Carbon-Centered Radicals in Protein Manipulation

Engineered Half-Unit-Cell MoS2/ZnIn2S4 Monolayer Photocatalysts and Adsorbed Hydroxyl Radicals-Assisted Activation of Cα-H Bond for Efficient Cβ-O Bond Cleavage in Lignin to Aromatic Monomers

Photocatalysis has high potential in the cleavage of Cβ-O bond in lignin into high-value aromatic monomers; however, the inefficient Cα-H bond activation in lignin and a low hydrogen transfer efficiency on the photocatalyst's surfaces have limited its application in photocatalytic lignin conversion. This study indicates that the cleavage of the Cβ-O bond can be improved by the generation of the Cα radical intermediate through Cα-H bond activation, and the formation of desirable aromatic products can be significantly improved by the enhanced hydrogen transfer efficiency from photocatalyst surfaces to aromatic monomeric radicals. We elaborately designed the half-unit-cell MoS2/ZnIn2S4 monolayer with a thickness of ∼1.7 nm to promote the hydrogen transfer efficiency on the photocatalyst surfaces. The ultrathin structure can shorten the diffusion distance of charge carriers from the interior to the surfaces and tight interface between MoS2 and ZnIn2S4 to facilitate the migration of photogenerated electrons from ZnIn2S4 to MoS2, therefore improving the selectivity of desirable products. The adsorbed hydroxyl radical (*OH) on the surfaces of MoS2/ZnIn2S4 from water oxidation can significantly reduce the bond dissociation energy (BDE) of Cα-H bond in PP-ol from 2.38 to 1.87 eV, therefore improving the Cα-H bond activation. The isotopic experiments of H2O/D2O indicate that the efficiency of *OH generation is an important step in Cα-H bond activation for PP-ol conversion to aromatic monomers. In summary, PP-ol can completely convert to 86.6% phenol and 82.3% acetophenone after 1 h of visible light irradiation by using 3% MoS2/ZnIn2S4 and the assistance of *OH, which shows the highest conversion rate compared to previous works.

Overlooked Roles and Transformation of Carbon-Centered Radicals Produced from Natural Organic Matter in a Thermally Activated Persulfate System

The presence and induced secondary reactions of natural organic matter (NOM) significantly affect the remediation efficacy of in situ chemical oxidation (ISCO) systems. However, it remains unclear how this process relates to organic radicals generated from reactions between the NOM and oxidants. The study, for the first time, reported the vital roles and transformation pathways of carbon-centered radicals (CCR•) derived from NOM in activated persulfate (PS) systems. Results showed that both typical terrestrial/aquatic NOM isolates and collected NOM samples produced CCR• by scavenging activated PS and greatly enhanced the dehalogenation performance under anoxic conditions. Under oxic conditions, newly formed CCR• could be oxidized by O2 and generate organic peroxide intermediates (ROO•) to catalytically yield additional •OH without the involvement of PS. Nuclear magnetic resonance (NMR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) results indicated that CCR• predominantly formed from carboxyl and aliphatic structures instead of aromatics within NOM through hydrogen abstraction and decarboxylation reactions by SO4•- or •OH. Specific anoxic reactions (i.e., dehalogenation and intramolecular cross-coupling reactions) further promoted the transformation of CCR• to more unsaturated and polymerized/condensed compounds. In contrast, oxic propagation of ROO• enhanced bond breakage/ring cleavage and degradation of CCR• due to the presence of additional •OH and self-decomposition. This study provides novel insights into the role of NOM and O2 in ISCO and the development of engineered strategies for creating organic radicals capable of enhancing the remediation of specific contaminants and recovering organic carbon.

α-Silylated Diazoalkynes: New Tools for Bioconjugation of Proteins

α-Silylated diazoalkynes are stabilized diazo compounds that can selectively react with carboxylic residues in buffered aqueous media. In-situ fluoride induced desilylation increases this reactivity, leading to a very fast reaction. Application to the selective functionalization of RNase A, followed by post-functionalization using click chemistry, is described. These new reagents expand the toolbox for native protein modification at carboxylic residues.

Development of an oxazole-based cleavable linker for peptides

We report the development of a new oxazole-based cleavable linker to release peptides from attached cargo. Oxazoles are stable to most reaction conditions, yet they can be rapidly cleaved in the presence of single-electron oxidants like cerium ammonium nitrate (CAN). An oxazole linker could be synthesized and attached to peptides through standard solid-phase peptide coupling reactions. Cleavage of these peptide-oxazole conjugates is demonstrated on a broad scope of peptides containing various natural and unnatural amino acids. These results represent the first example of a peptide-based linker that is cleaved through single-electron oxidation. The oxazole is also demonstrated to be a suitable linker for both the release of a peptide from a conjugated small molecule and the orthogonal release of cargo from a peptide containing multiple cleavable linkers. Oxazole linkers could serve as a promising tool for peptide screening platforms such as peptide-encoded libraries.

