The objective of the studies was to synthesize and characterize new mono- and diesters with an imidazoquinolin-2-one ring with the use of 2,3-dihydro-2-thioxo-1H-imidazo[4 ,5-c]-quinolin-4(5H)-ones and ethyl bromoacetate. The products were isolated at high yield and characterized by instrumental methods (IR, 1H-, 13C-, and 15N- NMR, MS-ESI, HR-MS, EA). In order to clarify the places of substitution and the structure of the derivatives obtained, molecular modeling of substrates and products was performed. Consideration of the possible tautomeric structures of the substrates confirmed the existence only the most stable keto form. Based on the free energy of monosubstituted ester derivatives, the most stable form were derivatives substituted at sulfur atom of enolic form the used imidazoquinolones. Enolic form referred only to nitrogen atom no 1. The modeling results were consistent with the experimental data. The HOMO electron densities at selected atoms of each substrate has shown that the most reactive atom is sulfur atom. It explained the formation of monoderivatives substituted at sulfur atom. The diester derivatives of the used imidazoquinolones had second substituent at nitrogen atom no. 3. The new diesters can be used as raw material for synthesis of thermally stable polymers, and they can also have biological activity.

• Klíčová slova
• 3-hydroxyquinolinediones, ammonium thiocyanate, debenzylation, molecular modeling, thioxoimidazoquinolinone ring,
• MeSH
• chinolony chemická syntéza   chemie   MeSH
• estery chemie   MeSH
• imidazoly chemie   MeSH
• kvantová teorie MeSH
• molekulární konformace MeSH
• molekulární modely * MeSH
• thiokyanatany chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chinolony MeSH
• estery MeSH
• imidazole MeSH Prohlížeč
• imidazoly MeSH
• thiocyanic acid MeSH Prohlížeč
• thiokyanatany MeSH

The structure of Zn4Al2 Layered Double Hydroxide intercalated with benzencarboxylate (C6H5COO-) was solved using molecular modeling combined with experiment (X-ray powder diffraction, IR spectroscopy, TG measurements). Molecular modeling revealed the arrangement of guest molecules, layer stacking, water content and water location in the interlayer space of the host structure. Molecular modeling using empirical force field was carried out in Cerius(2) modeling environment. Results of modeling were confronted with experiment that means comparing the calculated and measured diffraction pattern and comparing the calculated water content with the thermogravimetric value. Good agreement has been achieved between calculated and measured basal spacing: d(calc) = 15.3 A and d(exp) = 15.5 A. The number of water molecules per formula unit (6H2O per Zn4Al2(OH)12) obtained by modeling (i.e., corresponding to the energy minimum) agrees with the water content estimated by thermogravimetry. The long axis of guest molecules are almost perpendicular to the LDH layers, anchored to the host layers via COO- groups. Mutual orientation of benzoate ring planes in the interlayer space keeps the parquet arrangement. Water molecules are roughly arranged in planes adjacent to host layers together with COO- groups.

• MeSH
• anionty chemie   MeSH
• benzen MeSH
• difrakce rentgenového záření MeSH
• hliník MeSH
• hydroxid hlinitý chemie   MeSH
• hydroxid hořečnatý chemie   MeSH
• hydroxidy chemie   MeSH
• krystalizace MeSH
• kyselina benzoová chemie   MeSH
• kyseliny karboxylové chemie   MeSH
• molekulární modely MeSH
• spektrofotometrie infračervená MeSH
• vazebná místa MeSH
• zinek MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• anionty MeSH
• benzen MeSH
• hliník MeSH
• hydrotalcite MeSH Prohlížeč
• hydroxid hlinitý MeSH
• hydroxid hořečnatý MeSH
• hydroxidy MeSH
• kyselina benzoová MeSH
• kyseliny karboxylové MeSH
• zinek MeSH

In silico methods like molecular docking and pharmacophore modeling are established strategies in lead identification. Their successful application for finding new active molecules for a target is reported by a plethora of studies. However, once a potential lead is identified, lead optimization, with the focus on improving potency, selectivity, or pharmacokinetic parameters of a parent compound, is a much more complex task. Even though in silico molecular modeling methods could contribute a lot of time and cost-saving by rationally filtering synthetic optimization options, they are employed less widely in this stage of research. In this review, we highlight studies that have successfully used computer-aided SAR analysis in lead optimization and want to showcase sound methodology and easily accessible in silico tools for this purpose.

