Journal: Computational and Structural Biotechnology Journal

Article Title: Computational Simulations Identified Two Candidate Inhibitors of Cdk5/p25 to Abrogate Tau-associated Neurological Disorders

doi: 10.1016/j.csbj.2019.04.010

Figure Lengend Snippet: Designing and virtual screening of natural product drug-like databases. InterBioScreen (IBS) and Zinc natural product database (ZNPD) were used to design a drug-like database. Lipinski's rule of five (ROF) and absorption, distribution, metabolism, excretion, and toxicity (ADMET) filtration evaluated 4563 and 29,183 compounds as drug-like molecules from IBSD and ZNPD, respectively. The selected pharmacophore was used as a 3D query and a total of 155, and 1605 drug-like molecules were retrieved from IBSD and ZNPD, respectively. A fit value (≥ 1.00) was used and a total of 90 and 1036 natural product drug-like molecules were identified as the best-fitted molecules on pharmacophore.

Article Snippet: InterBioScreen (IBS) and Zinc natural product database (ZNPD) were used to design a drug-like database.

Techniques: Filtration

Journal: Pharmaceuticals

Article Title: A Hybrid Approach Combining Shape-Based and Docking Methods to Identify Novel Potential P2X7 Antagonists from Natural Product Databases

doi: 10.3390/ph17050592

Figure Lengend Snippet: Schematic representation of the hierarchical sequence of selection filters applied to the MEGx and NATx databases aiming at the selection of potential P2X7 antagonists.

Article Snippet: The MEGx (~5.8 × 10 3 compounds) and NATx (~32 × 10 3 compounds) natural product databases from the AnalytiCon Discovery library (release 04/2022; available at https://ac-discovery.com/ , (accessed on 2 January 2024)) were obtained in SDF format and used for the VS protocols in this study.

Techniques: Sequencing, Selection

Journal: Pharmaceuticals

Article Title: A Hybrid Approach Combining Shape-Based and Docking Methods to Identify Novel Potential P2X7 Antagonists from Natural Product Databases

doi: 10.3390/ph17050592

Figure Lengend Snippet: Some physicochemical properties * and docking scores of the selected compounds from the MegX and NatX databases as potential P2X7 antagonists.

Article Snippet: The MEGx (~5.8 × 10 3 compounds) and NATx (~32 × 10 3 compounds) natural product databases from the AnalytiCon Discovery library (release 04/2022; available at https://ac-discovery.com/ , (accessed on 2 January 2024)) were obtained in SDF format and used for the VS protocols in this study.

Techniques:

Journal: Pharmaceuticals

Article Title: A Hybrid Approach Combining Shape-Based and Docking Methods to Identify Novel Potential P2X7 Antagonists from Natural Product Databases

doi: 10.3390/ph17050592

Figure Lengend Snippet: Schematic representation of the predicted binding modes (docking solutions with the best score) of two representative compounds selected by our VS protocol as potential P2X7 antagonists. ( A ) Superposition between the best scoring poses from the GOLD (carbon atoms in yellow) and DockThor (carbon atoms in pink) programs for compound NP-016468 from the MEGx database. ( B ) Superposition between the best scoring poses from the GOLD (carbon atoms in yellow) and DockThor (carbon atoms in pink) programs for compound NAT13-340161 from the NATx database. The Am P2X7 structure is represented as a green cartoon. Representative compound structures and binding site residues that make hydrophobic and/or hydrogen bond interactions with the representative compounds are shown as sticks. Oxygen, nitrogen, and fluorine atoms are colored red, blue, and light blue, respectively. Hydrogen bonds are represented by dashed lines (in cyan for GOLD docking poses and in magenta for DockThor docking poses). Residues from different subunits are labeled in black and in blue. The figure was prepared using the PyMOL v.2.5.0 software.

Article Snippet: The MEGx (~5.8 × 10 3 compounds) and NATx (~32 × 10 3 compounds) natural product databases from the AnalytiCon Discovery library (release 04/2022; available at https://ac-discovery.com/ , (accessed on 2 January 2024)) were obtained in SDF format and used for the VS protocols in this study.

Techniques: Binding Assay, Labeling, Software

Journal: Pharmaceuticals

Article Title: Recent Advances in the Discovery of SIRT1/2 Inhibitors via Computational Methods: A Perspective

doi: 10.3390/ph17050601

Figure Lengend Snippet: A perspective of the successful computational studies applied in the search of SIRT2 modulators. Activators (A) and inhibitors (I) are listed. Structure-based virtual screening (SBVS) studies and ligand-based (LB) ones or LB/SBVS are highlighted in light cyan and light yellow. The release date (R.D.) and the corresponding reference (Ref.) are reported.

Article Snippet: 11 , 2021 , [ ] , SBVS pharmacophore model combined with (SB+LB) QSAR , Not tested , AnalytiCon Discovery database of purified natural products (5637) , Asperphenamate , I , 1.94 μM (IC 50 ).

Techniques: Generated, Inhibition, Purification

Journal: International Journal of Molecular Sciences

Article Title: Profiling Chemobiological Connection between Natural Product and Target Space Based on Systematic Analysis

doi: 10.3390/ijms241411265

Figure Lengend Snippet: Count of LOTUS natural products library. ( A ) Number of natural products in different pathways. ( B ) Number of natural products of different pathways and the kingdom of plants.

Article Snippet: LOTUS natural product database (MongoDB dump) was downloaded from https://lotus.naturalproducts.net/download and accessed on 15 February 2023 [ ].

Techniques: