Discovery of High-Affinity Amyloid Ligands Using a Ligand-Based Virtual Screening Pipeline

Abstract

Fibrillar protein aggregates are characteristic of neurodegenerative diseases but represent difficult targets for ligand design, because limited structural information about the binding sites is available. Ligand-based virtual screening has been used to develop a computational method for the selection of new ligands for Aβ(1–42) fibrils, and five new ligands have been experimentally confirmed as nanomolar affinity binders. A database of ligands for Aβ(1–42) fibrils was assembled from the literature and used to train models for the prediction of dissociation constants based on chemical structure. The virtual screening pipeline consists of three steps: a molecular property filter based on charge, molecular weight, and logP; a machine learning model based on simple chemical descriptors; and machine learning models that use field points as a 3D description of shape and surface properties in the Forge software. The three-step pipeline was used to virtually screen 698 million compounds from the ZINC15 database. From the top 100 compounds with the highest predicted affinities, 46 compounds were experimentally investigated by using a thioflavin T fluorescence displacement assay. Five new Aβ(1–42) ligands with dissociation constants in the range 20–600 nM and novel structures were identified, demonstrating the power of this ligand-based approach for discovering new structurally unique, high-affinity amyloid ligands. The experimental hit rate using this virtual screening approach was 10.9%.

A closer look at amyloid ligands, and what they tell us about protein aggregates

“…We compiled a database of 3457 measurements of ligand–amyloid fibril interactions from the scientific literature. 50–385 The requirements to be included in this database were (1) a known chemical structure, (2) a structure that does not contain metals (metalloligands have been thoroughly reviewed elsewhere in the literature 43,386–391 ), (3) a K d or IC 50 measurement, and (4) a fibril target related to Aβ, tau, or αSyn. Nearly half of the database reports on binding to Aβ fibrils formed in vitro , although recent years has seen a shift in focus toward tau and αSyn fibrils formed in vitro (Table 1).…”

Ligand Profiling as a Diagnostic Tool to Differentiate Patient-Derived α-Synuclein Polymorphs

“…We have previously shown that amyloid fibrils contain a collection of binding sites which are morphology-dependent . Different ligands and different binding assays report on different ligand binding sites. − These binding sites, and the fibril morphology, can therefore be characterized by ligand binding assays. Figure shows a schematic illustration of the experiment for a fibril that has two different types of binding site (blue and orange).…”

Ligand Profiling to Characterize Different Polymorphic Forms of α-Synuclein Aggregates

“…Protein fibrils possess multiple structurally distinct binding sites that bind different structural classes of ligands. − The nature of the binding sites and their spatial distribution differs between fibrils composed of different proteins . Characterization of the ligand binding sites present on amyloid fibrils may therefore provide a methodology for fingerprinting fibril morphology.…”