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1.
Acc Chem Res ; 2024 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-38333993

RESUMO

ConspectusThe enzyme acetylcholinesterase (AChE) hydrolyzes the neurotransmitter acetylcholine (ACh) at cholinergic synapses of the peripheral and central nervous system. Thus, it is a prime therapeutic target for diseases that occur with a cholinergic deficit, prominently Alzheimer's disease (AD). Working at a rate near the diffusion limit, it is considered one of nature's most efficient enzymes. This is particularly meritorious considering that its catalytic site is buried at the bottom of a 20-Å-deep cavity, which is preceded by a bottleneck with a diameter shorter than that of the trimethylammonium group of ACh, which has to transit through it. Not only the particular architecture and amino acid composition of its active site gorge enable AChE to largely overcome this potential drawback, but it also offers plenty of possibilities for the design of novel inhibitor drug candidates.In this Account, we summarize our different approaches to colonize the vast territory of the AChE gorge in the pursuit of increased occupancy and hence of inhibitors with increased affinity. We pioneered the use of molecular hybridization to design inhibitors with extended binding at the CAS, reaching affinities among the highest reported so far. Further application of molecular hybridization to grow CAS extended binders by attaching a PAS-binding moiety through suitable linkers led to multisite inhibitors that span the whole length of the gorge, reaching the PAS and even interacting with midgorge residues. We show that multisite AChE inhibitors can also be successfully designed the other way around, by starting with an optimized PAS binder and then colonizing the gorge and CAS. Molecular hybridization from a multicomponent reaction-derived PAS binder afforded a single-digit picomolar multisite AChE inhibitor with more than 1.5 million-fold increased potency relative to the initial hit. This illustrates the powerful alliance between molecular hybridization and gorge occupancy for designing potent AChE inhibitors.Beyond AChE, we show that the stereoelectronic requirements imposed by the AChE gorge for multisite binding have a templating effect that leads to compounds that are active in other key biological targets in AD and other neurological and non-neurological diseases, such as BACE-1 and the aggregation of amyloidogenic proteins (ß-amyloid, tau, α-synuclein, prion protein, transthyretin, and human islet amyloid polypeptide). The use of known pharmacophores for other targets as the PAS-binding motif enables the rational design of multitarget agents with multisite binding within AChE and activity against a variety of targets or pathological events, such as oxidative stress and the neuroinflammation-modulating enzyme soluble epoxide hydrolase, among others.We hope that our results can contribute to the development of drug candidates that can modify the course of neurodegeneration and may inspire future works that exploit the power of molecular hybridization in other proteins featuring large cavities.

2.
Chem Biol Interact ; 386: 110741, 2023 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-37839515

RESUMO

Based on previous finding showing 2,3,6,11-tetrahydro-1H-azocino[4,5-b]indole as suitable scaffold of novel inhibitors of acetylcholinesterase (AChE), a main target of drugs for the treatment of Alzheimer's disease and related dementias, herein we investigated diverse newly and previously synthesized ß-enamino esters (and ketones) derivatives of 1,4,7,8-tetrahydroazocines (and some azonines) fused with benzene, 1H-indole, 4H-chromen-4-one and pyrimidin-4(3H)-one. Twenty derivatives of diversely annelated eight-to-nine-membered azaheterocyclic ring, prepared through domino reaction of the respective tetrahydropyridine and azepine with activated alkynes, were assayed for the inhibitory activity against AChE and butyrylcholinesterase (BChE). As a major outcome, compound 7c, an alkylamino derivative of tetrahydropyrimido[4,5-d]azocine, was found to be a highly potent BChE-selective inhibitor, which showed a noncompetitive/mixed-type inhibition mechanism against human BChE with single digit nanomolar inhibition constant (Ki = 7.8 ± 0.2 nM). The four-order magnitude BChE-selectivity of 7c clearly reflects the effect of lipophilicity upon binding to the BChE binding cavity. The ChEs' inhibition data, interpreted by chemoinformatic tools and an in-depth in-silico study (molecular docking combined with molecular dynamics calculations), not only highlighted key structural factors enhancing inhibition potency and selectivity toward BChE, but also shed light on subtle differences distinguishing the binding sites of equine BChE from the recombinant human BChE. Compound 7c inhibited P-glycoprotein with IC50 of 0.27 µM, which may support its ability to permeate blood-brain barrier, and proved to be no cytotoxic in human liver cancer cell line (HepG2) at the BChE bioactive concentrations. Overall, the biological profile allows us to envision 7c as a promising template to improve design and development of BChE-selective ligands of pharmaceutical interest, including inhibitors and fluorogenic probes.


