Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space

Abstract

Abstract. The search for a new drug to cure a particular disease involves to find a chemical compound that influences a corresponding biological process, e.g., by inhibiting or activating an involved biological target molecule. A potential drug candidate however does not only need to show a sufficient amount of biological activity, but also needs to adhere to additional rules that define the basic limits of druglikeness, including for example restrictions regarding solubility and molecular weight. The sheer size of the search space, i.e., the chemical space that contains the available compounds, the large number of potentially relevant data annotations per compound, the incomplete knowledge on those properties, and the complex relation between the molecular properties and the actual effects in a living organism, complicate the search and may turn the discovery process into a tedious challenge. We describe Scaffold Hunter, an interactive software tool for the exploration and analysis of chemical compound databases. Scaffold Hunter allows to explore the chemical space spanned by a compound database, fosters intuitive recognition of complex structural and bioactivity relationships, and helps to identify interesting compound classes with a desired bioactivity. Thus, the tool supports chemists during the complex and time-consuming drug discovery process to gain additional knowledge and to focus on regions of interest, facilitating the search for promising drug candidates.

Exploring β‐Tubulin Inhibitors from Plant Origin using Computational Approach

“…Scaffold(s) analysis involves the construction of scaffold trees and dendrograms. In our study, we have used Scaffold Hunter (Klein et al, ) which is a Java‐based tool used for hierarchical classification based on compound structure, exploration of chemical space to find “virtual scaffolds” that should share bioactivity properties with their parent compound or child scaffolds (Wetzel et al, ; Klein et al, ). The analysis was done in two parts.…”

Breaking free from chemical spreadsheets

“…To illustrate this we will describe one such approach, called Card View TM , which is implemented in the StarDrop TM software platform. Other examples of environments that have explored some of these concepts are Scaffold Explorer [26] and Scaffold Hunter [27].…”

A Novel Customized Big Data Analytics Framework for Drug Discovery

“…Some of the interesting applications of analytic platforms reported in the literature that includes Octopus [26] tool perform Virtual HTS by integrating docking and visualization tools. Scaffold Hunter [27] Figure 2 Outline methodology for drug discovery. is a visual analytic framework for drug discovery.…”