Rational Polypharmacology: Systematically Identifying and Engaging Multiple Drug Targets To Promote Axon Growth

TY - JOUR

T1 - Rational Polypharmacology

T2 - Systematically Identifying and Engaging Multiple Drug Targets To Promote Axon Growth

AU - Al-Ali, Hassan

AU - Lee, Do-Hun

AU - Danzi, Matt C

AU - Nassif, Houssam

AU - Gautam, Prson

AU - Wennerberg, Krister

AU - Zuercher, Bill

AU - Drewry, David H

AU - Lee, Jae K

AU - Lemmon, Vance P

AU - Bixby, John L

PY - 2015/8/21

Y1 - 2015/8/21

N2 - Mammalian central nervous system (CNS) neurons regrow their axons poorly following injury, resulting in irreversible functional losses. Identifying therapeutics that encourage CNS axon repair has been difficult, in part because multiple etiologies underlie this regenerative failure. This suggests a particular need for drugs that engage multiple molecular targets. Although multitarget drugs are generally more effective than highly selective alternatives, we lack systematic methods for discovering such drugs. Target-based screening is an efficient technique for identifying potent modulators of individual targets. In contrast, phenotypic screening can identify drugs with multiple targets; however, these targets remain unknown. To address this gap, we combined the two drug discovery approaches using machine learning and information theory. We screened compounds in a phenotypic assay with primary CNS neurons and also in a panel of kinase enzyme assays. We used learning algorithms to relate the compounds' kinase inhibition profiles to their influence on neurite outgrowth. This allowed us to identify kinases that may serve as targets for promoting neurite outgrowth as well as others whose targeting should be avoided. We found that compounds that inhibit multiple targets (polypharmacology) promote robust neurite outgrowth in vitro. One compound with exemplary polypharmacology was found to promote axon growth in a rodent spinal cord injury model. A more general applicability of our approach is suggested by its ability to deconvolve known targets for a breast cancer cell line as well as targets recently shown to mediate drug resistance.

AB - Mammalian central nervous system (CNS) neurons regrow their axons poorly following injury, resulting in irreversible functional losses. Identifying therapeutics that encourage CNS axon repair has been difficult, in part because multiple etiologies underlie this regenerative failure. This suggests a particular need for drugs that engage multiple molecular targets. Although multitarget drugs are generally more effective than highly selective alternatives, we lack systematic methods for discovering such drugs. Target-based screening is an efficient technique for identifying potent modulators of individual targets. In contrast, phenotypic screening can identify drugs with multiple targets; however, these targets remain unknown. To address this gap, we combined the two drug discovery approaches using machine learning and information theory. We screened compounds in a phenotypic assay with primary CNS neurons and also in a panel of kinase enzyme assays. We used learning algorithms to relate the compounds' kinase inhibition profiles to their influence on neurite outgrowth. This allowed us to identify kinases that may serve as targets for promoting neurite outgrowth as well as others whose targeting should be avoided. We found that compounds that inhibit multiple targets (polypharmacology) promote robust neurite outgrowth in vitro. One compound with exemplary polypharmacology was found to promote axon growth in a rodent spinal cord injury model. A more general applicability of our approach is suggested by its ability to deconvolve known targets for a breast cancer cell line as well as targets recently shown to mediate drug resistance.

KW - Animals

KW - Cells, Cultured

KW - Central Nervous System/cytology

KW - Drug Discovery/methods

KW - Humans

KW - Machine Learning

KW - Nerve Regeneration/drug effects

KW - Neurites/drug effects

KW - Neurons/drug effects

KW - Polypharmacology

KW - Protein Kinase Inhibitors/pharmacology

KW - Protein Kinases/genetics

KW - RNA, Small Interfering/genetics

KW - Rats

U2 - 10.1021/acschembio.5b00289

DO - 10.1021/acschembio.5b00289

M3 - Journal article

C2 - 26056718

SN - 1554-8929

VL - 10

SP - 1939

EP - 1951

JO - A C S Chemical Biology

JF - A C S Chemical Biology

IS - 8

ER -