A new chiral boron-dipyrromethene (BODIPY)-based fluorescent probe: molecular docking, DFT, antibacterial and antioxidant approaches

Synthesis and characterization of novel BODIPYs and their antioxidant, antimicrobial, photodynamic antimicrobial, antibiofilm and DNA interaction activities

In the current study, we synthesized and characterized new BODIPY derivatives (1-4) having pyridine or thienyl-pyridine substituents at meso- position and 4-dibenzothienyl or benzo[b]thien-2-yl moieties at 2-,6- positions. We investigated fluorescence properties and the ability to form singlet oxygen. In addition, various biological activities of BODIPYs such as DPPH scavenging, DNA binding/cleavage ability, cell viability inhibition, antimicrobial activity, antimicrobial photodynamic therapy (aPDT) and biofilm inhibition properties were performed. BODIPY derivatives BDPY-3 (3) and BDPY-4 (4) have high fluorescence quantum yields as 0.50 and 0.61 and 1 O2 quantum yields were calculated as 0.83 for BDPY-1 (1), 0.12 for BDPY-2 (2), 0.11 for BDPY-3 and 0.23 for BDPY-4. BODIPY derivatives BDPY-2, BDPY-3 and BDPY-4 displayed 92.54 ± 5.41%, 94.20 ± 5.50%, and 95.03 ± 5.54% antioxidant ability, respectively. BODIPY compounds showed excellent DNA chemical nuclease activity. BDPY-2, BDPY-3 and BDPY-4 also exhibited 100% APDT activity against E. coli at all tested concentrations. In addition to these, they demonstrated a highly effective biofilm inhibition activity against Staphyloccous aureus and Pseudomans aeruginosa. BDPY-4 showed the most effective antioxidant and DNA cleavage activity, while BDPY-3 exhibited the most effective antimicrobial and antibiofilm activity.

Synthesis of Metallo-Chromone Porphyrin Nano-Starch Sensitizers as Photodynamic Therapeutics for the Eradication of Enterococci Dental Pathogens

Photodynamic therapy (PDT), as an advanced, alternative, and promising treatment, can inhibit dental pathogens. PDT employs the activation of photosensitizers via the light of a particular wavelength and molecular oxygen to inhibit dental pathogens. Herein, we present a comprehensive study on the synthesis and characterization of three chromone-porphyrins [Zn(II)-5-[4-chromone]-15-(4-phenyl)porphyrin (ZnCP), 5-[4-chromone]-15-(4-12 phenyl)porphyrin (DMCP), and Pd(II)-5-[4-chromone]-15-(4-phenyl)porphyrin (PdCP)]. Next, the computational study was also performed to establish the correlation between photophysical properties and theoretical calculations for those chromone-porphyrins using density functional theory and time-dependent density functional theory. Furthermore, chromone-porphyrins were encapsulated in starch nanoparticles to develop soluble nano-starch sensitizers (ZnCP-SNPs, DMCP-SNPs, and PdCP-SNPs) via the nanoprecipitation technique. Upon green light exposure, these nano-starch sensitizers exhibited excellent singlet oxygen generation ability. Moreover, final nanoformulations have been explored for pH responsiveness. Based on our intriguing findings, the chromone-porphyrin-loaded nano-starch sensitizers displayed great potential as prospective PDT to treat enterococci dental pathogens.

Hydrogen peroxide enhanced photoinactivation of Candida albicans by a novel boron-dipyrromethene (BODIPY) derivative

Photodynamic inactivation (PDI) has received increasing attention as a promising approach to combat Candida albicans infections. This study aimed to evaluate the synergistic effect of a new BODIPY (4,4-difluoro-boradiazaindacene) derivative and hydrogen peroxide on C. albicans. BDP-4L in combination with H₂O₂ demonstrated enhanced photokilling efficacy. In suspended cultures of C. albicans, the maximum decrease was 6.20 log and 2.56 log for PDI using BDP-4L (2.5 μM) with or without H₂O₂, respectively. For mature C. albicans biofilms, 20 μM BDP-4L plus H₂O₂ eradicated C. albicans, causing an over 6.7 log count reduction in biofilm-associated cells, while only a reduction of ~ 1 log count was observed when H₂O₂ was omitted. Scanning electron microscopy analysis and LIVE/DEAD assays suggested that PDI using BDP-4L plus H₂O₂ induced more damage to the cell membrane. Correspondingly, amplification of nucleic acids release was observed in biofilms treated with the combined PDI. Additionally, we also discovered that the addition of hydrogen peroxide potentiated the generation of ¹O₂ in PDI using the singlet oxygen sensor green probe. Collectively, BDP-4L combined with H₂O₂ presents a promising approach in the treatment of C. albicans infections.