• Klíčová slova
• Docking, Lead optimization, Molecular modeling, Pharmacophore modeling, Structure-activity relationship,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

The surface area of various types of montmorillonites (MMT) with different values of layer charge plays a very important role in surface arrangement of methylene blue cations (MB). Photoluminescence measurements can be strongly or partially influenced by this surface arrangement of cations. For these reasons and on the basis of our previous results, molecular simulations were performed for various types of montmorillonites covered with methylene blue cations. Adsorption of methylene blue cations on Na-Wyoming MMT surface is different from Ca-Cheto MMT. In the case of Wyoming with a lower layer charge, MB cations lie parallel to the silicate layer for all investigated samples. On the other hand, Cheto surface is covered with a higher amount of MB cations. The results obtained from molecular modeling indicate that MB lies parallel to low loading case and become tilted with respect to layer for a higher loading. Moreover, a higher amount of MB cations covering the silicate layer are much less energy-stable. A higher loading of MB cations leads to aggregates but at low loading MB cations degrade to monomers.

• MeSH
• bentonit chemie   MeSH
• kationty chemie   MeSH
• methylenová modř chemie   MeSH
• molekulární modely * MeSH
• povrchové vlastnosti MeSH
• termodynamika MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bentonit MeSH
• kationty MeSH
• methylenová modř MeSH
• voda MeSH

Human DHRS7 (SDR34C1) is one of insufficiently described enzymes of the short-chain dehydrogenase/reductase superfamily. The members of this superfamily often play an important pato/physiological role in the human body, participating in the metabolism of diverse substrates (e.g. retinoids, steroids, xenobiotics). A systematic approach to the identification of novel, physiological substrates of DHRS7 based on a combination of homology modeling, structure-based virtual screening and experimental evaluation has been used. Three novel substrates of DHRS7 (dihydrotestosterone, benzil and 4,4'-dimetylbenzil) have been described.

• Klíčová slova
• DHRS7, Homology modeling, Molecular modeling, SDR superfamily, SDR34C1,
• MeSH
• dihydrotestosteron metabolismus   MeSH
• fenylglyoxal analogy a deriváty   metabolismus   MeSH
• konformace proteinů MeSH
• lidé MeSH
• oxidoreduktasy chemie   metabolismus   MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 4,4'-dimethylbenzil MeSH Prohlížeč
• benzil MeSH Prohlížeč
• DHRS7 protein, human MeSH Prohlížeč
• dihydrotestosteron MeSH
• fenylglyoxal MeSH
• oxidoreduktasy MeSH

A simple molecular modeling method for the characterization of polymeric drug carriers is presented. Six biodegradable polymers have been investigated as drug carriers using molecular simulations: l-polylactide, d-polylactide, chitosan, polyglycolic acid, polyethylene glycol and cellulose. Cyclosporine A has been chosen as a model drug substance. Classical molecular dynamics and docking calculations were employed to model and predict polymer-drug interactions. These interactions have been analyzed by non-bond interaction energy and interaction parameter calculated using Flory-Huggins theory. Flexibility of polymer chains has been characterized by the change of gyration radius along the molecular dynamics trajectory. The relationship between mixing energy, chain length and chain flexibility has been revealed for each polymer/drug system.

• MeSH
• cyklosporin chemie   MeSH
• molekulární modely * MeSH
• nosiče léků chemie   MeSH
• polymery chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cyklosporin MeSH
• nosiče léků MeSH
• polymery MeSH