Assuntos
Acetilcolinesterase , Butirilcolinesterase , Animais , Humanos , Acetilcolinesterase/metabolismo , Butirilcolinesterase/metabolismo , Inibidores da Colinesterase/química , Ésteres/farmacologia , Indóis , Simulação de Acoplamento Molecular , Relação Estrutura-Atividade
3.
Front Mol Biosci ; 8: 760026, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34805275

RESUMO

Adenosine monophosphate-activated protein kinase (AMPK) is a key energy sensor regulating the cell metabolism in response to energy supply and demand. The evolutionary adaptation of AMPK to different tissues is accomplished through the expression of distinct isoforms that can form up to 12 heterotrimeric complexes, which exhibit notable differences in the sensitivity to direct activators. To comprehend the molecular factors of the activation mechanism of AMPK, we have assessed the changes in the structural and dynamical properties of ß1- and ß2-containing AMPK complexes formed upon binding to the pan-activator PF-739. The analysis revealed the molecular basis of the PF-739-mediated activation of AMPK and enabled us to identify distinctive features that may justify the slightly higher affinity towards the ß1-isoform, such as the ß1-Asn111 to ß2-Asp111 substitution, which seems to be critical for modulating the dynamical sensitivity of ß1- and ß2 isoforms. The results are valuable in the design of selective activators to improve the tissue specificity of therapeutic treatment.

4.
Chemistry ; 27(19): 6015-6027, 2021 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-33666306

RESUMO

Many (poly-)phenolic natural products, for example, curcumin and taxifolin, have been studied for their activity against specific hallmarks of neurodegeneration, such as amyloid-ß 42 (Aß42) aggregation and neuroinflammation. Due to their drawbacks, arising from poor pharmacokinetics, rapid metabolism, and even instability in aqueous medium, the biological activity of azobenzene compounds carrying a pharmacophoric catechol group, which have been designed as bioisoteres of curcumin has been examined. Molecular simulations reveal the ability of these compounds to form a hydrophobic cluster with Aß42, which adopts different folds, affecting the propensity to populate fibril-like conformations. Furthermore, the curcumin bioisosteres exceeded the parent compound in activity against Aß42 aggregation inhibition, glutamate-induced intracellular oxidative stress in HT22 cells, and neuroinflammation in microglial BV-2 cells. The most active compound prevented apoptosis of HT22 cells at a concentration of 2.5 µm (83 % cell survival), whereas curcumin only showed very low protection at 10 µm (21 % cell survival).


Assuntos
Amiloidose , Curcumina , Amiloide/metabolismo , Peptídeos beta-Amiloides/metabolismo , Curcumina/farmacologia , Humanos , Estresse Oxidativo
5.
J Chem Inf Model ; 59(6): 2859-2870, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-30924649

RESUMO

Mammalian AMP-activated protein kinase (AMPK) is a Ser/Thr protein kinase with a key role as a sensor in cellular energy homeostasis. It has a major role in numerous metabolic disorders, such as type 2 diabetes, obesity, and cancer, and hence it has gained progressive interest as a potential therapeutic target. AMPK is a heterotrimeric enzyme composed by an α-catalytic subunit and two regulatory subunits, ß and γ. It is regulated by several mechanisms, including indirect activators such as metformin and direct activators such as compound A-769662. The crystal structure of AMPK bound to A-769662 has been recently reported, suggesting a hypothetical allosteric mechanism of AMPK activation assisted by phosphorylated Ser108 at the ß-subunit. Here, we have studied the direct activation mechanism of A-769662 by means of molecular dynamics simulations, suggesting that the activator may act as a glue, coupling the dynamical motion of the ß-subunit and the N-terminal domain of the α-subunit, and assisting the preorganization of the ATP-binding site. This is achieved through the formation of an allosteric network that connects the activator and ATP-binding sites, particularly through key interactions formed between αAsp88 and ßArg83 and between ßpSer108 and αLys29. Overall, these studies shed light into key mechanistic determinants of the allosteric regulation of this cellular energy sensor, and pave the way for the fine-tuning of the rational design of direct activators of this cellular energy sensor.


