1
|
Lahmy R, Hübner H, Lachmann D, Gmeiner P, König B. Development of Photoswitchable Tethered Ligands that Target the μ-Opioid Receptor. ChemMedChem 2023; 18:e202300228. [PMID: 37817331 DOI: 10.1002/cmdc.202300228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/12/2023]
Abstract
Converting known ligands into photoswitchable derivatives offers the opportunity to modulate compound structure with light and hence, biological activity. In doing so, these probes provide unique control when evaluating G-protein-coupled receptor (GPCR) mechanism and function. Further conversion of such compounds into covalent probes, known as photoswitchable tethered ligands (PTLs), offers additional advantages. These include localization of the PTLs to the receptor binding pocket. Covalent localization increases local ligand concentration, improves site selectivity and may improve the biological differences between the respective isomers. This work describes chemical, photophysical and biochemical characterizations of a variety of PTLs designed to target the μ-opioid receptor (μOR). These PTLs were modeled on fentanyl, with the lead disulfide-containing agonist found to covalently interact with a cysteine-enriched mutant of this medically-relevant receptor.
Collapse
Affiliation(s)
- Ranit Lahmy
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Daniel Lachmann
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Burkhard König
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
| |
Collapse
|
2
|
Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
Collapse
Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
3
|
Hu J, Hu X, Zeng Z, Zhang J, Li M, Geng F, Wu D. Interaction between a photoisomerizable azobenzene compound and alpha-lactalbumin: Spectroscopic and computational simulation studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122965. [PMID: 37327501 DOI: 10.1016/j.saa.2023.122965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/18/2023]
Abstract
The combination of light and photoresponsive compounds provides a peculiar way of regulating biological systems. Azobenzene is a classical organic compound with photoisomerization properties. Exploring the interactions between azobenzene and proteins can deepen the biochemical applications of the azobenzene compounds. In this paper, the interaction of 4-[(2,6-dimethylphenyl)diazenyl]-3,5-dimethylphenol with alpha-lactalbumin was investigated by UV-Vis absorption spectra, multiple fluorescence spectra, computer simulations, and circular dichroism spectra. Most critically, the interaction differences between proteins and the trans- and cis-isomer of ligands have been analyzed and compared. Results showed that both isomers of ligands were bound to alpha-lactalbumin to form ground state complexes and statically quenched the steady-state fluorescence of alpha-lactalbumin. The van der Waals forces and hydrogen bonding dominated the binding; the difference is that the binding of the cis-isomer to alpha-lactalbumin is more rapidly stabilized, and the binding strength is greater than the trans-isomer. These binding differences were modeled and analyzed by molecular docking and kinetic simulations, and we found that both isomers bind through the hydrophobic aromatic cluster 2 of alpha-lactalbumin. However, the bent structure of the cis-isomer is more closely aligned with the construction of the aromatic cluster and may have contributed to the above differences.
Collapse
Affiliation(s)
- Jie Hu
- School of Mechanical Engineering, Chengdu University, Chengdu 610106, China
| | - Xia Hu
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Zhen Zeng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Jing Zhang
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Mohan Li
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Di Wu
- School of Mechanical Engineering, Chengdu University, Chengdu 610106, China; Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China.
| |
Collapse
|
4
|
Oger S, Duchemin N, Bendiab YM, Birlirakis N, Skiredj A, Rharrabti S, Jullian JC, Poupon E, Smietana M, Arseniyadis S, Evanno L. Expanding the 'aplysinospin cascade' through DNA-templated [2+2] photocycloaddition. Chem Commun (Camb) 2023; 59:4221-4224. [PMID: 36939749 DOI: 10.1039/d3cc00673e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Inspired by the unique ability of nucleic acids to template chemical transformations that are otherwise impossible in solution, we embarked on the generalisation of our DNA-templated [2+2] photo-induced homo- and heterodimerization of aplysinopsins. Our process ensures a straightforward access to cyclobutane containing natural products and analogues thereof. Most importantly, this conceptual biomimetic achievement presents interesting arguments to build a biosynthetic scenario.