A novel series of 7-methoxytacrine (7-MEOTA)-donepezil like compounds was synthesized and tested for their ability to inhibit electric eel acetylcholinesterase (EeAChE), human recombinant AChE (hAChE), equine serum butyrylcholinesterase (eqBChE) and human plasmatic BChE (hBChE). New hybrids consist of a 7-MEOTA unit, representing less toxic tacrine (THA) derivative, connected with analogues of N-benzylpiperazine moieties mimicking N-benzylpiperidine fragment from donepezil. 7-MEOTA-donepezil like compounds exerted mostly non-selective profile in inhibiting cholinesterases of different origin with IC50 ranging from micromolar to sub-micromolar concentration scale. Kinetic analysis confirmed mixed-type inhibition presuming that these inhibitors are capable to simultaneously bind peripheral anionic site (PAS) as well as catalytic anionic site (CAS) of AChE. Molecular modeling studies and QSAR studies were performed to rationalize studies from in vitro. Overall, 7-MEOTA-donepezil like derivatives can be considered as interesting candidates for Alzheimer's disease treatment.

• Klíčová slova
• 7-MEOTA, AChE/BChE inhibitors, Alzheimer's disease, Molecular modeling, QSAR, Tacrine,
• MeSH
• acetylcholinesterasa metabolismus   MeSH
• butyrylcholinesterasa krev   metabolismus   MeSH
• cholinesterasové inhibitory chemická syntéza   chemie   farmakologie   MeSH
• donepezil MeSH
• Electrophorus MeSH
• indany chemie   farmakologie   MeSH
• koně MeSH
• kvantitativní vztahy mezi strukturou a aktivitou * MeSH
• lidé MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• piperidiny chemie   farmakologie   MeSH
• rekombinantní proteiny metabolismus   MeSH
• takrin analogy a deriváty   chemie   farmakologie   MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 7-methoxytacrine MeSH Prohlížeč
• acetylcholinesterasa MeSH
• butyrylcholinesterasa MeSH
• cholinesterasové inhibitory MeSH
• donepezil MeSH
• indany MeSH
• piperidiny MeSH
• rekombinantní proteiny MeSH
• takrin MeSH

The present work aimed to compare the small, neutral and monoaromatic oxime, isatin-3-oxime (isatin-O), to the commercial ones, pralidoxime (2-PAM) and obidoxime, in a search for a new potential reactivator for acetylcholinesterase (AChE) inhibited by the pesticide paraoxon (AChE/POX) as well as a novel potential scaffold for further synthetic modifications. The multicriteria decision methods (MCDM) allowed the identification of the best docking poses of those molecules inside AChE/POX for further molecular dynamic (MD) studies, while Ellman's modified method enabled in vitro inhibition and reactivation assays. In corroboration with the theoretical studies, our experimental results showed that isatin-O have a reactivation potential capable of overcoming 2-PAM at the initial moments of the assay. Despite not achieving better results than obidoxime, this molecule is promising for being an active neutral oxime with capacity of crossing the blood⁻brain barrier (BBB), to reactivate AChE/POX inside the central and peripheral nervous systems. Moreover, the fact that isatin-O can also act as anticonvulsant makes this molecule a possible multipotent reactivator. Besides, the MCDM method showed to be an accurate method for the selection of the best docking poses generated in the docking studies.

• Klíčová slova
• Ellman’s method, TOPSIS-AHP, acetylcholinesterase, molecular modeling, multicriteria decision making, neutral oxime,
• MeSH
• cholinesterasové inhibitory farmakologie   MeSH
• erytrocyty účinky léků   enzymologie   MeSH
• molekulární modely * MeSH
• molekulární struktura MeSH
• oximy chemie   farmakologie   MeSH
• paraoxon chemie   farmakologie   MeSH
• reaktivátory cholinesterasy chemie   farmakologie   MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cholinesterasové inhibitory MeSH
• oximy MeSH
• paraoxon MeSH
• reaktivátory cholinesterasy MeSH

