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Su K, Vázquez O. Enlightening epigenetics: optochemical tools illuminate the path. Trends Biochem Sci 2024; 49:290-304. [PMID: 38350805 DOI: 10.1016/j.tibs.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024]
Abstract
Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where specific events occur. Therefore, these are invaluable for studying both histone and nucleotide modifications and exploring disease-related mechanisms. We systematically report and assess current examples in the field, and identify open challenges and future directions. These outstanding proof-of-concept investigations will inspire other chemical biologists to participate in these emerging fields given the potential of photochromic molecules in research and biomedicine.
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Affiliation(s)
- Kaijun Su
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg D-35043, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg D-35043, Germany.
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2
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Laczi D, Johnstone MD, Fleming CL. Photoresponsive Small Molecule Inhibitors for the Remote Control of Enzyme Activity. Chem Asian J 2022; 17:e202200200. [PMID: 35446477 PMCID: PMC9322446 DOI: 10.1002/asia.202200200] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Indexed: 12/14/2022]
Abstract
The development of new and effective therapeutics is reliant on the ability to study the underlying mechanisms of potential drug targets in live cells and multicellular systems. A persistent challenge in many drug development programmes is poor selectivity, which can obscure the mechanisms involved and lead to poorly understood modes of action. In efforts to improve our understanding of these complex processes, small molecule inhibitors have been developed in which their OFF/ON therapeutic activity can be toggled using light. Photopharmacology is devoted to using light to modulate drugs. Herein, we highlight the recent progress made towards the development of light-responsive small molecule inhibitors of selected enzymatic targets. Given the size of this field, literature from 2015 onwards has been reviewed.
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Affiliation(s)
- Dóra Laczi
- Centre for Biomedical and Chemical SciencesSchool of ScienceAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
| | - Mark D. Johnstone
- Centre for Biomedical and Chemical SciencesSchool of ScienceAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
| | - Cassandra L. Fleming
- Centre for Biomedical and Chemical SciencesSchool of ScienceAuckland University of TechnologyPrivate Bag 92006Auckland1142New Zealand
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3
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Fast E/Z UV-light response T-type photoswitching of phenylene-thienyl imines. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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4
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Kobauri P, Galenkamp NS, Schulte AM, de Vries J, Simeth NA, Maglia G, Thallmair S, Kolarski D, Szymanski W, Feringa BL. Hypothesis-Driven, Structure-Based Design in Photopharmacology: The Case of eDHFR Inhibitors. J Med Chem 2022; 65:4798-4817. [PMID: 35258959 PMCID: PMC8958501 DOI: 10.1021/acs.jmedchem.1c01962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Photopharmacology
uses light to regulate the biological activity
of drugs. This precise control is obtained through the incorporation
of molecular photoswitches into bioactive molecules. A major challenge
for photopharmacology is the rational design of photoswitchable drugs
that show light-induced activation. Computer-aided drug design is
an attractive approach toward more effective, targeted design. Herein,
we critically evaluated different structure-based approaches for photopharmacology
with Escherichia coli dihydrofolate reductase (eDHFR)
as a case study. Through the iterative examination of our hypotheses,
we progressively tuned the design of azobenzene-based, photoswitchable
eDHFR inhibitors in five design–make–switch–test–analyze
cycles. Targeting a hydrophobic subpocket of the enzyme and a specific
salt bridge only with the thermally metastable cis-isomer emerged as the most promising design strategy. We identified
three inhibitors that could be activated upon irradiation and reached
potencies in the low-nanomolar range. Above all, this systematic study
provided valuable insights for future endeavors toward rational photopharmacology.
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Affiliation(s)
- Piermichele Kobauri
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nicole S Galenkamp
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Albert M Schulte
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jisk de Vries
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nadja A Simeth
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Institute for Organic and Biomolecular Chemistry, University of Goettingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Giovanni Maglia
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Dušan Kolarski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,DWI-Leibniz Institut für interaktive Materialien e.V., RWTH Aachen University, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Matsuo K, Tamaoki N. Rational design and development of a lit-active photoswitchable inhibitor targeting CENP-E. Org Biomol Chem 2021; 19:6979-6984. [PMID: 34346473 DOI: 10.1039/d1ob01332g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the emerging field of photopharmacology, synthetic photoswitches based on reversible photochemical reactions are fused to bioactive molecules. Azobenzene derivatives, which can undergo trans-cis photoisomerization, are typical photoswitches. Most azobenzene-based photochemical tools are active in the thermodynamically stable trans, but not cis, form. cis-Active photochemical tools would be ideal because they can be "initially inactive and active after light illumination" in a reversible mode only by light illumination. However, only a few rational strategies for constructing such "lit-active" photopharmacological tools has been developed. Herein, we report a rationally designed lit-active photoswitchable inhibitor targeting centromere-associated protein E (CENP-E). Using the lit-active inhibitor, we were able to photoregulate CENP-E-dependent mitotic chromosome location in cells. This study provides a framework to facilitate further progress in the development of photopharmacological tools.
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Affiliation(s)
- Kazuya Matsuo
- Research Institute for Electronic Science, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan.
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