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Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 14898

Special Issue Editors

Dr. Ioannis Kostakis

E-Mail Website
Guest Editor
Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
Interests: development of new synthetic methods; design and synthesis of organic molecules with pharmacological activity [antineoplastic, antiviral, antibacterial, trypanocidal and central nervous system (CNSs)]; structural modification of bioactive natural products and their derivatives aiming at the improvement of their potency; synthesis of natural compounds
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Evagelos Gikas

E-Mail Website
Guest Editor
Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
Interests: pharmaceutical analysis; method development for the determination of bioactive substances in biological fluids; separation methods (GC, HPLC, UPLC); mass spectrometry (TQ, QqToF, orbitrap, ion-trap); synthesis of fluorescent probes; computational chemistry (αb initio, DFT, CASSCF)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The need for ultra-sensitive ultra-fast highly specific monitoring of biological processes or trace levels of endogenous substances or xenobiotics and toxicants has forcefully pushed the frontiers of fluorescence-based probe science towards novel approaches. The developments in instrumentation as in fluorescence microscopy or LIF, as well as methodological approaches such as FRET, time-resolved fluorescence, or immunofluorescence, proved that fluorescence has unlimited potential to reveal “difficult” to follow biological processes. In contrast, new developments in fluorescence-aided chromatographic science have enabled the precise mapping of target substance distribution in the human body. This Special Issue will collect recent advances in the exciting field of fluorescence probes that span over quantum-chemistry or molecular modeling-based design, synthetic approaches, and their application in biological phenomena. The contributions will be focused on the pharmaceuticals/drugs filed, including applications for API/impurity/degradation product detection, bioavailability/pharmacodynamics methodologies, receptor probes, cellular enzymatic reactions monitoring, organelle targeting probes, and any other application related to the modulating or probing processes of the human body.

Dr. Ioannis Kostakis
Prof. Dr. Evagelos Gikas
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Quantum mechanical molecular modeling drug design
  • Synthesis (small molecules/peptides, hybrid peptide-probe molecules)
  • Receptor based probes
  • Probes for organelle detection – modulation 
  • Chemical derivatization reagents

Published Papers (6 papers)

