Patrick Pfaff1, Kusal T G Samarasinghe2, Craig M Crews2,3,4, Erick M Carreira1. 1. Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland. 2. Department of Molecular, Cell, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States. 3. Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States. 4. Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States.
Abstract
Off-tissue effects are persistent issues of modern inhibition-based therapies. By merging the strategies of photopharmacology and small-molecule degraders, we introduce a novel concept for persistent spatiotemporal control of induced protein degradation that potentially prevents off-tissue toxicity. Building on the successful principle of bifunctional all-small-molecule Proteolysis Targeting Chimeras (PROTACs), we designed photoswitchable PROTACs (photoPROTACs) by including ortho-F4-azobenzene linkers between both warhead ligands. This highly bistable yet photoswitchable structural component leads to reversible control over the topological distance between both ligands. The azo-cis-isomer is observed to be inactive because the distance defined by the linker is prohibitively short to permit complex formation between the protein binding partners. By contrast, the azo-trans-isomer is active since it can engage both protein partners to form the necessary and productive ternary complex. Importantly, due to the bistable nature of the ortho-F4-azobenzene moiety employed, the photostationary state of the photoPROTAC is persistent, with no need for continuous irradiation. This technique offers reversible on/off switching of protein degradation that is compatible with an intracellular environment and, therefore, could be useful in experimental exploration of biological signaling pathways-such as those crucial for oncogenic signal transduction. Additionally, this strategy may be suitable for therapeutic intervention to address a variety of diseases. By enabling reversible activation and deactivation of protein degradation, photoPROTACs offer advantages over conventional photocaging strategies that irreversibly release active agents.
Off-tissue effects are persistent issues of modern inhibition-based therapies. By merging the strategies of photopharmacology and small-molecule degraders, we introduce a novel concept for persistent spatiotemporal control of induced protein degradation that potentially prevents off-tissue toxicity. Building on the successful principle of bifunctional all-small-molecule Proteolysis Targeting Chimeras (PROTACs), we designed photoswitchable PROTACs (photoPROTACs) by including ortho-F4-azobenzene linkers between both warhead ligands. This highly bistable yet photoswitchable structural component leads to reversible control over the topological distance between both ligands. The azo-cis-isomer is observed to be inactive because the distance defined by the linker is prohibitively short to permit complex formation between the protein binding partners. By contrast, the azo-trans-isomer is active since it can engage both protein partners to form the necessary and productive ternary complex. Importantly, due to the bistable nature of the ortho-F4-azobenzene moiety employed, the photostationary state of the photoPROTAC is persistent, with no need for continuous irradiation. This technique offers reversible on/off switching of protein degradation that is compatible with an intracellular environment and, therefore, could be useful in experimental exploration of biological signaling pathways-such as those crucial for oncogenic signal transduction. Additionally, this strategy may be suitable for therapeutic intervention to address a variety of diseases. By enabling reversible activation and deactivation of protein degradation, photoPROTACs offer advantages over conventional photocaging strategies that irreversibly release active agents.
In recent years, the
transition from inhibition of aberrant protein
function to specific degradation of undesired proteins with Proteolysis Targeting Chimeras (PROTACs) has resulted in remarkable progress and is currently
effecting a paradigm shift in drug discovery and therapy development.[1,2] PROTACs effect highly efficient protein degradation by commandeering
the endogenous ubiquitin–proteasome system. PROTACs engage
proteins of interest and E3 ligases in a ternary complex, leading
to specific polyubiquitination and labeling of proteins for degradation
via the proteasome. This approach has allowed quick expansion of the
“druggable proteome” beyond proteins that bear distinct
functional sites responsible for their respective mode of action.