Assuntos
Adenilato Quinase/química , Adenilato Quinase/metabolismo , Simulação de Dinâmica Molecular , Regulação Alostérica , Entropia , Ativação Enzimática , Multimerização Proteica , Estrutura Quaternária de Proteína
6.
Phys Chem Chem Phys ; 20(33): 21404-21416, 2018 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-30105318

RESUMO

The light-harvesting mechanisms of cryptophyte antenna complexes have attracted considerable attention due to their ability to exhibit maximal photosynthetic activity under very low-light conditions and to display several colors, as well as the observation of vibronic coherent features in their two-dimensional electronic spectra. However, detailed investigations on the interplay between the protein environment and their light-harvesting properties are hampered by the uncertainty related to the protonation state of the underlying bilin pigments. Here we study the protonation preferences of four types of bilin pigments including 15,16-dihydrobiliverdin (DBV), phycoerythrobilin (PEB), phycocyanobilin (PCB) and mesobiliverdin (MBV), which are found in phycoerythrin PE545 and phycocyanin PC577, PC612, PC630 and PC645 complexes. We apply quantum chemical calculations coupled to continuum solvation calculations to predict the intrinsic acidity of bilins in aqueous solution, and then combine molecular dynamics simulations with empirical pKa estimates to investigate the impact of the local protein environment on the acidity of the pigments. We also report measurements of the absorption spectra of the five complexes in a wide range of pH in order to validate our simulations and investigate possible changes in the light harvesting properties of the complexes in the range of physiological pH found in the lumen (pH ∼ 5-7). The results suggest a pKa > 7 for DBV and MBV pigments in the α polypeptide chains of PE545 and PC630/PC645 complexes, which are not coordinated to a negatively charged amino acid. For the other PEB, DBV and PCB pigments, which interact with a Glu or Asp side chain, higher pKa values (pKa > 8) are estimated. Overall, the results support a preferential population of the fully protonated state for bilins in cryptophyte complexes under physiological conditions regardless of the specific type of pigment and local protein environment.


Assuntos
Ficobilinas/química , Ficobiliproteínas/química , Prótons , Criptófitas/química , Concentração de Íons de Hidrogênio , Luz , Modelos Químicos , Simulação de Dinâmica Molecular , Ficobilinas/efeitos da radiação , Ficobiliproteínas/efeitos da radiação , Teoria Quântica , Termodinâmica
7.
Chemistry ; 24(54): 14513-14521, 2018 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-29974986

RESUMO

Multiple multicomponent reactions rapidly assemble complex structures. Despite being very productive, the lack of selectivity and the reduced number of viable transformations restrict their general application in synthesis. Hereby, we describe a rationale for a selective version of these processes based in the preferential generation of intermediates which are less reactive than the initial substrates. In this way, applying the Groebke-Blackburn-Bienaymé reaction on a range of α-polyamino-polyazines, we prepared a family compact heterocyclic scaffolds with relevant applications in medicinal and biological chemistry (live cell imaging probes, selective binders for DNA quadruplexes, and antiviral agents against human adenoviruses). The approach has general character and yields complex molecular targets in a selective, tunable and direct manner.


Assuntos
Compostos Macrocíclicos/síntese química , Células A549 , Adenoviridae/efeitos dos fármacos , Antivirais/síntese química , Antivirais/química , Antivirais/farmacologia , Sobrevivência Celular/efeitos dos fármacos , Corantes Fluorescentes/síntese química , Corantes Fluorescentes/química , Quadruplex G , Compostos Heterocíclicos com 3 Anéis/síntese química , Compostos Heterocíclicos com 3 Anéis/química , Compostos Heterocíclicos com 3 Anéis/farmacologia , Humanos , Compostos Macrocíclicos/química , Compostos Macrocíclicos/farmacologia , Modelos Moleculares , Sondas Moleculares/síntese química , Sondas Moleculares/química , Estrutura Molecular , Oligonucleotídeos/química , Imagem Óptica
8.
Eur J Med Chem ; 146: 108-122, 2018 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-29407943

