Molecular Interactions of Selective Agonists and Antagonists with the Retinoic Acid Receptor γ.

All-trans retinoic acid (ATRA), the major active metabolite of all-trans retinol (vitamin A), is a key hormonal signaling molecule. In the adult organism, ATRA has a widespread influence on processes that are crucial to the growth and differentiation of cells and, in turn, the acquisition of mature cell functions. Therefore, there is considerable potential in the use of retinoids to treat diseases. ATRA binds to the retinoic acid receptors (RAR) which, as activated by ATRA, selectively regulate gene expression. There are three main RAR isoforms, RARα, RARß, and RARγ. They each have a distinct role, for example, RARα and RARγ regulate myeloid progenitor cell differentiation and hematopoietic stem cell maintenance, respectively. Hence, targeting an isoform is crucial to developing retinoid-based therapeutics. In principle, this is exemplified when ATRA is used to treat acute promyelocytic leukemia (PML) and target RARα within PML-RARα oncogenic fusion protein. ATRA with arsenic trioxide has provided a cure for the once highly fatal leukemia. Recent in vitro and in vivo studies of RARγ have revealed the potential use of agonists and antagonists to treat diseases as diverse as cancer, heterotopic ossification, psoriasis, and acne. During the final drug development there may be a need to design newer compounds with added modifications to improve solubility, pharmacokinetics, or potency. At the same time, it is important to retain isotype specificity and activity. Examination of the molecular interactions between RARγ agonists and the ligand binding domain of RARγ has revealed aspects to ligand binding that are crucial to RARγ selectivity and compound activity and key to designing newer compounds.

Surface-Bioengineered Extracellular Vesicles Seeking Molecular Biotargets in Lung Cancer Cells.

Personalized medicine is a new approach to modern oncology. Here, to facilitate the application of extracellular vesicles (EVs) derived from lung cancer cells as potent advanced therapy medicinal products in lung cancer, the EV membrane was functionalized with a specific ligand for targeting purposes. In this role, the most effective heptapeptide in binding to lung cancer cells (PTHTRWA) was used. The functionalization process of EV surface was performed through the C- or N-terminal end of the heptapeptide. To prove the activity of the EVs functionalized with PTHTRWA, both a model of lipid membrane mimicking normal and cancerous cell membranes as well as human adenocarcinomic alveolar basal epithelial cells (A549) and human normal bronchial epithelial cells (BEAS-2B) have been exposed to these bioconstructs. Magnetic resonance imaging (MRI) showed that the as-bioengineered PTHTRWA-EVs loaded with superparamagnetic iron oxide nanoparticle (SPIO) cargos reach the growing tumor when dosed intravenously in NUDE Balb/c mice bearing A549 cancer. Molecular dynamics (MD) in silico studies elucidated a high affinity of the synthesized peptide to the α5ß1 integrin. Preclinical safety assays did not evidence any cytotoxic or genotoxic effects of the PTHTRWA-bioengineered EVs.

Structure and the Anticancer Activity of Vitamin D Receptor Agonists.

Vitamin D is a group of seco-steroidal fat-soluble compounds. The two basic forms, vitamin D2 (ergocalciferol) and vitamin D3 (cholecalciferol), do not have biological activity. They are converted in the body by a two-step enzymatic hydroxylation into biologically active forms, 1α,25-dihydroxyvitamin D2 [ercalcitriol, 1,25(OH)2D2] and 1α,25-dihydroxyvitamin D3 [calcitriol, 1,25(OH)2D3], which act as classical steroid hormones. 1,25(OH)2D3 exerts most of its physiological functions by binding to the nuclear vitamin D receptor (VDR), which is present in most body tissues to provide support to a broad range of physiological processes. Vitamin D-liganded VDR controls the expression of many genes. High levels of 1,25(OH)2D3 cause an increase in calcium in the blood, which can lead to harmful hypercalcemia. Several analogs of 1,25(OH)2D3 and 1,25(OH)2D2 have been designed and synthesized with the aim of developing compounds that have a specific therapeutic function, for example, with potent anticancer activity and a reduced toxic calcemic effect. Particular structural modifications to vitamin D analogs have led to increased anticancer activity and reduced calcemic action with the prospect of extending work to provide future innovative therapies.

