Rational Design of a Profluorescent Substrate for S-adenosylhomocysteine Hydrolase and its Applications in Bioimaging and Inhibitor Screening

Identification of novel inhibitors of S-adenosyl-L-homocysteine hydrolase via structure-based virtual screening and molecular dynamics simulations

S-adenosyl-L-homocysteine hydrolase (SAHase) is an important regulator in the methylation reactions in many organisms and thus is crucial for numerous cellular functions. In recent years, SAHase has become one of the popular targets for drug design, and SAHase inhibitors have exhibited potent antiviral activity. In this study, we established the complex-based pharmacophore models based on the known crystal complex of SAHase (PDB ID: 1A7A) to screen the drug-likeness compounds of ChEMBL database. Then, three molecular docking programs were used to validate the reliability of compounds, involving Libdock, CDOCKER, and AutoDock Vina programs. The four promising hit compounds (CHEMBL420751, CHEMBL346387, CHEMBL1569958, and CHEMBL4206648) were performed molecular dynamics simulations and MM-PBSA calculations to evaluate their stability and binding-free energy in the binding site of SAHase. After screening and analyzing, the hit compounds CHEMBL420751 and CHEMBL346387 were suggested to further research to obtain novel potential SAHase inhibitors. A series of computer-aided drug design methods, including pharmacophore, molecular docking, molecular dynamics simulation and MM-PBSA calculations, were employed in this study to identity novel inhibitors of S-adenosyl-L-homocysteine hydrolase (SAHase). Some compounds from virtual screening could form various interactions with key residues of SAHase. Among them, compounds CHEMBL346387 and CHEMBL420751 exhibited potent binding affinity from molecular docking and MM-PBSA, and maintained good stability at the binding site during molecular dynamics simulations as well. All these results indicated that the selected compounds might have the potential to be novel SAHase inhibitors.

Amphipolar, Amphiphilic 2,4-diarylpyrano[2,3-b]indoles as Turn-ON Luminophores in Acidic and Basic Media

A versatile amphiphilic pyrano[2,3-b]indole for halochromic turn-ON luminescence in acidic or basic media is accessed by an insertion-coupling-cycloisomerization and adjusting solubilizing and phenolic functionalities. While almost non-emissive in neutral solutions, treatment with acids or bases like trifluoroacetic acid (TFA) or 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) reveals distinct luminescence at wavelengths of 540 nm or 630 nm in propan-2-ol, respectively. Turn-ON emission can be detected at pH values as mild as pH = 5.31 or 8.70. Quantum yields in propan-2-ol are substantial for protonated (Φf = 0.058) and deprotonated (Φf = 0.059) species. Photometrically, pKa1 of 3.5 and pKa2 of 10.5 were determined in propan-2-ol. With lipophilic polyether sidechains and hydrophilic protonation and deprotonation sites the molecule can be regarded as amphipolar, which results in good solubility properties for different organic solvents. In aqueous media, an organic co-solvent like propan-2-ol (35%) or tetrahydrofuran (25%) is needed, and the solution can be diluted with pure water without precipitation of the compound. At higher concentrations of water, a turbid solution is formed, which indicates the formation of micellar structures or clusters. With dynamic light scattering we could show that these clusters increase in size with increasing water content.

A small molecule fluorescent probe for mercury ion analysis in broad low pH range: Spectral, optical mechanism and application studies

Development of new fluorescent probes for mercury ion analysis in environmental or living organism is undergoing quick growth due to its detrimental toxicity to environmental safety, ecological security, and human being. However, in most cases, the industrial waste water is acidic whereas it remains a great challenge to real-time monitor mercury ion directly at low pH using small molecule fluorescence probe. In this study, we have successfully designed and synthesized the Naph (1, 8-Naphthalimide derivative) -based small molecule probe termed as Naph-NSS capable of monitoring mercury ion in a broad range at low pH (from 2.0 to 7.0). The solid spectral studies demonstrated the high sensitivity and selectivity of the probe towards mercury ion among various species. After binding with Hg²⁺, the fluorescence of Naph-NSS greatly enhanced, and the mechanism of which was investigated by DFT studies. The probe was able to be loaded on paper strip for instant and fast detection of mercury ions. In addition, the probe is also suitable for detection of mercury ion in environmental samples, living cells and in vivo.

Profiling Cystathionine β/γ-Lyase in Complex Biosamples Using Novel Activatable Fluorogens

Cystathionine lyase, the key enzyme in transsulfuration and reverse transsulfuration pathways, is involved in a wide array of physiological and pathophysiological processes in both mammals and nonmammals. Though the biological significance of the hydrogen sulfide/cystathionine lyase system in disease states is extensively discussed, the absence of molecular methods for direct monitoring of cystathionine lyase in complex biosamples renders the result unreliable and perplexing. Here, we present the first attempt at designing and developing effective activatable fluorescent probes for cystathionine lyase based on the naphthylamide scaffold. CBLP and CSEP were designed based on the catalytic preference of cystathionine β-lyase (CBL) and cystathionine γ-lyase (CSE). Briefly, incorporation of cysteine/homocysteine as the recognition moiety and a carbamate ethyl sulfide group as a self-immolated linker proved to be an effective strategy for cystathionine lyase fluorescence reporting. CBLP exhibits high selectivity and sensitivity in vitro in semiquantifying CBL levels in roots of wild-type Arabidopsis thaliana and cbl mutants (cbl knockout: SALK_014740C, overexpressed: OE-CBL). Meanwhile, CSEP successfully detected CSE levels in HCC-LM3 cells, zebrafish models, and upregulated CSE in frozen section slides from the liver tissue of cecal ligation and puncture (CLP)-induced septic rats, which was also validated by Western blotting and immunohistochemical analysis. In summary, the practical design strategy facilitates profiling of cystathionine lyase activity in biological processes. It may pave the way for the development of accurate and efficient methods for the direct estimation of cystathionine lyase.

