Lipophilic Interactions Research Articles

671. Potent Anti-Tumor Effects of ApDCs (Aptamer Drug Conjugates) for Targeted Therapeutics in Pancreatic Cancer

Aptamer Drug Conjugates (ApDCs) are a potential class of targeting therapeutics to improve therapeutic index over traditional chemotherapy. As most existing chemotherapies are absorbed into cells non-specifically through lipophilic interaction, to improve the therapeutic index, the drugs were attached to pancreatic cancer specific RNA aptamer, P19, as targeting moieties that preferentially delivered the payload to tumor cells. Active metabolites of gemcitabine (dFdCMP) and 5FdU (5FdUMP) were incorporated P19 intrinsically to make conjugates. The conjugates of P19-dFdCMP or P19-5FdUMP kept their structural functionality getting internalized in their target cells, PANC-1. P19-dFdCMP and P19-5FdUMP was incorporated into replicating DNA, resulting in chain termination and stalling of replication forks in nuclear. They induced the phosphorylation of histone H2AX on Ser139 (γ-H2AX), markers of double-strand DNA breaks, and increased the forms of nuclear foci at the sites of DNA damage. In consequence, the cell proliferation was significantly inhibited 51-53% in PANC-1 and 54-34% in gemcitabine resistance AsPC-1. Targeted anti-mitotic therapies have emerged as a new concept of cancer drugs. Chemotoxine, monomethyl auristatin E (MMAE) is a very potent antimitotic agent that inhibits cell division by blocking the polymerization of tubulin. However, it can't be used by drug itself because of high toxicity. Herein, toxic molecule, MMAE, was conjugated to P19 for the targeted anti-mitotic therapies. P19-MMAE caused mitotic G2/M phase arrest, consequently inhibited 56% of cell proliferation on dose-dependent manner comparing control. In vivo assay, P19-MMAE induced the tumor regression via tail vein injection. In this study, the drug attached aptamer significantly decreased non-specific uptake of the drug and increase specific uptake of the conjugate in tumor cells. Our approaches suggest guiding cytotoxic drugs into malignant cancer cells specifically without causing significant harm to the normal cells.

Selective complexation of di-n-hexylammonium salts by tailed porphyrin host

A di-n-hexylammonium ion was selectively encapsulated in the cavity of tailed porphyrins due to induced fit and lipophilic interactions.

Integrated Free Energy Model (IFEM) for microemulsions

The Integrated Free Energy Model (IFEM) is a platform used to predict the solubilization of nonpolar oils in nonionic alkyl-polyethylene oxide (CXEOY) micelles starting from a free energy balance of costs and gains when surfactants from empty micelles and oil from a continuous oil phase assemble to form an oil-swollen micelle. IFEM considers lipophilic interactions between surfactant tails and oil solubilized in the core of micelles, and the interaction between surfactant tails and the oil solubilized in the surfactant tail domain, as well as oil–oil and surfactant–surfactant tail interactions. Expressions to calculate these lipophilic interactions from van der Waals (VDW) interaction potential were introduced in a previous publication. In this article, two new surfactant–water interactions are considered, surfactant headgroup dehydration during solubilization, and surfactant tail group dehydration. These six interaction terms, in addition to two entropy of mixing contributions (in the lipophilic and in the hydrophilic domains) make up the eight terms of the IFEM platform. Of these terms, only the headgroup dehydration requires a calibrated parameter. After calibrating this parameter, the model is capable of predicting experimental solubilization data, and the experimental trends reflected by a semi-empirical model, the Hydrophilic–Lipophilic-Difference+Net-Average-Curvature (HLD–NAC). Although there are numerous approaches to predict the surfactant–oil–water (SOW) phase behavior, the IFEM platform is the only one, to the knowledge of the authors that produces an explicit connection between molecular interactions and experimental data for real SOW systems. The IFEM platform can be programmed in a personal computer using relatively inexpensive software and its explicit nature opens the possibility to introduce additional interaction terms for more complex SOW systems.

Role of the phenolic OH moiety of GluN2B-selective NMDA antagonists with 3-benzazepine scaffold.