Binding mechanism of pentamidine derivatives with human serum acute phase protein α1-acid glycoprotein.

Drug binding and interactions with plasma proteins play a crucial role in determining the efficacy of drug delivery, thus significantly impacting the overall pharmacological effect. AGP, the second most abundant plasma protein in blood circulation, has the unique capability to bind drugs and transport various compounds. In our present study, for the first time, we investigated whether AGP, a major component of the acute phase lipocalin in human plasma, can bind with pentamidine derivatives known for their high activity against the fungal pathogen Pneumocystis carinii. This investigation was conducted using integrated spectroscopic techniques and computer-based approaches. According to the results, it was concluded that compounds having heteroatoms (-NCH3) in the aliphatic linker and the addition of a Br atom and a methoxy substituent at the C-2 and C-6 positions on the benzene ring, exhibit strong interactions with the AGP binding site. These compounds are identified as potential candidates for recognition by this protein. MD studies indicated that the tested analogues complexed with AGPs reach an equilibrium state after 60 ns, suggesting the stability of the complexes. This observation was further corroborated by experimental results. Therefore, exploring the interaction mechanism of pentamidine derivatives with plasma proteins holds promise for the development of bis-benzamidine-designed pharmaceutically important drugs.

Improving the Selectivity of the C-C Coupled Product Electrosynthesis by Using Molecularly Imprinted Polymer─An Enhanced Route from Phenol to Biphenol.

We developed a procedure for selective 2,4-dimethylphenol, DMPh, direct electro-oxidation to 3,3',5,5'-tetramethyl-2,2'-biphenol, TMBh, a C-C coupled product. For that, we used an electrode coated with a product-selective molecularly imprinted polymer (MIP). The procedure is reasonably selective toward TMBh without requiring harmful additives or elevated temperatures. The TMBh product itself was used as a template for imprinting. We followed the template interaction with various functional monomers (FMs) using density functional theory (DFT) simulations to select optimal FM. On this basis, we used a prepolymerization complex of TMBh with carboxyl-containing FM at a 1:2 TMBh-to-FM molar ratio for MIP fabrication. The template-FM interaction was also followed by using different spectroscopic techniques. Then, we prepared the MIP on the electrode surface in the form of a thin film by the potentiodynamic electropolymerization of the chosen complex and extracted the template. Afterward, we characterized the fabricated films by using electrochemistry, FTIR spectroscopy, and AFM, elucidating their composition and morphology. Ultimately, the DMPh electro-oxidation was performed on the MIP film-coated electrode to obtain the desired TMBh product. The electrosynthesis selectivity was much higher at the electrode coated with MIP film in comparison with the reference nonimprinted polymer (NIP) film-coated or bare electrodes, reaching 39% under optimized conditions. MIP film thickness and electrosynthesis parameters significantly affected the electrosynthesis yield and selectivity. At thicker films, the yield was higher at the expense of selectivity, while the electrosynthesis potential increase enhanced the TMBh product yield. Computer simulations of the imprinted cavity interaction with the substrate molecule demonstrated that the MIP cavity promoted direct coupling of the substrate to form the desired TMBh product.

Nonaqueous Capillary Electrophoretic Separation of Analogs of (24R)-1,24-Dihydroxyvitamin D3 Derivative as Predicted by Quantum Chemical Calculations.

Nonaqueous capillary electrophoretic (NACE) separation was obtained of analogs of (24R)-1,24-dihydroxyvitamin D3 derivative (calcipotriol) as predicted by quantum chemical calculations supported by the density functional theory (DFT). Among the key electronic properties investigated, absolute values of the dipole polarizability and energy gap between HOMO and LUMO molecular orbitals of the analog molecules differ significantly for particular analogs, and there is a direct relationship with their electrophoretic migration time. These differences and relationships suggest that the structurally related analogs should be separable in the electrostatic field. Indeed, the robust, sensitive, and rapid NACE method was first developed for the identification and determination of the anticancer analog of calcipotriol (coded PRI-2205) and its process-related impurities (coded PRI-2201, PRI-2203, and PRI-2204) in organic and aqueous biological solutions. The direct relation between the calculated electronic properties of the analogs and the experimental electrophoretic migration time could be a promising prospect for theoretically predicting the electrophoretic separations.

