Photopharmacology: Beyond Proof of Principle Velema, Willem A; Szymanski, Wiktor; Feringa, Ben L
Journal of the American Chemical Society,
02/2014, Letnik:
136, Številka:
6
Journal Article
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Pharmacotherapy is often severely hindered by issues related to poor drug selectivity, including side effects, environmental toxicity, and the emergence of resistance. Lack of selectivity is caused ...by the inability to control drug activity in time and space. Photopharmacology aims at solving this issue by incorporating photoswitchable groups into the molecular structure of bioactive compounds. These switching units allow for the use of light as an external control element for pharmacological activity, which can be delivered with very high spatiotemporal precision. This Perspective presents the reader with the current state and outlook on photopharmacology. In particular, the principles behind photoregulation of bioactivity, the challenges of molecular design, and the possible therapeutic scenarios are discussed.
Antibiotic resistance is an enormous problem that is accountable for over a million deaths annually, with numbers expected to significantly increase over the coming decades. Although some of the ...underlying causes leading up to antibiotic resistance are well understood, many of the molecular processes involved remain elusive. To better appreciate at a molecular level how resistance emerges, customized chemical biology tools can offer a solution. This Feature Article attempts to provide an overview of the wide variety of tools that have been developed over the last decade, by highlighting some of the more illustrative examples. These include the use of fluorescent, photoaffinity and activatable antibiotics and bacterial components to start to unravel the molecular mechanisms involved in resistance. The antibiotic crisis is an eminent global threat and requires the continuous development of creative chemical tools to dissect and ultimately counteract resistance.
The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed ...photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely on wavelength-selective cleavage of photo-removable protecting groups. Here we report the orthogonal and reversible control of two distinct types of photoswitches in one solution, that is, a donor-acceptor Stenhouse adduct (DASA) and an azobenzene. The control is achieved by using three different wavelengths of irradiation and a thermal relaxation process. The reported combination tolerates a broad variety of differently substituted photoswitches. The presented system is also extended to an intramolecular combination of photoresponsive units. A model application for an intramolecular combination of switches is presented, in which the DASA component acts as a phase-transfer tag, while the azobenzene moiety independently controls the binding to α-cyclodextrin.
Photocleavable protecting groups (PPGs) are extensively used in chemical and biological sciences. In their application, advantage is taken of using light as an external, non-invasive stimulus, which ...can be delivered with very high spatiotemporal precision. More recently, orthogonally addressing multiple PPGs, in a single system and with different wavelengths of light, has been explored. This approach allows one to independently control multiple functionalities in an external, non-invasive fashion. In this tutorial review, we discuss the design principles for dynamic systems involving wavelength-selective deprotection, focusing on the choice and optimization of PPGs, synthetic methods for their introduction and strategies for combining multiple PPGs into one system. Finally, we illustrate the design principles with representative examples, aiming at providing the reader with an instructive overview on how the wavelength-selective cleavage of photoprotecting groups can be applied in materials science, organic synthesis and biological systems.
Cancer treatment suffers from limitations that have a major impact on the patient’s quality of life and survival. In the case of chemotherapy, the systemic distribution of cytotoxic drugs reduces ...their efficacy and causes severe side effects due to nonselective toxicity. Photopharmacology allows a novel approach to address these problems because it employs external, local activation of chemotherapeutic agents by using light. The development of photoswitchable histone deacetylase (HDAC) inhibitors as potential antitumor agents is reported herein. Analogues of the clinically used chemotherapeutic agents vorinostat, panobinostat, and belinostat were designed with a photoswitchable azobenzene moiety incorporated into their structure. The most promising compound exhibits high inhibitory potency in the thermodynamically less stable cis form and a significantly lower activity for the trans form, both in terms of HDAC activity and proliferation of HeLa cells. This approach offers a clear prospect towards local photoactivation of HDAC inhibition to avoid severe side effects in chemotherapy.
Bright therapy: Chemotherapeutic histone deacetylase (HDAC) inhibitors with photocontrolled activity are presented. On HDAC2, the best compound shows high potency (similar to the clinically used parent hydroxamic acid; see figure) in the thermodynamically less stable state and 40× lower potency in the resting state. This approach offers prospects towards local photoactivation of HDAC inhibition to avoid severe side effects in chemotherapy.
