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Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping.

Hiroshi Nakano¹, Tomoyuki Miyao^1,2, Jasial Swarit^1,2

¹Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.

Journal of Chemical Information and Modeling

|July 15, 2021

Summary

This summary is machine-generated.

Sparse pharmacophore graphs (SPhGs) offer an interpretable method for scaffold hopping (SH) in drug discovery. This new approach maintains virtual screening performance while enhancing chemical space exploration.

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Area of Science:

Computational chemistry
Medicinal chemistry
Drug discovery

Background:

Scaffold hopping (SH) aims to identify novel compounds with different molecular structures but similar biological activity.
Pharmacophore graphs (PhGs) have been used for SH, but their complexity as complete graphs hinders interpretability.
Existing methods require improved ways to explore unexplored chemical space for new drug candidates.

Purpose of the Study:

To introduce sparse pharmacophore graphs (SPhGs) as an intuitive molecular representation for scaffold hopping.
To reduce graph complexity while preserving essential topological distances between pharmacophoric features.
To evaluate the performance and interpretability of SPhGs in virtual screening for scaffold hopping.

Main Methods:

Development of sparse pharmacophore graphs (SPhGs) by reducing edges in traditional pharmacophore graphs (PhGs).
Quantitative validation of SPhG sparseness and topological distance preservation through benchmark calculations.
Virtual screening (VS) trials using SPhGs on ChEMBL and PubChem databases for thrombin, tyrosine kinase ABL1, and κ-opioid receptor targets.

Main Results:

Benchmark calculations confirmed the effectiveness of SPhGs in reducing graph complexity while maintaining topological accuracy.
Virtual screening performance using SPhGs was comparable to that of traditional, fully connected PhGs.
Highly ranked SPhGs provided interpretable results, particularly for thrombin, aligning with structure-based interpretations.

Conclusions:

SPhGs provide an interpretable and effective method for scaffold hopping in drug discovery.
The SPhG approach facilitates exploration of novel chemical space with maintained virtual screening efficacy.
SPhGs represent a valuable tool for identifying new drug candidates with diverse scaffolds.