By avoiding high drug doses and acting via novel mechanisms, PROTACs
show promise as therapeutic candidates for disease phenotypes that
display resistance to conventional inhibition-based therapy.[3]With the evolution from peptide- to small-molecule-based
PROTACs,
the therapeutic potential of PROTACs is quickly expanding. Selective
degradation of transcriptional regulators (BRD4,[4,5] CDK9,[6] TRIM24[7]), trans-membrane
receptor tyrosine kinases (EGFR,[8] c-Met,[8] ALK[9]), hormone receptors
(ERRα, AR),[10] or proteins linked
to neurodegenerative diseases (Tau[11]) extends
the potential of PROTACs for treatment of a variety of diseases, such
as cancer of the hematopoietic tissue[12] or hormone receptor-mediated solid malignancies.[13] Recent additions to the portfolio of chimeric degraders
include functional molecules specifically targeting degradation of
extracellular proteins.[14,15]In spite of the
tremendous advancements outlined, current PROTAC
approaches may still have undesired effects because systemic application
can affect untargeted tissue, a disadvantage shared with traditional
inhibitor-based therapeutics. As an example, ARV-771, a highly active
BET protein degrader, has been shown to achieve complete regression
of prostate cancer in a CRPC mouse xenograft model.[13] However, an on-target, general cytotoxic effect was also
observed, most notably with the occurrence of skin deterioration at
the injection site. This demonstrates the need for a switchable element
within the PROTAC scaffold, that would allow reversible degradation
in a spatiotemporal manner.A strategy to potentially circumvent
systemic undesired effects
of PROTACs involves the use of designed peptides, known as phosphoPROTACs,
that can be conditionally activated via phosphorylation by specific
growth-factor stimuli.[16] Other approaches
couple light stimuli to irreversibly induce protein degradation. This
includes photocaging[17] and the use of inducible
degrons.[18] However, both of those techniques
require the fusion of protein domains. Nonetheless, the use of light
stimuli is a highly attractive approach due to the high spatiotemporal
precision with which it can be applied.[19] Thus, there is a need for light-based strategies complementing optogenetic
approaches. In this regard, the growing field of photopharmacology
includes many examples enabling optical control of receptor function
by employment of photoswitchable ligands.[20,21] This prompted us to evaluate possible ways of introducing a photoswitchable
handle within the PROTAC scaffold.
Rationale
Despite
the published work with a variety of small molecules, PROTAC
linkers have been the subject of only nominal variation, which most
often has been restricted to alkyl and polyether linkers of varying
lengths. This has highlighted the subtle sensitivity of ternary complex
formation to linker length and composition.[22,23] Analysis of the small-molecule PROTAC literature suggests that a
minimum linker length is necessary between the warheads, because shorter
linkers are otherwise unable to span the gap needed to simultaneously
bind both the recruited proteins in a ternary complex.[24]The critical difference in linker length
between active and inactive
degraders in many of the reported examples is about 3 Å.[3,25] Strikingly, the switch between trans- and cis-azobenzenes corresponds
to a very similar difference of 3–4 Å in topological distance.
Making use of this observation, we envisioned generation of photoswitchable
PROTACs (photoPROTACs) in which the typical linear polyether
linker is replaced by azobenzenes. This would serve to introduce a
novel photoswitchable functionality to the PROTAC linker beyond passive
tethering of the two ligands. At the heart of the idea is the design
of a trans-photoPROTAC that corresponds
to the optimized linker length for efficient induction of ternary
complex formation between protein of interest (POI) and E3 ligase
(Figure A). By contrast,
the photoswitched cis-photoPROTAC would
span a prohibitively short distance and thus be unable to reach the
binding pocket of the second binding partner, precluding ternary complex
formation, target ubiquitination, and eventual degradation.
Figure 1
Concept of photoPROTACs. (A) The functional azobenzene
handle allows for photoinduced switching between an active trans- and inactive cis-photoPROTAC isomer which is prohibitively short to engage both proteins in a
ternary complex. (B) Features of photoPROTACs: catalytic,
bistable, and switchable with visible light. (C) Structure of highly
active BET protein degrader ARV-771 displaying a maximal distance
of 11 Å between both warhead moieties. (D) “Pull–pull”
and “push–pull” modes of modular connectivity
for introduction of an o-F4 azobenzene
moiety. (E) Devised BRD-degrading photoPROTAC, representatively
shown with “pull–pull” diacid linker. The trans-isomer retains the maximal distance displayed by ARV-771
while the cis-isomer is considerably shorter.