In Silico Studies of Novel Vemurafenib Derivatives as BRAF Kinase Inhibitors.

BRAF inhibitors have improved the treatment of advanced or metastatic melanoma in patients that harbor a BRAFT1799A mutation. Because of new insights into the role of aberrant glycosylation in drug resistance, we designed and studied three novel vemurafenib derivatives possessing pentose-associated aliphatic ligands-methyl-, ethyl-, and isopropyl-ketopentose moieties-as potent BRAFV600E kinase inhibitors. The geometries of these derivatives were optimized using the density functional theory method. Molecular dynamic simulations were performed to find interactions between the ligands and BRAFV600E kinase. Virtual screening was performed to assess the fate of derivatives and their systemic toxicity, genotoxicity, and carcinogenicity. The computational mapping of the studied ligand-BRAFV600E complexes indicated that the central pyrrole and pyridine rings of derivatives were located within the hydrophobic ATP-binding site of the BRAFV600E protein kinase, while the pentose ring and alkyl chains were mainly included in hydrogen bonding interactions. The isopropyl-ketopentose derivative was found to bind the BRAFV600E oncoprotein with more favorable energy interaction than vemurafenib. ADME-TOX in silico studies showed that the derivatives possessed some desirable pharmacokinetic and toxicologic properties. The present results open a new avenue to study the carbohydrate derivatives of vemurafenib as potent BRAFV600E kinase inhibitors to treat melanoma.

Drug Repurposing to Inhibit Histamine N-Methyl Transferase.

Lower activity of the histaminergic system is associated with neurological disorders, including Alzheimer's disease (AD). Thus, the enhancement of histaminergic neurotransmission by inhibition of histamine N-methyl transferase (HNMT), which degrades histamine, appears as an important approach. For this purpose, rigid and flexible molecular docking studies of 185 FDA-approved drugs with the HNMT enzyme were carried out to select two compounds to perform molecular dynamics (MD) simulations to evaluate the binding free energies and stability of the enzyme-drug complexes. Finally, an HNMT inhibition assay was performed to corroborate their effect towards HNMT. Molecular docking studies with HNMT allowed the selection of dihydroergotamine and vilazodone since these molecules showed the lowest Gibbs free energy values. Analysis of the binding mode of vilazodone showed interactions with the binding pocket of HNMT with Glu28, Gln143, and Asn283. In contrast, dihydroergotamine binds to the HNMT active site in a different location, apparently because it is overall the more rigid ligand compared to flexible vilazodone. HNMT inhibitory activity for dihydroergotamine and vilazodone was corroborated (IC50 = 72.89 µM and 45.01 µM, respectively) by in vitro assays. Drug repurposing of HNMT was achieved by employing computational studies.

In Silico Prediction of the Metabolic Resistance of Vitamin D Analogs against CYP3A4 Metabolizing Enzyme.

The microsomal cytochrome P450 3A4 (CYP3A4) and mitochondrial cytochrome P450 24A1 (CYP24A1) hydroxylating enzymes both metabolize vitamin D and its analogs. The three-dimensional (3D) structure of the full-length native human CYP3A4 has been solved, but the respective structure of the main vitamin D hydroxylating CYP24A1 enzyme is unknown. The structures of recombinant CYP24A1 enzymes have been solved; however, from studies of the vitamin D receptor, the use of a truncated protein for docking studies of ligands led to incorrect results. As the structure of the native CYP3A4 protein is known, we performed rigid docking supported by molecular dynamic simulation using CYP3A4 to predict the metabolic conversion of analogs of 1,25-dihydroxyvitamin D2 (1,25D2). This is highly important to the design of novel vitamin D-based drug candidates of reasonable metabolic stability as CYP3A4 metabolizes ca. 50% of the drug substances. The use of the 3D structure data of human CYP3A4 has allowed us to explain the substantial differences in the metabolic conversion of the side-chain geometric analogs of 1,25D2. The calculated free enthalpy of the binding of an analog of 1,25D2 to CYP3A4 agreed with the experimentally observed conversion of the analog by CYP24A1. The metabolic conversion of an analog of 1,25D2 to the main vitamin D hydroxylating enzyme CYP24A1, of unknown 3D structure, can be explained by the binding strength of the analog to the known 3D structure of the CYP3A4 enzyme.

