Daryono H. Tjahjono

CATIONIC PORPHYRINS BEARING DIAZOLIUM RINGS : SYNTHESIS AND THEIR INTERACTION WITH CALF THYMUS DNA

Two novel cationic porphyrins bearing five-membered rings at the meso-positions, meso-tetrakis(1,3-dimethylimidazolium-2-yl)porphyrin (H2TDMImP) and meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin (H2TDMPzP), have been synthesized. These two compounds interact with calf thymus DNA (CTDNA) in different binding modes from that of mesotetrakis(N-methylpyridinium-4-yl)porphyrin (H2TMPyP). H2TDMImP outside binds to the minor groove of CTDNA while H2TDMPzP intercalates into CTDNA. These two novel cationic porphyrins strongly bind to CTDNA even at high ionic strength and the binding constant of H2TDMPzP to CTDNA is comparable to that of H2TMPyP. The binding of H2TDMImP to CTDNA is enthalpically driven. The favorable free energy changes in binding of H2TDMPzP to CTDNA come from the large negative enthalpy changes accompanied by small positive entropy changes.

The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study

Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid–DNA complexes during 2 ns was performed by Amber9 molecular dynamics package. The binding energy calculation of best four complexes was then carried out using MMPBSA method. The hybrid compounds interacted to DNA duplexes through intercalation and groove binding modes. The minor groove binding of DNA was energetically preferred by cationic porphyrin hybrids due to favorable electrostatic and van der Waals interactions. Both electrostatic and van der Waals contributions were able to distinguish the binding mode of porphyrin hybrid to DNA duplexes.

A selective distance-based paper analytical device for copper(II) determination using a porphyrin derivative

Meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin sulfonate (TDMPzP), a water-soluble porphyrin derivative, was synthesized and used as a colorimetric reagent for Cu2+ detection on a microfluidic paper-based analytical device (µPAD) using distance-based quantification. TDMPzP showed a high selectivity for Cu2+ detection in aqueous solutions. When Cu2+ was added to the TDMPzP under acidic conditions, a color change from green to a pink was observed by the naked eye. Under optimized conditions, the application of this system to a distance-based μPAD exhibited good analytical response. The presence of common metal ions (Al3+, Fe3+, Mg2+, Co2+, Mn2+, Zn2+, Pb2+, Cd2+, Sn2+, and Ni2+) did not interfere with Cu2+ detection within reasonable tolerance ratios. The lowest concentration of copper that could be measured was 1mgL-1 (1ppm) which meets the requirements for drinking water contamination regulations from the US Environmental Protection Agency (EPA) and World Health Organization (WHO) guidelines for drinking water. Real drinking water samples were analyzed to confirm the practical application of this system and the results showed good agreement with ICP-MS data. This distance-based µPAD based on TDMPzP for Cu2+ detection is convenient and effective for real-time drinking water analysis.

In silico study of porphyrin-anthraquinone hybrids as CDK2 inhibitor

Cyclin-Dependent Kinases (CDKs) are known to play crucial roles in controlling cell cycle progression of eukaryotic cell and inhibition of their activity has long been considered as potential strategy in anti-cancer drug research. In the present work, a series of porphyrin-anthraquinone hybrids bearing meso-substituents, i.e. either pyridine or pyrazole rings were designed and computationally evaluated for their Cyclin Dependent Kinase-2 (CDK2) inhibitory activity using molecular docking, molecular dynamics simulation, and binding free energy calculation. The molecular docking simulation revealed that all six porphyrin hybrids were able to bind to ATP-binding site of CDK2 and interacted with key residues constituted the active cavity of CDK2, while molecular dynamics simulation indicated that all porphyrins bound to CDK2 were stable for 6ns. The binding free energies predicted by MM-PBSA method showed that most compounds exhibited higher affinity than that of native ligand (4-anilinoquinazoline, DTQ) and the affinity of mono-H2PyP-AQ was about three times better than that of DTQ, indicating its potential to be advanced as a new CDK2 inhibitor.

Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes

A series of cationic porphyrin–anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the meso-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.

Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors

Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research.

DNA-Binding Properties of Iron(II) Mixed-Ligand Complexes Containing 1,10-Phenanthroline and Dipyrido(3,2-a:2',3'-c)phenazine

An iron(II) mixed-ligand complex with 1,10-phenanthroline (phen) and dipyrido[3,2-a:2’,3’- c]phenazine (dppz), [Fe(phen)2(dppz)]2+, has been synthesized. The DNA-binding properties of the mixed-ligand complex have been studied in terms of equilibrium binding constant, thermodynamic parameter, thermal denaturation as well as Pfeiffer effect upon binding to DNA. The spectrophotometric titration of [Fe(phen)2(dppz)]2+ with calf thymus DNA (ct-DNA) has shown that the iron(II) mixed-ligand complex binds effectively to ct-DNA in an intercalation mode as indicated by remarkable hypochromicity (ca. 36%) and moderate bathochromic shift (8 nm) of the absorption spectra. This intercalative mode is supported by a significant increase (Δ Tm = 21 °C) in the melting temperature (Tm) of ct-DNA at R([complex]/[ct-DNA]) = 1.5. The binding of [Fe(phen)2(dppz)]2+ to ct-DNA is entropically driven as characterized by a positive enthalpy change and a large negative TΔ S term. An intense CD signal in the UV and visible region develops upon addition of ct-DNA to the racemate solution of [Fe(phen)2(dppz)]2+. This has revealed that a shift in diastereomeric inversion equilibrium takes place in the solution to yield an excess of one enantiomer of the DNA-iron(II) complex (Pfeiffer effect). The striking resemblance of the CD spectral profiles to those of the corresponding Δ -enantiomer indicates that Δ -[Fe(phen)2(dppz)]2+ is preferentially bound to ct-DNA

