Visualizing and Analyzing the Chemical Space of Natural Product Databases for Drug Discovery

Summary

Here, we provide a methodology that uses different molecular representations to display and analyze the chemical space of natural compound data sets, with a focus on applications related to drug discovery.

Abstract

Chemical space is a multidimensional descriptor space that encloses all possible molecules, and at least 1 x 10⁶⁰ organic substances with a molecular weight below 500 Da are thought to be potentially relevant for drug discovery. Natural products have been the primary source of the new pharmacological entities marketed during the past forty years and continue to be one of the most productive sources for the creation of innovative medications. Chemoinformatics-based computational tools accelerate the drug development process for natural products. Methods including estimating bioactivities, safety profiles, ADME, and natural product likeness measurement have been used. Here, we go over recent developments in chemoinformatic tools designed to visualize, characterize, and expand the chemical space of natural compound data sets using various molecular representations, create visual representations of such spaces, and investigate structure-property relationships within chemical spaces. With an emphasis on drug discovery applications, we evaluate the open-source databases BIOFACQUIM and PeruNPDB as proof of concept.

Introduction

Natural products (NPs), which are chemical compounds created by living things, have been utilized as traditional treatments for centuries. Individual NPs have been created as medications in the modern era and successfully exploited as lead compounds in drug discovery¹. Marine, fungal, bacterial, plant, and endogenous substances created by humans and animals are included in the category of bioactive compounds, as are venoms and poisons produced by various animals². As a result, for forty years, the number of medications made by NPs represented a significant source of new pharmacological substances³, emphasizing that NPs have been crucial in the development of new medications, particularly for the treatment of cancer and infectious diseases, as well as for other therapeutic conditions like multiple sclerosis and cardiovascular disease⁴. Furthermore, 64.9% of the 185 small compounds that were authorized to treat cancer between 1981 and 2019 were unmodified NPs or synthetic medicines with an NP pharmacophore³.

Chemoinformatics, a well-established inter-discipline that rests on the concept of chemical space, has been used to analyze and visualize the chemical space of NPs' physicochemical qualities linked to drug-like traits⁵. Chemoinformatics has shown a substantial impact on drug design and discovery based on NPs⁶. The chemical space of a group of compounds is not always unique. It will depend on the collection of descriptors used to define it, which means that studying the chemical space of NPs as any other set of compounds, presents particular challenges that rest on molecular representation⁷. This endeavor can be approached using a variety of molecular descriptors and data visualization techniques. In contrast, the most often utilized techniques are principal component analysis (PCA), scaffold trees, self-organizing maps, generative topographic mapping (GTM), and a novel visualization technique called tree maps (TMAPs)⁸. Also, the collection, evaluation, and dissemination of NP's chemical information in compound databases is one of the uses of chemoinformatics in NP research. In contrast, with the introduction of big data, this is especially pertinent⁹.

Here, the open-source NP databases BIOFACQUIM¹⁰ and PeruNPDB¹¹ are used to describe the protocol that searches for visualization and characterization of the chemical space of natural compound data sets using various molecular representations, creates visual representations of such spaces and investigates structure-property relationships within chemical spaces, with an emphasis on drug discovery applications.

Protocol

1. Software download and installation

1. Make this project's directory fresh. For convenient access, put the executables and files in this directory.
2. Install the required software packages after downloading them.
3. Download the latest version of The Osiris DataWarrior (OSIRIS) software, which can be found at https://openmolecules.org/datawarrior/
4. Download the latest version of The Konstanz Information Miner (KNIME) Analytics Platform, which can be found at https://www.knime.com/
5. Download the latest version of The GraphPad Prism software, which can be found at https://www.graphpad.com/
   NOTE: The Osiris DataWarrior software and The Konstanz Information Miner (KNIME) Analytics Platform can be used on a personal computer and are free for individual use, while the GraphPad Prism software can be purchased at (https://www.graphpad.com/).

2. Construction and curation of a compound database

NOTE: Find substances and sources that have the necessary data. The user is advised to have the following details for each compound in a spreadsheet.

