The in silico drug-like profile was determined using QikProp software (QikProp release 2018, Schrödinger, LLC, New York, NY, USA, 2018). Pan Assay Interference Compounds (PAINS) evaluation was performed by the FAFDrugs4 web server [70 (link)] (https://fafdrugs4.rpbs.univ-paris-diderot.fr/ (accessed on 15 February 2021)) as previously described [71 (link)].
Qikprop software
Manufactured by Schrödinger
Sourced in United States
QikProp is a software tool developed by Schrödinger that calculates physicochemical properties of drug-like molecules. It predicts important properties such as solubility, permeability, and other parameters relevant to drug discovery and development.
Automatically generated - may contain errors
4 protocols using qikprop software
1
In silico Drug-like Profile Evaluation
2
In silico Screening of Propolis Constituents
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Filtration of propolis constituents imported from the database was carried out using Qikprop software (Schrodinger suite 2017A) by calculation of absorption, distribution, metabolism, and excretion (ADME) criteria and applying Lipinski's rule of five.17 (link) In this study, compounds with projected oral bioavailability (OB) of less than 30 were excluded. In addition, compounds that satisfied less than three criteria from Lipinski's rule of five were also excluded.
3
Physico-Chemical Evaluation of Compounds
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The evaluation of physico-chemical properties was performed using QikProp software (Schrödinger release 2018, Schrödinger, LLC, NY, 2018). Compounds were built in Maestro suite (Schrödinger release 2018, Schrödinger, LLC, NY, 2018) using the available drawing tools. The resulting structures were minimized employing Macromodel software (Schrödinger release 2018, Schrödinger, LLC, NY, 2018) and subsequently treated by LigPrep (Schrödinger release 2018, Schrödinger, LLC, NY, 2018) in order to obtain the most plausible protonation state at physiological pH (7.4 ± 0.2) as previously described [31] (link), [32] (link). Potential aggregator effects of the selected molecules were evaluated using the web-server Aggregator Advisor (http://advisor.bkslab.org/search/ ) [33] (link).
4
Physicochemical Properties Evaluation
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Octanol/water partition coefficient (logP), water solubility (logS), Caco-2 and MDCK apparent cell permeability, Lipinski and Jorgensen parameters were calculated using QikProp software within Schrodinger suite [43] . Prior to the ADME properties calculation, the ligands were subjected to torsional sampling conformational search (MCMM) and energy minimization, which were performed using the Macromodel module included in Maestro modeling package [55] .
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