Structure determination of high-energy states in a dynamic protein ensemble.

Macromolecular function frequently requires that proteins change conformation into high-energy states1-4. However, methods for solving the structures of these functionally essential, lowly populated states are lacking. Here we develop a method for high-resolution structure determination of minorly populated states by coupling NMR spectroscopy-derived pseudocontact shifts5 (PCSs) with Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion6 (PCS-CPMG). Our approach additionally defines the corresponding kinetics and thermodynamics of high-energy excursions, thereby characterizing the entire free-energy landscape. Using a large set of simulated data for adenylate kinase (Adk), calmodulin and Src kinase, we find that high-energy PCSs accurately determine high-energy structures (with a root mean squared deviation of less than 3.5 angström). Applying our methodology to Adk during catalysis, we find that the high-energy excursion involves surprisingly small openings of the AMP and ATP lids. This previously unresolved high-energy structure solves a longstanding controversy about conformational interconversions that are rate-limiting for catalysis. Primed for either substrate binding or product release, the high-energy structure of Adk suggests a two-step mechanism combining conformational selection to this state, followed by an induced-fit step into a fully closed state for catalysis of the phosphoryl-transfer reaction. Unlike other methods for resolving high-energy states, such as cryo-electron microscopy and X-ray crystallography, our solution PCS-CPMG approach excels in cases involving domain rearrangements of smaller systems (less than 60 kDa) and populations as low as 0.5%, and enables the simultaneous determination of protein structure, kinetics and thermodynamics while proteins perform their function.

Design principles for cyclin K molecular glue degraders.

Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

Controlling the Photophysical Properties of a Series of Isostructural d6 Complexes Based on Cr0, MnI, and FeII.

Development of first-row transition metal complexes with similar luminescence and photoredox properties as widely used RuII polypyridines is attractive because metals from the first transition series are comparatively abundant and inexpensive. The weaker ligand field experienced by the valence d-electrons of first-row transition metals challenges the installation of the same types of metal-to-ligand charge transfer (MLCT) excited states as in precious metal complexes, due to rapid population of energetically lower-lying metal-centered (MC) states. In a family of isostructural tris(diisocyanide) complexes of the 3d6 metals Cr0, MnI, and FeII, the increasing effective nuclear charge and ligand field strength allow us to control the energetic order between the 3MLCT and 3MC states, whereas pyrene decoration of the isocyanide ligand framework provides control over intraligand (ILPyr) states. The chromium(0) complex shows red 3MLCT phosphorescence because all other excited states are higher in energy. In the manganese(I) complex, a microsecond-lived dark 3ILPyr state, reminiscent of the types of electronic states encountered in many polyaromatic hydrocarbon compounds, is the lowest and becomes photoactive. In the iron(II) complex, the lowest MLCT state has shifted to so much higher energy that 1ILPyr fluorescence occurs, in parallel to other excited-state deactivation pathways. Our combined synthetic-spectroscopic-theoretical study provides unprecedented insights into how effective nuclear charge, ligand field strength, and ligand π-conjugation affect the energetic order between MLCT and ligand-based excited states, and under what circumstances these individual states become luminescent and exploitable in photochemistry. Such insights are the key to further developments of luminescent and photoredox-active first-row transition metal complexes.

Pseudocontact Shifts in Biomolecular NMR Spectroscopy.

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

An Artificial Metalloenzyme Based on a Copper Heteroscorpionate Enables sp3 C-H Functionalization via Intramolecular Carbene Insertion.

The selective functionalization of sp3 C-H bonds is a versatile tool for the diversification of organic compounds. Combining attractive features of homogeneous and enzymatic catalysts, artificial metalloenzymes offer an ideal means to selectively modify these inert motifs. Herein, we report on a copper(I) heteroscorpionate complex embedded within streptavidin that catalyzes the intramolecular insertion of a carbene into sp3 C-H bonds. Target residues for genetic optimization of the artificial metalloenzyme were identified by quantum mechanics/molecular mechanics simulations. Double-saturation mutagenesis yielded detailed insight on the contribution of individual amino acids on the activity and the selectivity of the artificial metalloenzyme. Mutagenesis at a third position afforded a set of artificial metalloenzymes that catalyze the enantio- and regioselective formation of ß- and γ-lactams with high turnovers and promising enantioselectivities.

Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins.

