Synthesis, photodynamic activity, and quantitative structure-activity relationship modelling of a series of BODIPYs

Predicting fluorescence to singlet oxygen generation quantum yield ratio for BODIPY dyes using QSPR and machine learning

Functional dyes that are capable of both bright fluorescence and efficient singlet oxygen generation are crucial for theranostic techniques, which integrate fluorescence imaging and photodynamic therapy (PDT). The development of new functional dyes for theranostics is often costly and time-consuming due to laborious synthesis and post-synthetic screening of large libraries of compounds. In this work, we describe machine learning methods suitable for simultaneous prediction of fluorescence and photosensitizing ability of heavy-atom-free boron dipyrromethene (BODIPY) compounds. We analysed the ratio between fluorescence quantum yield (ΦFl) and singlet oxygen quantum yield (ΦΔ) for over 70 BODIPY structures in polar (acetonitrile) and non-polar (toluene) solvents, which mimic hydrophilic and hydrophobic cell environments, respectively. QSPR models were developed based on more than 5000 calculated molecular descriptors, including quantum chemical and topological descriptors. We applied multiple linear regression (MLR), support vector regression (SVR), and random forest regression (RFR) methods for model building and optimization. The resulting models demonstrated robust statistical parameters (R2 = 0.73-0.91) for both polar and non-polar media. The relative contributions of the descriptors to the models were assessed, identifying Eig03_EA(dm), F01[C-N], and TDB06p as the most influential. These results demonstrate that QSPR machine learning methods are effective in predicting key photochemical parameters of BODIPY photosensitizers, thereby potentially streamlining the development of theranostic agents.

BODIPY-Based Molecules for Biomedical Applications

BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) derivatives have attracted attention as probes in applications like imaging and sensing due to their unique properties like (1) strong absorption and emission in the visible and near-infrared regions of the electromagnetic spectrum, (2) strong fluorescence and (3) supreme photostability. They have also been employed in areas like photodynamic therapy. Over the last decade, BODIPY-based molecules have even emerged as candidates for cancer treatments. Cancer remains a significant health issue world-wide, necessitating a continuing search for novel therapeutic options. BODIPY is a flexible fluorophore with distinct photophysical characteristics and is a fascinating drug development platform. This review provides a comprehensive overview of the most recent breakthroughs in BODIPY-based small molecules for cancer or disease detection and therapy, including their functional potential.

Microwave-assisted direct synthesis of BODIPY dyes and derivatives

A microwave-assisted one-pot synthesis of BODIPY dyes from pyrroles and acyl chlorides is reported. This protocol features short reaction times, low temperatures, minimum amount of solvent, scalability, versatility, and good yields of the products. These simple, efficient and sustainable conditions can be also applied to the synthesis of derivatives such as BOPHY, BOAHY and BOPAHY.

BODIPYs in PDT: A Journey through the Most Interesting Molecules Produced in the Last 10 Years

Over the past 30 years, photodynamic therapy (PDT) has shown great development. In the clinical setting the few approved molecules belong almost exclusively to the porphyrin family; but in the scientific field, in recent years many researchers have been interested in other families of photosensitizers, among which BODIPY has shown particular interest. BODIPY is the acronym for 4,4-difluoro-4-bora-3a, 4a-diaza-s-indacene, and is a family of molecules well-known for their properties in the field of imaging. In order for these molecules to be used in PDT, a structural modification is necessary which involves the introduction of heavy atoms, such as bromine and iodine, in the beta positions of the pyrrole ring; this change favors the intersystem crossing, and increases the ¹O₂ yield. This mini review focused on a series of structural changes made to BODIPYs to further increase ¹O₂ production and bioavailability by improving cell targeting or photoactivity efficiency.