Polytyramine Film-Coated Single-Walled Carbon Nanotube Electrochemical Chemosensor with Molecularly Imprinted Polymer Nanoparticles for Duloxetine-Selective Determination in Human Plasma.

We devised, fabricated, and tested differential pulse voltammetry (DPV) and impedance spectroscopy (EIS) chemosensors for duloxetine (DUL) antidepressant determination in human plasma. Polyacrylic nanoparticles were synthesized by precipitation polymerization and were molecularly imprinted with DUL (DUL-nanoMIPs). Then, together with the single-walled carbon nanotube (SWCNT) scaffolds, they were uniformly embedded in polytyramine films, i.e., nanoMIPs-SWCNT@(polytyramine film) surface constructs, deposited on gold electrodes by potentiodynamic electropolymerization. These constructs constituted recognition units of the chemosensors. The molecular dynamics (MD) designing of DUL-nanoMIPs helped select the most appropriate functional and cross-linking monomers and determine the selectivity of the chemosensor. Three different DUL-nanoMIPs and non-imprinted polymer (nanoNIPs) were prepared with these monomers. DUL-nanoMIPs, synthesized from respective methacrylic acid and ethylene glycol dimethyl acrylate as the functional and cross-linking monomers, revealed the highest affinity to the DUL analyte. The linear dynamic concentration range, extending from 10 pM to 676 nM DUL, and the limit of detection (LOD), equaling 1.6 pM, in the plasma were determined by the DPV chemosensor, outperforming the EIS chemosensor. HPLC-UV measurements confirmed the results of DUL electrochemical chemosensing.

In Vitro and Computational Studies of Perezone and Perezone Angelate as Potential Anti-Glioblastoma Multiforme Agents.

Glioblastoma multiforme (GBM) represents the most malignant type of astrocytoma, with a life expectancy of two years. It has been shown that Poly (ADP-ribose) polymerase 1 (PARP-1) protein is over-expressed in GBM cells, while its expression in healthy tissue is low. In addition, perezone, a phyto-compound, is a PARP-1 inhibitor with anti-neoplastic activity. As a consequence, in the present study, both in vitro and computational evaluations of perezone and its chemically related compound, perezone angelate, as anti-GBM agents were performed. Hence, the anti-proliferative assay showed that perezone angelate induces higher cytotoxicity in the GBM cell line (U373 IC50 = 6.44 µM) than perezone (U373 IC50 = 51.20 µM) by induction of apoptosis. In addition, perezone angelate showed low cytotoxic activity in rat glial cells (IC50 = 173.66 µM). PARP-1 inhibitory activity (IC50 = 5.25 µM) and oxidative stress induction by perezone angelate were corroborated employing in vitro studies. In the other hand, the performed docking studies allowed explaining the PARP-1 inhibitory activity of perezone angelate, and ADMET studies showed its probability to permeate cell membranes and the blood-brain barrier, which is an essential characteristic of drugs to treat neurological diseases. Finally, it is essential to highlight that the results confirm perezone angelate as a potential anti-GBM agent.

Cilostazol-imprinted polymer film-coated electrode as an electrochemical chemosensor for selective determination of cilostazol and its active primary metabolite.

An electrochemical chemosensor for cilostazol (CIL) determination was devised, engineered, and tested. For that, a unique conducting film of the functionalized thiophene-appended carbazole-based polymer, molecularly imprinted with cilostazol (MIP-CIL), was potentiodynamically deposited on a Pt disk electrode by oxidative electropolymerization. Thanks to electro-oxidation potentials lower than that of CIL, the carbazole monomers outperformed pyrrole, thiophene, and phenol monomers, in this electropolymerization. The pre-polymerization complexes quantum-mechanical and molecular dynamics analysis allowed selecting the most appropriate monomer from the three thiophene-appended carbazoles examined. The electrode was then used as a selective CIL chemosensor in the linear dynamic concentration range of 50 to 924 nM with a high apparent imprinting factor, IF = 10.6. The MIP-CIL responded similarly to CIL and CIL's pharmacologically active primary metabolite, 3,4-dehydrocilostazol (dhCIL), thus proving suitable for their determination together. Simulated models of the MIP cavities binding of the CIL, dhCIL, and interferences' molecules allowed predicting chemosensor selectivity. The MIP film sorption of CIL and dhCIL was examined using DPV by peak current data fitting with the Langmuir (L), Freundlich (F), and Langmuir-Freundlich (LF) isotherms. The LF isotherm best described this sorption with the sorption equilibrium constant (KLF) for CIL and dhCIL of 12.75 × 10-6 and 0.23 × 10-6 M, respectively. Moreover, the chemosensor cross-reactivity to common interferences study resulted in the selectivity to cholesterol and dehydroaripiprazole of 1.52 and 8.0, respectively. The chemosensor proved helpful in determining CIL and dhCIL in spiked human plasma with appreciable recovery (99.3-134.1%) and limit of detection (15 nM).