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Research

12 pages, 2026 KiB  
Communication
A BODIPY-Based Probe Enables Fluorogenicity via Thiol-Dependent Modulation of Fluorophore Aggregation
by Tak Ian Chio, Akiva J. Grimaldi, Thomas I. Radford and Susan L. Bane
Molecules 2022, 27(8), 2455; https://doi.org/10.3390/molecules27082455 - 11 Apr 2022
Cited by 2 | Viewed by 2037
Abstract
Given the popular usage of BODIPY fluorophores in biological research, their propensity to aggregate in aqueous solution and impact their spectroscopic properties arguably warrants more attention. The probe under study herein serves as a case in point. A para-maleimide-substituted meso-phenyl BODIPY [...] Read more.
Given the popular usage of BODIPY fluorophores in biological research, their propensity to aggregate in aqueous solution and impact their spectroscopic properties arguably warrants more attention. The probe under study herein serves as a case in point. A para-maleimide-substituted meso-phenyl BODIPY (p-MB) had previously been characterized in organic media, where its inherently high fluorescence ruled out its fluorogenic potential. Here, we have found that in aqueous solution, p-MB behaves differently, exhibiting a much-reduced fluorescence as a result of aggregation-caused quenching (ACQ). Additionally, p-MB is capable of responding to complementarily reactive substrates, including thiols and TCEP, to generate a substantial turn-on signal. The fluorescence restoration is largest when it reacts with those containing adjacent ionizable groups. By being part of a polar conjugate, p-MB assumes a disaggregated form, circumventing ACQ and unleashing up to ~1000-fold fluorescence enhancement through apparent disaggregation-induced emission (DIE). While our results support DIE as the turn-on mechanism, we found that the reactivity of the probe is much lower when it is given time to form stable aggregates. Therefore, contrary to the conventional depiction that a DIE probe works by dispersing from preformed aggregates to react with the target, our results suggest that it functions via a target-mediated inhibition of probe aggregation. Altogether, our work highlights the aggregation issue often faced by BODIPY-based probes and demonstrates how that can be exploited for turn-on sensing application. Furthermore, it reconstructs a different pathway for the DIE mechanism. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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20 pages, 5892 KiB  
Article
An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection
by Steve Vincent, Suman Mallick, Guillaume Barnoin, Hoang-Ngoan Le, Benoît Y. Michel and Alain Burger
Molecules 2022, 27(7), 2267; https://doi.org/10.3390/molecules27072267 - 31 Mar 2022
Cited by 2 | Viewed by 1722
Abstract
The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of [...] Read more.
The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of this task, as they do not exhibit good brightness in aqueous buffer media, develop aggregation and/or are not easily conjugated to oligodeoxynucleotides (ODNs) while keeping their photophysics intact. Herein, an important modification strategy was employed for a well-known fluorophore, 2-(4-(diethylamino)phenyl)-3-hydroxychromone (dEAF). Although this push–pull dye absorbs intensively in the visible range and shows emission with large Stokes shifts in all organic solvents, it is strongly quenched in water. This Achilles’ heel prompted us to implement a new strategy to obtain a series of dyes that retain all the photophysical features of dEAF in water, conjugate readily with oligonucleotides, and furthermore demonstrate sensitivity to hydration, thus paving the way for a high-performance fluorogenic DNA hybridization probe. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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12 pages, 2249 KiB  
Article
Chemometrically Assisted Optimization of Pregabalin Fluorescent Derivatization Reaction with a Novel Xanthone Analogue and Validation of the Method for the Determination of Pregabalin in Bulk via a Plate Reader
by Nikolaos Kritikos, Aikaterini Iliou, Amalia D. Kalampaliki, Evangelos Gikas, Ioannis K. Kostakis, Benoît Y. Michel and Yannis Dotsikas
Molecules 2022, 27(6), 1954; https://doi.org/10.3390/molecules27061954 - 17 Mar 2022
Cited by 2 | Viewed by 2022
Abstract
Quantitation of chromophore-free analytes is always a challenge. To this purpose, derivatization of the analyte constitutes a common strategy, leading to a product with a strong signal. In the current study, a novel xanthone analogue was utilized for the first time for the [...] Read more.
Quantitation of chromophore-free analytes is always a challenge. To this purpose, derivatization of the analyte constitutes a common strategy, leading to a product with a strong signal. In the current study, a novel xanthone analogue was utilized for the first time for the derivatization of pregabalin, a model analyte with a primary amine moiety that lacks a chromophore. The fact that only the xanthene-based derivative, formed after the derivatization reaction fluoresces, enables avoiding its chromatographic separation from the reagent and thus reducing the analysis time of a series of samples in 1–2 min via a plate reader. The reaction conditions were optimized via a central composite design (CCD), with fluorescence signal as the measure of the yield. The following factors that affect the derivatization reaction were chosen: (a) temperature, (b) reaction time, and (c) triethylamine solution volume used to drive the reaction to completion. After the identification of the optimal conditions, the method was validated according to ICH guidelines, using a fluorescence plate reader for signal measurement (λex = 540, λem = 615 nm). Finally, the newly developed high-throughput method was applied to the determination of drug content in pregabalin bulk. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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15 pages, 3284 KiB  