In order to analyze the role of the phenolic OH moiety of ifenprodil (1) and 3-benzazepin-1,7-diol 2 for the affinity and selectivity at GluN2B subunit containing NMDA receptors, the 3-benzazepin-1-ols 3 were designed, synthesized and pharmacologically evaluated and furthermore, the molecular interactions of the phenylbutyl derivative 3c with the GluN2B receptor were investigated. In order to avoid decarbonylation during the intramolecular Friedel-Crafts acylation of 11, the N-atom has to be protected with a trifluoromethylsulfonyl group. The second key step of the synthesis was the removal of the N-triflyl group, which was realized by K2CO3 induced elimination of trifluoromethanelsulfinate (F3CSO2(-)). In receptor binding studies with the radioligand [(3)H]ifenprodil the 3-benzazepin-1-ol 3c revealed a GluN2B affinity of 73 nM indicating that the phenolic OH moiety of 1 and 2 is not essential but favorable for high GluN2B affinity. In docking studies 3-benzazepin-1-ol 3c shows the same binding pose as ifenprodil-keto 1A in the X-ray crystal structure. H-bond interactions and lipophilic interactions of 3c and 1A are very similar.

Ligand efficient tetrahydro-pyrazolopyridines as inhibitors of ERK2 kinase.

A series of structure based drug design hypotheses and focused screening efforts drove improvements in the potency and lipophilic efficiency of tetrahydro-pyrazolopyridine based ERK2 inhibitors. Elaboration of a fragment chemical lead established a new lipophilic aryl-Tyr interaction resulting in a substantial potency improvement. Subsequent cleavage of the lipophilic moiety led to reconfiguration of the ligand bound binding cleft. The reconfiguration established a polar contact between a newly liberated N-H and a vicinal Asp, resulting in further improvements in lipophilic efficiency and in vitro clearance.

Optimisation and validation of ultra-high performance liquid chromatographic-tandem mass spectrometry method for qualitative and quantitative analysis of potato steroidal alkaloids.

An ultra-high performance liquid chromatographic-tandem mass spectrometry (UHPLC-MS/MS) method for quantification of potato steroidal alkaloids, namely α-solanine, α-chaconine, solanidine and demissidine was developed and validated. Three different column chemistries, i.e. ethylene bridged hybrid (BEH) C18, hydrophilic lipophilic interaction and amide columns, were assessed. The BEH C18 column showed best separation and sensitivity for the alkaloids. Validation data (inter-day and intra-day combined) for accuracy and recovery ranged from 94.3 to 107.7% and 97.0 to 103.5%, respectively. The accuracy data were within the acceptable range of 15% as outlined in the United States Food and Drug Administration (USFDA) guidelines. The recovery data were consistent and reproducible with a coefficient of variation (CV) ranging from 6.2 to 9.7%. In addition, precision of the method also met the criteria of the USFDA with CV values lower than 15% even at lower limit of quantification (LLOQ), while the permissible variation is considered acceptable below 20%. The limit of detection and LLOQ of the four alkaloids were in the range of 0.001-0.004μg/mL whereas the linearities of the standard curves were between 0.980 and 0.995.

Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability

An increasing number of macrocyclic peptides that cross biological membranes are being reported, suggesting that it might be possible to develop peptides into orally bioavailable therapeutics; however, current understanding of what makes macrocyclic peptides cell permeable is still limited. Here, we synthesized 62 cyclic hexapeptides and characterized their permeability using in vitro assays commonly used to predict in vivo absorption rates, i.e. the Caco-2 and PAMPA assays. We correlated permeability with experimentally measured parameters of peptide conformation obtained using rapid methods based on chromatography and nuclear magnetic resonance spectroscopy. Based on these correlations, we propose a model describing the interplay between peptide permeability, lipophilicity and hydrogen bonding potential. Specifically, peptides with very high permeability have high lipophilicity and few solvent hydrogen bond interactions, whereas peptides with very low permeability have low lipophilicity or many solvent interactions. Our model is supported by molecular dynamics simulations of the cyclic peptides calculated in explicit solvent, providing a structural basis for the observed correlations. This prospective exploration into biomarkers of peptide permeability has the potential to unlock wider opportunities for development of peptides into drugs.

Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.