Poisoning with organophosphorus compounds used as pesticides or misused as chemical weapons remains a serious threat to human health and life. Their toxic effects result from irreversible blockade of the enzymes acetylcholinesterase and butyrylcholinesterase, which causes overstimulation of the cholinergic system and often leads to serious injury or death. Treatment of organophosphorus poisoning involves, among other strategies, the administration of oxime compounds. Oximes reactivate cholinesterases by breaking the covalent bond between the serine residue from the enzyme active site and the phosphorus atom of the organophosphorus compound. Although the general mechanism of reactivation has been known for years, the exact molecular aspects determining the efficiency and selectivity of individual oximes are still not clear. This hinders the development of new active compounds. In our research, using relatively simple and widely available molecular docking methods, we investigated the reactivation of acetyl- and butyrylcholinesterase blocked by sarin and tabun. For the selected oximes, their binding modes at each step of the reactivation process were identified. Amino acids essential for effective reactivation and those responsible for the selectivity of individual oximes against inhibited acetyl- and butyrylcholinesterase were identified. This research broadens the knowledge about cholinesterase reactivation and demonstrates the usefulness of molecular docking in the study of this process. The presented observations and methods can be used in the future to support the search for new effective reactivators.

• Klíčová slova
• acetylcholinesterase, butyrylcholinesterase, docking studies, molecular modeling, organophosphates, reactivation process, reactivators,
• MeSH
• acetylcholinesterasa metabolismus   MeSH
• aktivace enzymů MeSH
• butyrylcholinesterasa metabolismus   MeSH
• cholinesterasové inhibitory farmakologie   MeSH
• fosfor chemie   MeSH
• katalytická doména MeSH
• konformace proteinů MeSH
• kvantová teorie MeSH
• lidé MeSH
• ligandy MeSH
• molekulární modely MeSH
• myši MeSH
• organofosfáty chemie   MeSH
• oximy chemie   MeSH
• proteosyntéza MeSH
• reaktivátory cholinesterasy farmakologie   MeSH
• sarin chemie   MeSH
• shluková analýza MeSH
• simulace molekulového dockingu * MeSH
• vazba proteinů MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• acetylcholinesterasa MeSH
• butyrylcholinesterasa MeSH
• cholinesterasové inhibitory MeSH
• fosfor MeSH
• ligandy MeSH
• organofosfáty MeSH
• oximy MeSH
• reaktivátory cholinesterasy MeSH
• sarin MeSH
• tabun MeSH Prohlížeč

Phenyl valerate (PV) is a substrate for measuring the PVase activity of neuropathy target esterase (NTE), a key molecular event of organophosphorus-induced delayed neuropathy. A protein with PVase activity in chicken (model for delayed neurotoxicity) was identified as butyrylcholinesterase (BChE). Purified human butyrylcholinesterase (hBChE) showed PVase activity with a similar sensitivity to inhibitors as its cholinesterase (ChE) activity. Further kinetic and theoretical molecular simulation studies were performed. The kinetics did not fit classic competition models among substrates. Partially mixed inhibition was the best-fitting model to acetylthiocholine (AtCh) interacting with PVase activity. ChE activity showed substrate activation, and non-competitive inhibition was the best-fitting model to PV interacting with the non-activated enzyme and partial non-competitive inhibition was the best fitted model for PV interacting with the activated enzyme by excess of AtCh. The kinetic results suggest that other sites could be involved in those activities. From the theoretical docking analysis, we deduced other more favorable sites for binding PV related with Asn289 residue, situated far from the catalytic site ("PV-site"). Both substrates acethylcholine (ACh) and PV presented similar docking values in both the PV-site and catalytic site pockets, which explained some of the observed substrate interactions. Molecular dynamic simulations based on the theoretical structure of crystallized hBChE were performed. Molecular modeling studies suggested that PV has a higher potential for non-competitive inhibition, being also able to inhibit the hydrolysis of ACh through interactions with the PV-site. Further theoretical studies also suggested that PV could yet be able to promote competitive inhibition. We concluded that the kinetic and theoretical studies did not fit the simple classic competition among substrates, but were compatible with the interaction with two different binding sites.

• Klíčová slova
• Docking, Human butyrylcholinesterase, Inhibition kinetics, Molecular dynamics, Phenyl valerate,
• MeSH
• acetylthiocholin metabolismus   MeSH
• butyrylcholinesterasa metabolismus   MeSH
• lidé MeSH
• molekulární modely * MeSH
• simulace molekulového dockingu MeSH
• valeráty metabolismus   MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• acetylthiocholin MeSH
• butyrylcholinesterasa MeSH
• phenyl valerate MeSH Prohlížeč
• valeráty MeSH