Issues surrounding the reversible photocontrol of biological systems by the incorporation of molecular photoswitches are examined. Photoswitches are used for photoregulation of biological processes.
Riboswitches are structural RNA elements that control gene expression. These naturally occurring RNA sensors are of continued interest as antibiotic targets, molecular sensors, and functional ...elements of synthetic circuits. Here, we describe affinity-based profiling of the flavin mononucleotide (FMN) riboswitch to characterize ligand binding and structural folding. We designed and synthesized photoreactive ligands and used them for photoaffinity labeling. We showed selective labeling of the FMN riboswitch and used this covalent interaction to quantitatively measure ligand binding, which we demonstrate with the naturally occurring antibiotic roseoflavin. We measured conditional riboswitch folding as a function of temperature and cation concentration. Furthermore, combining photoaffinity labeling with reverse transcription revealed ligand binding sites within the aptamer domain with single-nucleotide resolution. The photoaffinity probe was applied to cellular extracts of Bacillus subtilis to demonstrate conditional folding of the endogenous low-abundant ribD FMN riboswitch in biologically derived samples using quantitative PCR. Lastly, binding of the riboswitch-targeting antibiotic roseoflavin to the FMN riboswitch was measured in live bacteria using the photoaffinity probe.
Terminal deoxynucleotidyl Transferase (TdT) is a template‐independent DNA polymerase that plays an essential role in the human adaptive immune system and is upregulated in several types of leukemia. ...It has therefore gained interest as a leukemia biomarker and potential therapeutic target. Herein, we describe a FRET‐quenched fluorogenic probe based on a size‐expanded deoxyadenosine that reports directly on TdT enzymatic activity. The probe enables real‐time detection of primer extension and de novo synthesis activity of TdT and displays selectivity over other polymerase and phosphatase enzymes. Importantly, TdT activity and its response to treatment with a promiscuous polymerase inhibitor could be monitored in human T‐lymphocyte cell extract and Jurkat cells using a simple fluorescence assay. Finally, employing the probe in a high‐throughput assay resulted in the identification of a non‐nucleoside TdT inhibitor.
A fluorogenic probe based on size‐expanded adenosine is used to monitor activity of the leukemia biomarker and therapeutic target Terminal deoxynucleotidyl Transferase (TdT). The probe can measure TdT activity in cancer cell extract in real‐time and report on its response to treatment. Use of the probe in a high‐throughput screening led to the identification of the non‐nucleoside inhibitor SCH202676.
RNA is a versatile biomolecule with a broad range of biological functions that go far beyond its initially described role as a simple information carrier. The development of chemical methods to ...control, manipulate and modify RNA has the potential to yield new insights into its many functions and properties. Traditionally, most of these methods involved the chemical modification of RNA structure using solid-state synthesis or enzymatic transformations. However, over the past 15 years, the direct functionalization of RNA by selective acylation of the 2′-hydroxyl (2′-OH) group has emerged as a powerful alternative that enables the simple modification of both synthetic and transcribed RNAs. In this Review, we discuss the chemical properties and design of effective reagents for RNA 2′-OH acylation, highlighting the unique problem of 2′-OH reactivity in the presence of water. We elaborate on how RNA 2′-OH acylation is being exploited to develop selective chemical probes that enable interrogation of RNA structure and function, and describe new developments and applications in the field.The direct functionalization of RNA by selective acylation at the 2′-hydroxyl position is a powerful tool for structural and functional studies. This Review describes the chemical properties and design of effective acylating reagents, highlighting the various applications of RNA acylation.
Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly‐evolving resistant bacteria. Nucleic acid therapeutics hold promise as ...powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore‐mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore‐conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono‐catechol group showed equally effective. Targeting the lacZ transcript resulted in dose‐dependent decreased β‐galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii also showed concentration‐dependent growth inhibition. Whole‐genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore‐mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics.
Synthetic siderophores are conjugated to antibacterial antisense sequences to efficiently deliver them into bacteria. The conjugates display effective protein downregulation and potent antibacterial properties. Whole‐genome sequencing of resistant mutants and competition experiments with the endogenous siderophore demonstrate transport through the siderophore‐mediated iron uptake pathway.
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