Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1.

Detection of cryptic pockets (hidden protein pockets) is a hot topic in structure-based drug discovery, especially for drugging the yet undruggable proteome. The experimental detection of cryptic pockets is still considered an expensive endeavor. Thus, computational methods, such as atomistic simulations, are used instead. These simulation methods can provide a perspective on protein dynamics that overpasses the experimental X-ray structures' static and average view. Nonetheless, unbiased molecular dynamics (MD) simulations fall short to detect transient and cryptic pockets requiring the crossing of high-energy barriers. Enhanced sampling methods, such as Metadynamics, provide a solution to overcome the time-scale problem faced by unbiased MD simulations. However, these methods are still limited by the availability of collective variable space to capture the intricate parameters, leading to the opening of cryptic pockets. Unfortunately, the design of such collective variables requires a priori knowledge of the binding site, information that is by definition lacking for cryptic pockets. In this work, we evaluated the use of the Metadynamics biasing scheme on essential coordinates space as a general method for cryptic pocket detection. This approach was applied to an antiapoptotic protein: Mcl-1 as a test model. In addition to providing a broader characterization of Mcl-1's conformational space, we show the effectiveness of this method in drawing the full repository of Mcl-1's known and novel cryptic pockets in an unsupervised manner.

Effect of oral exposure to the acaricide pirimicarb, a new varroacide candidate, on Apis mellifera feeding rate.

BACKGROUND: The ectoparasitic honey bee mite Varroa destructor is a main cause of the gradual decline in honey bees Apis mellifera. Beekeepers currently utilize a wide range of different synthetic acaricides, organic acids and essential oils to keep mite populations under control. Previous work has indicated that pirimicarb may be a new varroacide candidate. The aim of this study was to observe chronic effects on feeding activity in worker honey bees after oral exposure to 1.05 mm pirimicarb. The long-term effects of 24 h exposure to pirimicarb were also tested. RESULTS: After three successive trials, no mortality could be detected at the tested concentration, although oral exposure to pirimicarb had a significant effect on honey bees feeding behavior. Pirimicarb added to a sucrose solution led to a rapid decrease in food intake. These tendencies may be reversed when the pesticide is removed. However, recovery seemed to be trial dependent. CONCLUSION: This study highlights seasonal variation in honey bee susceptibility, which should be considered in toxicology studies. © 2018 Society of Chemical Industry.

Protective effects of caffeic acid against hypothalamic neuropeptides alterations induced by malathion in rat.

Exposure to pesticides is suspected to cause human health problems. Our study aimed to evaluate preventive effects of caffeic acid (3,4-dihydroxycinnamic acid) in the hypothalamus against malathion-induced neuropeptides gene expression alterations. Malathion at 100 mg/kg was administered intragastrically to rats alone or in combination with caffeic acid at 100 mg/kg during 4 weeks. A molecular expression of hypothalamic neuropeptides and plasmatic cholinesterase activity was investigated. Furthermore, we used in silico analysis, known as computational docking, to highlight the nature of acetylcholinesterase-malathion/caffeic acid interactions. Our findings showed differences in the responses and indicate that caffeic acid reversed malathion-induced decrease in corticotropin-releasing hormone mRNA but not brain-derived neurotrophic factor which presented an increased tendency. We suggest that caffeic acid can interact with acetylcholinesterase as the primary target of organophosphorus compounds. Results predict that caffeic acid can block partly the acetylcholinesterase gorge entrance via π-π stacking interaction with Tyr 124 and Trp 286 residues of the peripheral site leading to its stricture. Under this condition, we suggested that acetylcholine trafficking toward the catalytic site is ameliorated compared to malaoxon according to their sizes.

Synthesis of novel 7-oxo and 7-hydroxy trifluoroallocolchicinoids with cytotoxic effect.

The synthesis of 7-oxo and 7-hydroxy trifluoroallocolchicinoids was achieved through the intramolecular cyclization of o-phenyl-ß-phenylalanines. The resulting compounds were evaluated for their cytotoxic activity against KB cells and their inhibitory effect towards the polymerization of tubulin. The results yielded some potent cytotoxic compounds with correlated partial antitubulin effect.

Structural characterizations of oligopyridyl foldamers, α-helix mimetics.

Protein-protein interactions are central to many biological processes, from intracellular communication to cytoskeleton assembly, and therefore represent an important class of targets for new therapeutics. The most common secondary structure in natural proteins is an α-helix. Small molecules seem to be attractive candidates for stabilizing or disrupting protein-protein interactions based on α-helices. In our study, we assessed the ability of oligopyridyl scaffolds to mimic the α-helical twist. The theoretical as well as experimental studies (X-ray diffraction and NMR) on conformations of bipyridines in the function of substituent and pyridine nitrogen positions were carried out. Furthermore, the experimental techniques showed that the conformations observed in bipyridines are maintained within a longer oligopyridyl scaffold (quaterpyridines). The alignment of the synthesized quaterpyridine with two methyl substituents showed that it is an α-helix foldamer; their methyl groups overlap very well with side chain positions, i and i + 3, of an ideal α-helix.

Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study.