NMR chemical shift changes can report on the functional dynamics of biomacromolecules in solution with sizes >1 MDa. However, their interpretation requires chemical shift assignments to individual nuclei, which for large molecules often can only be obtained by tedious point mutations that may interfere with function. We present here an efficient pseudocontact shift NMR method to assign biomacromolecules using bound antibodies tagged with lanthanoid DOTA chelators. The stability of the antibody allows positioning the DOTA tag at many surface sites, providing triangulation of the macromolecule nuclei at distances >60 Å. The method provides complete assignments of valine and tyrosine 1H-15N resonances of the ß1-adrenergic receptor in various functional forms. The detected chemical shift changes reveal strong forces exerted onto the backbone of transmembrane helix 3 during signal transmission, which are absorbed by its electronic structure. The assignment method is applicable to any soluble biomacromolecule for which suitable complementary binders exist.

Geländer Molecules with Orthogonal Joints: Synthesis of Macrocyclic Dimers.

Orthogonal joints, understood as connections with an angle of 90°, were introduced in the design of the "Geländer" model compounds 1 and 2. The banister, consisting of a conjugated carbazole dimer linked by either 1,3-butadiyne (2) or a single thiophene (1), wraps around an axis composed of a phthalimide dimer due to the dimensional mismatch of both subunits, which are interconnected by phenylene rungs. The "Geländer" structure was assembled from a monomer comprising the 1,4-diaminobenzene rung with one amino substituent as part of a 4-bromo phthalimide subunit forming the orthogonal junction to the axis, and the other as part of a masked 2-ethynyl carbazole as orthogonal joint to the banister. The macrocycle was obtained by two sequential homocoupling steps. A first dimerization by a reductive homocoupling assembled the axis, while an oxidative acetylene coupling served as ring-closing reaction. The formed butadiyne was further derivatized to a thiophene, rendering all carbons of the model compound sp2 hybridized. Both helical structures were fully characterized and chirally resolved. Assignment of the enantiomers was achieved by simulation of chiroptical properties and enantiopure synthesis.

Manganese(I) Complex with Monodentate Arylisocyanide Ligands Shows Photodissociation Instead of Luminescence.

Recently reported manganese(I) complexes with chelating arylisocyanide ligands exhibit luminescent metal-to-ligand charge-transfer (MLCT) excited states, similar to ruthenium(II) polypyridine complexes with the same d6 valence electron configuration used for many different applications in photophysics and photochemistry. However, chelating arylisocyanide ligands require substantial synthetic effort, and therefore it seemed attractive to explore the possibility of using more readily accessible monodentate arylisocyanides instead. Here, we synthesized the new Mn(I) complex [Mn(CNdippPhOMe2)6]PF6 with the known ligand CNdippPhOMe2 = 4-(3,5-dimethoxyphenyl)-2,6-diisopropylphenylisocyanide. This complex was investigated by NMR spectroscopy, single-crystal structure analysis, high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) measurements, IR spectroscopy supported by density functional theory (DFT) calculations, cyclic voltammetry, and time-resolved as well as steady-state UV-vis absorption spectroscopy. The key finding is that the new Mn(I) complex is nonluminescent and instead undergoes arylisocyanide ligand loss during continuous visible laser irradiation into ligand-centered and charge-transfer absorption bands, presumably owed to the population of dissociative d-d excited states. Thus, it seems that chelating bi- or tridentate binding motifs are essential for obtaining emissive MLCT excited states in manganese(I) arylisocyanides. Our work contributes to understanding the basic properties of photoactive first-row transition metal complexes and could help advance the search for alternatives to precious metal-based luminophores, photocatalysts, and sensors.

Characterization and Quantification of Particle-Bound Criegee Intermediates in Secondary Organic Aerosol.

The ozonolysis of alkenes contributes substantially to the formation of secondary organic aerosol (SOA), which are important modulators of air quality and the Earth's climate. Criegee intermediates (CIs) are abundantly formed through this reaction. However, their contributions to aerosol particle chemistry remain highly uncertain. In this work, we present the first application of a novel methodology, using spin traps, which simultaneously quantifies CIs produced from the ozonolysis of volatile organic compounds in the gas and particle phases. Only the smallest CI with one carbon atom was detected in the gas phase of a ß-caryophyllene ozonolysis reaction system. However, multiple particle-bound CIs were observed in ß-caryophyllene SOA. The concentration of the most abundant CI isomer in the particle phase was estimated to constitute ∼0.013% of the SOA mass under atmospherically relevant conditions. We also demonstrate that the lifetime of CIs in highly viscous SOA particles is at least on the order of minutes, substantially greater than their gas-phase lifetime. The confirmation of substantial concentrations of large CIs with elongated lifetimes in SOA raises new questions regarding their influence on the chemical evolution of viscous SOA particles, where CIs may be a previously underestimated source of reactive species.

