Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family

The engineering of efficient enzymes for large-scale production of industrially relevant compounds is a challenging task. Utilizing rational protein design, which relies on a comprehensive understanding of mechanistic information, holds significant promise for achieving success in this endeavor. Pre-steady-state kinetic measurements, obtained either through fast-mixing techniques or photoswitchable substrates, provide crucial mechanistic insights. The latter approach not only furnishes mechanistic clarity but also affords real-time structural elucidation of reaction intermediates via time-resolved femtosecond crystallography. Unfortunately, only a limited number of such valuable mechanistic probes are available. To address this gap, we applied a multidisciplinary approach, including computational analysis, chemical synthesis, physicochemical property screening, and enzyme kinetics to identify promising candidates for photoswitchable probes. We demonstrate the approach by designing an azobenzene-based photoswitchable substrate tailored for haloalkane dehalogenases, a prototypic class of enzymes pivotal in developing computational tools for rational protein design. The probe was subjected to steady-state and pre-steady-state kinetic analysis, which revealed new insights about the catalytic behavior of the model biocatalysts. We employed laser-triggered Z-to-E azobenzene photoswitching to generate the productive isomer in situ, opening avenues for advanced mechanistic studies using time-resolved femtosecond crystallography. Our results not only pave the way for the mechanistic understanding of this model enzyme family, incorporating both kinetic and structural dimensions, but also propose a systematic approach to the rational design of photoswitchable enzymatic substrates.

A Double Photocage Strategy to Construct Light-Controllable and Spatiotemporally Trackable Cathepsin B Activity-Based Probes

Utilizing multiple cages to selectively modulate the activity of biomolecules is indispensable to achieving controllable and trackable activity manipulation. However, trackable cages that can be used to monitor the activation of biomolecules are rare. In this work, we utilized a double photocage strategy to achieve light-controllable and spatiotemporally trackable activation. To demonstrate biological applicability, we used the well-known cancer cell biomarker cathepsin B as the target and constructed double photocaged cathepsin B activity-based probe 2PPG-FK-AcRha that performed well in cancer cell cultures. Using our probe, we could monitor the light-activation by the blue fluorescence of 7-diethylamino-4-hydroxymethyl-coumarin (DEACM) and simultaneously probe the activity of cathepsin B through the green fluorescence of acetyl rhodamine (AcRha). Additionally, by partially irradiating the cell cultures, the regional photoactivation experiments also demonstrated great spatial controllability and trackability of our probe.

Protein-Mediated Fluorescence Resonance Energy Transfer (P-FRET) Probe: Fabrication and Hydroxyl Radical Detection

Fluorescent probes based on fluorescence resonance energy transfer (FRET) are highly promising for diverse bioapplications. The key to constructing FRET probes is to confine the donor and acceptor within a sufficiently close distance. However, the commonly used covalent linkage often requires elaborate design and complex organic synthesis, and sometimes causes changes in the fluorescence properties of the donor and acceptor. Inspired by the binding between small molecules and protein in nature, herein, we propose a protein-mediated strategy to fabricate FRET probe. In such protein-mediated FRET (P-FRET) probe, protein acts as a carrier to simultaneously confine donor and acceptor in its cavity. As a proof of concept, we use bovine serum albumin (BSA) as a model protein, coumarin derivative as a donor and hydroxyl radical (·OH)-responsive dye fluorescein as an acceptor. Through a series of investigations, including binding parameters, fluorescence properties and detection performance, we prove that the construction of P-FRET probe is simple and feasible and the detection is sensitive. Our P-FRET strategy will provide new insights for the design of FRET probes.

Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets

Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.

Redirecting natural killer cells to potentiate adoptive immunotherapy in solid tumors through stabilized Y-type bispecific aptamer

Modulating interactions between immune effector cells and tumor cells in vivo using a bispecific aptamer (Ap) is a promising strategy for cancer immunotherapy. However, it remains a technical challenge owing to the complex and dynamic internal environment accompanied by severe degradation. Herein, by using a Y-shaped DNA scaffold, a bispecific and stabilized Y-type Ap is designed to redirect natural killer (NK) cells to enhance adoptive immunotherapy of hepatocellular carcinoma (HCC) solid tumors. Y-type Ap is constituted by the HCC-specific Ap TLS11a linked with the CD16-specific Ap through a Y-shaped DNA scaffold. Owing to the rigid structure, Y-type Ap shows high stability in 10% serum for over 72 h and resistance to denaturation by 8 M urea. Additionally, the Y-type Ap exhibits more potent avidity to bind with NK cells and tumor cells both in vitro and in vivo, resulting in higher cytokine secretion and excellent antitumor efficiency. Collectively, this study offers a translational platform for constructing stable bispecific Ap, offering considerable potential to enhance adoptive immunotherapy of solid tumors.