New insights into ESIPT mechanism of three sunscreen compounds in solution: A combined experimental and theoretical study

In this present work, we have successfully designed and investigated three flavonoid sunscreen compounds. Based on steady-state spectroscopy and time-dependent density functional theory (TDDFT), the mechanism of excited state intramolecular proton transfer (ESIPT) of sunscreen compounds was studied. The calculated UV-vis absorption spectra and fluorescence emission spectra are in good agreement with the experimental results in methanol solution. The potential energy curve demonstrates that the ESIPT process can easily occur in the three sunscreen compounds without energy barrier. Therefore, the absorbed excitation energy can get back to the ground state through a non-radiative relaxation process. Light stability tests ensure that the three flavonoids have the potential as sunscreens. This work provides not only an application of the ESIPT process in sunscreen mechanisms, but also a theory basis for the development of novel sunscreen molecules.

Excited state electronic structures and photochemistry of different oxidation states of 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)

The molecular structures of 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), were calculated by using time-dependent density functional theory (TDDFT) model with M062X method with 6-311G (d, p) basis set. In this work, the ABTS were theoretically investigated from the geometric structure, the energy levels of the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO), the energy level gap ΔE_HOMO-LUMO of the molecular ground state, excited stated properties and the electronic absorption spectra of different oxidation states. We studied the energy levels of LUMO and HOMO of ABTS in different oxidation states. Frontier molecular orbital analysis can provide insight into the nature of excited states. ABTS was synthesized from N-ethylamine by total synthesis. Then, we measured the UV-Vis spectra of ABTS before and after being oxidized by K₂S₂O₈. The calculated electronic structures and photochemical properties of different oxidation state of ABTS were in accordance with the experimental result. This work demonstrates the relationship between the electronic structures and photochemistry of different oxidation states ABTS hence paves the way for the rationally synthesis and deepen understanding of the photophysical properties of ABTS materials.

Fluorogenic probes for disease-relevant enzymes

Traditional biochemical methods for enzyme detection are mainly based on antibody-based immunoassays, which lack the ability to monitor the spatiotemporal distribution and, in particular, the in situ activity of enzymes in live cells and in vivo. In this review, we comprehensively summarize recent progress that has been made in the development of small-molecule as well as material-based fluorogenic probes for sensitive detection of the activities of enzymes that are related to a number of human diseases. The principles utilized to design these probes as well as their applications are reviewed. Specific attention is given to fluorogenic probes that have been developed for analysis of the activities of enzymes including oxidases and reductases, those that act on biomacromolecules including DNAs, proteins/peptides/amino acids, carbohydrates and lipids, and those that are responsible for translational modifications. We envision that this review will serve as an ideal reference for practitioners as well as beginners in relevant research fields.

Development of a fluorogenic small substrate for dipeptidyl peptidase-4

A series of aniline and m-phenylenediamine derivatives with electron-withdrawing 3,3,3-trifluoropropenyl substituents were synthesized as small and chemically stable fluorescent organic compounds. Their fluorescence performances were evaluated by converting 2,4-disubstituted aniline 1 to the non-fluorescent dipeptide analogue H-Gly-Pro-1 for the use as a fluorogenic substrate for dipeptidyl peptidase-4 (DPP-4). The progress of the enzymatic hydrolysis of H-Gly-Pro-1 with DPP-4 was monitored by fluorometric determination of 1 released into the reaction medium. The results suggest that 1 could be used as fluorophore in OFF–ON-type fluorogenic probes.

Naphthalimide-Based Fluorophore for Soft Anionic Interface Monitoring

A naphthalimide-based low-molecular-mass fluorophore (NA) was designed and synthesized by introducing an azetidine unit onto the aromatic ring of the compound as an electron-donating structure, and a hydrophilic (2-(2-aminoethyl-amino)ethanol) moiety into the "N-imide site" of the core structure. UV-vis absorption and fluorescence measurements revealed that the fluorophore is soluble in water and shows a fluorescent quantum yield of ∼20% and lifetime of ∼3.7 ns in the solvent within a wide pH range. Moreover, the fluorescence emission and anisotropy of the fluorophore as produced are both dependent upon the viscosity and polarity of the medium. Further studies demonstrated that NA can be used as a selective probe to monitor the aggregation of anionic surfactants owing to its accumulation onto the anionic surfaces of the aggregates as formed. Inspired by the discovery, NA was successfully applied for detection of cell membranes and E. coli via monitoring of their negatively charged surfaces, which is important for fast checking of biological contamination of water. Importantly, all the tests could be performed in a visualized manner. We believe that the new, low-molecular-mass fluorophore as created may find applications in chemical and biochemical sensing and imaging.