The computationally predicted drug-likeness, pharmacokinetics properties, medicinal chemistry parameters, and toxicity properties of Cucurbita maxima compounds.

Introduction

Natural products (NP), such as plants and their extracts, have been used to cure diseases in humans and livestock since ancient times (Daina et al., 2017; Greenwell & Rahman, 2015). In modern computer-aided drug design approaches, NPs are considered to be a significant foundation for drug discovery due to their diverse chemical components and their often-unique biomedical properties (Süntar, 2020). Among their unique properties, the NPs are often rich in stereogenic centres and occupy portions of the chemical space that is usually not covered by most synthetic drugs (Marxer et al., 2012).

Cucurbita maxima (commonly known as giant pumpkin) is rich in phenolics, tannins, flavonoids, alkaloids, saponins, terpenoids, carbohydrates and proteins (Salehi et al., 2019; Sorescu et al., 2020). For centuries, extracts from different parts of the plant have been used to treat various diseases such as intestinal infections, renal failure, hyperplasia, constipation, and parasite infestation (Menendez-Baceta et al., 2014; Kujawska & Pieroni, 2015; Mahomoodally et al., 2016; Mtemeli et al. 2021). Thus, CADD approaches can be applied to investigate the potential of some compounds from this plant to act as drug leads. Before synthesising a compound in the laboratory for testing, modern computational approaches require that the compounds be computationally screened for drug-likeness and potential toxicity.

The standard method to evaluate drug-likeness of a compound is to assess compliance to Lipinski's Rule of Five (Lipinski et al., 1997), which covers the molecular weight, numbers of hydrophilic groups and hydrophobicity. This data note presents a list of C. maxima natural compounds and their computationally calculated data on drug-likeness characteristics, pharmacokinetics, medicinal chemistry parameters and predicted toxicity. Toxicity predictions are important because substructures with known toxic, teratogenic or mutagenic properties negatively affects the usefulness of a designed drug. With data produced in this work, researchers can better predict which C. maxima compounds have a better chance of succeeding throughout all stages of clinical trials, through to drug approval.

Materials and methods

To create a library of C. maxima natural compounds, the term 'Cucurbita maxima' was entered into the search box of the Lotus Natural Compounds Database (https://lotus.naturalproducts.net/). The search returned 130 natural products. A file containing the 130 compounds in the structure-data file (SDF) format was downloaded and then fed into BIOVIA Discovery Studio v21.1.0.20298, RRID:SCR_015651 to get the molecular structures in the corresponding simplified molecular-input line-entry system (SMILE) format. The SMILEs were then used to calculate the various properties of the compounds using the SwissADME (Daina et al., 2017) web tool and the DataWarrior v5.5.0 (Sander et al., 2015) software.

Dataset validation and limitations

An inherent limitation of computational prediction of drug-likeness is the lack of validated datasets of drugs and non-drugs. Therefore, the classification presented here is solely based on the similarity of structure of the compounds to known drugs. Also compounds from completely new classes are likely to be wrongly classified. Another important limitation of computationally predicted drug-likeness is that it does not predict the biological/pharmacological activity of a compound. Wet bench methods are required to validate the biological/pharmacological activity.

In summary, the dataset presented here will probably be most useful in lead discovery where they could be used for prioritizing compounds for synthesis or for purchasing from external suppliers.