Theoretical evaluation of EGFR kinase inhibition and toxicity of di-indol-3-yl disulphides with anti-cancer potency.

Research aimed at developing potent di-indol-3-yl disulphides for cancer diseases makes use of various theoretical techniques to evaluate the drug-likeness parameters and the mode of action. A drug-likeness filter helps evaluate the therapeutic potency of four bis-indole derivatives, structurally related to 3,3'-methanediyl-bis-indole (DIM) but having the S-S instead of the methylene linker and showing a high inhibitory impact on the variants of cancer cell lines (among them HL-60 and DU-145). Based on in vitro experimental results for their close analogues, a correlation was found between the epidermal growth factor receptor kinase (EGFR) inhibition and the theoretical energy of complexation. Docking studies of ligands followed by molecular dynamics were performed at the ATP-binding site of EGFR tyrosine kinase to scrutinize the inhibition of the di-indol-3-yl disulphides at a molecular level. Derivatives with bromine or iodine substituents at C-5 positions of the indole moieties made strong complexes by interaction with the most important hinge region residues Met-793 and Cys-733. The inhibition model for EGFR kinase and the proposed procedures can be very informative in the biological testing of selected bis-indoles and may be useful for future research on effective inhibitors for the treatment of EGFR-related cancer.Communicated by Ramaswamy H. Sarma.

Molecularly imprinted polymer nanoparticles-based electrochemical chemosensors for selective determination of cilostazol and its pharmacologically active primary metabolite in human plasma.

Molecularly imprinted polymer (MIP) nanoparticles-based differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) chemosensors for antiplatelet drug substance, cilostazol (CIL), and its pharmacologically active primary metabolite, 3,4-dehydrocilostazol (dhCIL), selective determination in human plasma were devised, prepared, and tested. Molecular mechanics (MM), molecular dynamics (MD), and density functional theory (DFT) simulations provided the optimum structure and predicted the stability of the pre-polymerization complex of the CIL template with the chosen functional acrylic monomers. Moreover, they accounted for the MIP selectivity manifested by the molecularly imprinted cavity with the CIL molecule complex stability higher than that for each interference. On this basis, a fast and reliable method for determining both compounds was developed to meet an essential requirement concerning the personalized drug dosage adjustment. The limit of detection (LOD) at the signal-to-noise ratio of S/N = 3 in DPV and EIS determinations using the ferrocene redox probe in a "gate effect" mode was 93.5 (±2.2) and 86.5 (±4.6) nM CIL, respectively, and the linear dynamic concentration range extended from 134 nM to 2.58 µM in both techniques. The chemosensor was highly selective to common biological interferences, including cholesterol and glucose, and less selective to structurally similar dehydroaripiprazole. Advantageously, it responded to dhCIL, thus allowing for the determination of CIL and dhCIL together. The EIS chemosensor appeared slightly superior to the DPV chemosensor concerning its selectivity to interferences. The CIL DPV sorption data were fitted with Langmuir, Freundlich, and Langmuir-Freundlich isotherms. The determined sorption parameters indicated that the imprinted cavities were relatively homogeneous and efficiently interacted with the CIL molecule.

Deposition of pentamidine analogues in the human body - spectroscopic and computational approaches.