1. Name each compound. Add the names of all the compounds that are described at the source in the first column of a spreadsheet.
2. Assign an internal, standardized code if creating an in-house collection, or assign a number that uniquely identifies this compound in the consulted database.
3. Provide the structure input using canonical SMILES notation, which can be imported into other molecular editing tools.
   1. Save the database ideally in .csv format once this data is gathered in the spreadsheet.
   2. Employ OSIRIS software to generate the dataset's structure data files (SDF), molecular data file (mol), and mol2, which also contain chemical information and are interoperable with most software packages. For this, upload the .csv archive by clicking the File button and then the Open button.
   3. Upload the dataset to the KNIME analytics platform to improve the data's quality and prevent inaccurate results. For this, upload the .sdf or .mol2 file by clicking the File button and then the Open button.
4. Ensure uniformity in chemical structures.
   1. Examine each chemical structure for valid atom types and valence checks. Standardize the structures by converting them to a canonical tautomeric form, kekulizing aromatic structures, standardizing the positioning of stereo bonds, and turning all implicit hydrogens into explicit hydrogens using the Standardizing Molecular Structures workflow of KNIME.
   2. Find and eliminate duplicates after the molecules have been correctly standardized by employing the Standardizing Molecular Structures workflow of KNIME. Utilize InChI keys as a linear notation to locate various protonation states and tautomers.
   3. Eliminate duplicates.
   4. Enumerate tautomers and stereoisomers. This step is crucial in virtual screening studies, especially when using search methods such as docking or pharmacophore-based filtering.

3. Molecular descriptors and diversity analysis

NOTE: Molecular descriptors, such as physicochemical qualities, and molecular fingerprints and chemical scaffolds, are the most common approaches to represent molecules in chemoinformatic applications. Analysis can be performed here: http://132.248.103.152:3838/PUMA/. All steps described below are detailed on the PUMA website.

1. Calculate the six most prevalent physicochemical qualities of pharmacological relevance: molecular weight (MW), octanol/water partition coefficient (clogP), topological surface area (TPSA), aqueous solubility (clogS), number of H-bond donor atoms (HBD), and number of H-bond acceptor atoms (HBA). Refer to the PUMA website for more information.
2. Calculate the 166-bit MACCS keys, the pairwise Tanimoto similarity, and extended connectivity fingerprints of diameter 4 (ECFP4), along with other circular fingerprints suitable for virtual screening, activity landscape modeling, and structure-activity relationships (SAR) research.
3. Compute a central tendency statistic for each pairwise comparison. Ensure diversity in the dataset with a smaller mean or median contrary to Euclidean distance or any general distance metric.
4. Check if the calculated values have been recorded in the literature or computed for other reference databases for comparison purposes. For this, consult websites such as PubChem or CHEMBL.
5. Generate violin plots for visualization within the GraphPad Prism software, displaying the maximum and minimum values.

4. Visualization of the chemical space

NOTE: It is possible to condense the majority of the pertinent data into a small number of variables using PCA and other dimensionality reduction techniques. Visualizations of the chemical space are therefore made possible.

1. Select all the six descriptors to determine similarity or distance. Create the similarity (or distance) matrix accordingly.
2. Perform PCA analysis on the matrix. Select two or three main components for plotting. Consider the proportion of variance captured by each primary component.
3. Generate two or three-dimensional scatter-plot representations for PCA using the Plotly KNIME node.

5. Consensus diversity plots

NOTE: Visual representations have been developed to summarize a few characteristics that can be used to quantify variety. The consensus diversity plots (CDPs)¹² analysis can be performed here http://132.248.103.152:3838/CDPlots/.

1. Create a plot with the number of compounds in the database to determine the data point size. Use the diversity of molecular fingerprints for the x-axis, diversity of scaffolds for the y-axis, diversity based on physicochemical properties for the color continuous scale, and the relative number of compounds in the dataset for data point size.
2. Generate the multiple-variable plot using the GraphPad Prism software.

Results

Molecular properties and visualization of the chemical space
All compounds in the BIOFACQUIM¹⁰, PeruNPDB¹¹, and FDA¹³ datasets had six physicochemical properties calculated for them. These qualities were then plotted onto violin plots, which allow one to see how the properties of the three studied datasets are distributed (Figure 1). The distribution profiles of the six physicochemical parameters o...

Discussion

Due to its many potential uses, such as compound classification, compound selection, exploring structure-activity links, and navigating through structure-property interactions, the concept of chemical space is nowadays widely employed in the drug discovery and development process¹⁴. Also, the creation of NP databases is a fundamental procedure to perform various computational studies, including the design of chemical libraries, characterization and comparison of the chemical space, the study of SA...

Materials

Name	Company	Catalog Number	Comments
GraphPad Prism	GraphPad Prism	https://www.graphpad.com/
KNIME platform	KNIME	https://www.knime.com
Osiris DataWarrior (OSIRIS) software	openmolecules.org	https://openmolecules.org/datawarrior/
PUMA	PUMA: Platform for Unified Molecular Analysis	http://132.248.103.152:3838/PUMA/