Halogenated BODIPY photosensitizers: Photophysical processes for generation of excited triplet state, excited singlet state and singlet oxygen

We have systematically examined the formation of singlet oxygen O₂(¹Δ_g), the excited triplet state (T₁), and excited singlet state (S₁) for halogenated BODIPY photosensitizers (halogen = Cl, Br, and I) in eight solvents to understand how halogen atoms and solvent affect these properties. The phosphorescence spectra and lifetimes of singlet oxygen generated by these halogenated BODIPYs have been measured by steady state/time resolved NIR emission, while the formation quantum yield of singlet oxygen (Φ_Δ) has been determined by chemical method using diphenylisobenzofuran (DPBF) as the trapping agent. The formation quantum yield Φ_Δ of singlet oxygen can be as high as 0.96 for iodinated BODIPY and 0.71 for brominated BODIPY. The triplet state T₁ absorption spectra of brominated and iodinated BODIPYs have been recorded by laser flash photolysis method, in which T₁ shows high formation efficiency and long lifetime. The formation and decay of excited singlet state S₁ of four BODIPYs have been measured by ground state (S₀) absorption and steady state/time resolved fluorescence. The results show that larger halogen atoms on BODIPY core lead to smaller fluorescence quantum yield, shorter fluorescence lifetime and higher singlet oxygen formation quantum yield due to heavy atom effect that promotes the formation of triplet state. On the other hand, higher solvent polarity causes lower singlet oxygen formation quantum yield, smaller fluorescence quantum yield, and shorter fluorescence lifetime. This solvent effect is explained by the presence of photoinduced charge transfer (ICT) process from halogen atoms to BODIPY. The ICT efficiency has been estimated and the results are agreed with ICT theory. ICT process in halogenated BODIPYs has never been revealed in literature. HOMO/LUMO obtained from DFT calculation also supports the presence of ICT. The involvement of ICT in the photosensitizing process of halogenated BODIPYs provides new insights for designing BODIPY photosensitizers for photodynamic therapy of tumor.

Searching for antimicrobial photosensitizers among a panel of BODIPYs

In recent years, antimicrobial Photodynamic Therapy (aPDT) gained increasing attention for its potential to inhibit the growth and spread of microorganisms, both as free-living cells and/or embedded in biofilm communities. In this scenario, compounds belonging to the family of boron-dipyrromethenes (BODIPYs) represent a very promising class of photosensitizers for applications in antimicrobial field. In this study, twelve non-ionic and three cationic BODIPYs were assayed for the inactivation of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans. As expected, S. aureus showed to be very sensitive to BODIPYs and mild conditions were sufficient to reach good rates of photoinactivation with both neutral and monocationic ones. Surprisingly, one neutral compound (named B9 in this study) resulted the best BODIPY to photoinactivate P. aeruginosa PAO1. The photoinactivation of C. albicans was reached with both neutral and mono-cationic BODIPYs. Furthermore, biofilms of the three model microorganisms were challenged with BODIPYs in light-based antimicrobial technique. S. aureus biofilms were successfully inhibited with milder conditions than those applied to P. aeruginosa and C. albicans. Notably, it was possible to eradicate 24-h-old biofilms of both S. aureus and P. aeruginosa. In conclusion, this study supports the potential of neutral BODIPYs as pan-antimicrobial PSs.

Deep neural network model for highly accurate prediction of BODIPYs absorption

A possibility to accurately predict the absorption maximum wavelength of BODIPYs was investigated. We found that previously reported models had a low accuracy (40-57 nm) to predict BODIPYs due to the limited dataset sizes and/or number of BODIPYs (few hundreds). New models developed in this study were based on data of 6000-plus fluorescent dyes (including 4000-plus BODIPYs) and the deep neural network architecture. The high prediction accuracy (five-fold cross-validation room mean squared error (RMSE) of 18.4 nm) was obtained using a consensus model, which was more accurate than individual models. This model provided the excellent accuracy (RMSE of 8 nm) for molecules previously synthesized in our laboratory as well as for prospective validation of three new BODIPYs. We found that solvent properties did not significantly influence the model accuracy since only few BODIPYs exhibited solvatochromism. The analysis of large prediction errors suggested that compounds able to have intermolecular interactions with solvent or salts were likely to be incorrectly predicted. The consensus model is freely available at https://ochem.eu/article/134921 and can help the other researchers to accelerate design of new dyes with desired properties.

