PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies

The rapidly increasing amount of publicly available data in biology and chemistry enables researchers to revisit interaction problems by systematic integration and analysis of heterogeneous data. Herein, we developed a comprehensive python package to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for drug discovery. PyDPI (drug–protein interaction with Python) is a powerful python toolkit for computing commonly used structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of drug molecules from their topology, and protein–protein interaction and protein–ligand interaction descriptors. It computes 6 protein feature groups composed of 14 features that include 52 descriptor types and 9890 descriptors, 9 drug feature groups composed of 13 descriptor types that include 615 descriptors. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pair fingerprints, topological torsion fingerprints, and Morgan/circular fingerprints. By combining different types of descriptors from drugs and proteins in different ways, interaction descriptors representing protein–protein or drug–protein interactions could be conveniently generated. These computed descriptors can be widely used in various fields relevant to chemoinformatics, bioinformatics, and chemogenomics. PyDPI is freely available via https://sourceforge.net/projects/pydpicao/

A new neolignan from <i>Selaginella moellendorffii</i> Hieron

<p>A new neolignan, selamoellenin A (<b>1</b>), was isolated from the whole plants of <i>Selaginella moellendorffii</i> Hieron. The structure was elucidated on the basis of comprehensive spectroscopic methods (1D/2D NMR and HRMS). Compound <b>1</b> was evaluated for its protective effect against high glucose-induced human umbilical vein endothelial cells (HUVECs) damage <i>in vitro</i>.</p

Two new anthraquinone derivatives and one new triarylbenzophenone analog from <i>Selaginella tamariscina</i>

<p>Two new anthraquinone derivatives, selaginones A (<b>1</b>) and B (<b>2</b>), and one new triarylbenzophenone analog, selagibenzophenone B (<b>3</b>), were isolated from <i>Selaginella tamariscina</i> (Beauv.) Spring. Their structures were established by 1D-, 2D-NMR and HR-ESI-MS data. Compounds <b>1</b> and <b>2</b> represent the uncommon examples of aryl substituted anthraquinone derivatives. Especially, compound <b>2</b> is a unique anthranone with exceptional structural feature, in which a <i>p</i>-hydroxyphenyl moiety is attached to the C-10 position. Compound <b>3</b> is the second naturally occurring triarylbenzophenone and showed moderate activity against SMCC-7721 and MHCC97-H cell lines with IC₅₀ values of 39.8, 51.5 μM respectively.</p

New adenine analogues and a pyrrole alkaloid from <i>Selaginella delicatula</i>

<p>Phytochemical study on the <i>n</i>-BuOH extract of <i>Selaginella delicatula</i> lead to the isolation, characterization and structure elucidation of two new adenine analogues, delicatulines A (<b>1</b>) and B (<b>2</b>), one new pyrrole alkaloid (<b>4</b>), and five known compounds (<b>3</b>, <b>5</b>–<b>8</b>). These new substances all contain an aliphatic chain in their parent nucleus, which were unusual to find in plants. In the present study, they were identified from Selaginellaceae for the first time. The structures and absolute configurations of these new compounds were determined by a combination of NMR and CD spectroscopic analyses. Compounds <b>1</b>, <b>3</b> and <b>4</b> were evaluated for their inhibitory activities on HBV surface antigen and HBV DNA in HepAD38 cells. The results showed that these compounds had only weak or no inhibitive effects on HBV.</p