Concept of photoPROTACs. (A) The functional azobenzene
handle allows for photoinduced switching between an active trans- and inactive cis-photoPROTAC isomer which is prohibitively short to engage both proteins in a
ternary complex. (B) Features of photoPROTACs: catalytic,
bistable, and switchable with visible light. (C) Structure of highly
active BET protein degrader ARV-771 displaying a maximal distance
of 11 Å between both warhead moieties. (D) “Pull–pull”
and “push–pull” modes of modular connectivity
for introduction of an o-F4 azobenzene
moiety. (E) Devised BRD-degrading photoPROTAC, representatively
shown with “pull–pull” diacid linker. The trans-isomer retains the maximal distance displayed by ARV-771
while the cis-isomer is considerably shorter.In considering the potential applications, the
ideal photoswitchable
PROTAC-based therapeutic would have long-lived photostationary states
(∼days) that are populated following initial light stimuli
and persist throughout treatment, thereby avoiding the need for continued
or pulsed irradiation exposure. This requires the design of inactive azo-cis-isomers that are configurationally
stable in biological settings. In this respect, bistable ortho-tetrafluoroazobenzenes (o-F4-azobenzenes)
have been recently introduced,[26] and their azo-cis-isomers may display thermal τ1/2’s as high as two years at 25 °C compared to
a few hours for the parent cis-azobenzene.[27] Within these design boundaries, rationally designed photoPROTACs possess important characteristics summarized
in Figure B: a highly
stable, inactive cis-photoPROTAC is
isomerized by means of a visible light stimulus to a catalytically
active trans-photoPROTAC, that induces
polyubiquitination of a POI by complexation with an E3 ligase. The
labeled POI then proceeds to degradation by the proteasome while the trans-photoPROTAC remains active until isomerization
via a second light stimulus of a different wavelength regenerates
the inactive cis-photoPROTAC.As a photoPROTAC proof-of-concept, ARV-771[13] (Figure C) was selected as the lead structure for the generation of
a photoswitchable BET protein degrader. To introduce the o-F4-azobenzene fragment within the PROTAC scaffold as
part of a highly modular synthesis approach, two different amide linkers
(Figure D) were envisioned
involving either a precursor o-F4-azobenzene
diacid, as shown embedded in 1, or, alternatively, an o-F4-azobenzene amino-acid, as shown in 2. The designed replacement of the oligoether linker in ARV-771
with photoswitchable linkers furnishes the isomeric photoPROTAC pair shown in Figure E, which maintain an optimal distance of 11 Å between both warheads
for the putatively active trans-photoPROTAC-1 and a diminished distance of 8 Å in cis-photoPROTAC-1.
Results
Synthetic efforts commenced with the generation of unsymmetrical
amino acid o-F4-azobenzene linker as shown
in Figure D (right)
which had been predicted to possess a cis-τ1/2 of about 80 days.[28] The use
of Feringa’s method[29] gave access
to 6 from diazonium salt 4 and the organolithium
derivative generated from protected 3,5-difluoroaniline 5 (Figure A). Subsequent
palladium-catalyzed carbonylative esterification furnished aminoester 7.[30] Initial efforts to remove
the bisallyl protecting group under classical Pd-mediated conditions[31] were not met with success. Instead, ruthenium-catalyzed
isomerization and subsequent hydrolysis of the enamine produced gave
the targeted aniline 8.[32] Acetylation
of aniline 8 gave 9, which served as a model
to examine bistability. Switching between trans-9 and cis-9 occurred by irradiation
at the well-separated n−π* absorption bands at 415 nm
(cis–trans) and 530 nm (trans–cis), respectively. Unfortunately, cis-9 generated under 530 nm irradiation quickly isomerized to the thermodynamically
more stable trans-9 with a thermal half-life
of ∼2 h (Figure B). On the basis of our design criteria, this observation rendered
azobenzene linker building block 8 unsuitable. It is
important to note that this observation is in line with the general
concept of diminished bistability of “push–pull”
azobenzenes.[33,34]
Figure 2
(A) Synthetic approach toward unsymmetrical
amino acid azobenzene
linker 8. (B) Bistability measurement of model substrate 9, starting with enriched cis-9 (t = 0) after a 20 min irradiation at 530 nm (50
μM in CH3CN). (C) Synthetic approach toward monoprotected
diacid azobenzene building block 14. (D) Classical Curtius
conditions mainly generated urea 16 under reflux conditions,
preventing access to 18. Milder Curtius conditions under
Lewis-acid catalysis allowed isolation of 17 which could
be transformed into JQ-1 amine 18.