We have identified several series of small molecule inhibitors of TrkA with unique binding modes. The starting leads were chosen to maximize the structural and binding mode diversity derived from a high throughput screen of our internal compound collection. These leads were optimized for potency and selectivity employing a structure based drug design approach adhering to the principles of ligand efficiency to maximize binding affinity without overly relying on lipophilic interactions. This endeavor resulted in the identification of several small molecule pan-Trk inhibitor series that exhibit high selectivity for TrkA/B/C versus a diverse panel of kinases. We have also demonstrated efficacy in both inflammatory and neuropathic pain models upon oral dosing. Herein we describe the identification process, hit-to-lead progression, and binding profiles of these selective pan-Trk kinase inhibitors.

Deaggregators inhibit TNF-α-induced leukocyte adhesion in vitro by breaking up hydrophobic lipophilic interactions.

Deaggregators (deAgrs) are nontoxic organic molecules that possess the ability to deaggregate simple aggregates formed by hydrophobic lipophilic interactions (HLI). Since HLI-driven organic molecule aggregates may induce leukocyte adhesion, we investigated the influence of deAgrs on TNF-α-mediated leukocyte adhesion in vitro. For adhesion studies, vascular endothelial cells or smooth muscle cells monolayers were treated with TNF-α (10 μg/L) and deAgrs for 24 h, followed by addition of monocytes or neutrophils suspension. The non-adherent leukocytes were rinsed, and the number of attached leukocytes was measured using an ELISA plate reader. Simultaneously, fluorescence probes Np-12 and Np-Ch were used to measure the deaggregating efficiencies of these deAgrs. Among the nine deAgrs tested,eight significantly reduced the cell adhesion rates with the order of efficiencies: 260 > 160 > 568 > ZPMOP > R68 > 640 > TB6PMOP > CNS, but TBHQ had no effect. The deAgrs for deaggregating an aggregated probe (Np-12 or Np-Ch) exhibited a similar order of efficiencies: 260 > 160 > 568 > ZPMOP > R68 > 640 > TB6PMOP > CNS > 12-AA > 11-AA > TBHQ. Spearman correlation coefficient analyses indicated that the adherent rates of leukocytes to endothelial cells or smooth muscle cells treated with deAgrs had significantly negative correlation to their deaggregating abilities. DeAgrs effectively inhibit TNF-α-mediated leukocyte adhesion in vitro by breaking up hydrophobic lipophilic interactions, thus may be further tested for blocking atherogenesis.

Investigation of the retention behavior of structurally diverse drugs on alpha1 acid glycoprotein column: Insight on the molecular factors involved and correlation with protein binding data

Retention of 49 structurally diverse drugs on alpha1 acid glycoprotein column was investigated under different chromatographic conditions. Acetonitrile and 2-propanol were used as organic modifiers at different percentages and the pH was adjusted at 7.0 using PBS. Analysis of extrapolated and isocratic retention in terms of lipophilicity and electrostatic interactions revealed significant effect of the nature and percentage of organic modifier, which was attributed to the different shielding degree of the charged sites on the stationary phase by the buffer constituents. AGP retention factors were compared to HSA retention factors analyzed previously. Application of LSER analysis, extended to incorporate fractions ionized, demonstrated hydrogen bond acidity, dipolarity/polarizability and excess molar refraction as the most significant parameters for all AGP chromatographic indices, elucidating the differentiation of AGP retention from octanol–water partitioning and HSA retention. An attempt to correlate AGP chromatographic indices to AGP association constants, available in literature, supported the importance of stationary shielding in retention mechanism. Thus, isocratic retention factors logk10(ACN)AGP show a moderate but still better performance than lipophilicity in the case of A variant and may be a useful tool for the estimation of relevant association constants. For F1/S binding simulation lower stationary phase shielding is needed to obtain a significant two term regression equation, where logk20(ACN)AGP exerts a secondary contribution next to the most important bulk effect expressed by molecular weight.

Self-assembly and secondary nucleation in ZnO nanostructures derived from a lipophilic precursor

Crystal growth and self-assembly in iono-covalent nanomaterials can be directed via lipophilic interactions between a variety of metal soaps and amphiphilic lipids.

Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents

The discovery and optimization of a new class of bacterial topoisomerase (DNA gyrase and topoisomerase IV) inhibitors binding in the ATP domain are described. A fragment molecule, 1-ethyl-3-(2-pyridyl)urea, provided sufficiently potent enzyme inhibition (32 μM) to prompt further analogue work. Acids and acid isosteres were incorporated at the 5-pyridyl position of this fragment, bridging to a key asparagine residue, improving enzyme inhibition, and leading to measurable antibacterial activity. A CF3-thiazole substituent at the 4-pyridyl position improved inhibitory potency due to a favorable lipophilic interaction. Promising antibacterial activity was seen versus the Gram-positive pathogens Staphylococcus aureus and Streptococcus pneumoniae and the Gram-negative pathogens Haemophilus influenzae and Moraxella catarrhalis . Precursor metabolite incorporation and mutant analysis studies support the mode-of-action, blockage of DNA synthesis by dual target topoisomerase inhibition. Compound 35 was efficacious in a mouse S. aureus disease model, where a 4.5-log reduction in colony forming units versus control was demonstrated.

Molecular docking and quantitative structure–activity relationship (QSAR) analyses of indolylarylsulfones as HIV-1 non-nucleoside reverse transcriptase inhibitors

Indolylarylsulfones (IASs) have received considerable interest during the last decades due to high potency against HIV-1 as non-nucleoside reverse transcriptase inhibitors. In present work, quantitative structure–activity relationship (QSAR) and molecular docking analyses were performed to model the anti-HIV-1 activity of 36 IASs. 2D and 3D-descriptors, genetic algorithm, internal and external validations were used to develop statistically robust four-parametric QSAR models. The best QSAR model is with R tr 2 = 0.8608. The QSAR analysis reveals that the activity of IASs depends on the presence of electronegative and heavy atoms at the internal atmosphere of the compounds. The docking analysis reveals that lipophilic and H-bonding interactions are the prominent interactions among IASs and the receptor. The QSAR analysis proved to be a useful tool in the prediction of anti-HIV-1 activity of congeneric compounds and some important insights were also found that will be useful to guide for the synthesis of new IASs with improved activity.

Characterization of human β,β-carotene-15,15′-monooxygenase (BCMO1) as a soluble monomeric enzyme

The formal first step in in vitamin A metabolism is the conversion of its natural precursor β,β-carotene (C40) to retinaldehyde (C20). This reaction is catalyzed by the enzyme β,β-carotene-15,15′-monooxygenase (BCMO1). BCMO1 has been cloned from several vertebrate species, including humans. However, knowledge about this protein’s enzymatic and structural properties is scant. Here we expressed human BCMO1 in Spodoptera frugiperda 9 insect cells. Recombinant BCMO1 is a soluble protein that displayed Michaelis–Menten kinetics with a KM of 14μM for β,β-carotene. Though addition of detergents failed to increase BCMO1 enzymatic activity, short chain aliphatic detergents such as C8E4 and C8E6 decreased enzymatic activity probably by interacting with the substrate binding site. Thus we purified BCMO1 in the absence of detergent. Purified BCMO1 was a monomeric enzymatically active soluble protein that did not require cofactors and displayed a turnover rate of about 8 molecules of β,β-carotene per second. The aqueous solubility of BCMO1 was confirmed in mouse liver and mammalian cells. Establishment of a protocol that yields highly active homogenous BCMO1 is an important step towards clarifying the lipophilic substrate interaction, reaction mechanism and structure of this vitamin A forming enzyme.