The remarkably safe anesthetics xenon (Xe) and, to lesser extent, nitrous oxide (N(2)O) possess neuroprotective properties in preclinical studies. To investigate the mechanisms of pharmacological action of these gases, which are still poorly known, we performed both crystallography under a large range of gas pressure and biochemical studies on urate oxidase, a prototype of globular gas-binding proteins whose activity is modulated by inert gases. We show that Xe and N(2)O bind to, compete for, and expand the volume of a hydrophobic cavity located just behind the active site of urate oxidase and further inhibit urate oxidase enzymatic activity. By demonstrating a significant relationship between the binding and biochemical effects of Xe and N(2)O, given alone or in combination, these data from structure to function highlight the mechanisms by which chemically and metabolically inert gases can alter protein function and produce their pharmacological effects. Interestingly, the effects of a Xe:N(2)O equimolar mixture were found to be equivalent to those of Xe alone, thereby suggesting that gas mixtures containing Xe and N(2)O could be an alternative and efficient neuroprotective strategy to Xe alone, whose widespread clinical use is limited due to the cost of production and availability of this gas.

Synthesis of 3-amino-thiochromanes from 4-benzyl 2-thiazolines, via an unprecedented intramolecular electrophilic aromatic substitution.

A one-pot synthesis of various N-substituted 3-amino-thiochromanes from 4-benzyl-2-methyl thiazoline via a thiazolinium salt is described. The obtained 3-amino-thiochromanes are enantiopure, as their precursors derive from chiral 2-aminoalcohols. The reaction involves the formation of a disulfide, which subsequently takes part in an unprecedented intramolecular electrophilic aromatic substitution.

Fluoride ion and phosphines as nucleophilic catalysts: synthesis of 1,4-benzothiazepines from cyclic sulfenamides.

A new methodology, using fluoride ion as a nucleophilic catalyst, was applied for the synthesis of enantiopure 1,4-benzothiazepine from cyclic sulfenamide and electron-deficient acetylene, with high efficiency and atom economy.

Toward safer thrombolytic agents in stroke: molecular requirements for NMDA receptor-mediated neurotoxicity.

Current thrombolytic therapy for acute ischemic stroke with tissue-type plasminogen activator (tPA) has clear global benefits. Nevertheless, evidences argue that in addition to its prohemorrhagic effect, tPA might enhance excitotoxic necrosis. In the brain parenchyma, tPA, by binding to and then cleaving the amino-terminal domain (ATD) of the NR1 subunit of N-methyl-D-aspartate (NMDA) glutamate receptors, increases calcium influx to toxic levels. We show here that tPA binds the ATD of the NR1 subunit by a two-sites system (K(D)=24 nmol/L). Although tenecteplase (TNK) and reteplase also display two-sites binding profiles, the catalytically inactive mutant TNKS478A displays a one-site binding profile and desmoteplase (DSPA), a kringle 2 (K2) domain-free plasminogen activator derived from vampire bat, does not interact with NR1. Moreover, we show that in contrast to tPA, DSPA does not promote excitotoxicity. These findings, together with three-dimensional (3D) modeling, show that a critical step for interaction of tPA with NR1 is the binding of its K2 domain, followed by the binding of its catalytic domain, which in turn cleaves the NR1 subunit at its ATD, leading to a subsequent potentiation of NMDA-induced calcium influx and neurotoxicity. This could help design safer new generation thrombolytic agents for stroke treatment.

Straightforward stereoselective synthesis of spiro-epoxyoxindoles.

[reaction: see text] The in situ preparation of a sulfonium ylide reagent achieved the highly diastereoselective epoxidation of isatins, so that a new and straightforward access to biologically significant spiro-epoxyoxindoles is provided. The first investigations of an asymmetric version are reported with enantiopure sulfides.

A straightforward asymmetric synthesis of 1,2-disubstituted ferrocenylalkyl amines with the unusual (S(Fc),S) configuration.

A useful synthesis of rare 1,2-disubstituted ferrocenylalkyl amines with (S(Fc),S) configuration has been achieved in a sequential one-pot methodology from (S)-p-tolylsulfinylferrocene.

Diastereoselective addition of enantiopure lithium tert-butylsulfinylferrocene to imines.

(S)-tert-Butylsulfinylferrocene was submitted to ortho-metalation, and the corresponding lithium derivative was trapped by alkyl or aryl imines bearing various electron-withdrawing groups on the nitrogen atom (Ts, Dpp, Boc). New aminosulfoxides were obtained with complete diastereocontrol when Dpp or Boc groups were used. The absolute configuration (SS,SFc,S) has been determined by single-crystal X-ray analysis and chemical correlation. An unusual pseudocyclic boatlike transition state has been proposed to explain the stereochemical course of this reaction.

Synthesis and biological evaluation as AChE inhibitors of new indanones and thiaindanones related to donepezil.

Sixty-four new indanones and thiaindanones related to donepezil were synthesized and evaluated in vitro as potential AChE inhibitors. Among them, 11 derivatives were found to inhibit the enzyme in the submicromolar range; the best compound revealed its inhibitory activity with an IC50 in the same range (0.06 microM) than the reference compound, donepezil (IC50=0.02 microM).

Synthesis and biological evaluation of thienopyrrolizines, a new family of CDK/GSK-3 inhibitors.

Fifteen new thieno[2,3-b ]- and thieno[3,4-b]pyrrolizines were synthesized and tested against two protein kinases, CDK1/cyclin B and GSK-3. Among these compounds, 3-(3-hydroxy-4-methoxyphenyl)-8H-thieno[2,3-b]pyrrolizin-8-one 4g was identified as a moderate inhibitor of these kinases. Its molecular modeling study brought to the fore the pivotal role of the 2-methoxyphenol grouping and the interest in replacing it by bioisosteric moieties in future pharmacomodulations.