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

Abstract

We carried out surveys on the use of Cordia nodosa 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 Naja atra (5Z2G, −10.03 kcal/mol). Good results were also obtained from the venom of the Latin American Bothrops pirajai (3CYL, −9.71 kcal/mol) and that of Ecuadorian Bothrops asper snakes (5TFV, −9.47 kcal/mol) and Bothrops atrox (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.

A review on traditional uses and applications of Cordia spp. (Boraginaceae) as a natural polymer in the development of food and pharmaceutical products

“…been traditionally used to treat cough, spider bites, and snake bites and as an energizer (Saltos et al 2016, Vacas et al 2015. The antiophidic properties of this specie have been demonstrated by molecular coupling between the quercetin in its extract and toxins obtained from different snakes (Luzuriaga-Quichimbo et al 2019). The chemical structure of quercetin is shown in Fig.…”

“…In Ecuador, it is estimated that there are about 25 species of this genus distributed in the 4 natural regions that comprise it (Ulloa & Moller 2002). Some of them have been used ancestrally for their medicinal effect, however, the metabolites behind this activity are not scientifically known (Luzuriaga-Quichimbo et al 2019, Vacas et al 2015.…”

“…tree has been used in South American countries, including the Amazon region of Ecuador, to treat snake and spider bites, to reduce inflammation and prevent gangrene. (De Filipps et al 2004, De la Torre et al 2008, Luzuriaga-Quichimbo et al 2019. The infusion of the leaves of Cordia verbenacea DC.…”