Bis-benzamidines are a diverse group of compounds with high potential in pharmacotherapy, and among them, pentamidine is a drug of great therapeutic significance in Pneumocystis jiroveci pneumonia (PJP) prophylaxis and therapy. Pharmacokinetic properties of these cationic species such as transport, acid/base equilibria, and interactions with potential target molecules are still of interest, especially for recently designed compounds. To broaden our knowledge drug-likeness, human serum albumin binding, and acidity constants (Ka) were experimentally and theoretically examined for five pentamidine analogues 1 - 5 with -NH-CO-chain-CO-NH-bridges of increasing length and O, N, and S atoms in the chain. The studied analogues display very marked activity against Pneumocystis carinii without cytotoxicity that inspired us to perform an in silico analysis of their mode of action based on the hypothesis that the small DNA groove of rich in adenine-thymine pairs is their molecular target. These studies allowed us to classify them as very promising lead molecules.

Low-oxidation-potential thiophene-carbazole monomers for electro-oxidative molecular imprinting: Selective chemosensing of aripiprazole.

New thiophene-carbazole functional and cross-linking monomers electropolymerizing at potentials sufficiently low for molecular imprinting of an electroactive aripiprazole antipsychotic drug were herein designed and synthesized. Numerous conducting molecularly imprinted polymer (MIP) films are deposited by electropolymerization at relatively low potentials by electro-oxidation of pyrrole, aniline, phenol, or 3,4-ethylenedioxythiophene (EDOT). However, their interactions with templates are not sufficiently strong. Hence, it is necessary to introduce additional recognizing sites in these cavities to increase their affinity to the target molecules. For that, functional monomers derivatized with substituents forming stable complexes with the templates are used. However, oxidation potentials of these derivatives are often, disadvantageously, higher than that of parent monomers. Therefore, we designed and synthesized new functional and cross-linking monomers, which are oxidized at sufficiently low potentials. The deposited MIP and non-imprinted polymer (NIP) films were characterized by PM-IRRAS and UV-vis spectroscopy and imaged with AFM. The structure of the aripiprazole pre-polymerization complex with functional monomers was optimized with density functional theory (DFT), and aripiprazole interactions with imprinted cavities were simulated with molecular mechanics (MM) and molecular dynamics (MD). MIP-aripiprazole film-coated electrodes were used as extended gates for selective determination of aripiprazole with the extended-gate field-effect transistor (EG-FET) chemosensor. The linear dynamic concentration range was 30-300 pM, and the limit of detection was 22 fM. An apparent imprinting factor of the MIP-1 was IF = 4.95. The devised chemosensor was highly selective to glucose, urea, and creatinine interferences. The chemosensor was successfully applied for aripiprazole determination in human plasma. The results obtained were compared to those of the validated HPLC-MS method.

Evaluation of blood-brain barrier penetration and examination of binding to human serum albumin of 7-O-arylpiperazinylcoumarins as potential antipsychotic agents.

The delivery of drugs to the brain is complicated by the multiple factors including low blood-brain barrier (BBB) passive permeability, active BBB efflux systems, and plasma protein binding. Thus, a detailed understanding of the transport of the new potent substances through the membranes is vitally important and their physico-chemical characteristics should be analyzed at first. This work presents an evaluation of drug likeness of eight 7-O-arylpiperazinylcoumarin derivatives with high affinity towards serotoninergic receptors 5-HT1A and 5-HT2A with particular analysis of the requirements for the CNS chemotherapeutics. The binding constants to human serum albumin (HSA) were determined at physiological pH using fluorescence spectroscopy, and then their mode of action was explained by analysis of theoretical HSA complexes. Dynamic simulation of systems allowed for reliable evaluation of the interaction strength. The analyzed coumarins were able to pass BBB, and they present good drug likeness properties. They showed high affinities to HSA (log KQ = 5.3-6.0 which corresponds to -8.12 to -7.15 kcalmol-1 of Gibbs free energy). The changes of the emission intensity upon binding to HSA were scrutinized showing the different mode of action for 4-phenylpiperazinylcoumarins. The values of computed Gibbs free energy and determined on the basis of experimentally obtained binding constants log KQ coincide suggesting a good quality of the theoretical model. Overall the 8-acetyl-7-O-arylpiperazinyl-4-methylcoumarin derivatives represent valuable lead compounds to be further tested in various preclinical assays as a possible chemotherapeutics against CNS diseases. Studied coumarins can be metabolized by cytochrome P450 to aldehydes and hydroxy derivatives. The existence of other binding sites inside HSA than Sudlow's site 1 was postulated. The longer aliphatic linker between coumarin and piperazine moieties favored binding to HSA in other than Sudlow site 1 pocket.