RESUMO

In Plasmodium falciparum the bifunctional enzyme glucose-6-phosphate dehydrogenase‒6-phosphogluconolactonase (PfG6PD‒6PGL) is involved in the catalysis of the first reaction of the pentose phosphate pathway. Since this enzyme has a key role in parasite development, its unique structure represents a potential target for the discovery of antimalarial drugs. Here we describe the first 3D structural model of the G6PD domain of PfG6PD‒6PGL. Compared to the human enzyme (hG6PD), the 3D model has enabled the identification of a key difference in the substrate-binding site, which involves the replacement of Arg365 in hG6PD by Asp750 in PfG6PD. In a prospective validation of the model, this critical change has been exploited to rationally design a novel family of substrate analog-based inhibitors that can display the necessary selectivity towards PfG6PD. A series of glucose derivatives featuring an α-methoxy group at the anomeric position and different side chains at position 6 bearing distinct basic functionalities has been synthesized, and their PfG6PD and hG6PD inhibitory activities and their toxicity against parasite and mammalian cells have been assessed. Several compounds displayed micromolar affinity (Ki up to 23 µM), favorable selectivity (up to > 26-fold), and low cytotoxicity. Phenotypic assays with P. falciparum cultures revealed high micromolar IC50 values, likely as a result of poor internalization of the compounds in the parasite cell. Overall, these results endorse confidence to the 3D model of PfG6PD, paving the way for the use of target-based drug design approaches in antimalarial drug discovery studies around this promising target.


Assuntos
Antimaláricos/farmacologia , Descoberta de Drogas , Glucosefosfato Desidrogenase/antagonistas & inibidores , Plasmodium falciparum/efeitos dos fármacos , Antimaláricos/síntese química , Antimaláricos/química , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Glucosefosfato Desidrogenase/metabolismo , Células Hep G2 , Humanos , Modelos Moleculares , Estrutura Molecular , Testes de Sensibilidade Parasitária , Plasmodium falciparum/citologia , Plasmodium falciparum/enzimologia , Relação Estrutura-Atividade , Células Tumorais Cultivadas
9.
Nat Chem ; 9(3): 201-206, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28221352

RESUMO

There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. This non-equilibrium property is surprisingly effective in virtual screening because true ligands form more-resilient interactions than decoys. Notably, DUck is orthogonal to docking and other 'thermodynamic' methods. We demonstrate the potential of the docking-undocking combination in a fragment screening against the molecular chaperone and oncology target Hsp90, for which we obtain novel chemotypes and a hit rate that approaches 40%.


Assuntos
Descoberta de Drogas , Simulação de Acoplamento Molecular , Preparações Farmacêuticas/química , Proteínas de Choque Térmico HSP90/antagonistas & inibidores , Proteínas de Choque Térmico HSP90/química , Humanos , Ligantes , Estrutura Molecular , Preparações Farmacêuticas/síntese química , Termodinâmica
10.
Peptides ; 78: 68-76, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26854383

RESUMO

The TcTLE peptide (TLEEFSAKL) is a CD8(+) T cell HLA-A*0201-restricted epitope derived from the Trypanosoma cruzi KMP-11 protein that is efficiently processed, presented and recognized by CD8(+) T cells from chagasic patients. Since the immunogenic properties of wild-type epitopes may be enhanced by suitable substitutions in secondary anchor residues, we have studied the effect of introducing specific mutations at position 3, 6 and 7 of the TcTLE peptide. Mutations (E3L, S6V and A7F) were chosen on the basis of in silico predictions and in vitro assays were performed to determine the TcTLE-modified peptide binding capacity to the HLA-A*0201 molecule. In addition, the functional activity of peptide-specific CD8(+) T cells in HLA-A2(+) chagasic patients was also interrogated. In contrast to bioinformatics predictions, the TcTLE-modified peptide was found to have lower binding affinity and stability than the original peptide. Nevertheless, CD8(+) T cells from chronic chagasic patients recognized the TcTLE-modified peptide producing TNF-α and INF-γ and expressing CD107a/b, though in less extension than the response triggered by the original peptide. Overall, although the amino acids at positions 3, 6 and 7 of TcTLE are critical for the peptide affinity, they have a limited effect on the immunogenic properties of the TcTLE epitope.