Circularly Polarized Luminescence in a Möbius Helicene Carbon Nanohoop.

We present the first helicene carbon nanoohop that integrates a [6]helicene into [7]cycloparaphenylene. The [6]helicene endows the helicene carbon nanohoop with chiroptical properties and configurational stability typical for higher helicenes, while the radially conjugated seven para-phenylenes largely determine the optoelectronic properties. The structure of the helicene carbon nanoohop was unambiguously characterized by NMR, MS and X-ray analysis that revealed that it possesses a topology of a Möbius strip in the solid state and in solution. The chirality transfers from the [6]helicene to the para-phenylenes and leads to a pronounced circular dichroism and bright circularly polarized luminescence, which is affected by the structural topology of the nanohoop.

Pyrene-Decoration of a Chromium(0) Tris(diisocyanide) Enhances Excited State Delocalization: A Strategy to Improve the Photoluminescence of 3d6 Metal Complexes.

There is a long-standing interest in iron(II) complexes that emit from metal-to-ligand charge transfer (MLCT) excited states, analogous to ruthenium(II) polypyridines. The 3d6 electrons of iron(II) are exposed to a relatively weak ligand field, rendering nonradiative relaxation of MLCT states via metal-centered excited states undesirably efficient. For isoelectronic chromium(0), chelating diisocyanide ligands recently provided access to very weak MLCT emission in solution at room temperature. Here, we present a concept that boosts the luminescence quantum yield of a chromium(0) isocyanide complex by nearly 2 orders of magnitude, accompanied by a significant increase of the MLCT lifetime. Pyrene units in the diisocyanide ligand backbone lead to an enlarged π-conjugation system and to a strongly delocalized MLCT state, from which nonradiative relaxation is less dominant despite a sizable redshift of the emission. While the pyrene moiety is electronically coupled to the core of the chromium(0) complex in the excited state, UV-vis absorption and 2D NMR spectroscopy show that this is not the case in the ground state. Luminescence lifetimes and quantum yields for our pyrenyl-decorated chromium(0) complex exhibit an unusual bell-shaped dependence on solvent polarity, indicative of two counteracting effects governing the MLCT deactivation. These two effects are identified as predominant deactivation either through an energetically nearby lying metal-centered state in the most apolar solvents, or alternatively via direct nonradiative relaxation to the ground state following the energy gap law in more polar solvents. This is the first example of a 3d6 MLCT emitter to benefit from an increased π-conjugation network.

An Ortho-Tetraphenylene-Based "Geländer" Architecture Consisting Exclusively of 52 sp2 -Hybridized C Atoms.

A new type of "Geländer" molecule based on a ortho-tetraphenylene core is presented. The central para-quaterphenyl backbone is wrapped by a 4,4'-di((Z)-styryl)-1,1'-biphenyl banister, with its aryl rings covalently attached to all four phenyl rings of the backbone. The resulting helical chiral bicyclic architecture consists exclusively of sp2 -hybridized carbon atoms. The target structure was assembled by expanding the central ortho-tetraphenylene subunit with the required additional phenyl rings followed by a twofold macrocyclization. The first macrocyclization attempts based on a twofold McMurry coupling were successful but low yielding; the second strategy, profiting from olefin metathesis, provided satisfying yields. Hydrogenation of the olefins resulted in a saturated derivative of similar topology, thereby allowing the interdependence between saturation and physico-chemical properties to be studied. The target structures, including their solid-state structures, were fully characterized. The helical chiral bicycle was synthesized as a racemate and separated into pure enantiomers by HPLC on a chiral stationary phase. Comparison of recorded and simulated chiroptical properties allowed the enantiomers to be assigned.

Bicyclic Phenyl-Ethynyl Architectures: Synthesis of a 1,4-Bis(phenylbuta-1,3-diyn-1-yl) Benzene Banister.