Efficient and specific cardiac IK1 inhibition by a new pentamidine analogue

In excitable cells, KIR2.x ion-channel-carried inward rectifier current (IK₁) is thought to set the negative and stable resting membrane potential, and contributes to action potential repolarization. Loss- or gain-of-function mutations correlate with cardiac arrhythmias and pathological remodelling affects normal KIR2.x protein levels. No specific IK1 inhibitor is currently available for in vivo use, which severely hampers studies on the precise role of IK1 in normal cardiac physiology and pathophysiology. The diamine antiprotozoal drug pentamidine (P) acutely inhibits IK₁ by plugging the cytoplasmic pore region of the channel. We aim to develop more efficient and specific IK₁ inhibitors based on the P structure. We analysed seven pentamidine analogues (PA-1 to PA-7) for IK₁ blocking potency at 200 nM using inside-out patches from KIR2.1 expressing HEK-293 cells. PA-6 showed the highest potency and was tested further. PA-6 blocked KIR2.x currents of human and mouse with low IC₅₀ values (12-15 nM). Modelling indicated that PA-6 had less electrostatic but more lipophilic interactions with the cytoplasmic channel pore than P, resulting in a higher channel affinity for PA-6 (ΔG -44.1 kJ/Mol) than for P (ΔG -31.7 kJ/Mol). The involvement of acidic amino acid residues E224 and E299 in drug-channel interaction was confirmed experimentally. PA-6 did not affect INav1.5, ICa-L, IKv4.3, IKv11.1, and IKv7.1/minK currents at 200 nM. PA-6 inhibited the inward (50 nM 40%; 100 nM 59%; 200 nM 77%) and outward (50 nM 40%; 100 nM 76%; 200 nM 100%) components of IK₁ in isolated canine adult-ventricular cardiomyocytes (CMs). PA-6 prolonged action potential duration of CMs by 8 (n = 9), 26 (n = 5), and 34% (n = 11) at 50, 100, and 200 nM, respectively. Unlike P, PA-6 had no effect on KIR2.1 channel expression at concentrations from 0.1 to 3 μM. However, PA-6 at 10 μM increased KIR2.1 expression levels. Also, PA-6 did not affect the maturation of hERG, except when applied at 10 μM. PA-6 has higher efficiency and specificity to KIR2.x-mediated current than P, lengthens action potential duration, and does not affect channel trafficking at concentrations relevant for complete IK₁ block.

On the Solubility and Lipophilicity of Metallacarborane Pharmacophores

Metallacarborane moieties have been identified as promising pharmacophores. The pharmaceutical use of such compounds is, however, complicated by their low solubility and tendency to self-assemble in aqueous solution. In this work, we estimated the solubilities of a vast series of metallacarboranes [cobalt bis(dicarbollide) derivatives] in pure water, saline, and saline with human serum albumin as a model of blood plasma. In addition, we determined the octanol-water partition coefficients (Pow) as a lipophilicity descriptor. Pow weakly correlates with the water solubility of metallacarboranes, whereas the ability of HSA to increase the solubility of metallacarboranes correlates well with their Pow values. Because metallacarboranes are known inhibitors of HIV protease, the possible correlation between Pow and the ability to inhibit HIV protease was investigated. Results from this study indicate that interaction of metallacarborane inhibitors with HIV protease is driven by specific binding rather than by promiscuous lipophilic interactions. The most promising candidates for further drug development were identified by ligand lipophilicity efficiency analysis.

Selective Targeting of Dendritic Cell‐Specific Intercellular Adhesion Molecule‐3‐Grabbing Nonintegrin (DC‐SIGN) with Mannose‐Based Glycomimetics: Synthesis and Interaction Studies of Bis(benzylamide) Derivatives of a Pseudomannobioside

Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) and Langerin are C-type lectins of dendritic cells (DCs) that share a specificity for mannose and are involved in pathogen recognition. HIV is known to use DC-SIGN on DCs to facilitate transinfection of T-cells. Langerin, on the contrary, contributes to virus elimination; therefore, the inhibition of this latter receptor is undesired. Glycomimetic molecules targeting DC-SIGN have been reported as promising agents for the inhibition of viral infections and for the modulation of immune responses mediated by DC-SIGN. We show here for the first time that glycomimetics based on a mannose anchor can be tuned to selectively inhibit DC-SIGN over Langerin. Based on structural and binding studies of a mannobioside mimic previously described by us (2), a focused library of derivatives was designed. The optimized synthesis gave fast and efficient access to a group of bis(amides), decorated with an azide-terminated tether allowing further conjugation. SPR inhibition tests showed improvements over the parent pseudomannobioside by a factor of 3-4. A dimeric, macrocyclic structure (11) was also serendipitously obtained, which afforded a 30-fold gain over the starting compound (2). The same ligands were tested against Langerin and found to exhibit high selectivity towards DC-SIGN. Structural studies using saturation transfer difference NMR spectroscopy (STD-NMR) were performed to analyze the binding mode of one representative library member with DC-SIGN. Despite the overlap of some signals, it was established that the new ligand interacts with the protein in the same fashion as the parent pseudodisaccharide. The two aromatic amide moieties showed relatively high saturation in the STD spectrum, which suggests that the improved potency of the bis(amides) over the parent dimethyl ester can be attributed to lipophilic interactions between the aromatic groups of the ligand and the binding site of DC-SIGN.