Drug delivery systems for the photodynamic application of two photosensitizers belonging to the porphyrin family

Photodynamic therapy involves the concomitant action of three components, light with an appropriate wavelength, molecular oxygen, and a molecule, able to absorb an electromagnetic radiation, called photosensitizer (PS). A fundamental aspect is the bioavailability of the PS that is directly related to some physicochemical properties of the PS itself as it should feature a certain degree of lipophilicity to easily cross the cell membrane, however, at the same time, should be sufficiently water-soluble to navigate in the bloodstream. Consequently, the use of a system for drug delivery becomes essential when photosensitizers with a high degree of lipophilicity are considered. In this work, we present three different drug delivery systems, microemulsions, emulsions and liposomes all capable of carrying a PS belonging to the porphyrin family: the tetraphenyl porphyrin (TPP) and the 4-hydroxyphenyl porphyrin (THPP), which show a relevant different degree of lipophilicity. A series of microemulsions (ME) and emulsions (E) were prepared, among which two formulations, one for THPP and one for TPP, have been chosen. The stability of these two carriers was monitored over time and under various temperature conditions. With the same criteria, two liposomal formulations have been also identified and analyzed. The four formulations mentioned above (one ME, one E and two liposomes) have been tested on SKOV3 tumor cell line comparing the photodynamic activity of the porphyrin formulations versus the aqueous/organic (DMSO) solution of the same two PSs. The results show that all the formulations have proved to be excellent carriers and that the liposomal formulation enhance the photodynamic efficacy of both porphyrins.

Tuning Photodynamic Properties of BODIPY Dyes, Porphyrins' Little Sisters

The photodynamic properties of a series of non-halogenated, dibrominated and diiodinated BODIPYs with a phthalimido or amino end modification on the phenoxypentyl and phenoxyoctyl linker in the meso position were investigated. Halogen substitution substantially increased the singlet oxygen production based on the heavy atom effect. This increase was accompanied by a higher photodynamic activity against skin melanoma cancer cells SK-MEL-28, with the best compound reaching an EC50 = 0.052 ± 0.01 µM upon light activation. The dark toxicity (toxicity without light activation) of all studied dyes was not detected up to the solubility limit in cell culture medium (10 µM). All studied BODIPY derivatives were predominantly found in adiposomes (lipid droplets) with further lower signals colocalized in either endolysosomal vesicles or the endoplasmic reticulum. A detailed investigation of cell death indicated that the compounds act primarily through the induction of apoptosis. In conclusion, halogenation in the 2,6 position of BODIPY dyes is crucial for the efficient photodynamic activity of these photosensitizers.

Quantitative Structure-Property Relationship Modelling for the Prediction of Singlet Oxygen Generation by Heavy-Atom-Free BODIPY Photosensitizers*

Heavy-atom-free sensitizers forming long-living triplet excited states via the spin-orbit charge transfer intersystem crossing (SOCT-ISC) process have recently attracted attention due to their potential to replace costly transition metal complexes in photonic applications. The efficiency of SOCT-ISC in BODIPY donor-acceptor dyads, so far the most thoroughly investigated class of such sensitizers, can be finely tuned by structural modification. However, predicting the triplet state yields and reactive oxygen species (ROS) generation quantum yields for such compounds in a particular solvent is still very challenging due to a lack of established quantitative structure-property relationship (QSPR) models. In this work, the available data on singlet oxygen generation quantum yields (ΦΔ ) for a dataset containing >70 heavy-atom-free BODIPY in three different solvents (toluene, acetonitrile, and tetrahydrofuran) were analyzed. In order to build reliable QSPR model, a series of new BODIPYs were synthesized that bear different electron donating aryl groups in the meso position, their optical and structural properties were studied along with the solvent dependence of singlet oxygen generation, which confirmed the formation of triplet states via the SOCT-ISC mechanism. For the combined dataset of BODIPY structures, a total of more than 5000 quantum-chemical descriptors was calculated including quantum-chemical descriptors using density functional theory (DFT), namely M06-2X functional. QSPR models predicting ΦΔ values were developed using multiple linear regression (MLR), which perform significantly better than other machine learning methods and show sufficient statistical parameters (R=0.88-0.91 and q2 =0.62-0.69) for all three solvents. A small root mean squared error of 8.2 % was obtained for ΦΔ values predicted using MLR model in toluene. As a result, we proved that QSPR and machine learning techniques can be useful for predicting ΦΔ values in different media and virtual screening of new heavy-atom-free BODIPYs with improved photosensitizing ability.

