efficiency based on original documents. The structured chemical information database can facilitate the access to medical intelligence and accelerate the transformation of scientific research achievements.

Analysis of traditional Chinese medicine prescriptions based on support vector machine and analytic hierarchy process / 中国中药杂志

Combined use of drugs is a hot spot in the research of new drugs nowadays, and traditional Chinese medicine (TCM) is a classic practice in the combined use of drugs. In this paper, the compatibility of TCM prescriptions and the related properties of composed herbs were calculated and studied to verify and discuss the feasibility of the results in guiding compatibility. Research Group on New Drug Design, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences had established a structured database of TCM prescriptions by using traditional Chinese medicine inheritance support system (TCMISS V2.0), including 4 012 prescription compatibilities, 2 072 drug components, 381 kinds of TCM diseases, 316 kinds of TCM syndromes and 26 kinds of drug properties. On the basis of the created database above, Support Vector Machine (SVM) was used to analyze the prescription compatibility data and establish a model for predicting feasibility of drug compatibilities. Analytic Hierarchy Process (AHP) and cluster analysis were used to study the influence of drug properties in the rationality of prescription compatibility. The computational results showed that the accuracy in efficacy prediction of two data sets, i.e. prescription-disease and prescription-syndrome, was up to 90% in the linear SVM model. The macro₋averaging and micro₋averaging of the two models were around 0.92, 0.46, respectively. After AHP mapping, most of the incompatible combinations showed significant difference with other drug combinations during the clustering process in the vertical icicle, indicating that the proper machine learning algorithm can be used to lay the foundation for further exploring the combination rules in TCM and establishing more detailed drug-disease and syndrome predicting models, and provide theoretical guidance for the study of the combined use of drugs to a certain degree.

Advances on anti-neoplastic STAT3 inhibitors / 药学学报

Signal transducer and activator of transcription 3 (STAT3) is a kind of signal transduction protein involved in cell proliferation, differentiation, apoptosis and other important physiological processes in response to a large number of cytokines and growth factors in cells. It has been shown that constitutive activation of STAT3 is closely associated with oncogenesis and tumorigenesis. Inhibition of aberrant STAT3 signaling has been one of promising strategies for the development of anti-neoplastic therapeutics. The review summarizes the latest progress of STAT3 inhibitors in recent years from the perspective of targeting N-terminal domain, DNA binding domain, SH2 domain and C-terminal transactivation domain of STAT3.

Synthesis, antifungal activity and molecular docking of (E)-3-(((1,3,4-thiadiazol-2-yl)amino)methylene)-thiochroman-4-ones / 药学学报

Thiochromanones and 1,3,4-thiadazoles as heterocyclic compounds have broad biological activities. In order to find novel compounds with antifungal activity, we synthesized a novel series of (E)-3-(((1,3,4-thiadiazol-2-yl) amino)methylene)-thiochroman-4-ones. Structures of these compounds were established by HR-MS, 1H NMR, 13C NMR and 1D-noesy. All of the synthesized compounds were screened for antifungal activity by using an established agar double dilution method (plate method) against ten fungi species in vitro. Compound 5j showed significant inhibitory activity to Colletotrichum capsici, Rhizoctonia cerealis and Aspergillus niger compared with that of the positive control carbendazim. Compounds 5h exhibited better antifungal activity to Canidia albicans and Aspergillus funigatus than the positive control fluconazole, in which the minimum inhibition concentration can reach 8 μg·mL-1 and 16 μg·mL-1. Moreover, the molecular docking method was used to study the interaction mode of compound 5h and CYP51, and the results will be helpful for designing of CYP51 inhibitors in the future.

Identification of novel selective TRPV3 antagonists based on virtual screening, molecular docking and bioassay / 药学学报

Transient receptor potential vanilloid member 3 (TRPV3) is a temperature-sensitive cation channel protein, which contributes to nociception, itch, hair growth, emotional control and the pathophysiology of migraine. However, research progress on TRPV3 fundamental molecular biology is rather slow, compared to other TRP channels due to the lack of its selective antagonists. It's necessary to identify TRPV3 selective antagonists for the study on TRPV3 physiological functions. In this study, several selective TRPV3 antagonists were identified by ligand-based virtual screening of shape-based similarity and electrostatic matching. The most potent one (V-39) blocked 2-APB-activated currents in a stable human TRPV3 expressed HEK293T cell line with IC50=18.0 ±1.1 μmol·L-1 (n=4). Besides, the interaction pattern between TRPV3 and its antagonists were studied through docking the antagonists into a homology model (TRPV3_HM4) generated from the crystal structure of TPRV1. The docking results show that the binding site of TRPV3 locates between linker domain (of N-terminus and TM1) and TRP Box. There are a π-π stacking interaction and hydrogen bonding interactions between compound V-39 and residues His-310, His-314 and Arg-577 of the pocket. Identification of these antagonists provides new probes for understanding the pharmacological function of TRPV3 channel.

A review of ANO1-based calcium activated chloride channel modulators / 药学学报

Calcium-activated chloride channel (CaCC) is an anion channel, widely distributed in the human body, taking a part in cell functions including secretion, heart muscle repolarization, nerve signal transmission and several physiological activities. The anoctamin 1 (ANO1) protein is the molecular basis of CaCC and the modification of ANO1 protein will produce a variety of pharmacological effects, such as analgesia, treating dysentery and asthma, even tumor proliferation and migration inhibition. In the past decade, many methods in screening of ANO1 regulators have been developed. Although a series of the ANO1-based CaCC regulatory molecules have been identified, the pharmacological effects of these molecules are not consistent. In this review, we introduce ANO1 protein regulators from many aspects including bio-test methods, structure-activity relationships, and the potential applications.

Exploiture and application of an internet-based Computation Platform for Integrative Pharmacology of Traditional Chinese Medicine / 中国中药杂志

Recently, integrative pharmacology(IP) has become a pivotal paradigm for the modernization of traditional Chinese medicines(TCM) and combinatorial drugs discovery, which is an interdisciplinary science for establishing the in vitro and in vivo correlation between absorption, distribution, metabolism, and excretion/pharmacokinetic(ADME/PK) profiles of TCM and the molecular networks of disease by the integration of the knowledge of multi-disciplinary and multi-stages. In the present study, an internet-based Computation Platform for IP of TCM(TCM-IP, www.tcmip.cn) is established to promote the development of the emerging discipline. Among them, a big data of TCM is an important resource for TCM-IP including Chinese Medicine Formula Database, Chinese Medical Herbs Database, Chemical Database of Chinese Medicine, Target Database for Disease and Symptoms, et al. Meanwhile, some data mining and bioinformatics approaches are critical technology for TCM-IP including the identification of the TCM constituents, ADME prediction, target prediction for the TCM constituents, network construction and analysis, et al. Furthermore, network beautification and individuation design are employed to meet the consumer's requirement. We firmly believe that TCM-IP is a very useful tool for the identification of active constituents of TCM and their involving potential molecular mechanism for therapeutics, which would wildly applied in quality evaluation, clinical repositioning, scientific discovery based on original thinking, prescription compatibility and new drug of TCM, et al.