The results with 9 prompted us to revise the design
of the photoPROTAC conjugate to include a “pull–pull”
system by the introduction of diacid linker as shown for 1 (Figure D,E), bearing
two electron-withdrawing substituents. Notably, this permutation in
design necessitated transposition of the amide bond joining BET protein
ligand JQ-1 and the azobenzene linker moiety (Figure C,E). For ease of handling, generation of
building block 14 was targeted, which would allow for
facile discrimination of both substitution sites. Aniline 10 was generated in a 3-step sequence starting from 2,6-difluoro-4-iodoaniline
(Figure C). Treatment
of 10 with NOBF4 in EtOAc afforded diazonium
tetrafluoroborate 11.[35] The
diazonium salt was trapped with lithiated TBS-protected 3,5-difluorobenzylalcohol 12 to furnish unsymmetrically substituted o-F4-azobenzene 13.[29] After TBS deprotection with TBAF and oxidation[36] of the obtained benzylic alcohol desired bifunctional azobenzene
linker 14 was generated.(A) Synthetic approach toward unsymmetrical
amino acid azobenzene
linker 8. (B) Bistability measurement of model substrate 9, starting with enriched cis-9 (t = 0) after a 20 min irradiation at 530 nm (50
μM in CH3CN). (C) Synthetic approach toward monoprotected
diacid azobenzene building block 14. (D) Classical Curtius
conditions mainly generated urea 16 under reflux conditions,
preventing access to 18. Milder Curtius conditions under
Lewis-acid catalysis allowed isolation of 17 which could
be transformed into JQ-1 amine 18.To synthesize required JQ1-amine 18, a sequence was
devised to convert JQ1-acid 15 to the corresponding amine
via Curtius rearrangement. However, under classical conditions, the
isocyanate generated could not be trapped by alcohols such as tert-butanol or benzyl alcohol but instead led to the formation
of urea 16 (Figure D). We hypothesized that intramolecular reaction of
the intermediate isocyanate with the diazepine was leading to complications
and examined alternative conditions involving the use of TMSN3 under mild conditions.[37,38] Under these conditions
JQ1-carbamoyl azide 17 was isolated, which could then
be easily deprotected within minutes by employing KOt-Bu in aq. t-BuOH. This facile sequence may be generally
applicable with challenging substrates for the Curtius rearrangement.With all necessary building blocks in hand the desired BRD-photoPROTAC-1 was assembled by a series of amide couplings
(Figure A). After
coupling of VHL ligand[39,40]19 to the azobenzene,
the tert-butyl ester was hydrolyzed with TFA, and
JQ-1 amine 18 was attached furnishing o-F4-azobenzene linked BRD-photoPROTAC-1.
Next, the photochemical properties of the conjugate generated were
examined. In DMSO, the cis–trans switch occurred efficiently by irradiation at 415 nm (Figure B), producing a photostationary
state (PSS) consisting of 95% trans-photoPROTAC-1 as determined by separation of both isomers via HPLC (Figure C). Irradiation at 530 nm established
a PSS consisting of 68% cis-photoPROTAC-1, which is slightly reduced when compared to examples of o-F4-azobenzenes with higher cis-PSSs[27,41] although the n−π* absorption
maxima of both isomers are well-separated by 47 nm (Figure S7 for calculated spectra of pure cis- and trans-photoPROTAC-1).
Figure 3
(A) Modular
assembly of photoPROTAC-1. (B) UV–vis
spectra of photoenriched trans-photoPROTAC-1 (irradiated at 415 nm, shown in orange) and cis-photoPROTAC-1 (irradiated at 530 nm, shown in dark
blue) in DMSO; left panel, UV–vis spectra in the range 290–600
nm; right panel, enlargement of the spectra in the range 390–600
nm. (C) RP-HPLC chromatograms of photoenriched trans-photoPROTAC-1 (415 nm, left panel) and cis-photoPROTAC-1 (530 nm, right panel) in DMSO shown at
isosbestic wavelength (275 nm in CH3CN/H2O).