Assuntos
Substituição de Aminoácidos , Anticorpos Antiprotozoários/biossíntese , Epitopos de Linfócito T/imunologia , Antígeno HLA-A2/imunologia , Peptídeos/imunologia , Proteínas de Protozoários/imunologia , Trypanosoma cruzi/química , Sequência de Aminoácidos , Sítios de Ligação , Linfócitos T CD8-Positivos/citologia , Linfócitos T CD8-Positivos/efeitos dos fármacos , Linfócitos T CD8-Positivos/imunologia , Linhagem Celular , Doença de Chagas/imunologia , Doença de Chagas/parasitologia , Epitopos de Linfócito T/química , Epitopos de Linfócito T/genética , Regulação da Expressão Gênica , Antígeno HLA-A2/química , Antígeno HLA-A2/genética , Humanos , Interferon gama/genética , Interferon gama/imunologia , Proteína 1 de Membrana Associada ao Lisossomo/genética , Proteína 1 de Membrana Associada ao Lisossomo/imunologia , Proteína 2 de Membrana Associada ao Lisossomo/genética , Proteína 2 de Membrana Associada ao Lisossomo/imunologia , Mutação , Peptídeos/síntese química , Peptídeos/farmacologia , Ligação Proteica , Proteínas de Protozoários/química , Trypanosoma cruzi/imunologia , Fator de Necrose Tumoral alfa/genética , Fator de Necrose Tumoral alfa/imunologia
11.
Eur J Med Chem ; 81: 35-46, 2014 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-24942641

RESUMO

The α4ß2 nicotinic acetylcholine receptor (nAChR) is a molecular target of 3,4-methylenedioxymethamphetamine (MDMA), a synthetic drug also known as ecstasy, and it modulates the MDMA-mediated reinforcing properties. However, the enantioselective preference of the α4ß2 nAChR subtype still remains unknown. Since the two enantiomers exhibit different pharmacological profiles and stereoselective metabolism, the aim of this study is to assess a possible difference in the interaction of the MDMA enantiomers with this nAChR subtype. To this end, we report a novel simple, yet highly efficient enantioselective synthesis of the MDMA enantiomers, in which the key step is the diastereoselective reduction of imides derived from optically pure tert-butylsulfinamide. The enantioselective binding to the receptor is examined using [(3)H]epibatidine in a radioligand assay. Even though the two enantiomers induced a concentration-dependent binding displacement, (S)-MDMA has an inhibition constant 13-fold higher than (R)-MDMA, which shows a Hill's coefficient not significantly different from unity, implying a competitive interaction. Furthermore, when NGF-differentiated PC12 cells were pretreated with the compounds, a significant increase in binding of [(3)H]epibatidine was found for (R)-MDMA, indicating up-regulation of heteromeric nAChR in the cell surface. Finally, docking and molecular dynamics studies have been used to identify the binding mode of the two enantiomers, which provides a structural basis to justify the differences in affinity from the differential interactions played by the substituents at the stereogenic centre of MDMA. The results provide a basis to explore the distinct psychostimulant profiles of the MDMA enantiomers mediated by the α4ß2 nAChR subtype.


Assuntos
3,4-Metilenodioxianfetamina/análogos & derivados , Receptores Nicotínicos/metabolismo , 3,4-Metilenodioxianfetamina/síntese química , 3,4-Metilenodioxianfetamina/química , 3,4-Metilenodioxianfetamina/metabolismo , 3,4-Metilenodioxianfetamina/farmacologia , Animais , Sítios de Ligação/efeitos dos fármacos , Relação Dose-Resposta a Droga , Estrutura Molecular , Células PC12 , Ratos , Estereoisomerismo , Relação Estrutura-Atividade
12.
Eur J Med Chem ; 60: 479-89, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23354070

RESUMO

Glycogen synthase kinase 3ß (GSK-3ß) is widely recognised as a relevant player in the pathogenesis of several highly prevalent disorders such as Alzheimer's disease, mood disorders, diabetes and cancer. Therefore, this enzyme constitutes a highly attractive therapeutic target for the development of selective inhibitors as new promising drugs for the treatment of these pathologies. We describe here the isolation and biochemical characterization of the marine natural sesquiterpene palinurin as a GSK-3ß inhibitor. Experimental studies performed for characterizing the inhibitory mechanism indicate that GSK-3ß inhibition by palinurin cannot be competed out by ATP nor peptide substrate. Molecular modelling techniques have enabled us to propose an unconventional binding mode to GSK-3ß. Moreover, molecular dynamics simulations have identified an allosteric mechanism by which binding of palinurin leads to GSK-3ß inhibition. The inhibitory activities determined for a series of structurally related analogues support the proposed binding mode of palinurin, which is the first compound described to target this allosteric site. The results offer new opportunities for designing and developing selective inhibitors with novel mechanisms of action.