The novel diacetylene bridged terphenylic macrocycle 1 is presented and discussed in the context of rotationally restricted "Geländer" oligomers. The 1,4-bis(phenylbuta-1,3-diyn-1-yl) benzene bridge of diacetylene 1 is significantly longer than its terphenyl backbone, forcing the bridge to bend around the central pylon. The synthesis of molecule 1 is based to a large extent on acetylene scaffolding strategies, profiting from orthogonal alkyne protection groups to close both macrocyclic subunits by oxidative acetylene coupling sequentially. The spatial arrangement and the dynamic enantiomerization process of the bicyclic target structure 1 are analyzed. In-depth NMR investigations not only reveal an unexpected spatial arrangement with both oligomer strands bent alongside the backbone, but also display the limited stability of the model compound in the presence of molecular oxygen.

Sulfone "Geländer" Helices: Revealing Unexpected Parameters Controlling the Enantiomerization Process.

The two sulfonyl-bridged Geländer helices 1a and 2a are obtained by oxidation of the corresponding sulfide bridged precursors 1b and 2b. Both Geländer structures are fully characterized by NMR, high-resolution mass spectrometry, and optical spectroscopies. X-ray diffraction with a single crystal of 2a provides its solid-state structure. Both Geländer helices 1a and 2a are separated into enantiomers, and their racemizations are monitored by circular dichroism. For 1a, consisting of two equally sized macrocycles, a substantial increase in the enantiomerization barrier is observed upon going from the sulfide to the sulfone, and only a subtle rise is detected for the constitutional isomer 2a with two macrocycles of different size during the same transformation. This results not only in 1a with the highest configurational stability in the series of hitherto investigated Geländer structures but also challenges the so far hypothesized correlations between bridging structures and the Gibbs free energy of enantiomerization. The simulation of the enantiomerization process in the macrocyclic subunits suggests the proximity of the endotopic hydrogens as parameter responsible for the heights of the enantiomerization barrier.

NMR pseudocontact shifts in a symmetric protein homotrimer.

NMR pseudocontact shifts are a valuable tool for structural and functional studies of proteins. Protein multimers mediate key functional roles in biology, but methods for their study by pseudocontact shifts are so far not available. Paramagnetic tags attached to identical subunits in multimeric proteins cause a combined pseudocontact shift that cannot be described by the standard single-point model. Here, we report pseudocontact shifts generated simultaneously by three paramagnetic Tm-M7PyThiazole-DOTA tags to the trimeric molecular chaperone Skp and provide an approach for the analysis of this and related symmetric systems. The pseudocontact shifts were described by a "three-point" model, in which positions and parameters of the three paramagnetic tags were fitted. A good correlation between experimental data and predicted values was found, validating the approach. The study establishes that pseudocontact shifts can readily be applied to multimeric proteins, offering new perspectives for studies of large protein complexes by paramagnetic NMR spectroscopy.

Divergent Synthesis of Bioactive Dithiodiketopiperazine Natural Products Based on a Double C(sp3 )-H Activation Strategy.

This article provides a detailed report of our efforts to synthesize the dithiodiketopiperazine (DTP) natural products (-)-epicoccin G and (-)-rostratin A using a double C(sp3 )-H activation strategy. The strategy's viability was first established on a model system lacking the C8/C8' alcohols. Then, an efficient stereoselective route including an organocatalytic epoxidation was secured to access a key bis-triflate substrate. This bis-triflate served as the functional handles for the key transformation of the synthesis: a double C(sp3 )-H activation. The successful double activation opened access to a common intermediate for both natural products in high overall yield and on a multigram scale. After several unsuccessful attempts, this intermediate was efficiently converted to (-)-epicoccin G and to the more challenging (-)-rostratin A via suitable oxidation/reduction and protecting group sequences, and via a final sulfuration that occurred in good yield and high diastereoselectivity. These efforts culminated in the synthesis of (-)-epicoccin G and (-)-rostratin A in high overall yields (19.6 % over 14 steps and 12.7 % over 17 steps, respectively), with the latter being obtained on a 500 mg scale. Toxicity assessments of these natural products and several analogues (including the newly synthesized epicoccin K) in the leukemia cell line K562 confirmed the importance of the disulfide bridge for activity and identified dianhydrorostratin A as a 20x more potent analogue.