(A) Modular
assembly of photoPROTAC-1. (B) UV–vis
spectra of photoenriched trans-photoPROTAC-1 (irradiated at 415 nm, shown in orange) and cis-photoPROTAC-1 (irradiated at 530 nm, shown in dark
blue) in DMSO; left panel, UV–vis spectra in the range 290–600
nm; right panel, enlargement of the spectra in the range 390–600
nm. (C) RP-HPLC chromatograms of photoenriched trans-photoPROTAC-1 (415 nm, left panel) and cis-photoPROTAC-1 (530 nm, right panel) in DMSO shown at
isosbestic wavelength (275 nm in CH3CN/H2O).In addition, quantum yields for both isomerization
reactions at
either 415 or 530 nm irradiation were calculated on the basis of kinetic
data (Figures S6–S10; see section
S2.9 for technical details). The obtained quantum yields [ϕEZ (530 nm) = 0.28, ϕZE (415 nm) = 0.65] were
of similar order as those reported previously for underivatized o-F4-azobenzenes[27] indicating efficient isomerization upon photon absorption. Importantly,
the reported bistability of the “pull–pull” ortho-F4 azobenzene was also retained in the photoPROTAC-1 derivative, and no thermal back-isomerization
of cis-photoPROTAC-1 was observed in
DMSO, acetonitrile, or aq. buffer for several days at 37 °C.
The suitability for biological applications was further demonstrated
by retained stability of a 50 μM solution of photoPROTAC-1 in the presence of 10 mM reduced glutathione over 3 days (Figure S5A). Additionally, stability of photoPROTAC-1 in cells was evaluated. Cells were incubated
with or without photoPROTAC-1 at 25 μM, and after
different time periods of up to 24 h, cells were harvested and lysed
in PBS by multiple freeze–thaw cycles. Then, cell lysates were
analyzed by LC-MS for nonreduced and reduced forms of photoPROTAC-1. Consistent with the data presented in Figure S5A, masses matching a potentially reduced form were not detected.
However, fully retained isotopic distribution after 24 h matching
the nonreduced form of the photoPROTAC indicated the
stability of the photoPROTAC under biological conditions
(Figure S5B,C).Having confirmed
stability under biological conditions and efficient
switching between cis- and trans-configurations upon irradiation at 530 and 415 nm, we next carried
out biological experiments in Ramos cells. PhotoPROTAC-1 solutions were irradiated using 415 or 530 nm LEDs initially for
20 min to obtain trans- and cis-isomers, respectively; after 1 min of rest and brief vortexing, irradiation
was continued for another 10 min. Trans- and cis-photoPROTAC-1 solutions were diluted to
the desired concentrations and added to Ramos cells. Incubation of trans-photoPROTAC-1 for 6.5 h significantly
induced BRD2 degradation at low nanomolar concentrations (Figure A). Conversely, cis-photoPROTAC-1 did not induce BRD2 degradation
in the range of concentrations tested. Longer 18 h incubation with
either cis- or trans-photoPROTAC-1 did not improve or affect the BRD2degradation efficiencies (Figure B). Interestingly, photoPROTAC-1 did not induce efficient BRD2 degradation in
cells without an initial 415 nm irradiation indicating that the presence
of a mixture of trans- and cis-photoPROTAC-1 (35% cis-isomer after equilibrating
for 5 days under daylight) led to diminished BRD2 degradation (Figure S3). One possible explanation for this
observation would be that the inactive cis-isomer
has a higher affinity for either BRD2 or VHL than does trans-photoPROTAC-1, which blocks binding of the active isomer
and thereby prevents induction of degradation. As a result, ratios
well below the PSS of 68% cis at 530 nm evidently
suffice to prevent degradation.
Figure 4
PhotoPROTAC-1 can be converted
to active trans- and inactive cis-isomers to induce differential
degradation of BRD2. PhotoPROTAC-1 working solutions
were irradiated for 30 min using 415 or 530 nm LEDs and added to Ramos
cells at varying concentrations. Cells were incubated in the dark
for (A) 6.5 h or (B) 18 h prior to cell lysis. Treatment of active
trans-photoPROTAC induced significant
BRD2 degradation within 6.5 h whereas inactive cis-photoPROTAC-1 did not show a significant effect on BRD2
levels. BRD4 degradation was not observed under indicated conditions.
(C) Time-dependent degradation of BRD proteins by photoPROTAC-1. Singly irradiated photoPROTAC-1 (trans and cis) were treated at 500 nM concentrations,
and BRD protein levels were analyzed after indicated time points.