Synthesis of a new sulfadimidine Schiff base and their nano complexes as potential anti-COVID-19 and anti-cancer activity

The primary objective of this study was to describe the cytotoxicity on HEPG-2 cells and to study the COVID‑19 activities of the novel H₂L ligand and its Cr and Cu nano-complexes. As well as exploring the chemistry of the prepared nano-complexes. In this paper novel Schiff base, N-(4, 6-dimethyl pyrimidin-2-yl)-4-(((2-hydroxyl naphthalene-1-y l) methylene) amino) benzene-sulfonamidesulfonyl) amide has been synthesized. The novel Schiff base H₂L is used to synthesize novel nano and micro-complexes with CrCl₂.6H₂O and CuCl₂.2H₂O. The prepared ligand and micro complexes were interpreted by different spectroscopic techniques. The nano-sized Cr and Cu complexes were synthesized in an environmentally friendly manner using Coriandrum sativum (CS) media extract in ethanol. The structure, morphologies and particle size of the nano-sized complexes were determined using FT-IR, TEM, and PXRD. The results showed that the nano-domain complexes are on the Sub-nano scale. Furthermore, using TGA, we studied the effect of heat on the size of newly prepared nano-complexes. Experimental data were supported by DFT calculations. The findings revealed that the metal complexes investigated are more stable than the free ligand H₂L. The antitumor activity was examined before and after heating the nano-complexes at 200 °C. The results reveal the Cr nano complex, after heating, exhibited strong antitumor activity with IC₅₀ value (3.349 μg/ml). The tested Cu nano-complex shows good DNA cleavage. The liver cancer and COVID19 proteins were examined using molecular docking to identify the potential binding energy of inhibitors.

A Review on the Recent Advancements on Therapeutic Effects of Ions in the Physiological Environments

This review focuses on the therapeutic effects of ions when released in physiological environments. Recent studies have shown that metallic ions like Ag+, Sr2+, Mg2+, Mn2+, Cu2+, Ca2+, P+5, etc., have shown promising results in drug delivery systems and regenerative medicine. These metallic ions can be loaded in nanoparticles, mesoporous bioactive glass nanoparticles (MBGNs), hydroxyapatite (HA), calcium phosphates, polymeric coatings, and salt solutions. The metallic ions can exhibit different functions in the physiological environment such as antibacterial, antiviral, anticancer, bioactive, biocompatible, and angiogenic effects. Furthermore, the metals/metalloid ions can be loaded into scaffolds to improve osteoblast proliferation, differentiation, bone development, fibroblast growth, and improved wound healing efficacy. Moreover, different ions possess different therapeutic limits. Therefore, further mechanisms need to be developed for the highly controlled and sustained release of these ions. This review paper summarizes the recent progress in the use of metallic/metalloid ions in regenerative medicine and encourages further study of ions as a solution to cure diseases.

AoPEX1 and AoPEX6 Are Required for Mycelial Growth, Conidiation, Stress Response, Fatty Acid Utilization, and Trap Formation in Arthrobotrys oligospora

Arthrobotrys oligospora (A. oligospora) is a typical nematode-trapping (NT) fungus that can capture nematodes by producing adhesive networks. Peroxisomes are single membrane-bound organelles that perform multiple physiological functions in filamentous fungi. Peroxisome biogenesis proteins are encoded by PEX genes, and the functions of PEX genes in A. oligospora and other NT fungi remain largely unknown. Here, our results demonstrated that two PEX genes (AoPEX1 and AoPEX6) are essential for mycelial growth, conidiation, fatty acid utilization, stress tolerance, and pathogenicity in A. oligospora. AoPEX1 and AoPEX6 knockout resulted in a failure to produce traps, conidia, peroxisomes, and Woronin bodies and damaged cell walls, reduced autophagosome levels, and increased lipid droplet size. Transcriptome data analysis showed that AoPEX1 and AoPEX6 deletion resulted in the upregulation of the proteasome, membranes, ribosomes, DNA replication, and cell cycle functions, and the downregulation of MAPK signaling and nitrogen metabolism. In summary, our results provide novel insights into the functions of PEX genes in the growth, development, and pathogenicity of A. oligospora and contribute to the elucidation of the regulatory mechanism of peroxisomes in trap formation and lifestyle switching in NT fungi.

