Range Of Ki Research Articles

Selective probes and antagonists for G protein-coupled receptor LPAR1.

The G protein-coupled receptors (GPCRs) constitute the largest class of signaling molecules in the human genome with diverse disease pathogenesis, yet many of receptors with unknown antagonists continue to remain. The complex biology and potential for drug discovery within this class provides strong incentives for chemical biology approaches that seek to develop small molecule probes. In addition to this, it will also help to facilitate the elucidation of mechanistic pathways and enable the specific manipulation of the individual receptors’ activity. We have initiated a small molecule antagonist that actively targets lysophosphatidic acid receptor (LPAR1), a clinically important target that is linked to several metabolic and inflammatory diseases including cancer, fibrosis, and rheumatoid arthritis. While numerous selective LPAR1 antagonists have been developed their clinical efficacy has only been evaluated in idiopathic pulmonary fibrosis. As a useful aid in the various efforts of identifying novel effective LPAR1 antagonists, diverse computational methods can serve as an important and valuable tool. In particular, the sequent in-silico approaches such as virtual screening, molecular docking, molecular dynamics simulation, and protein-ligand binding free energy are able to refine the accuracy of in-silico approaches of GPCR-antagonist complexes. In our study, we focused on trying to identify novel LPAR1 antagonists using the in-silico virtual screening of commercial databases on the human LPAR1 model. Various molecular modeling methodologies such as molecular docking and dynamics simulation, along with different drug likeness filtering criteria, were applied to select anti-LPAR1 antagonists as promising candidate molecules based on different known lead compounds. In-vitro binding assays of the selected molecules are expected to demonstrate activity within the nanomolar range of Ki or IC50. The current integrated computational and experimental methods used in this work can provide new insights for systematic hit identification for novel anti-LPAR1 agents.

Synthesis characterization and evaluation of novel triazole based analogs as a acetylcholinesterase and α-glucosidase inhibitors

A series of novel triazole analogs (10a-k) bearing piperidine were synthesized in an aprotic solvent on the most effective pharmacophore with acetylcholinesterase (AChE) and α-glucosidase inhibitory activity. Triazole analogs (10a-k) were obtained in excellent yields (75–90 %) and characterized by EI-MS, IR, 13C NMR and 1H NMR. The newly synthesized triazole analogs (10a-k) showed potent AChE inhibitory activity in the range of Ki = 0.0155 ± 1.25 µM to 0.557 ± 0.50 µM, IC50 = 0.031 ± 0.85 to 0.537 ± 0.76 µM than Eserine (0.04 ± 0.001 µM) having strong electron-withdrawing fluorine group on the pyridine ring was recorded as a most potent inhibitor of AChE while (%) inhibition against α-glucosidase was ranging between 52.36 ± 1.67 to 85.35 ± 1.39. The kinetic study predicted that triazole analogs (10a-k) followed the un-competitive and mixed type of inhibition against AChE. In silico molecular docking was performed at the active site of the AChE co-crystal structure (PDB ID:1NEN). The results of molecular docking corelate will with the experimental findings.

Synthesis, characterization, evaluation of metabolic enzyme inhibitors and in silico studies of thymol based 2-amino thiol and sulfonic acid compounds

Eight new aminothiols (4a-g and 5) and three new sulfonic acid derivatives (6a-c) were synthesized, and their structures were characterized. Inhibitory effects of the obtained compounds on carbonic anhydrase I and II isoforms (hCA I and hCA II), butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), enzymes were investigated. The newly synthesized compounds have inhibited hCA I with Kis ranging from 7.11 ± 1.46 nM (6a) to 670.52 ± 300.41 nM (4b) and, hCA II with Kis ranging from 16.83 ± 5.72 nM (6a) to 453.34 ± 208.56 nM (4c). Acetazolamide was employed as the positive control for both hCA isoforms (Ki for hCA I 198.81 ± 14.13 nM and Ki for hCA II 211.42 ± 13.10 nM), and among the new compounds obtained, it was observed that there were compounds that were active at much lower nM levels. All compounds were also evaluated for inhibition of AChE and BChE. They inhibited AChE and BChE enzymes in the range of Ki 5.24 ± 2.27 (6c) - 48.44 ± 21.82 (4g) for AChE and 4.86 ± 0.64 (6c) - 51.75 ± 12.56 (4a) for BChE, and the results were compared with the standard inhibitor Tacrine (Ki: 14.20 ± 8.83 nM toward AChE and Ki: 3.39 ± 1.91 nM for BChE). Cholinesterase (BChE and AChE) inhibitory abilities of all synthesized molecules were also performed in situ and molecular docking and molecular dynamics (MD) simulation studies. The molecular coupling scores of the compounds and the free binding energies calculated by MM/GBSA were found to be compatible. Examining the results obtained from this study shows that it may have the potential to develop new drugs to treat some global patients such as glaucoma and Alzheimer's disease (AD).

