The biotech giant will pay $420m (€312m) in cash to buy the San Francisco-based company, and after the completion of the transaction Ilypsa will become a wholly-owned subsidiary of Amgen.
Directors from each company said that the deal should close by the third quarter of 2007.
"We are delighted to reach an agreement with Amgen that will help drive Ilypsa's most promising therapeutic program closer to commercialisation as an important new option for patients," said Jay Shepard, president and CEO of Ilypsa.
Ilypsa's flagship drug is the experimental clinical candidate ILY101, a non-absorbed polymeric agent that works by preventing the absorption of ingested phosphate, treating the elevated levels of phosphate in blood that CKD patients often suffer when undergoing haemodialysis.
ILY101 has been designed for the selective binding and removal of phosphate anions from the gastrointestinal (GI) tract.
Current studies suggest that ILY101 could lead a new generation of non-absorbed polymeric drugs for the treatment of renal and metabolic disorders, said Ilypsa.
According to the company, the non-absorbed feature means a simpler toxicology and pharmacology testing requirement for this class of drugs, which leads to superior safety and risk profiles as the drug is not absorbed systemically.
ILY101 may also provide an enhanced phosphate binding selectivity and capacity compared to currently available polymeric drugs, such as Genzyme's Renagel (sevelamer HCl) and Shire's Fosrenol (lanthanum carbonate).
ILY101 has recently completed enrollment of Phase II trials in patients with CKD.
Ilypsa has built a portfolio of non-absorbed polymeric phosphate and potassium binder compounds to treat CKD using a proprietary development platform created and validated at Symyx Technologies.
The ILY101 programme endorses the speed of the platform in bringing drugs through development swiftly, as it has gone from winning approval to start clinical trials to completion of Phase II enrollment in just one year.
If Ilypsa's clinical candidate is proved to be effective and becomes available on the market, it will join Amgen's other array of products aimed at fighting complications related to CKD, such as Aranesp (darbepoetin alfa) and Epogen (epoetin alfa), which treat anaemia by boosting blood red cells.
To date, Ilypsa has raised $46m in its first and second rounds of financing.
Investors include The Sprout Group, 5AM Ventures, US Venture Partners, Johnson & Johnson Development Corporation and Delphi Ventures.