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1. Structure and dynamics of the ASB9 CUL-RING E3 Ligase

   https://doi.org/10.1038/s41467-020-16499-9  

   Lumpkin, Ryan J.; Baker, Richard W.; Leschziner, Andres E.; Komives, Elizabeth A. (June 2020, Nature Communications)

   Abstract The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18-member ankyrin and SOCS box (ASB) family is the largest substrate receptor family. Here we report cryo-EM data for the substrate, creatine kinase (CKB) bound to ASB9-ELOB/C, and for full-length CUL5 bound to the RING protein, RBX2, which binds various E2s. To date, no full structures are available either for a substrate-bound ASB nor for CUL5. Hydrogen–deuterium exchange (HDX-MS) mapped onto a full structural model of the ligase revealed long-range allostery extending from the substrate through CUL5. We propose a revised allosteric mechanism for how CUL-E3 ligases function. ASB9 and CUL5 behave as rigid rods, connected through a hinge provided by ELOB/C transmitting long-range allosteric crosstalk from the substrate through CUL5 to the RBX2 flexible linker. 

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2. High‐Resolution Photoelectron Imaging of IrB ₃ ⁻ : Observation of a π‐Aromatic B ₃ ⁺ Ring Coordinated to a Transition Metal

   https://doi.org/10.1002/anie.201902406  

   Czekner, Joseph; Cheung, Ling Fung; Kocheril, G. Stephen; Kulichenko, Maksim; Boldyrev, Alexander I.; Wang, Lai‐Sheng (May 2019, Angewandte Chemie International Edition)

   Abstract In a high‐resolution photoelectron imaging and theoretical study of the IrB₃⁻cluster, two isomers were observed experimentally with electron affinities (EAs) of 1.3147(8) and 1.937(4) eV. Quantum calculations revealed two nearly degenerate isomers competing for the global minimum, both with a B₃ring coordinated with the Ir atom. The isomer with the higher EA consists of a B₃ring with a bridge‐bonded Ir atom (C_s,²A′), and the second isomer features a tetrahedral structure (C_3v,²A₁). The neutral tetrahedral structure was predicted to be considerably more stable than all other isomers. Chemical bonding analysis showed that the neutralC_3visomer involves significant covalent Ir−B bonding and weak ionic bonding with charge transfer from B₃to Ir, and can be viewed as an Ir–(η³‐B₃⁺) complex. This study provides the first example of a boron‐to‐metal charge‐transfer complex and evidence of a π‐aromatic B₃⁺ring coordinated to a transition metal. 

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3. Mechanistic analysis of carbon–carbon bond formation by deoxypodophyllotoxin synthase

   https://doi.org/10.1073/pnas.2113770119  

   Tang, Haoyu; Wu, Min-Hao; Lin, Hsiao-Yu; Han, Meng-Ru; Tu, Yueh-Hua; Yang, Zhi-Jie; Chien, Tun-Cheng; Chan, Nei-Li; Chang, Wei-chen (January 2022, Proceedings of the National Academy of Sciences)

   Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate–dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (±)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS’s catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel–Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs. 

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4. Aromatic ouroboroi: heterocycles involving a σ-donor–acceptor bond and 4 n + 2 π-electrons

   https://doi.org/10.1039/c9cp05071j  

   Báez-Grez, Rodrigo; Inostroza, Diego; García, Victor; Vásquez-Espinal, Alejandro; Donald, Kelling J.; Tiznado, William (January 2020, Physical Chemistry Chemical Physics)

   null (Ed.)

   The aromaticity and dynamics of a set of recently proposed neutral 5- and 6-membered heterocycles that are closed by dative (donor–acceptor) or multi-center σ bonds, and have resonance forms with a Hückel number of π-electrons, are examined. The donors and acceptors in the rings include N, O, and F, and B, Be, and Mg, respectively. The planar geometry of the rings, coupled with evidence from different measures of aromaticity, namely the NICS zz , and NICS πzz components of the conventional nucleus independent chemical shifts (NICS), and ring current strengths (RCS), indicate non-trivial degrees of aromaticity in certain cases, including the cyclic C 3 B 2 OH 6 and C 3 BOH 5 isomers, both with three bonds to the O site in the ring. The former is lower in energy by at least 17.6 kcal mol −1 relative to linear alternatives obtained from molecular dynamics simulations in this work. Some of the other systems examined are best described as non-aromatic. Ring opening, closing, and isomerization are observed in molecular dynamics simulations for some of the systems studied. In a few cases, the ring indeed persists. 

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5. Synthesis of model bacteriochlorophylls containing substituents of native rings A, C and E

   https://doi.org/10.1039/d1nj02469h  

   Chung, Duy T.; Tran, Phuong Vy; Chau Nguyen, Khiem; Wang, Pengzhi; Lindsey, Jonathan S. (August 2021, New Journal of Chemistry)

   null (Ed.)

   A route under development for the synthesis of bacteriochlorophyll a and analogues relies on joining an AD-dihydrodipyrrin (bearing a D-ring carboxaldehyde) and a BC-dihydrodipyrrin (bearing a C-ring β-ketoester group and a B-ring dimethoxymethyl group) via Knoevenagel condensation followed by double-ring closure (Nazarov cyclization, electrophilic aromatic substitution, and elimination of methanol). Prior synthetic studies afforded the bacteriochlorophyll skeleton containing a gem-dimethyl group in ring B, a trans -dialkyl group in ring D, and a carboethoxy group at the 3-position of ring A. To explore the incorporation of native substituents, the synthesis of two bacteriochlorophyll analogues thereof was pursued, one with 12-methyl and 3-carboethoxy groups and the other with 2,12-dimethyl and 3-acetyl groups. The 12-methyl group resulted in half the yield ( versus the unsubstituted analogue) in the Knoevenagel reaction, but insignificant effects in all other steps including the rate and yield of double-ring closure despite the known effects of alkyl groups to facilitate electrophilic substitution of pyrroles. The 2-methyl-3-acetyl group, however, resulted in diminished yields in several steps, including the Knoevenagel reaction, but not the double-ring closure. The results point to obstacles and openings on the path to total syntheses of the native pigments. 

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