Physiologically-based pharmacokinetic model-based translation of OATP1B-mediated drug-drug interactions from coproporphyrin I to probe drugs.

The accurate prediction of OATP1B‐mediated drug–drug interactions (DDIs) is challenging for drug development. Here, we report a physiologically‐based pharmacokinetic (PBPK) model analysis for clinical DDI data generated in heathy subjects who received oral doses of cyclosporin A (CysA; 20 and 75 mg) as an OATP1B inhibitor, and the probe drugs (pitavastatin, rosuvastatin, and valsartan). PBPK models of CysA and probe compounds were combined assuming inhibition of hepatic uptake of endogenous coproporphyrin I (CP‐I) by CysA. In vivo Ki of unbound CysA for OATP1B (Ki,OATP1B), and the overall intrinsic hepatic clearance per body weight of CP‐I (CLint,all,unit) were optimized to account for the CP‐I data (Ki,OATP1B, 0.536 ± 0.041 nM; CLint,all,unit, 41.9 ± 4.3 L/h/kg). DDI simulation using Ki,OATP1B reproduced the dose‐dependent effect of CysA (20 and 75 mg) and the dosing interval (1 and 3 h) on the time profiles of blood concentrations of pitavastatin and rosuvastatin, but DDI simulation using in vitro Ki,OATP1B failed. The Cluster Gauss–Newton method was used to conduct parameter optimization using 1000 initial parameter sets for the seven pharmacokinetic parameters of CP‐I (β, CLint, all, FaFg, Rdif, fbile, fsyn, and v syn), and Ki,OATP1B and Ki,MRP2 of CysA. Based on the accepted 546 parameter sets, the range of CLint, all and Ki,OATP1B was narrowed, with coefficients of variation of 12.4% and 11.5%, respectively, indicating that these parameters were practically identifiable. These results suggest that PBPK model analysis of CP‐I is a promising translational approach to predict OATP1B‐mediated DDIs in drug development.

Inhibitory Potential of New Phenolic Hydrazide-Hydrazones with a Decoy Substrate Fragment towards Laccase from a Phytopathogenic Fungus: SAR and Molecular Docking Studies

Laccase from pathogenic fungi participates in both the delignification and neutralization of phytoantibiotics. Furthermore, it interferes with the hormone signaling in plants and catalyzes melanization. Infections of these pathogens contribute to loss in forestry, agriculture, and horticulture. As there is still a need to expand knowledge on efficient defense strategies against phytopathogenic fungi, the present study aimed to reveal more information on the molecular mechanisms of laccase inhibition with natural and natural-like carboxylic acid semi-synthetic derivatives. A set of hydrazide-hydrazones derived from carboxylic acids, generally including electron-rich arene units that serve as a decoy substrate, was synthesized and tested with laccase from Trametes versicolor. The classic synthesis of the title inhibitors proceeded with good to almost quantitative yield. Ninety percent of the tested molecules were active in the range of KI = 8–233 µM and showed different types of action. Such magnitude of inhibition constants qualified the hydrazide-hydrazones as strong laccase inhibitors. Molecular docking studies supporting the experimental data explained the selected derivatives’ interactions with the enzyme. The results are promising in developing new potential antifungal agents mitigating the damage scale in the plant cultivation, gardening, and horticulture sectors.