Probing the functional hotspots inside protein hydrophobic pockets by in situ photochemical trifluoromethylation and mass spectrometry

Due to the complex high-order structures and interactions of proteins within an aqueous solution, a majority of chemical functionalizations happen on the hydrophilic sites of protein external surfaces which are naturally exposed to the solution. However, the hydrophobic pockets inside proteins are crucial for ligand binding and function as catalytic centers and transporting tunnels. Herein, we describe a reagent pre-organization and in situ photochemical trifluoromethylation strategy to profile the functional sites inside the hydrophobic pockets of native proteins. Unbiased mass spectrometry profiling was applied for the characterization of trifluoromethylated sites with high sensitivity. Native proteins including myoglobin, trypsin, haloalkane dehalogenase, and human serum albumin have been engaged in this mild photochemical process and substantial hydrophobic site-specific and structure-selective trifluoromethylation substitutes are obtained without significant interference to their bioactivity and structures. Sodium triflinate is the only reagent required to functionalize the unprotected proteins with wide pH-range tolerance and high biocompatibility. This "in-pocket" activation model provides a general strategy to modify the potential binding pockets and gain essential structural insights into the functional hotspots inside protein hydrophobic pockets.

The Minimum Protein Staple? - Towards 'bio'-Baldwin's rules via inter-phosphosite linking in the MEK1 activation loop

In small molecule organic chemistry, the heuristic insight into ring-forming processes that was enabled by Baldwin's rules some 50 years ago proved a step-change in the role of mechanistically guided synthesis. It created a lens upon and marker of fundamental stereoelectronic and conformation-guided chemical processes. However, despite the widespread role of stereoelectronics and conformational control in Biology, no equivalent coherent exploitation of trapped, ring-forming processes yet exists in biomolecules. In the development of a minimal ring-closing process in intact proteins that might prove suitable in a coherent rule-set, we have tested endo-trig ring-closing conjugate thioether lanthionine (Lan) -CH2-S-CH2- formation as a limiting cyclization. Spontaneous Lan formation in proteins is rare if not non-existent and when found in natural product cyclic peptides it requires the mediation of corresponding biosynthetic enzymes as well as productive reactive conformations to guide it. Here, we show that within a conformationally flexible and functionally important protein loop - the MAPK kinase phosphorylation-targeted activation loop - Lan ring-closing is possible. Ring-closing proves to be critically dependent on the location of a trig electrophilic site in just one of two regioisomeric potential precursors to allow phosphosite-to-phosphosite 'stapling'. This first example of spontaneous protein thioether ring-closing/'stapling' and its accessibility from just one precursor (despite the potential for both to form an identical 'staple') now reveals the potential for Lan formation not only as an accessible form of minimal stapling in proteins but also as an exquisitely sensitive probe of associated protein geometries. We suggest that the use of this (as well as the development of other such, intramolecular protein traps that are dependent on inherent protein-controlled reactivity rather than forced crosslinking) may allow the broader trapping and mapping of relevant, even minor, protein states. In this way, protein ring formation may enable a form of extended 'bio-Baldwin's rules' that help to delineate relevant protein conformational space.

Cross aldol OPAL bioconjugation outcompetes intramolecular hemiaminal cyclisation of proline adjacent N-terminal α-oxo aldehydes at acidic pH

Novel methods to construct small molecule-protein bioconjugates are integral to the development of new biomedicines for a variety of diseases. C-C linked bioconjugates are increasingly desirable in this application due to their in vivo stability and can be accessed through cross aldol bioconjugation of reactive α-oxo aldehyde handles easily introduced at the N-terminus of proteins by periodate oxidation. We previously developed an organocatalyst-mediated protein aldol ligation (OPAL) for chemical modification of these reactive aldehydes, but the efficiency of this method was limited when a proline residue was directly adjacent to the N-terminus due to intramolecular hemiaminal formation. Herein we explore the competition between this cyclisation and the OPAL modification and demonstrate bioconjugation can be favoured through use of acidic pH for both oxidation and OPAL, and optimisation of reaction conditions and organocatalyst. We then showcase the utility of this acidic-OPAL in modification of the cholera toxin B-subunit (CTB), a homo-pentameric protein of biomedical promise.

Nickel-Catalyzed Antibody Bioconjugation

New biocompatible methods for post-translational protein modification are challenging to develop but crucial to create improved chemical probes and optimize next-generation biologic therapies such as antibody-drug conjugates (ADCs). Herein, we describe the bottom-up construction of an aqueous nickel-catalyzed cross-coupling for the chemospecific arylation of cysteine residues on peptides and proteins and its use for the preparation of ADCs. A variety of arene linkages are exemplified, enabling the incorporation of small molecules, probes, and cytotoxic payloads. The utility of this new bioconjugation platform in a drug discovery setting is highlighted by the construction of novel ADCs with target-mediated in vitro cytotoxic activity.