Collapse
Affiliation(s)
- Samuel Oger
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| | - Nicolas Duchemin
- Queen Mary University of London, Department of Chemistry, Mile End Road, E1 4NS, London, UK.
| | - Yara Mayssa Bendiab
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| | - Nicolas Birlirakis
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolecules (LBM), 24 rue Lhomond, 75005, Paris, France
| | - Adam Skiredj
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| | - Somia Rharrabti
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| | | | - Erwan Poupon
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 Route de Mende, 34095, Montpellier, France.
| | - Stellios Arseniyadis
- Queen Mary University of London, Department of Chemistry, Mile End Road, E1 4NS, London, UK.
| | - Laurent Evanno
- Université Paris-Saclay, CNRS, BioCIS, 17, Avenue des Sciences, 91400, Orsay, France.
| |
Collapse
|
5
|
Xavier P, Bhat SA, Yelamaggad CV, Viswanath P. Phase behaviour and adsorption of deoxyribonucleic acid onto an azobenzene liquid crystalline ligand at the interfaces. Biophys Chem 2023; 296:106980. [PMID: 36889134 DOI: 10.1016/j.bpc.2023.106980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
Azobenzene liquid crystalline (ALC) ligand contains a cholesteryl group linked to an azobenzene moiety through a carbonyl dioxy spacer (C7) and terminated with an amine group as a polar head. The phase behaviour of the C7 ALC ligand at the air-water (A-W) interface is investigated employing surface manometry. The surface pressure-area per molecule isotherm shows that C7 ALC ligand exhibit two different phases following the phase sequence viz., liquid expanded (LE1 and LE2) and then collapse to three-dimensional crystallites. Further, our investigations under different pH conditions and in the presence of DNA reveal the following. Compared to the bulk, the acid dissociation constant (pKa) of an individual amine reduces to 5 at the interfaces. For pH (3.5) < pKa, the protonation of amine groups of C7 ALC ligand facilitates the condensation of the film and enhances the stability. For pH values > pKa, the phase behaviour of the ligand remains the same due to the partial dissociation of the amine groups. The presence of DNA in the sub-phase result in the expansion of isotherm to the higher area per molecule and the compressional modulus extracted reveals the phase sequence; liquid expanded, liquid condensed, followed by a collapse. Further, the kinetics of adsorption of DNA to the amine groups of the ligand is investigated, suggesting the interactions are influenced by surface pressure corresponding to different phases and pH of the sub-phase. Brewster angle microscope studies are carried out at different surface densities of the ligand as well as in the presence of DNA also supports this inference. Atomic force microscope is employed to acquire the surface topography and height profile of C7 ALC ligand (1 layer) after transferring on onto a silicon substrate using Langmuir Blodgett deposition. The difference in the surface topography and thickness of the film indicates the adsorption of DNA onto the amine groups of the ligand. The characteristic UV-visible absorption bands of the ligand films (10 layers) at the air-solid interface are tracked and the hypsochromic shift of these bands is also attributed to these DNA interactions.
Collapse
Affiliation(s)
- Pinchu Xavier
- Centre for Nano and Soft Matter Sciences, Bengaluru 562 162, India; Manipal Academy of Higher Education, Manipal 576 104, India
| | - Sachin A Bhat
- Centre for Nano and Soft Matter Sciences, Bengaluru 562 162, India
| | | | | |
Collapse
|
6
|
Controllable DNA hybridization by host-guest complexation-mediated ligand invasion. Nat Commun 2022; 13:5936. [PMID: 36209265 PMCID: PMC9547909 DOI: 10.1038/s41467-022-33738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic regulation of nucleic acid hybridization is fundamental for switchable nanostructures and controllable functionalities of nucleic acids in both material developments and biological regulations. In this work, we report a ligand-invasion pathway to regulate DNA hybridization based on host-guest interactions. We propose a concept of recognition handle as the ligand binding site to disrupt Watson-Crick base pairs and induce the direct dissociation of DNA duplex structures. Taking cucurbit[7]uril as the invading ligand and its guest molecules that are integrated into the nucleobase as recognition handles, we successfully achieve orthogonal and reversible manipulation of DNA duplex dissociation and recovery. Moreover, we further apply this approach of ligand-controlled nucleic acid hybridization for functional regulations of both the RNA-cleaving DNAzyme in test tubes and the antisense oligonucleotide in living cells. This ligand-invasion strategy establishes a general pathway toward dynamic control of nucleic acid structures and functionalities by supramolecular interactions.
Collapse
|