Using photolabile ligands in drug discovery and development

doi:10.1016/S0167-7799(99)01402-X

Trends in Biotechnology

Volume 18, Issue 2, 1 February 2000, Pages 64-77

https://doi.org/10.1016/S0167-7799(99)01402-X Get rights and content

Abstract

Photoactivatable ligands are important tools used in drug discovery and drug development. These ligands enable researchers to identify the targets of durgs, to determine the affinity and selectivity of the drug–target interaction, and to identify the binding site on the target. Examples are presented from three fundamentally different approaches: (1) photoaffinity labeling of target macromolecules; (2) photoactivation and release of ‘caged ligands'; and (3) photoimmobilization of ligands onto surfaces.

Section snippets

General principles of the main photochemical techniques

Two main classes of photochemistry can be distinguished, which depend on whether or not a chemical bond is formed or cleaved (Fig. 2). In photoaffinity labeling (PAL), a new covalent linkage is created between a light-sensitive, detectable ligand and a biopolymer upon irradiation, in a reversibly bound state. As a result of the photoinitiated coupling reaction, the ligand-binding site of the biopolymer (e.g. a receptor protein or an enzyme) becomes irreversibly occupied, and can inactivate or

Basic concepts

Photochemical activation of biomaterials have recently been classified⁵¹ as either: ‘single-cycle’ photoswitches, in which irradiation of photocleavable functional groups causes instantaneous activation via a bond cleavage; or ‘multicycle’ photobiological switches, wherein the biologically active and inactive states can be accessed by irradiation with different wavelengths, providing reversible photochemical control.

For single-cycle photoswitches, speed is the critical factor and is achieved by

Future perspectives

The discovery of new therapeutic agents requires a coordinated interdisciplinary effort. Emerging techniques are accelerating the process from molecular biology and genomics to combinatorial synthesis and HTS. At each step, photochemistry provides mild, controllable and selective tools for scientists engaged in the drug-discovery process. In the future, additional innovative applications can be anticipated to increase the efficiency and resolution of the photochemical methods. Combining

Acknowledgements

We thank the US National Institutes of Health (Grants NS29632 and GM44836 to G.D.P.) for support and The University of Utah for providing funds for new initiatives. Special thanks are due to the Prestwich group co-workers whose published results are cited herein and to two conscientious reviewers for suggesting improvements to the text.

Glossary

AP-2: Assembly protein 2
AZ: Azide
Bhc: Brominated 7-hydroxycoumarinyl methyl esters
BP: Benzophenone
Bpa: 4-Benzoyl-phenylalanine
BZDC-IP³: 4-Benzoyldihydrocinnamoyl-P-1-O-aminopropyl Ins(1,4,5)P₃
DIA: Diazirine
HTS: High-throughput screening
Ins(1,4,5)P₃: Inositol 1,4,5-triphosphate
MALDI-TOF MS: Matrix-assisted laser-desorption and ionization coupled with time-of-flight mass spectrometry
MDR: Multidrug resistance
MTP: Microsomal triglyceride transfer protein
NSAID: Non-steroid anti-inflammatory drug
P-GP: P-glycoprotein
PAL

References (80)

J. Fedan
Photoaffinity labels as pharmacological tools
Biochem. Pharmacol.
(1984)
M. Page
Proteomics: a major new technology for the drug discovery process
Drug Discov. Today
(1999)
J.S. Mills
Identification of a ligand binding site in the human neutrophil formyl peptide receptor using a site-specific fluorescent photoaffinity label and mass spectrometry
J. Biol. Chem.
(1998)
J.W. Darrow
Structurally similar small molecule photoaffinity CCK-A agonists and antagonists as novel tools for directly probing 7TM receptor–ligand interactions
Bioorg. Med. Chem. Lett.
(1998)
A. Bisello
Parathyroid hormone–receptor interactions identified directly by photocross-linking and molecular modeling studies
J. Biol. Chem.
(1998)
M. Schwanstecher
Identification of a 38-kDa high affinity sulfonylurea binding peptide in insulin-secreting cells and cerebral cortex
J. Biol. Chem.
(1994)
H.M. Bömmel
Anti-pterins as tools to characterize the function of tetrahydrobiopterin in NO synthase
J. Biol. Chem.
(1998)
T. Dang
The binding site for an inhibitor of squalene:hopene cyclase determined using photoaffinity labeling and molecular modeling
Chem. Biol.
(1999)
M.F. Taylor
Photoaffinity labeling of rat steroid 5 alpha-reductase (isozyme-1) by a benzophenone derivative of a 4-methyl-4-azasteroid
Steroids
(1996)
H. Jamil
Evidence that microsomal triglyceride transfer protein is limiting in the production of apolipoprotein B-containing lipoproteins in hepatic cells
J. Lipid Res.
(1998)

J. Otto et al.

Photolabeling of prostaglandin endoperoxidase H synthase-1 with 3-trifluoro-3-(m[¹²⁵I]iodophenyl diazirine as a probe of membrane association and the cyclooxygenase active site

J. Biol. Chem.

(1996)

A. Chaudhary

Probing the phosphoinositide 4,5-bisphosphate binding site of human profilin I

Chem. Biol.

(1998)

A.A. Profit

Probing the phosphoinositide binding site of the clathrin assembly protein AP-2 with photoaffinity labels

Arch. Biochem. Biophys.