Article
Direct Visualization of Amlodipine Intervention into Living Cells by Means of Fluorescence Microscopy
by Christine Quentin, Rūta Gerasimaitė, Alexandra Freidzon, Levon S. Atabekyan, Gražvydas Lukinavičius, Vladimir N. Belov and Gyuzel Y. Mitronova
Molecules 2021, 26(10), 2997; https://doi.org/10.3390/molecules26102997 - 18 May 2021
Cited by 4 | Viewed by 3422
Abstract
Amlodipine, a unique long-lasting calcium channel antagonist and antihypertensive drug, has weak fluorescence in aqueous solutions. In the current paper, we show that direct visualization of amlodipine in live cells is possible due to the enhanced emission in cellular environment. We examined the [...] Read more.
Amlodipine, a unique long-lasting calcium channel antagonist and antihypertensive drug, has weak fluorescence in aqueous solutions. In the current paper, we show that direct visualization of amlodipine in live cells is possible due to the enhanced emission in cellular environment. We examined the impact of pH, polarity and viscosity of the environment as well as protein binding on the spectral properties of amlodipine in vitro, and used quantum chemical calculations for assessing the mechanism of fluorescence quenching in aqueous solutions. The confocal fluorescence microscopy shows that the drug readily penetrates the plasma membrane and accumulates in the intracellular vesicles. Visible emission and photostability of amlodipine allow confocal time-lapse imaging and the drug uptake monitoring. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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11 pages, 4204 KiB  
Article
Evaluation of Fluorescent Cu2+ Probes: Instant Sensing, Cell Permeable Recognition and Quantitative Detection
by Hao He, Zhao Cheng, Lei Zheng and Xuejiao Zhang
Molecules 2021, 26(2), 512; https://doi.org/10.3390/molecules26020512 - 19 Jan 2021
Cited by 6 | Viewed by 2139
Abstract
By incorporating a rhodamine spirolactam structure as the recognition site for Cu2+, two novel probes were synthesized through a connection of rhodamine 6G acylhydrazine and 5-formyl-6-hydroxyl-4-methylcoumarin/2,4-dihydroxybenzaldehyde. In the recognition process of probes towards Cu2+, the spirolactam ring exhibited opening [...] Read more.
By incorporating a rhodamine spirolactam structure as the recognition site for Cu2+, two novel probes were synthesized through a connection of rhodamine 6G acylhydrazine and 5-formyl-6-hydroxyl-4-methylcoumarin/2,4-dihydroxybenzaldehyde. In the recognition process of probes towards Cu2+, the spirolactam ring exhibited opening and closing, accompanying an instant and specific change in fluorescence and in color, which could also achieve a naked-eye and semiquantitative recognition of aqueous Cu2+ besides the fluorescent Cu2+ detection method. Fluorescent analyses and ECV304 cell imaging further revealed the probes’ good optical stability, instant response, low toxicity, and membrane permeability, which offers future possibilities for the probes’ instant detection and the real-time tracking of Cu2+ in biological systems. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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17 pages, 2553 KiB  
Article
New 1,3-Disubstituted Benzo[h]Isoquinoline Cyclen-Based Ligand Platform: Synthesis, Eu3+ Multiphoton Sensitization and Imaging Applications
by Sebastiano Di Pietro, Dalila Iacopini, Barbara Storti, Riccardo Nifosì, Valeria Di Bussolo, Mauro Pineschi, Aldo Moscardini, Giovanni Signore and Ranieri Bizzarri
Molecules 2021, 26(1), 58; https://doi.org/10.3390/molecules26010058 - 24 Dec 2020
Cited by 1 | Viewed by 2607
Abstract
The development of lanthanide-based luminescent probes with a long emission lifetime has the potential to revolutionize imaging-based diagnostic techniques. By a rational design strategy taking advantage of computational predictions, a novel, water-soluble Eu3+ complex from a cyclen-based ligand bearing 1,3-disubstituted benzo[h]isoquinoline arms [...] Read more.
The development of lanthanide-based luminescent probes with a long emission lifetime has the potential to revolutionize imaging-based diagnostic techniques. By a rational design strategy taking advantage of computational predictions, a novel, water-soluble Eu3+ complex from a cyclen-based ligand bearing 1,3-disubstituted benzo[h]isoquinoline arms was realized. The ligand has been obtained overcoming the lack of reactivity of position 3 of the isoquinoline moiety. Notably, steric hindrance of the heteroaromatic chromophore allowed selective and stoichiometry-controlled insertion of two or three antennas on the cyclen platform without any protection strategy. The complex bears a fourth heptanoic arm for easy conjugation to biomolecules. This new chromophore allowed the sensitization of the metal center either with one or two photons excitation. The suitability as a luminescent bioprobe was validated by imaging BMI1 oncomarker in lung carcinoma cells following an established immunofluorescence approach. The use of a conventional epifluorescence microscope equipped with a linear structured illumination module disclosed a simple and inexpensive way to image confocally Ln-bioprobes by single photon excitation in the 350–400 nm window, where ordinary confocal systems have no excitation sources. Full article
(This article belongs to the Special Issue Fluorescent Probes in Pharmaceutical and Drug Design Applications: Quantum Chemistry-Based Design, Synthesis, Photophysical and Chemical Properties, Biological Applications)
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