In Silico ADME/Tox Profiling of Natural Products: A Focus on BIOFACQUIM

Abstract

Natural products continue to be major sources of bioactive compounds and drug candidates not only because of their unique chemical structures but also because of their overall favorable metabolism and pharmacokinetic properties. The number of publicly accessible natural product databases has increased significantly in the past few years. However, the systematic ADME/ Tox profile has been reported on a limited basis. For instance, BIOFACQUIM was recently published as a public database of natural products from Mexico, a country with a rich source of biomolecules. However, its ADME/Tox profile has not been reported. Herein, we discuss the results of an in-depth in silico ADME/Tox profile of natural products in BIOFACQUIM and other large public collections of natural products. It was concluded that the absorption and distribution profiles of compounds in BIOFACQUIM are similar to those of approved drugs, while the metabolism profile is comparable to that in the other natural product databases. The excretion profile of compounds in BIOFACQUIM is different from that of the approved drugs, but their predicted toxicity profile is comparable. This work further contributes to the deeper characterization of natural product collections as major sources of bioactive compounds with therapeutic potential.

Identification of 1,2,3-triazole-phthalimide derivatives as potential drugs against COVID-19: a virtual screening, docking and molecular dynamic study

“…The blood–brain barrier (BBB) protects the central nervous system (CNS) preventing certain substances (mostly harmful) from entering the brain tissues. The BBB limits the passage of most of the external compounds to maintain CNS at a steady state (Durán-Iturbide et al, 2020 ; Miao et al, 2019 ). In addition, P-glycoprotein (P-gp) actively transports a wide variety of compounds out of cells.…”

“…This parameter has a direct impact in determining the dose regimen (how often) and dose size (how much) of a given drug. Thus, its prediction helps us to determine the feasibility of clinical dosing and provides a framework for the starting dose in in vivo studies (Durán-Iturbide et al, 2020 ). In this work, the TC values of 1,2,3-triazoles-phtalimide derivatives varied from −0.26 to 0.85 log (mL/min/kg), for H2 and E37 derivatives, respectively.…”

Cheminformatics to Characterize Pharmacologically Active Natural Products

“…Authors of that work found that the absorption and distribution profile of compounds in BIOFACQUIM is similar to approved drugs, while the metabolism profile is comparable to other NP databases. The excretion profile of compounds in BIOFACQUIM is different from approved drugs, but their predicted toxicity profile is comparable [ 30 ].…”

PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds

“…Additionally, PSC-db allows for computing the correlation between any pair of the available features among a subset of compounds (physicochemical properties, lipophilicity, water solubility, pharmacokinetics and drug-likeness). Interestingly, these types of correlations have been reported, for example, to validate the estimations of the permeability of compounds [ 21 ], the estimations of oral absorption [ 22 ], and to compare the ADME/Tox profiling of several important chemical compound databases [ 23 ]. Nowadays, it is useful to have a repository that helps the users to find natural compounds with potentially similar properties/bioactivities.…”