Riemannian geometry and molecular similarity I: spectrum of the Laplacian

Abstract

Ligand-based virtual screening aims to reduce the cost and duration of small molecule drug discovery campaigns. Shape similarity can be used to screen large databases, with the goal of predicting potential new hits by comparing with molecules with known favourable properties. This paper presents the theory underpinning RGMolSA, a new alignment-free and mesh-free surface-based molecular shape descriptor derived from the mathematical theory of Riemannian geometry. The treatment of a molecule as a series of intersecting spheres allows the description of its surface geometry using the Riemannian metric , obtained by considering the spectrum of the Laplacian. This gives a simple vector descriptor constructed of the weighted surface area and eight non-zero eigenvalues, which capture the surface shape. We demonstrate the potential of our method by considering a series of PDE5 inhibitors that are known to have similar shape as an initial test case. RGMolSA displays promise when compared with existing shape descriptors and in its capability to handle different molecular conformers.