IMPORTANCE Nematode-trapping (NT) fungi are important resources for the biological control of plant-parasitic nematodes. They are widely distributed in various ecological environments and capture nematodes by producing unique predatory organs (traps). However, the molecular mechanisms of trap formation and lifestyle switching in NT fungi are still unclear. Here, we provided experimental evidence that the AoPEX1 and AoPEX6 genes could regulate mycelial growth and development, trap formation, and nematode predation of A. oligospora. We further analyzed the global transcription level changes of wild-type and mutant strains using RNA-seq. This study highlights the important role of peroxisome biogenesis genes in vegetative growth, conidiation, trap formation, and pathogenicity, which contribute to probing the mechanism of organelle development and trap formation of NT fungi and lays a foundation for developing high-efficiency nematode biocontrol agents.

A New Ratiometric Design Strategy Based on Modulation of π-Conjugation Unit for Developing Fluorescent Probe and Imaging of Cellular Peroxynitrite

Ratiometric fluorescent probes could effectively offset the changes of the autofluorescence and compartmental localization. FRET, ICT, etc. are the common strategies to design probes for biosensing, but these strategies have some deficiencies. Here, we proposed a new design strategy based on π-conjugation modulation, giving two different emission bands in the absence and presence of the target. The new fluorescence probe named Rhod-DCM-B was rationally designed and synthesized, which displayed a fluorescence emission peak at 670 nm because the electron cloud focuses on the conjugated DCM unit. With the addition of ONOO^-, the fluorescence emission at 570 nm increased, accompanied by the decrease of fluorescence emission at 670 nm, showing a ratiometric signal change attributed to the opened spirane structure making the electron cloud concentrated on the xanthene core. The mechanism is well confirmed by MS and DFT calculations. Rhod-DCM-B exhibited outstanding sensitivity and excellent selectivity toward ONOO^-. Moreover, Rhod-DCM-B was effectively employed to determine endogenous and exogenous ONOO^- in living cells. As a marker for inflammation and drug-induced liver injury (DILI) process, ONOO^- in vivo was successfully monitored by Rhod-DCM-B and presented a dramatic ratiometric response.

A Novel Dicationic Boron Dipyrromethene-based Photosensitizer for Antimicrobial Photodynamic Therapy against Methicillin-Resistant Staphylococcus aureus

Background

We report herein the synthesis of a novel dicationic boron dipyrromethene derivative (compound 3) which is symmetrically substituted with two trimethylammonium styryl groups.

Methods

The antibacterial photodynamic activity of compound 3 was determined against sixteen methicillin-resistant Staphylococcus aureus (MRSA) strains, including four ATCC type strains (ATCC 43300, ATCC BAA-42, ATCC BAA-43, and ATCC BAA-44), two mutant strains [AAC(6’)-APH(2”) and RN4220/pUL5054], and ten non-duplicate clinical strains of hospital- and community-associated MRSA. Upon light irradiation, the minimum bactericidal concentrations of compound 3 were in the range of 1.56-50 µM against all the sixteen MRSA strains. Interestingly, compound 3 was not only more active than an analogue in which the ammonium groups are not directly connected to the n-conjugated system (compound 4), but also showed significantly higher (p < 0.05) antibacterial potency than the clinically approved photosensitizer methylene blue. The skin irritation of compound 3 during topical application was tested on human 3-D skin constructs and proven to be non-irritant in vivo at concentrations below 1.250 mM. In the murine MRSA infected wound study, the colony forming unit reduction of compound 3 + PDT group showed significantly (p < 0.05) higher value (>2.5 log₁₀) compared to other test groups except for the positive control.

Conclusion

In conclusion, the present study provides a scientific basis for future development of compound 3 as a potent photosensitizer for photodynamic therapy for MRSA wound infection.

