[citation needed] The company has been the subject of multiple regulatory investigations,[5] negative shorts-seller reports[6] and class action lawsuits amid allegations of securities fraud.

[14] Captisol, a Ligand indication, is a chemically modified clathrate compound of the cyclodextrin class designed to improve solubility, stability, bioavailability and dosing of active pharmaceutical ingredients.

[17] The same month the Securities and Exchange Commission of the company's financial reporting, which was characterized as "questionable," and resulted in a "lengthy scandal" according to The San Diego Union-Tribune.

[5] In November 2016, The Shareholder Foundation filed a class action lawsuit against Ligand, alleging the company had engaged in securities fraud by making false and misleading statements, overstating the value of its assets, mis-classifying its debt, and by failing to maintain control over its accounting.

Ligand executives, former high ranking-SEC lawyer Brad Bondi and congressmen Duncan Hunter subsequently lobbied the U.S. Securities and Exchange Commission to charge Lemelson.

On November 5, 2021, a federal jury rejected the allegations in a mixed verdict,[26] which cleared Lemelson of the commentary on Ligand in his reports but did find misstatements, including about a different company, Viking Therapeutics.