In Silico Molecular Studies of Antiophidic Properties of the Amazonian Tree Cordia nodosa Lam

• Published in: Molecules (Basel, Switzerland) Vol. 24; no. 22; p. 4160
• Main Authors: Luzuriaga-Quichimbo, Carmen X, Blanco-Salas, José, Muñoz-Centeno, Luz María, Peláez, Rafael, Cerón-Martínez, Carlos E, Ruiz-Téllez, Trinidad
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.11.2019; MDPI
• Subjects: Analgesics; Antidotes - chemistry; Antidotes - pharmacology; antiophidic; Binding Sites; Biodiversity; Biological activity; Bothrops asper; Bothrops atrox; Bothrops pirajai; cordia; Cordia - chemistry; Cordia nodosa; docking; Field study; Free energy; Homology; Hydrophobicity; in silico; Ligands; Literature reviews; Minority & ethnic groups; Models, Molecular; Molecular Conformation; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular Structure; Naja atra; Oligomerization; Phospholipase A2; Plant Extracts - chemistry; Plant Extracts - pharmacology; Protein Binding; Proteins; Quercetin; quercetrin; Snake Venoms - antagonists & inhibitors; Snake Venoms - chemistry; Snakes; Structure-Activity Relationship; Tocopherol; Toxins; Toxins, Biological - antagonists & inhibitors; Toxins, Biological - chemistry; Trees; validation; Venom; Ecuador; Cordia; docking; quercetrin; antiophidic; in silico; validation
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules24224160

We carried out surveys on the use of Lam. in the jungles of Bobonaza (Ecuador). We documented this knowledge to prevent its loss under the Framework of the Convention on Biological Diversity and the Nagoya Protocol. We conducted bibliographic research and identified quercetrin as a significant bioactive molecule. We studied its in silico biological activity. The selected methodology was virtual docking experiments with the proteins responsible for the venomous action of snakes. The molecular structures of quercetrin and 21 selected toxins underwent corresponding tests with SwissDock and Chimera software. The results point to support its antiophidic use. They show reasonable geometries and a binding free energy of -7 to -10.03 kcal/mol. The most favorable values were obtained for the venom of the Asian snake (5Z2G, -10.03 kcal/mol). Good results were also obtained from the venom of the Latin American (3CYL, -9.71 kcal/mol) and that of Ecuadorian snakes (5TFV, -9.47 kcal/mol) and (5TS5, -9.49 kcal/mol). In the 5Z2G and 5TS5 L-amino acid oxidases, quercetrin binds in a pocket adjacent to the FAD cofactor, while in the myotoxic homologues of PLA2, 3CYL and 5TFV, it joins in the hydrophobic channel formed when oligomerizing, in the first one similar to α-tocopherol. This study presents a case demonstration of the potential of bioinformatic tools in the validation process of ethnobotanical phytopharmaceuticals and how in silico methods are becoming increasingly useful for sustainable drug discovery.