PhotoPROTAC-1 can be converted
to active trans- and inactive cis-isomers to induce differential
degradation of BRD2. PhotoPROTAC-1 working solutions
were irradiated for 30 min using 415 or 530 nm LEDs and added to Ramos
cells at varying concentrations. Cells were incubated in the dark
for (A) 6.5 h or (B) 18 h prior to cell lysis. Treatment of active
trans-photoPROTAC induced significant
BRD2 degradation within 6.5 h whereas inactive cis-photoPROTAC-1 did not show a significant effect on BRD2
levels. BRD4 degradation was not observed under indicated conditions.
(C) Time-dependent degradation of BRD proteins by photoPROTAC-1. Singly irradiated photoPROTAC-1 (trans and cis) were treated at 500 nM concentrations,
and BRD protein levels were analyzed after indicated time points.To investigate time-dependent degradation profiles
of trans- and cis-photoPROTAC-1, Ramos cells
were harvested at different time points ranging from 1 to 24 h. Within
1 h, significant BRD2 degradation was not observed. However, after
3 h of incubation, trans-photoPROTAC-1 induced BRD2 degradation, which increased over the next 4 h. After
7 h, BRD2 degradation reached the maximum level and remained unchanged
over the following 17 h (Figure C). To confirm that trans-photoPROTAC-1 induced BRD2 degradation through the proteasomal pathway, we analyzed
the BRD2 degradation profile in the presence or absence of the selective
NEDD8 inhibitor MLN-4924. Treatment with MLN-4924 rescued BRD2 degradation
indicating that BRD2 degradation took place via the proteasomal pathway
(Figure S4).Curiously, the data
did not show a significant degradation of BRD4
in response to cis- or trans-photoPROTAC-1 treatments even though ARV-771 could degrade
both BRD4 and BRD2, and with greater potency (Figure S1). Although no structural data are currently available
for trans-photoPROTAC-1 bound to BRD4,
hypotheses for the observed differential degradation include a newly
gained selectivity of the trans-photoPROTAC-1 toward BRD2 over BRD4 due to the reversed amide bond between JQ-1
and o-F4-azobenzene moiety—a structural
feature differentiating it from ARV-771 (Figure C,E). Also, introduction of the azobenzene
to the PROTAC scaffold increased the overall stiffness[19] of the conjugate that could further account
for a potential loss of important interactions with BRD4. Both structural
changes might result in a less stable ternary complex, leading to
a more rapid dissociation and consequently to inefficient ubiquitination
and proteasomal degradation of BRD4. Overall, these data suggested
that the o-F4-azobenzene moiety within photoPROTAC-1 allows interconversion between active trans-photoPROTAC-1 and inactive cis-photoPROTAC-1 that is rapid and stable—the latter
made evident by the finding that continuous irradiation does not yield
a superior differential BRD2 degradation (Figure S3). Concordantly, the biological data indicate efficient degradation
of BRD2 by trans-photoPROTAC-1 and minimum
degradation by cis-photoPROTAC-1 obtained
from a single, initial irradiation.Next, to test the reversible
photoswitching between cis-photoPROTAC-1 and trans-photoPROTAC-1, we performed
a two-step irradiation process using both 415 and
530 nm LEDs before incubation with cells. Initial 415 and 530 nm irradiations
were carried out separately for 30 min to obtain active trans-photoPROTAC-1 and inactive cis-photoPROTAC-1, respectively. Trans-photoPROTAC-1 and cis-photoPROTAC-1 were then subdivided (50:50) into two tubes each. One tube of each photoPROTAC-1 isomer was set aside, while the remaining tube
of trans-photoPROTAC-1 was subjected
to a second round of irradiation at 530 nm, and the remaining tube
of cis-photoPROTAC-1 was exposed to
the 415 nm LED. To assess the reversible photoisomerization of photoPROTAC-1, Ramos cells were separately treated with varying
concentrations of either singly irradiated (415 nm, trans-photoPROTAC-1; or 530 nm, cis-photoPROTAC-1) or doubly irradiated (530/415 nm, trans-photoPROTAC-1; or 415/530 nm, cis-photoPROTAC-1) photoPROTAC-1. After 18 h of incubation
with photoPROTAC-1 obtained from different irradiation
combinations, cells were lysed and analyzed for levels of BRD4 and
BRD2. In line with the previous experiment (Figure ), similar BRD4/2 degradation patterns were
observed for trans-photoPROTAC-1 and cis-photoPROTAC-1 that were obtained through
single irradiation (Figure A, 415 or 530 nm). Regarding double-irradiated photoPROTAC-1 (Figure A, 530/415
or 415/530 nm), the data demonstrate a complete reversal of their
degradation potential following a second irradiation (i.e., 530 nm
followed by 415 nm LEDs or vice versa) indicating the dynamic switching
of photoPROTAC between active and inactive states.