Mechanical Fixation by Porphyrin Connection: Synthesis and Transport Studies of a Bicyclic Dimer.

The bowl-shaped, 3-fold interlinked porphyrin dimer 2 was obtained in respectable yields during macrocyclization attempts. Its bicyclic structure, consisting of a macrocycle made of a pair of acetylene interlinked tetraphenylporphyrins which are additionally linked by a C-C bond interlinking two pyrrole subunits, has been confirmed spectroscopically (2D-NMR, UV/vis, HR-MALDI-ToF MS). Late-stage functionalization provided the structural analogue 1 with acetyl-protected terminal thiol anchor groups enabling single molecule transport investigations in a mechanically controlled break junction experiment. The formation of single-molecule junctions was observed, displaying large variations in the observed conductance values pointing at a rich diversity in the molecular junctions.

Highly Stable Silver(I) Complexes with Cyclen-Based Ligands Bearing Sulfide Arms: A Step Toward Silver-111 Labeled Radiopharmaceuticals.

With a half-life of 7.45 days, silver-111 (ßmax 1.04 MeV, Eγ 245.4 keV [Iγ 1.24%], Eγ 342.1 keV [Iγ 6.7%]) is a promising candidate for targeted cancer therapy with ß- emitters as well as for associated SPECT imaging. For its clinical use, the development of suitable ligands that form sufficiently stable Ag+-complexes in vivo is required. In this work, the following sulfur-containing derivatives of tetraazacyclododecane (cyclen) have been considered as potential chelators for silver-111: 1,4,7,10-tetrakis(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO4S), (2S,5S,8S,11S)-2,5,8,11-tetramethyl-1,4,7,10-tetrakis(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO4S4Me), 1,4,7-tris(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO3S), 1,4,7-tris(2-(methylsulfanyl)ethyl)-10-acetamido-1,4,7,10-tetraazacyclododecane (DO3SAm), and 1,7-bis(2-(methylsulfanyl)ethyl)-4,10,diacetic acid-1,4,7,10-tetraazacyclododecane (DO2A2S). Natural Ag+ was used in pH/Ag-potentiometric and UV-vis spectrophotometric studies to determine the metal speciation existing in aqueous NaNO3 0.15 M at 25 °C and the equilibrium constants of the complexes, whereas NMR and DFT calculations gave structural insights. Overall results indicated that sulfide pendant arms coordinate Ag+ allowing the formation of very stable complexes, both at acidic and physiological pH. Furthermore, radiolabeling, stability in saline phosphate buffer, and metal-competition experiments using the two ligands forming the strongest complexes, DO4S and DO4S4Me, were carried out with [111Ag]Ag+ and promising results were obtained.

Catalyst-Controlled Transannular Polyketide Cyclization Cascades: Selective Folding of Macrocyclic Polyketides.

The biomimetic synthesis of aromatic polyketides from macrocyclic substrates by means of catalyst-controlled transannular cyclization cascades is described. The macrocyclic substrates, which feature increased stability and fewer conformational states, were thereby transformed into several distinct polyketide scaffolds. The catalyst-controlled transannular cyclizations selectively led to aromatic polyketides with a defined folding and oxygenation pattern, thus emulating ß-keto-processing steps of polyketide biosynthesis.

Iron in a Cage: Fixation of a Fe(II)tpy2 Complex by Fourfold Interlinking.

The coordination sphere of the Fe(II) terpyridine complex 1 is rigidified by fourfold interlinking of both terpyridine ligands. Profiting from an octa-aldehyde precursor complex, the ideal dimensions of the interlinking structures are determined by reversible Schiff-base formation, before irreversible Wittig olefination provided the rigidified complex. Reversed-phase HPLC enables the isolation of the all-trans isomer of the Fe(II) terpyridine complex 1, which is fully characterized. While temperature independent low-spin states were recorded with superconducting quantum interference device (SQUID) measurements for both, the open precursor 8 and the interlinked complex 1, evidence of the increased rigidity of the ligand sphere in 1 was provided by proton T2 relaxation NMR experiments. The ligand sphere fixation in the macrocyclized complex 1 even reaches a level resisting substantial deformation upon deposition on an Au(111) surface, as demonstrated by its pristine form in a low temperature ultra-high vacuum scanning tunneling microscope experiment.