Methods

Reference descriptions for methods used across entries

Entries link back to this page instead of repeating a method’s description each time. If a method here doesn’t match how it was applied in a specific entry, the entry’s own page takes precedence.

Molecular docking

Computational screening of a candidate compound against a target enzyme’s structure, producing a predicted binding pose and a docking score. Docking is a first pass: it flags candidates worth testing further, not a confirmed inhibitory effect.

Molecular dynamics simulation

A follow-up to docking that simulates how a compound and its target behave together over time, rather than in a single static pose. Used to tell a stable, likely-real interaction apart from one that only looks plausible in a single snapshot.

In vivo model

An AlCl₃/D-galactose-induced model in rats, used to study neurodegeneration-like changes, including oxidative stress and markers relevant to enzyme targets such as BACE1. Candidate compounds are tested in this model after computational screening, before any conclusions about biological effect are drawn.

Histology

Microscopic examination of tissue sections to assess structural and pathological changes, used alongside molecular measurements to confirm that an observed effect is reflected in the tissue itself.

qRT-PCR

Quantifies the expression level of a target gene, used here to confirm whether a candidate compound changes expression of its target (and any co-target) at the molecular level, following treatment in an in vivo model.

In vitro enzyme inhibition assay

Measures how much a candidate compound slows a target enzyme’s activity directly in a test tube or plate, without a cell or animal model, typically expressed as an IC50 (the concentration needed to inhibit 50% of activity) or a percent inhibition at a given concentration. This sits between purely computational screening and the animal models described above: it confirms an effect on the enzyme itself, but not yet in a living system.