(1998)

A. Chaudhary

Specific interaction of Golgi coatomer α-COP with phosphatidylinositol 3,4,5-trisphosphate

J. Biol. Chem.

(1998)

W. Beck et al.

Photoaffinity substrates for P-glycoprotein

Biochem. Pharmacol.

(1992)

R. Boer

Interaction of cytostatics and chemosensitizers with the dexniguldipine binding site on p-glycoprotein

Eur. J. Pharmacol.

(1996)

C.B. Herbert

Micropatterning gradients and controlling surface densities of photoactivatable biomolecules on self-assembled monolayers of oligo(ethylene glycol) alkanethiolates

Chem. Biol.

(1997)

M. Ayadim et al.

Photoimmobilization covalently anchored to the silica surface: modulation of the excitation state efficiency through electron transfer from the linking arm or from the surface

Tetrahedron Lett.

(1995)

F. Rossi

N-Nmoc-l-glutamate, a new caged glutamate with high chemical stability and low prephotolysis activity

J. Biol. Chem.

(1997)

W.H. Li

Membrane-permeant esters of inositol polyphosphates, chemical syntheses and biological applications

Tetrahedron

(1997)

T. Jiang

Membrane-permeant esters of phosphatidylinositol 3,4,5-trisphosphate

J. Biol. Chem.

(1998)

L. Qiao

Synthesis and evaluation of a photolyzable derivative of sphingosine 1-phosphate: caged SPP

Bioorg. Med. Chem. Lett.

(1998)

R. Shapiro

Identification of a ganglioside recognition domain of tetanus toxin using a novel ganglioside photoaffinity ligand

J. Biol. Chem.

(1997)

K. Curley et al.

Light-activated proteins

Curr. Opin. Chem. Biol.

(1999)

P. Pan et al.

Caged cysteine and thiophosphoryl peptides

FEBS Lett.

(1997)

V. Cornish et al.

A new tool for studying protein structure and function

Curr. Opin. Struct. Biol.

(1994)

Y. Wei

A photoactivated prodrug

Bioorg. Med. Chem. Lett.

(1998)

K. Nakatani

p-Cyano substituted benzophenone as an excellent photophore for one-electron oxidation of DNA

Tetrahedron Lett.

(1998)

F. Kotzyba-Hibert

Recent trends in photoaffinity labeling

Angew. Chem. Int. Ed. Engl.

(1995)

Y. Hatanaka

Diazirine-based photoaffinity labeling: chemical approach to biological interfaces

Rev. Heteroatom. Chem.

(1996)

J. Brunner

New photolabeling and crosslinking methods

Annu. Rev. Biochem.

(1993)

G.D. Prestwich

Benzophenone photoprobes for phosphoinositides, peptides, and drugs

Photochem. Photobiol.

(1997)

G. Marriott

Caged Compounds (Vol. 261)

(1998)

R. Amos

Biomaterial surface modification using photochemical coupling technology

M. Pirrung

Spatially addressable combinatorial libraries

Chem. Rev.

(1997)

R. Adams et al.

Controlling cell chemistry with caged compounds

Annu. Rev. Physiol.

(1993)

G. Dormán et al.

Benzophenone photophores in biochemistry

Biochemistry

(1994)

S.A. Fleming

Chemical reagents in photoaffinity labeling

Tetrahedron

(1995)

Koch, T. (1995) PhotoSelex, 23rd Annual Mtg. of the Am. Soc. for Photobiology, Washington, DC,...

B.A. Gilbert et al.

Modular design of biotinylated photoaffinity probes: synthesis and utilization of a biotinylated pepstatin photoprobe

J. Am. Chem. Soc.

(1995)

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Trends in Biotechnology

ReviewUsing photolabile ligands in drug discovery and development

Abstract

Section snippets

General principles of the main photochemical techniques

Basic concepts

Future perspectives

Acknowledgements

Glossary

Glossary

Biochem. Pharmacol.

Drug Discov. Today

J. Biol. Chem.

Bioorg. Med. Chem. Lett.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Chem. Biol.

Steroids

J. Lipid Res.

J. Biol. Chem.

Chem. Biol.

Arch. Biochem. Biophys.

J. Biol. Chem.

Biochem. Pharmacol.

Eur. J. Pharmacol.

Chem. Biol.

Tetrahedron Lett.

J. Biol. Chem.

Tetrahedron

J. Biol. Chem.

Bioorg. Med. Chem. Lett.

J. Biol. Chem.

Curr. Opin. Chem. Biol.

FEBS Lett.

Curr. Opin. Struct. Biol.

Bioorg. Med. Chem. Lett.

Tetrahedron Lett.

Recent trends in photoaffinity labeling

Angew. Chem. Int. Ed. Engl.

Diazirine-based photoaffinity labeling: chemical approach to biological interfaces

Rev. Heteroatom. Chem.

New photolabeling and crosslinking methods

Annu. Rev. Biochem.

Benzophenone photoprobes for phosphoinositides, peptides, and drugs

Photochem. Photobiol.

Caged Compounds (Vol. 261)

Biomaterial surface modification using photochemical coupling technology

Spatially addressable combinatorial libraries

Chem. Rev.

Controlling cell chemistry with caged compounds

Annu. Rev. Physiol.

Benzophenone photophores in biochemistry

Biochemistry

Chemical reagents in photoaffinity labeling

Tetrahedron

Modular design of biotinylated photoaffinity probes: synthesis and utilization of a biotinylated pepstatin photoprobe

J. Am. Chem. Soc.

Review
Using photolabile ligands in drug discovery and development