Assuntos
4-Butirolactona/análogos & derivados , Quinase 3 da Glicogênio Sintase/antagonistas & inibidores , Inibidores de Proteínas Quinases/farmacologia , 4-Butirolactona/química , 4-Butirolactona/farmacologia , Regulação Alostérica/efeitos dos fármacos , Animais , Sítios de Ligação/efeitos dos fármacos , Relação Dose-Resposta a Droga , Quinase 3 da Glicogênio Sintase/metabolismo , Glicogênio Sintase Quinase 3 beta , Humanos , Camundongos , Modelos Moleculares , Simulação de Dinâmica Molecular , Estrutura Molecular , Inibidores de Proteínas Quinases/química , Proteínas Recombinantes/antagonistas & inibidores , Proteínas Recombinantes/metabolismo , Relação Estrutura-Atividade , Células Tumorais Cultivadas
13.
J Med Chem ; 54(12): 4042-56, 2011 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-21500862

RESUMO

Development of kinase-targeted therapies for central nervous system (CNS) diseases is a great challenge. Glycogen synthase kinase 3 (GSK-3) offers a great potential for severe CNS unmet diseases, being one of the inhibitors on clinical trials for different tauopathies. Following our hypothesis based on the enhanced reactivity of residue Cys199 in the binding site of GSK-3, we examine here the suitability of phenylhalomethylketones as irreversible inhibitors. Our data confirm that the halomethylketone unit is essential for the inhibitory activity. Moreover, addition of the halomethylketone moiety to reversible inhibitors turned them into irreversible inhibitors with IC(50) values in the nanomolar range. Overall, the results point out that these compounds might be useful pharmacological tools to explore physiological and pathological processes related to signaling pathways regulated by GSK-3 opening new avenues for the discovery of novel GSK-3 inhibitors.


Assuntos
Fármacos do Sistema Nervoso Central/síntese química , Quinase 3 da Glicogênio Sintase/antagonistas & inibidores , Cetonas/síntese química , Trifosfato de Adenosina/química , Animais , Sítios de Ligação , Bovinos , Fármacos do Sistema Nervoso Central/química , Fármacos do Sistema Nervoso Central/farmacologia , Cerebelo/citologia , Desenho de Fármacos , Humanos , Técnicas In Vitro , Cetonas/química , Cetonas/farmacologia , Camundongos , Modelos Moleculares , Doenças Neurodegenerativas/tratamento farmacológico , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Fosforilação , Ligação Proteica , Ratos , Receptores de Neurotransmissores/antagonistas & inibidores , Estereoisomerismo , Relação Estrutura-Atividade , Proteínas tau/metabolismo
14.
J Comput Aided Mol Des ; 24(12): 1035-51, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20936494

RESUMO

Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, which play a central role in the immune response, is crucial to shed light into the details of peptide recognition and polymorphism. This work reports molecular modeling studies aimed at providing 3D models for two class I and two class II MHC alleles from Salmo salar (Sasa), as the lack of experimental structures of fish MHC molecules represents a serious limitation to understand the specific preferences for peptide binding. The reliability of the structural models built up using bioinformatic tools was explored by means of molecular dynamics simulations of their complexes with representative peptides, and the energetics of the MHC-peptide interaction was determined by combining molecular mechanics interaction energies and implicit continuum solvation calculations. The structural models revealed the occurrence of notable differences in the nature of residues at specific positions in the binding groove not only between human and Sasa MHC proteins, but also between different Sasa alleles. Those differences lead to distinct trends in the structural features that mediate the binding of peptides to both class I and II MHC molecules, which are qualitatively reflected in the relative binding affinities. Overall, the structural models presented here are a valuable starting point to explore the interactions between MHC receptors and pathogen-specific interactions and to design vaccines against viral pathogens.