BODIPY-Based Photosensitizers as Potential Anticancer and Antibacterial Agents: Role of the Positive Charge and the Heavy Atom Effect

Boron-dipyrromethene derivatives, including cationic and iodinated analogs, were obtained and subjected to physicochemical and in vitro photodynamic activity studies. Iodinated derivatives revealed a substantial heavy atom effect manifested by a bathochromic shift of the absorption band by about 30 nm and fluorescence intensity reduced by about 30-35 times, compared to that obtained for non-iodinated ones. In consequence, singlet oxygen generation significantly increased with Φ_Δ values in the range 0.69-0.97. The in vitro photodynamic activity was evaluated on Gram-positive Staphylococcus aureus, Gram-negative Escherichia coli, and on human androgen-sensitive prostate adenocarcinoma cells (LNCaP). The novel cationic, iodinated BODIPY, demonstrated the highest activity toward all studied cells. An excellent cytotoxic effect was found against LNCaP cells with an IC₅₀ value of 19.3 nM, whereas the viability of S. aureus was reduced by >5.6 log₁₀ at 0.25 μM concentration and by >5.3 log₁₀ in the case of E. coli at 5 μM. Thus, this analog seems to be a very promising candidate for the application in both anticancer and antimicrobial photodynamic therapy.

Microwave-assisted synthesis of meso-carboxyalkyl-BODIPYs and an application to fluorescence imaging

In this study, a significantly improved method for the synthesis of modular meso-BODIPY (boron dipyrromethene) derivatives possessing a free carboxylic acid group (which was subsequently coupled to peptides), is disclosed. This method provides a vastly efficient synthetic route with a > threefold higher overall yield than other reports. The resultant meso-BODIPY acid allowed for further easy incorporation into peptides. The meso-BODIPY peptides showed absorption maxima from 495-498 nm and emission maxima from 504-506 nm, molar absorptivity coefficients from 33 383-80 434 M-1 cm-1 and fluorescent quantum yields from 0.508-0.849. The meso-BODIPY-c(RGDyK) peptide was evaluated for plasma stability and (proved to be durable even up to 4 h) was then assessed for its fluorescence imaging applicability in vivo and ex vivo. The optical imaging in vivo was limited due to autofluorescence, however, the ex vivo tissue analysis displayed BODIPY-c(RGDyK) internalization and cancer detection thereby making it a novel tumor-integrin associated fluorescent probe while displaying the lack of interference the dye has on the properties of this ligand to bind the receptor.

In vitro photodynamic treatment of cancer cells induced by aza-BODIPYs

Two aza-BODIPY photosensitizes (PSs, compounds 7 and 8), featuring an iodine atom on each pyrrolic unit of their structure, were synthesized in fairly good yields starting from commercial products and tested in vitro on two human cancer cell lines (HCT116 and SKOV3) to assess their photodynamic efficacy. After treating the cell cultures with variable concentrations of 7 or 8 and incubating for the desired incubation time, the cells were irradiated for two hours with a red-light emitting diode (LED) device; afterwards the extent of cell death was determined by MTT assay. Besides the killing effect, the new PSs were also studied to determine further parameters related to photodynamic efficacy, such as the resistance towards photobleaching, the rate of singlet oxygen production, the fluorescence quantum yields, the cellular uptake and the localization inside the cells and, finally, flow cytometric analysis for apoptosis. Considering the results as a whole, these aza-BODIPYs can be considered to be promising photosensitizers because of their IC50 values being below micromolar concentrations and for more rather interesting features. Actually, these molecules have proved to be: (a) quite stable towards photobleaching; (b) good producers of singlet oxygen and (c) highly penetrating the cells with a wide distribution in the cytosol. Furthermore, in accordance with the good rate of singlet oxygen production, the apoptotic cells reach 30% and this allows us to assume a low inflammatory effect of the in vivo PDT treatment; thus a possible in vivo application of these aza-BODIPYs might be plausible.

