HIV has plagued humans for 30 years, infecting 60 million people and causing over 25 million deaths. AIDS patients can be effectively treated with Highly Active Antiretroviral Therapy (HAART), which usually comprises a combination of three anti-HIV drugs1
. However, the cost of current HAART therapy is prohibitive in developing countries. In addition, long-term HAART therapy can have serious side effects such as lipodystrophy, hyperglycemia, pancreatitis and liver toxicity2
. New therapies are needed to expand the current HAART repertoire, to provide hope for a cure and to reduce the cost of treatment and side-effects3
Combination therapies are also widely used to treat other infections including hepatitis C virus, malaria and bacterial infections such as pneumonia, in addition to non-infectious diseases such as cancer and asthma5
. Major benefits of combination therapy include a substantially reduced chance of evolving drug resistance, improved efficacy and reduced side-effects6
. The large combinatorial space of existing drugs provides a largely untapped resource for developing new treatments. Exploiting this resource could accelerate the drug development process since drugs in current or past use have favorable pharmacological properties. However, the large number of possible combinations from even a modest number of drugs makes a systematic search difficult without an efficient method. For example, for 10 drugs, there are 45 pair-wise combinations; for 100 drugs, 4950; and for 1000 drugs, 499,500.
Systematic searches for synergistic drug combinations have been performed previously in industrial settings using exhaustive combinations7, 8
, but the high cost of this method prevents wide adoption. Pooled screening methods have been explored to identify enzyme inhibitors9
and to look for synergistic anti-inflammatory compound pairs10
although the latter study did not yield novel synergistic compound pairs. Here we develop a pooled screening method named MuSIC
creen for I
ompounds) to screen a large collection of diverse FDA-approved or clinically-tested compounds. The MuSIC
screening library was designed to contain 10 compounds in each well of a 384-well plate and cover all the possible pair-wise combinations among these compounds using less than 3% of the number of wells needed in a standard pair-wise screen. For pools that contain potentially synergistic interactions, we deconvolute each pool into 45 drug pairs to identify efficacious drug pairs. Subsequently, we perform dose titration of the drug pairs to verify whether drugs act in synergy (). We validate our method using cell-based models of the HIV life cycle and show that it is effective at identifying pair-wise combinations that have anti-HIV activity.
MuSIC strategy and screening assay