Assuntos
Epitopos/química , Complexo Principal de Histocompatibilidade/imunologia , Simulação de Dinâmica Molecular , Peptídeos/química , Salmo salar/imunologia , Alelos , Sequência de Aminoácidos , Animais , Sítios de Ligação , Epitopos/imunologia , Epitopos/metabolismo , Humanos , Peptídeos/imunologia , Ligação Proteica/imunologia , Homologia de Sequência de Aminoácidos
15.
ChemMedChem ; 4(5): 866-76, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19350606

RESUMO

PDE7 inhibitors regulate pro-inflammatory and immune T-cell functions, and are a potentially novel class of drugs especially useful in the treatment of a wide variety of immune and inflammatory disorders. Starting from our lead family of thioxoquinazolines, we designed, synthesized, and characterized a novel series of thioxoquinazoline derivatives. Many of these compounds showed inhibitory potencies at sub-micromolar levels against the catalytic domain of PDE7A1 and at the micromolar level against PDE4D2. Cell-based studies showed that these compounds not only increased intracellular cAMP levels, but also had interesting anti-inflammatory properties within a therapeutic window. The in silico data predict that these compounds are capable of the crossing the blood-brain barrier. The X-ray crystal structure of the PDE7A1 catalytic domain in complex with compound 15 at a resolution of 2.4 A demonstrated that hydrophobic interactions at the active site pocket are a key feature. This structure, together with molecular modeling, provides insight into the selectivity of the PDE inhibitors and a template for the discovery of new PDE7 or PDE7/PDE4 dual inhibitors.


Assuntos
Anti-Inflamatórios/síntese química , Nucleotídeo Cíclico Fosfodiesterase do Tipo 7/antagonistas & inibidores , Inibidores de Fosfodiesterase/síntese química , Quinazolinas/química , Animais , Anti-Inflamatórios/química , Anti-Inflamatórios/farmacologia , Domínio Catalítico , Células Cultivadas , Cristalografia por Raios X , AMP Cíclico/metabolismo , Nucleotídeo Cíclico Fosfodiesterase do Tipo 4/metabolismo , Nucleotídeo Cíclico Fosfodiesterase do Tipo 7/metabolismo , Desenho de Fármacos , Humanos , Camundongos , Inibidores da Fosfodiesterase 4 , Inibidores de Fosfodiesterase/química , Inibidores de Fosfodiesterase/farmacologia , Quinazolinas/síntese química , Quinazolinas/farmacologia , Relação Estrutura-Atividade
16.
J Med Chem ; 52(9): 2724-32, 2009 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-19374444

RESUMO

Tacripyrines (1-14) have been designed by combining an AChE inhibitor (tacrine) with a calcium antagonist such as nimodipine and are targeted to develop a multitarget therapeutic strategy to confront AD. Tacripyrines are selective and potent AChE inhibitors in the nanomolar range. The mixed type inhibition of hAChE activity of compound 11 (IC(50) 105 +/- 15 nM) is associated to a 30.7 +/- 8.6% inhibition of the proaggregating action of AChE on the Abeta and a moderate inhibition of Abeta self-aggregation (34.9 +/- 5.4%). Molecular modeling indicates that binding of compound 11 to the AChE PAS mainly involves the (R)-11 enantiomer, which also agrees with the noncompetitive inhibition mechanism exhibited by p-methoxytacripyrine 11. Tacripyrines are neuroprotective agents, show moderate Ca(2+) channel blocking effect, and cross the blood-brain barrier, emerging as lead candidates for treating AD.


Assuntos
Doença de Alzheimer/tratamento farmacológico , Di-Hidropiridinas/química , Di-Hidropiridinas/farmacologia , Tacrina/análogos & derivados , Acetilcolinesterase/metabolismo , Doença de Alzheimer/enzimologia , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Peptídeos beta-Amiloides/metabolismo , Barreira Hematoencefálica/efeitos dos fármacos , Barreira Hematoencefálica/metabolismo , Butirilcolinesterase/metabolismo , Cálcio/metabolismo , Bloqueadores dos Canais de Cálcio/química , Bloqueadores dos Canais de Cálcio/metabolismo , Bloqueadores dos Canais de Cálcio/farmacologia , Bloqueadores dos Canais de Cálcio/uso terapêutico , Domínio Catalítico , Morte Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Inibidores da Colinesterase/química , Inibidores da Colinesterase/metabolismo , Inibidores da Colinesterase/farmacologia , Inibidores da Colinesterase/uso terapêutico , Citosol/efeitos dos fármacos , Citosol/metabolismo , Di-Hidropiridinas/metabolismo , Di-Hidropiridinas/uso terapêutico , Humanos , Peróxido de Hidrogênio/metabolismo , Cinética , Ligantes , Modelos Moleculares , Fragmentos de Peptídeos/metabolismo , Permeabilidade/efeitos dos fármacos
17.
J Chem Theory Comput ; 5(11): 3022-3031, 2009 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-21113276

RESUMO

A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances.