Figure 5
PhotoPROTACs are dynamically interchangeable between
active trans- and inactive cis-configurations.
(A) PhotoPROTAC-1 working solutions were initially irradiated
with 415 or 530 nm LEDs followed by second irradiation using 530 or
415 nm (415/530 and 530/415 nm) to reverse the initial configurations.
The treatment of singly irradiated trans-photoPROTAC-1 (415 nm) induced a significant BRD2 degradation relative to the cis-photoPROTAC-1 (530 nm) whereas no significant
BRD4 degradation was observed in response to both trans- and cis-photoPROTAC-1. Second irradiation
with either 530 or 415 nm significantly shifted the biologically active trans-isomer to inactive cis-isomer and
vice versa. (B) Temporal control of photoPROTAC-1 activity.
Singly irradiated photoPROTAC-1 (trans/415 nm and cis/530 nm) were added to cells. One
set of cis- and trans-photoPROTAC-1 treated cells were kept in the dark, and a parallel set of cells
treated with trans-photoPROTAC-1 were
exposed to irradiation at 530 nm (415 initial/530 nm in cells) to
induce the trans to cis isomerization
in cells.
PhotoPROTACs are dynamically interchangeable between
active trans- and inactive cis-configurations.
(A) PhotoPROTAC-1 working solutions were initially irradiated
with 415 or 530 nm LEDs followed by second irradiation using 530 or
415 nm (415/530 and 530/415 nm) to reverse the initial configurations.
The treatment of singly irradiated trans-photoPROTAC-1 (415 nm) induced a significant BRD2 degradation relative to the cis-photoPROTAC-1 (530 nm) whereas no significant
BRD4 degradation was observed in response to both trans- and cis-photoPROTAC-1. Second irradiation
with either 530 or 415 nm significantly shifted the biologically active trans-isomer to inactive cis-isomer and
vice versa. (B) Temporal control of photoPROTAC-1 activity.
Singly irradiated photoPROTAC-1 (trans/415 nm and cis/530 nm) were added to cells. One
set of cis- and trans-photoPROTAC-1 treated cells were kept in the dark, and a parallel set of cells
treated with trans-photoPROTAC-1 were
exposed to irradiation at 530 nm (415 initial/530 nm in cells) to
induce the trans to cis isomerization
in cells.To further investigate the reversibility
and temporal controllability
of photoPROTAC-1, one set of cells treated with trans-photoPROTAC-1 was incubated in the dark,
and another, parallel set of cells (trans-photoPROTAC-1 treated) was incubated under 530 nm irradiation. As anticipated, cis-photoPROTAC-1 was recovered by illuminating
530 nm light on cells at the desired time point. Intracellular conversion
was confirmed by suspension of BRD2 degradation in contrast to BRD2
levels in cells kept in the dark (Figure B). In addition, significant BRD2 degradation
was observed when cis-photoPROTAC-1 treated
cells were incubated under 415 nm LED (Figure S2) suggesting that the o-F4-azobenzene
moiety can be successfully incorporated into PROTAC linkers for light-induced,
spatiotemporal control of targeted protein degradation in a reversible
manner.Overall, our data indicate that initial irradiation
of photoPROTAC-1 holds the potential for successful spatiotemporal
control of photoPROTAC-1 and avoids laborious continuous-irradiation
efforts to induce the photoswitching between active and inactive states
of PROTACs. Moreover, sustained BRD2 degradation after an 18 h incubation
with trans-photoPROTAC-1 as well as
sustained suspension of BRD2 degradation after an 18 h incubation
with cis-photoPROTAC-1 (Figure B) indicate the bistability
of o-F4-azobenzene containing photoPROTAC-1. Had the active trans-isomer switched to the inactive cis-isomer over the course of the experiment, persistent
BRD2 degradation would have not been prominent considering the significant
resynthesis of BRD proteins that occurs as a feedback mechanism in
response to inhibition (Figure A,B, 530 nm treated cells).[42] Vice
versa, had the cis-isomer switched to the thermodynamically
more stable active trans-isomer within the time scale
of the experiment, degradation of BRD2 would have been induced over
time. Hence, our approach provides robust control over induced degradation.