Synthesis and exploration of 2-morpholino-4-phenylthiazol-5-yl acrylamide derivatives for their effects against carbonic anhydrase I, II, IX and XII isoforms as a non-sulfonamide class of inhibitors

Novel series of 2-morpholino-4-phenylthiazol-5-yl acrylamide derivatives (8a–s) have been synthesized and explored as a non-sulfonamide class of carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. The newly synthesized molecules were evaluated for their CA inhibitory potency against four isoforms: the cytosolic isozyme hCA I, II as well as trans-membrane tumor associated isoform hCA IX and hCA XII taking acetazolamide (AAZ) as standard drug. The results revealed that most of the compounds showed good activity against hCA II, IX, and XII whereas none of them were active against hCA I (Ki >100 μM). It is observed that the physiologically most important cytosolic isoform hCA II was inhibited by these molecules in the range of Ki 9.3–77.7 μM. It is also found the both the transmembrane isoforms hCA IX and XII were also inhibited with Kis ranging between 54.7–96.7 μM and 4.6–8.8 μM, respectively. The binding modes of the active compounds within the catalytic pockets of hCA II, IX and XII were evaluated by docking studies. This new non-sulfonamide class of selective inhibitors of hCA II, IX and XII over the hCA I isoform may be used for further understanding the physiological roles of some of these isoforms in various pathologies.

An Application of Fit Quality to Screen MDM2/p53 Protein-Protein Interaction Inhibitors.

The judicious application of ligand or binding efficiency (LE) metrics, which quantify the molecular properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Here we report for the first time the use of LE based metric, fit quality (FQ), in virtual screening (VS) of MDM2/p53 protein-protein interaction inhibitors (PPIIs). Firstly, a Receptor-Ligand pharmacophore model was constructed on multiple MDM2/ligand complex structures to screen the library. The enrichment factor (EF) for screening was calculated based on a decoy set to define the screening threshold. Finally, 1% of the library, 335 compounds, were screened and re-filtered with the FQ metric. According to the statistical results of FQ vs. activity of 156 MDM2/p53 PPIIs extracted from literatures, the cut-off was defined as FQ = 0.8. After the second round of VS, six compounds with the FQ > 0.8 were picked out for assessing their antitumor activity. At the cellular level, the six hits exhibited a good selectivity (larger than 3) against HepG2 (wt-p53) vs. Hep3B (p53 null) cell lines. On the further study, the six hits exhibited an acceptable affinity (range of Ki from 102 to 103 nM) to MDM2 when comparing to Nutlin-3a. Based on our work, FQ based VS strategy could be applied to discover other PPIIs.

Electrical Conductivity in Dimethyl Sulfoxide + Potassium Iodide Solutions at Different Concentrations and Temperatures

The direct current conductivity of DMSO + KI solutions was determined with the use of the impedance spectroscopy. The measurements were performed in the whole solubility range of KI and in the temperature range from (293.15 to 323.15) K. The limiting molar conductivities Λo(T) and λI–o(T), as well as the constant KA of ionic association, K+ + I–, were determined at different temperatures with the use of the Fuoss-Onsager method. The obtained data on KA, together with the literature data referred to the K+ + I– association in different solvents, allowed us to formulate an empirical dependence of KA on the molecular dipolar polarizability of the solvent used, KA ∝ exp(−μi2), where μi is the dipole moment of the molecules of ith solvent.

Identification of a Novel Phosphatidic Acid Binding Domain in Protein Phosphatase-1

Phosphatidic acid (PA) has been recognized as a lipid second messenger, yet few cellular targets for PA have been identified. Previous work demonstrated PA as a potent and noncompetitive tight-binding inhibitor of the catalytic subunit (gamma isoform) of protein phosphatase-1 (PP1c gamma) in vitro. The high potency of inhibition, coupled with high specificity for PA over other phospholipids, suggested the presence of a high-affinity PA binding domain on PP1c gamma. In the current study, quantification of the binding interaction and identification of the binding domain were pursued. Surface plasmon resonance was employed to quantitate the interaction between PP1c gamma and immobilized mixed lipid vesicles of PA/phosphatidylcholine (PC) or PC alone. The data disclosed a high-affinity interaction with a KD measured in the low (1-40) nanomolar range, consistent with the range of Ki previously obtained from in vitro enzymatic assays. Next, identification of the segment of PP1 necessary for PA binding was determined using a deletion mutagenesis strategy. Binding assays revealed that PP1c gamma residues between 274 and 299 were required for the interaction with the lipid. When fusions of PP1c gamma fragments with green fluorescent protein (GFP) were generated, it was then determined that PP1c gamma residues 286-296 were sufficient to confer PA binding to GFP, a protein that does not interact with PA. The minimal PA binding domain of PP1c gamma lacked similarity to the previously described PA binding segments of Raf-1 kinase and cyclic-AMP phosphodiesterase 4A1. When these results were taken together with the known crystallographic structure of PP1, they identified a novel PA binding region on PP1c gamma that contains a unique loop-strand structural fold responsible for the interaction with PA.