18.
Bioorg Med Chem ; 16(16): 7759-69, 2008 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-18640842

RESUMO

In this communication, we describe the synthesis and biological evaluation of tacripyrimedones 1-5, a series of new tacrine-1,4-dihydropyridine hybrids bearing the general structure of 11-amino-12-aryl-3,3-dimethyl-3,4,5,7,8,9,10,12-octahydrodibenzo[b,g][1,8]naphthyridine-1(2H)-one. These multifunctional compounds are moderately potent and selective AChEIs, with no activity toward BuChE. Kinetic analysis and molecular modeling studies point out that the new compounds preferentially bind the peripheral anionic site of AChE. In addition, compounds 1-5 show an excellent neuroprotective profile, and a moderate blocking effect of L-type voltage-dependent calcium channels due to the mitigation of [Ca(2+)] elevation elicited by K(+) depolarization. Therefore, they represent a new family of molecules with potential therapeutic application for the treatment of Alzheimer's disease.


Assuntos
Di-Hidropiridinas/síntese química , Di-Hidropiridinas/farmacologia , Tacrina/análogos & derivados , Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Animais , Cálcio/antagonistas & inibidores , Cálcio/metabolismo , Bloqueadores dos Canais de Cálcio/síntese química , Bloqueadores dos Canais de Cálcio/química , Bloqueadores dos Canais de Cálcio/farmacologia , Canais de Cálcio Tipo L/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Inibidores da Colinesterase/síntese química , Inibidores da Colinesterase/química , Inibidores da Colinesterase/farmacologia , Di-Hidropiridinas/química , Humanos , Concentração Inibidora 50 , Cinética , Espectroscopia de Ressonância Magnética , Espectrometria de Massas , Modelos Moleculares , Fármacos Neuroprotetores/síntese química , Fármacos Neuroprotetores/química , Fármacos Neuroprotetores/farmacologia , Espécies Reativas de Oxigênio/antagonistas & inibidores , Espécies Reativas de Oxigênio/metabolismo , Espectrofotometria Infravermelho , Tacrina/síntese química , Tacrina/química , Tacrina/farmacologia
19.
Phys Chem Chem Phys ; 10(19): 2616-24, 2008 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-18464976

RESUMO

The role of polarization in the stabilization of a series of biologically relevant alkali and alkaline-earth metal cations (Li(+), Na(+), K(+), Mg(2+) and Ca(2+)) with the pi-electron distribution of benzene is examined by means of MP2 computations using Sadlej's basis set. In all cases a full description of the energy profile for the approach of the metal cation along the axis normal to the molecular plane of benzene has been performed. Analysis of the different contributions to the interaction energy, performed within the framework of the symmetry-adapted perturbation theory (SAPT), illustrates the important role of the induction component in the definition of the geometrical and energetic properties of the pathway leading to the formation of cation-pi complex. Finally, the ability of classical polarization models based on models of implicitly and explicitly interacting distributed isotropic polarizabilities to describe the induction term has been examined and discussed in the context of the generation of new polarizable force fields.


Assuntos
Benzeno/química , Metais/química , Cátions , Estrutura Molecular
20.
J Am Chem Soc ; 128(11): 3608-19, 2006 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-16536534

RESUMO

Several very extended (0.5-1 micros) molecular dynamics (MD) simulations of parallel and antiparallel G-quadruplex DNA strongly suggest that in the presence of suitable cations the quadruplex not only remains stable in the gas phase, but also displays a structure that closely resembles that found in extended (25-ns long) trajectories in aqueous solution. In the absence of the crucial cations, the trajectories become unstable and in general the quadruplex structure is lost. To our knowledge, this is the first physiologically relevant structure of DNA for which very large MD simulations suggest that the structure in water and in the gas phase are indistinguishable.


Assuntos
DNA/química , Guanina/química , Simulação por Computador , Quadruplex G , Gases , Modelos Químicos , Modelos Moleculares , Conformação de Ácido Nucleico , Água/química
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