A New Family of Benzo[h]Chromene Based Azo Dye: Synthesis, In-Silico and DFT Studies with In Vitro Antimicrobial and Antiproliferative Assessment

The high biological activity of the chromene compounds coupled with the intriguing optical features of azo chromophores prompted our desire to construct novel derivatives of chromene incorporating azo moieties 4a-l, which have been prepared via a three-component reaction of 1-naphthalenol-4-[(4-ethoxyphenyl) azo], 1, with the benzaldehyde derivatives and malononitrile. The structural identities of the azo-chromene 4a-l were confirmed on the basis of their spectral data and elemental analysis, and a UV-visible study was performed in a Dimethylformamide (DMF) solution for these molecules. Additionally, the antimicrobial activity was investigated against four human pathogens (Gram-positive and Gram-negative bacteria) and four fungi, employing an agar well diffusion method, with their minimum inhibitory concentrations being reported. Molecules 4a, 4g, and 4h were discovered to be more efficacious against Syncephalastrum racemosum (RCMB 05922) in comparison to the reference drugs, while compounds 4b and 4h demonstrated the highest inhibitory activity against Escherichia coli (E. coli) in evaluation against the reference drugs. Moreover, their cytotoxicity was assessed against three different human cell lines, including human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), and human breast adenocarcinoma (MCF-7) with a selection of molecules illustrating potency against the HCT-116 and MCF-7 cell lines. Furthermore, the molecular modeling results depicted the binding interactions of the synthesized compounds 3b and 3h in the active site of the E. coli DNA gyrase B enzyme with a clear SAR (structure-activity relationship) analysis. Lastly, the density functional theory's (DFTs) theoretical calculations were performed to quantify the energy levels of the Frontier Molecular Orbitals (FMOs) and their energy gaps, dipole moments, and molecular electrostatic potentials. These data were utilized in the chemical descriptor estimations to confirm the biological activity.

Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases

New Schiff bases {N'-(phenyl(pyridin-2-yl)methylene) isonicotinohydrazide (L¹H), N¹ -(naphthalen-1-yl)-N² -(phenyl(pyridin-2-yl) methylidene) ethane-1,2-diamine (L²H), N-(6-chlorobenzo[d]thiazol-2-yl)-1-phenyl-1-(pyridin-2-yl) methanimine (L³H)}were synthesized by reaction of 2-benzoylpyridine with different amines (2-amino-6-chlorobenzothiazole, isonicotinohydrazide and N ¹-(naphthalen-1-yl)ethane-1,2-diamine) and characterized by ¹H-NMR, ¹³C-NMR, IR mass spectroscopy and elemental analysis. The compounds were assayed by the disc diffusion method for anti-bacterial against five pathogenic bacteria species (Staphylococcus aureus, Micrococcus luteus, Staphylococcus pyogenes, Bacillus subtilis, and E. coli). All prepared Schiff bases showed good activity compared to positive control (streptomycin), Moreover the L³H showed the highest activity against S. aureus, and M. luteus than the other compounds and streptomycin. In additional molecular docking studies with 3-chymotrypsin-like protease (3CLpro), the essential enzyme for SARS-CoV-2 proliferation. The rest of compounds have shown promising results as 3CLpro inhibitors interacting with the active sites of the enzymes. Finally, DFT 's estimated electrostatic molecular potential results were used to illustrate the molecular docking findings. The DFT calculations showed that L³H has the highest dipole moment and electrophilicity index. Interestingly, L²H of the largest energy gap ∆E = 2.49 eV, there are several hydrophilic interactions that could facilitate the binding with the receptors. All of these parameters could be shared to significantly affect the protein sites of binding affinity with different extent.

Modelling the Anti-Methicillin-Resistant Staphylococcus Aureus (MRSA) Activity of Cannabinoids: A QSAR and Docking Study

Twenty-four cannabinoids active against MRSA SA1199B and XU212 were optimized at WB97XD/6-31G(d,p), and several molecular descriptors were obtained. Using a multiple linear regression method, several mathematical models with statistical significance were obtained. The robustness of the models was validated, employing the leave-one-out cross-validation and Y-scrambling methods. The entire data set was docked against penicillin-binding protein, iso-tyrosyl tRNA synthetase, and DNA gyrase. The most active cannabinoids had high affinity to penicillin-binding protein (PBP), whereas the least active compounds had low affinities for all of the targets. Among the cannabinoid compounds, Cannabinoid 2 was highlighted due to its suitable combination of both antimicrobial activity and higher scoring values against the selected target; therefore, its docking performance was compared to that of oxacillin, a commercial PBP inhibitor. The 2D figures reveal that both compounds hit the protein in the active site with a similar type of molecular interaction, where the hydroxyl groups in the aromatic ring of cannabinoids play a pivotal role in the biological activity. These results provide some evidence that the anti-Staphylococcus aureus activity of these cannabinoids may be related to the inhibition of the PBP protein; besides, the robustness of the models along with the docking and Quantitative Structure–Activity Relationship (QSAR) results allow the proposal of three new compounds; the predicted activity combined with the scoring values against PBP should encourage future synthesis and experimental testing.

Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease M^pro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2'-Fluoro-2'-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.

Chair- and V-Shaped of H-bonded Supramolecular Complexes of Azophenyl Nicotinate Derivatives; Mesomorphic and DFT Molecular Geometry Aspects

New geometrical architectures of chair- and V-shaped supramolecular liquid crystalline complexes were molded through 1:1 intermolecular hydrogen bonding interactions between 4-(4-(hexyloxy)phenylazo)methyl)phenyl nicotinate and 4-alkoxybenzoic acids. The length of terminal alkoxy acid chains varied, n = 6 to 16 carbons. The mesomorphic behaviour of these complexes was examined through differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). Fourier-transform infrared spectroscopy (FT-IR) was carried out to confirm the presence of Fermi bands that appeared for the hydrogen bonding formation. Enantiotropic nematic phases were observed and covered all lengths of alkoxy chains. The geometrical structures of the prepared supramolecular complexes geometries were estimated by Density functional theory (DFT) calculations. The supramolecular complexes I/An are projected to exhibit a nonlinear geometry with V-shaped and chair-shaped geometry. The chair-shaped conformers of I/An were found to be more stable than V-shaped isomeric complexes. Moreover, the effect of the change of the mesogenic core on the mesophase thermal stability (TC) has been investigated by a comparative study of the present azo supramolecular H-bonding LCs (SMHBCs) I/An and our previously reported their Schiff base analogue complexes, II/An. The findings of the DFT illustrated the high impact of CH=N as a mesogenic core on the mesomorphic behavior in terms of the competitive lateral and terminal intermolecular interactions as well as the molecular electrostatic potential (MEP).

New Symmetrical U- and Wavy-Shaped Supramolecular H-Bonded Systems; Geometrical and Mesomorphic Approaches

New mesomorphic symmetrical 2:1 supramolecular H-bonded complexes of seven phenyl rings were prepared between 4-n-alkoxyphenylazobenzoic acids and 4-(2-(pyridin-3-yl)diazenyl)phenyl nicotinate. Mesomorphic studies of the prepared complexes were investigated using differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). Fermi bands of the formed H-bonded interactions were confirmed by FT-IR spectroscopy. Geometrical parameters for all complexes were performed using the density functional theory (DFT) calculations method. Theoretical results revealed that the prepared H-bonded complexes are in non-linear geometry with U-shaped and wavy-shaped geometrical structures; however, the greater linearity of the wavy-shaped compounds could be the reason for their stability with respect to the U-shaped conformer. Moreover, the stable, wavy shape of supramolecular H-bonded complexes (SMHBCs) has been used to illustrate mesomeric behavior in terms of the molecular interaction. The experimental mesomorphic investigations revealed that all complexes possess enantiotropic smectic C phase. Phases were confirmed by miscibility with a standard smectic C (SmC) compound. A comparison was constructed to investigate the effect of incorporating azophenyl moiety into the mesomeric behavior of the corresponding five-membered complexes. It was found that the addition of the extra phenylazo group to the acid moiety has a great increment of the mesophase stability (TC) values with respect to the monotropic SmC phase of the five aromatic systems to the high stable enantiotropic SmC mesophase.

Experimental and Theoretical Approaches of New Nematogenic Chair Architectures of Supramolecular H-Bonded Liquid Crystals

New four isomeric chair architectures of 1:1 H-bonded supramolecular complexes were prepared through intermolecular interactions between 4-(2-(pyridin-4-yl)diazenyl-(2-(or 3-)chlorophenyl) 4-alkoxybenzoates and 4-n-alkoxybenzoic acids. The H-bond formation of all complexes was confirmed by differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR). Mesomorphic characterization was carried by DSC and polarized optical microscopy (POM). It was found that all prepared laterally chloro-substituted supramolecular complexes were nematogenic, and exhibited nematic phase and low melting temperature. The thermal stability of the nematic mesophase observed depends upon the location and spatial orientation of the lateral Cl- atom in as well as the length of terminal chains. Theoretical calculations were carried out within the paradigm of the density functional theory (DFT) in order to establish the molecular conformation for the formed complexes and estimate their thermal parameters. The results of the computational calculations revealed that the H-bonded complexes were in a chair form molecular geometry. Additionally, out of the acquired data, it was possible to designate the influence of the position and orientation of the lateral group as well as the alkoxy chain length on the stability of the nematic phase.