Binding of nickel(II) tetrakis(dimethylpyrazolium-4-yl)porphyrin to poly(dG-dC)2 and poly(dA-dT)2

The interaction of nickel(II) complex of cationic porphyrins bearing five-membered rings, meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrinatonickel(II) (NiPzP), with synthetic polynucleotides poly(dG-dC)2 and poly(dA-dT)2 has been characterized by viscometric, visible absorption, CD and MCD spectroscopic, and melting temperature measurements. The nickel(II) complex NiPzP is intercalated into poly(dG-dC)2 but outside bound to the major groove of poly(dA-dT)2. The binding constants of NiPzP to poly(dG-dC)2 and poly(dA-dT)2 are in the order of 106 M-1 and comparable to those of other reported cationic metalloporphyrins. The binding process of NiPzP to poly(dG-dC)2 and poly(dA-dT)2 is endothermic and entropically driven.

In Silico Study, Synthesis, and Cytotoxic Activities of Porphyrin Derivatives

Five known porphyrins, 5,10,15,20-tetrakis(p-tolyl)porphyrin (TTP), 5,10,15,20-tetrakis(p-bromophenyl)porphyrin (TBrPP), 5,10,15,20-tetrakis(p-aminophenyl)porphyrin (TAPP), 5,10,15-tris(tolyl)-20-mono(p-nitrophenyl)porphyrin (TrTMNP), 5,10,15-tris(tolyl)-20-mono(p-aminophenyl)porphyrin (TrTMAP), and three novel porphyrin derivatives, 5,15-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-10,20-di(p-tolyl)porphyrin (DBECPDTP), 5,10-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-15,20-di-(methylpyrazole-4-yl)porphyrin (cDBECPDPzP), 5,15-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-10,20-di-(methylpyrazole-4-yl)porphyrin (DBECPDPzP), were used to study their interaction with protein targets (in silico study), and were synthesized. Their cytotoxic activities against cancer cell lines were tested using 3-(4,5-dimetiltiazol-2-il)-2,5-difeniltetrazolium bromide (MTT) assay. The interaction of porphyrin derivatives with carbonic anhydrase IX (CAIX) and REV-ERBβ proteins were studied by molecular docking and molecular dynamic simulation. In silico study results reveal that DBECPDPzP and TrTMNP showed the highest binding interaction with REV- ERBβ and CAIX, respectively, and both complexes of DBECPDPzP-REV-ERBβ and TrTMNP-CAIX showed good and comparable stability during molecular dynamic simulation. The studied porphyrins have selective growth inhibition activities against tested cancer cells and are categorized as marginally active compounds based on their IC50.

Computational Study of Imidazolylporphyrin Derivatives as a Radiopharmaceutical Ligand for Melanoma

BACKGROUND Melanoma is the most aggressive type of skin cancer. Metastatic melanoma is extremely difficult to treat with current therapy methods such as surgery. On the other hand, it is a good opportunity to develop a radiopharmaceutical using a radionuclide such as Technetium (Tc) for diagnostic and Rhenium (Re) for therapeutic purposes. T3,4BCPP has been be used as a radioimaging agent for melanoma cancers experimentally. The aim of the present research was to design new imidazolylporphyrin derivatives with better selectivity and higher affinity than those of T3,4BCPP by molecular modeling. METHODS Eight types of Re- and Tc-labeled imidazolylporphyrins were docked to Fibroblast Growth Factor Receptor 1 (FGFR1, PDB ID: 5AM6) using AutoDock 4.2. FGFR1 was simulated by Molecular Dynamic (MD) simulation for 30 ns using NAMD 2.10 at 37 °C. The obtained conformations were then applied in a molecular docking simulation. Dovitinib (natural ligand of FGFR1), Re- and Tc-T3, 4BCPP were used as references. RESULTS The MD simulation resulted in an RMSD of 3.8 Å. From all the studied imidazolylporphyrin derivatives, Tc-cD3, 4BCPMIP and Re-cD3, 4BCPIP had the best docking parameter. Tc-cD3, 4BCPMIP had a free binding energy of -4.06 kcal/mol, while that of Re-cD3, 4BCPIP was -4.35 kcal/mol. CONCLUSION It is concluded that cD3,4BCPMIP and cD3,4BCPIP are two potential candidate ligands for a melanoma radiopharmaceutical kit.