BODIPY Dyes Bearing Multibranched Fluorinated Chains: Synthesis, Structural, and Spectroscopic Studies

A small series of boron-dipyrromethene (BODIPY) dyes, characterized by the presence of multibranched fluorinated residues, were designed and synthesized. The dyes differ in both the position (para-perfluoroalkoxy-substituted phenyl ring or boron functionalization) and number of magnetically equivalent fluorine atoms (27 or 54 fluorine atoms per molecule). Photophysical and crystallographic characterization of the synthesized BODIPYs was carried out to evaluate the effect of the presence of highly fluorinated moieties on the optical and morphological properties of such compounds.

High Singlet Oxygen Yield Photosensitizer Based Polypeptide Nanoparticles for Low-Power Near-Infrared Light Imaging-Guided Photodynamic Therapy

NIR photosensitizer is attractive for photodynamic therapy (PDT). Low-power light irradiation and imaging-guided PDT makes it possible to increase tissue penetration depth. The pyrrole-substituted iodinated BODIPY (BDPI) molecule was designed and synthesized, and it possesses an intense NIR absorption and emission band, and exhibits a high singlet oxygen quantum yield (Φ_Δ = 0.80) which leads remarkable cytotoxicity upon low power illumination (IC50 = 0.60 μg/mL, 6.1 mW/cm²). After being encapsulated with biocompatibility polypeptide PEG-PLys, polymeric micelles nanoparticles (PBDPI NPs) was obtained that are water-dispersed and passively tumor-targetable. Such enhanced accumulation in tumor area makes it easily traced in vivo due to its NIR fluorescence. In addition, such nanoparticles offer an unprecedented photodynamic therapeutic effect by using a low-power irradiation light, which makes it possible to kill cancer cells in deep tissue efficiently.

Tailored-BODIPY/Amphiphilic Cyclodextrin Nanoassemblies with PDT Effectiveness

Amphiphilic cyclodextrins (aCDs) are an intriguing class of carrier systems which, recently, have been proposed to deliver porphyrinoids and anticancer drugs or combined dose of both for dual therapeutic applications. The design of nanoassemblies based on aCD and photosensitizers (PSs) aims to preserve the photodynamic therapy (PDT) efficacy of PS, reducing the tendency of PS to self-aggregate, without affecting the quantum yield of singlet oxygen (¹O₂) production, and, not less importantly, minimizing dark toxicity and reducing photosensitization effects. With this idea in mind, in this paper, we focus on nanoassemblies between a non-ionic aCD (SC6OH) and halo-alkyl tailored iodinated boron-dipyrromethenes (BODIPY) dye, a class of molecules which recently have been successfully proposed as a stimulating alternative to porphyrinoids for their high photodynamic efficacy. Nanoassemblies of BODIPY/aCD (BL01I@SC6OH) were prepared in different aqueous media by evaporation of mixed organic film of aCD and BODIPY, hydration, and sonication. The nanostructures were characterized, measuring their hydrodynamic diameter and ξ-potential and also evaluating their time-stability in biological relevant media. Taking advantage of emissive properties of the not-iodinated BODIPY analogue (BL01), nanoassemblies based on aCD and BL01 were investigated as model system to get insight on entanglement of BODIPY in the amphiphile in aqueous dispersion, pointing out that BODIPY is well-entrapped in monomeric form (τ ≅ 6.5 ns) within the colloidal carriers. Also morphology and fluorescence emission properties were elucidated after casting the solution on glass. BL01@SC6OH is easily detectable in cytoplasm of HCT116 cell lines, evidencing the remarkable intracellular penetration of this nanoassembly similar to free BODIPY. On the same cell lines, the photodynamically active assembly BL01I/aCD shows toxicity upon irradiation. Despite the fact that free BL01I is more PDT active than its assembly, aCD can modulate the cell uptake of BODIPY, pointing out the potential of this system for in vivo PDT application.