Screening of Protein Kinases by ATP-STD NMR Spectroscopy

ATP-STD NMR takes advantage of Mg2+ binding to ATP to adjust the ATP affinity for protein kinases permitting a wide range of Ki's to be determined for ATP competitive ligands. Substituting Mn2+ for Mg2+ creates a paramagnetic probe (MnATP) from which the proximity of non-ATP competitive ligands can be inferred. Internal standards and references are used to reduce false positives due to protein or compound degradation. Use of the natural ATP ligand confers active site-specificity that is not available a priori from other ligand binding experiments.

Aminocyclopentitol Inhibitors ofα-L-Fucosidases

Aminocyclopentitol analogs of α-L-fucose were synthesized stereoselectively from D-ribose. Alkyl substituents were attached at the NH2 group to mimic the glycosidic leaving group. The resulting (alkylamino)cyclopentitols inhibited α-L-fucosidases selectively with inhibition constants in the range of Ki=10−7 M. Comparisons with stereoisomers and acyclic analogs showed that this inhibition only occurs with N-alkyl substitution and proper configuration at the cyclopentane, as expected for transition-state-analog-type inhibition. These observations were supported by molecular-modeling comparisons between inhibitor and transition state.

大型試験片を用いた柱状結晶氷の破壊じん性の検討 ＩＩ 氷の破壊じん性に及ぼす負荷速度の影響

The effects of loading rate and specimen size on the fracture toughness KIc of columnar grained ice have been investigated at -10°C. Notched bend specimens with the section size of 50×50mm (medium size specimen) and 200×50mm (large size specimen) were used. The notch of specimen was made using a thin razor blade embedded in the mold. Several tests were carried out at each test condition, and probabilistic nature of fracture toghness was also investigated.The results obtained are as follows.(1) The value of KIc decreased as KI increased, and there was a transition in the range of KI≈10-100kPam1/2/s. The value of KIc was not substantially affected by KI in the high KI region beyond the transition.(2) Scatter of KIc for the large size specimens was considerably small compared with that for the medium size specimens.(3) The minimum value of KIc was not affected by the specimen size in the low KI range. However, in the high KI range, the minimum value of KIc of a large specimen showed a little higher value than that of a medium specimen.(4) The size effect was analyzed from the view point of the “weakest link theory”. It was observed that the experimental data did not agree with the theoretical prediction in the range of low values of KIc.(5) The relation between KI and KIc was compared with other experimental data on a similar kind of ice. Considerable difference in KIc, especially in the low loading rate range, was observed. The reason is not yet clear, and more studies are needed.

粗大結晶氷の破壊じん性および試験片寸法の影響

The effect of loading rate on fracture toughness of ice has been investigated using sharply edge-notched specimens by bending at -10°C. The loading rate KI ranged from 1 to about 103kPam1/2/s. The notch was made by molding a razor blade in the specimen in the ice growing process and removing it before the bending test. Two sizes of specimens, section sized 25×25mm (small size specimen) and 50×50mm (medium size specimen) respectively, were used. About thirty small size specimens or about ten medium size specimens were tested at each loading rate. The experimental results were as follows.(1) The values of KIc were lower in the higher KI range, and there was a transition in the range of KI=10-100kPam1/2/s.(2) The effect of KI was found to be very small in the range of KI larger than 100kPam1/2/s.(3) The effect of loading rate on the minimum value of fracture toughness KIc was small in the whole range of KI tested for both small and medium size specimens.(4) The minimum KIc values of small and medium size specimens seem to coinside each other approximately. The maximum and the median KIc values of medium size specimens were smaller than those of small size specimens.(5) It was found that a vinyl silicone impression material being used for dentistry was suitable to make replica of the fracture surface for macrofractography.