Taken together, our data provide evidence to support the use of o-F4-azobenzene moiety in PROTAC design to provide
a powerful strategy to spatiotemporally control PROTAC activity with
a single initial irradiation step.
Outlook
Bistable
heterodiazocine motifs, displaying >99% cis-content
in the dark with stable trans-isomers bearing
thermal half-lives of several days, are promising candidates that
may be amalgamated with our overarching strategy to generate cis-inactive photoPROTACs.[43] Future approaches could include azobenzenes sufficiently
red-shifted to allow irradiation in the NIR/IR window for optimal
tissue penetration.[44,45] Additionally, taking advantage
of two-photon excitation processes may further enable switching in
a more favorable window.[28,41]Applications
of our photoPROTAC method to target proteins
beyond BET domains are currently under investigation and will be reported
in due course. This also includes engagement of other E3 ligases such
as cereblon or MDM2. Moreover, photoPROTACs may serve
as a reversibly controllable platform for aggressively targeting central
parts of the cell machinery with high resolution, for example, for
the degradation of antiapoptotic proteins. Dilution via diffusion
of the on-site activated trans-photoPROTAC may suffice to prevent off-tissue effects; however, for even higher
resolution, back-switching of the activated trans-photoPROTAC to the inactive azo-cis-isomer by a second optical fiber light source at a defined distance
from the application site can be envisioned. As part of our studies
it was demonstrated that isomer compositions in ratios well below
the cis-rich PSS at 530 nm suffice to halt degradation,
which indicates that very short irradiation periods in the range of
minutes (for kinetic data cf. Figures S8 and S10) could be already satisfactory to persistently turn off degradation
activity. This is an advantage over conventional photocaging strategies
which release active drugs only irreversibly.While in the process
of preparing this manuscript, we became aware
of a preprint demonstrating an alternative approach by generating cis-active photoswitchable PROTACs.[46] In their complementary approach, Trauner et al. introduced azobenzene
moieties to ligands of E3 ligase cereblon. In contrast to our bistable
system, their strategy necessitates continued light pulses at 390
nm to induce prolonged degradation otherwise their degrader remains
inactive in the dark.
Conclusion
The combination of two
recently emerging areas in drug discovery,
namely, photopharmacology and small-molecule degraders, has led us
to develop the concept of photoswitchable, bistable photoPROTACs with potentially far reaching implications for manifold applications.
In combination with modern methods of proteomics, photoPROTACs offer further opportunity for studying downstream effects of signaling
pathways which are yet insufficiently understood.[47] More broadly, it should be noted that spatiotemporal activation/deactivation
of photoswitchable PROTACs by a single irradiation event may find
use in novel therapeutics.
Authors: Kanak Raina; Jing Lu; Yimin Qian; Martha Altieri; Deborah Gordon; Ann Marie K Rossi; Jing Wang; Xin Chen; Hanqing Dong; Kam Siu; James D Winkler; Andrew P Crew; Craig M Crews; Kevin G Coleman Journal: Proc Natl Acad Sci U S A Date: 2016-06-06 Impact factor: 11.205
Authors: George M Burslem; Blake E Smith; Ashton C Lai; Saul Jaime-Figueroa; Daniel C McQuaid; Daniel P Bondeson; Momar Toure; Hanqing Dong; Yimin Qian; Jing Wang; Andrew P Crew; John Hines; Craig M Crews Journal: Cell Chem Biol Date: 2017-11-09 Impact factor: 8.116
Authors: Andrew P Crew; Kanak Raina; Hanqing Dong; Yimin Qian; Jing Wang; Dominico Vigil; Yevgeniy V Serebrenik; Brian D Hamman; Alicia Morgan; Caterina Ferraro; Kam Siu; Taavi K Neklesa; James D Winkler; Kevin G Coleman; Craig M Crews Journal: J Med Chem Date: 2017-07-10 Impact factor: 7.446
Authors: Tao Wu; Hojong Yoon; Yuan Xiong; Sarah E Dixon-Clarke; Radosław P Nowak; Eric S Fischer Journal: Nat Struct Mol Biol Date: 2020-06-15 Impact factor: 15.369