Drug-likeness of linear pentamidine analogues and their impact on the hERG K+ channel - correlation with structural features.

This work presents drug-likeness and the cardiotoxicity profiles of six potent pentamidine analogs 1-6 and three new compounds 7-9 as chemotherapeutics for therapy of Pneumocystis jiroveci pneumonia. A combination of experimental and computational approaches was used in the cardiotoxicity examination. The hERG trafficking and functionality of the hERG currents were tested by western blot analyses, immunofluorescent staining procedures, and patch-clamp electrophysiological assays. Cardiotoxicity combined with blocking the hERG K+ channel was predicted, and then simulated by docking to the CSM-TM model 732 protein. Location of pentamidines in the proximity of Leu622, Thr623, Ser649, Tyr652, Ala653, and Phe656, and the high energies of interactions were in accordance with probable blocking of the hERG channel. However, in the biochemical experiments, no significant changes in I hERG densities and a minor effect on hERG maturation were observed. Predicted metabolic transformation of pentamidines with S atoms in the aliphatic linker leads to oxidation of one S atom, but those with the phenyl sulfanilide moiety can be oxidized to chinones. The tested pentamidines characterized by the presence of sulfur atoms or sulfanilide groups, have favorable drug-likeness parameters and are promising lead structures in the development of new potent chemotherapeutics against PJP.

Drug likeness prediction of 5-hydroxy-substituted coumarins with high affinity to 5-HT1A and 5-HT2A receptors.

One of the latest trends is search for the new anti-psychotic drugs among coumarin derivatives with piperazine moiety. Their therapeutic potential can be hampered by poor physico-chemical parameters as low brain penetration or limited transport in the body fluid. Herein, we predicted the drug likeness of six coumarins with high affinity towards 5-HT1A and 5-HT2A receptors. Subsequent experimental determination of their binding constants to human serum albumin (HSA) revealed the binding with a moderate strength (logK=4.8-5.8) at the Sudlow's site 1, which represents a possibility of temporary storage of tested coumarins on HSA. Computational mapping of the binding of coumarins - HSA complexes showed that the coumarin rings of all tested compounds were similarly located within the hydrophobic binding pocket of HSA, while the rest of molecules (composed with alkyl chains, piperazine and benzene rings) decided about the difference in binding modes by the hydrogen bonding interactions. The proton dissociation constants (pKa) of the compounds were also determined by UV-vis spectrophotometric titrations to obtain the distribution of the species in the different protonation states at physiological pH of 7.4. A good agreement of the computationally-determined free enthalpy values of the ligand - HSA complexes with the values determined by experimental fluorescence quenching data could be a promising prospect for proposed theoretical strategy.

Theoretical evaluation of ADMET properties for coumarin derivatives as compounds with therapeutic potential.

Coumarins have received a considerable attention in the last three decades as the lead structures for the discovery of orally administrated chemotherapeutics. Despite of the large amounts of in vitro activity information, relatively a little is known about their bioavailability in vivo. This paper presents an evaluation of drug-likeness of 31 coumarin derivatives on the basis of Lipinski's rule of five, and computed ADMET parameters (adsorption, distribution, metabolism, elimination and toxicity). Nine compounds which were predicted as showing the cardiotoxicity, were examined as hERG K+ channel blockers using in silico approach. Additionally, an impact of the acetyl group at benzene ring on pharmacokinetic profile was scrutinized for the tested coumarin derivatives. None of the analyzed coumarins violated the Lipinski's rule of five for orally administered drugs, and all tested compounds will remain in the qualitative likelihood of crossing the blood-brain barrier. 7-O-Alkilaminocoumarins showed no hepatotoxicity, but introduction of the nitrile or the amidine groups increased the levels of the hepatoxicity markers. Computed parameters of toxicity revealed cardiotoxic potency of twenty-five tested compounds. The proposed hERG K+ channel binding simulations helped in the understanding the molecular basis of coumarins cardiotoxicity. The presented theoretical studies explained some aspects of coumarin pharmacokinetics and identified the positive effect of the acetoxy substituent on the tested parameters.