Hypotheses concerning how Otx2 makes its incredible journey: a hitchhiker on the road to Rome?

OPINION article Front. Mol. Neurosci., 30 December 2013Sec. Neuroplasticity and Development Volume 6 - 2013 | https://doi.org/10.3389/fnmol.2013.00055

Lipophilic and polar interaction forces between acidic drugs and membrane phospholipids encoded in IAM-HPLC indexes: Their role in membrane partition and relationships with BBB permeation data

The membrane phospholipid affinity data, log kwIAM, for 18 acidic and unionized drugs spanning a wide lipophilicity range were measured by HPLC on two different phospholipid stationary phases, i.e. IAM.PC.MG and IAM.PC.DD2. These data related weakly with both logPN values, the n-octanol/water partition coefficients of the neutral forms, and logD7.4 values, the n-octanol/water partition coefficients of the mixtures of neutral and ionized forms at pH 7.4. The lack of collinearity confirms that, differently from partition in n-octanol/water, partition in phospholipids encodes not only lipophilic/hydrophobic intermolecular recognition forces but also ionic bonds, due to electrostatic interactions between electrically charged species and phospholipids, according to the “pH piston hypothesis”. Since, differently from bases, electrostatic interactions between acids and phospholipids take place at the surface of phospholipid layers (choline moieties), and not near their lipophilic core (phosphate moieties), they were parameterized by a new procedure yielding “Δ′ log kwIAM” parameters, i.e. the difference between the IAM retention factors observed for the analytes and those of neutral compounds with the same n-octanol partition values displayed by the analytes at pH 7.4. All acidic analytes, but one, and all unionized analytes, but the unionizable ones, showed positive Δ′ log kwIAM values, indicating that they partition stronger in phospholipids than in n-octanol. LogBB values (capability to pass BBB) weakly related with both lipophilicity and phospholipid affinity values; in contrast they are inversely related with Δ′ log kwIAM values. The relationships between logBB and Δ′ log kwIAM practically overlapped the previously found log BB/Δ log kwIAM relationships for bases. The excess of polar interaction component between acidic drugs and phospholipids, mainly electrostatic forces, although enhancing partition in phospholipids, hinders membrane passage, analogously to the behavior previously reported for bases.The study suggests that IAM-HPLC is an effective technique to perform simple and fast measurements of the intermolecular recognition forces related to membrane partition and permeation. This can contribute to better understand the mechanisms governing both partition of charged species in cell membranes and passage through them, also allowing the possible optimization of the pharmacokinetic properties of the drugs at the early stages of their development.

In‐silico prediction of gas chromatographic retention indices of some terpenols

A quantitative structure-retention relationship study based on multiple linear regression technique was carried out to investigate the gas chromatographic retention indices (RIs) of some terpenols on the HP 5 ms fused silica column. A collection of 75 terpene alcohols was chosen as dataset. The data were divided into two groups; a training set and a prediction set consist of 60 and 15 molecules, respectively. The best-selected descriptors that appear in the models are; the Randic index order 1, Kier shape index order 2, total charge weighted partial negatively charged surface area, and fractional atomic charge weighted partial positive surface area. These descriptors can encode different features of molecules that are responsible for their steric, electronic, and lipophilicity interactions. The best-obtained model had statistics of R(2)(t) = 0.959 and R(2)(p) = 0.952. The reliability of the model was evaluated by using the leave-many-out cross-validation method (Q(2) = 0.957 and SPRESS = 46.427) as well as by y-scrambling and jackknife test. Furthermore, the chemical applicability domains of these models were determined via leverage approach. The simple developed four-parameter linear model can predict the gas chromatographic RIs of terpenols.