Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 12 de 12
Filtrar
2.
Nat Methods ; 17(8): 777-787, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32661425

RESUMO

G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.


Assuntos
Simulação de Dinâmica Molecular , Receptores Acoplados a Proteínas G/química , Software , Metaboloma , Modelos Moleculares , Conformação Proteica
3.
Nucleic Acids Res ; 44(W1): W455-62, 2016 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-27166369

RESUMO

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results.


Assuntos
Internet , Modelos Moleculares , Receptores Acoplados a Proteínas G/química , Software , Algoritmos , Regulação Alostérica , Sequência de Aminoácidos , Humanos , Ligantes , Simulação de Dinâmica Molecular , Receptor Tipo 2 de Angiotensina/química
4.
Bioorg Med Chem Lett ; 26(4): 1355-9, 2016 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-26810314

RESUMO

Agonists of the angiotensin II receptor type 2 (AT2), a G-protein coupled receptor, promote tissue protective effects in cardiovascular and renal diseases, while antagonists reduce neuropathic pain. We here report detailed molecular models that explain the AT2 receptor selectivity of our recent series of non-peptide ligands. In addition, minor structural changes of these ligands that provoke different functional activity are rationalized at a molecular level, and related to the selectivity for the different receptor conformations. These findings should pave the way to structure based drug discovery of AT2 receptor ligands.


Assuntos
Bloqueadores do Receptor Tipo 1 de Angiotensina II/química , Receptor Tipo 2 de Angiotensina/metabolismo , Sequência de Aminoácidos , Bloqueadores do Receptor Tipo 1 de Angiotensina II/metabolismo , Sítios de Ligação , Ligantes , Simulação de Acoplamento Molecular , Ligação Proteica , Estrutura Terciária de Proteína , Receptor Tipo 1 de Angiotensina/química , Receptor Tipo 1 de Angiotensina/metabolismo , Receptor Tipo 2 de Angiotensina/agonistas , Receptor Tipo 2 de Angiotensina/química , Alinhamento de Sequência
5.
Eur J Med Chem ; 265: 116122, 2024 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-38199164

RESUMO

Two series of N-(heteroaryl)thiophene sulfonamides, encompassing either a methylene imidazole group or a tert-butylimidazolylacetyl group in the meta position of the benzene ring, have been synthesized. An AT2R selective ligand with a Ki of 42 nM was identified in the first series and in the second series, six AT2R selective ligands with significantly improved binding affinities and Ki values of <5 nM were discovered. The binding modes to AT2R were explored by docking calculations combined with molecular dynamics simulations. Although some of the high affinity ligands exhibited fair stability in human liver microsomes, comparable to that observed with C21 undergoing clinical trials, most ligands displayed a very low metabolic stability with t½ of less than 10 min in human liver microsomes. The most promising ligand, with an AT2R Ki value of 4.9 nM and with intermediate stability in human hepatocytes (t½ = 77 min) caused a concentration-dependent vasorelaxation of pre-contracted mouse aorta.


Assuntos
Receptor Tipo 2 de Angiotensina , Sulfonamidas , Camundongos , Humanos , Animais , Receptor Tipo 2 de Angiotensina/metabolismo , Ligantes , Sulfonamidas/química , Tiofenos/química , Aorta/metabolismo , Angiotensina II/metabolismo
6.
Biomolecules ; 10(4)2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32340100

RESUMO

Angiotensin II receptor type 1 and 2 (AT1R and AT2R) are two G-protein coupled receptors that mediate most biological functions of the octapeptide Angiotensin II (Ang II). AT2R is upregulated upon tissue damage and its activation by selective AT2R agonists has become a promising approach in the search for new classes of pharmaceutical agents. We herein analyzed the chemical evolution of AT2R agonists starting from octapeptides, through shorter peptides and peptidomimetics to the first drug-like AT2R-selective agonist, C21, which is in Phase II clinical trials and aimed for idiopathic pulmonary fibrosis. Based on the recent crystal structures of AT1R and AT2R in complex with sarile, we identified a common binding model for a series of 11 selected AT2R agonists, consisting of peptides and peptidomimetics of different length, affinity towards AT2R and selectivity versus AT1R. Subsequent molecular dynamics simulations and free energy perturbation (FEP) calculations of binding affinities allowed the identification of the bioactive conformation and common pharmacophoric points, responsible for the key interactions with the receptor, which are maintained by the drug-like agonists. The results of this study should be helpful and facilitate the search for improved and even more potent AT2R-selective drug-like agonists.


Assuntos
Angiotensina II/farmacologia , Peptídeos/farmacologia , Peptidomiméticos/farmacologia , Receptor Tipo 2 de Angiotensina/agonistas , Angiotensina II/química , Sítios de Ligação , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Peptídeos/química , Peptidomiméticos/química , Receptor Tipo 1 de Angiotensina/agonistas , Receptor Tipo 1 de Angiotensina/química , Receptor Tipo 2 de Angiotensina/química , Termodinâmica
7.
Mol Pharmacol ; 75(4): 982-90, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19168624

RESUMO

The extended classic ternary complex model predicts that a G protein-coupled receptor (GPCR) exists in only two interconvertible states: an inactive R, and an active R(*). However, different structural active R(*) complexes may exist in addition to a silent inactive R ground state (Rg). Here we demonstrate, in a cellular context, that several R(*) states of 5-hydroxytryptamine-4 (5-HT(4)) receptors involve different side-chain conformational toggle switches. Using site-directed mutagenesis and molecular modeling approaches, we show that the basal constitutive receptor (R(*)basal) results from stabilization of an obligatory double toggle switch (Thr3.36 from inactive g- to active g+ and Trp6.48 from inactive g+ to active t). Mutation of either threonine or tryptophan to alanine resulted in a lowering of the activity of the R(*)basal similar to the Rg. The T3.36A mutation shows that the Thr3.36 toggle switch plays a minor role in the stabilization of R(*) induced by 5-HT (R(*)-5-HT) and BIMU8 (R(*)-BIMU8) and is fully required in the stabilization of R(*) induced by (S)-zacopride, cisapride, and 1-(4-amino-5-chloro-2-methoxyphenyl)-3-(1-butyl-4-piperidinyl)-1-propanone (RS 67333) (R(*)-benzamides). Thus, benzamides stabilize R(*)-benzamides by forming a specific hydrogen bond with Thr3.36 in the active g+ conformation. Conversely, R(*)-BIMU8 was probably the result of a direct conformational transition of Trp6.48 from inactive g+ to active t by hydrogen bonding of this residue to a carboxyl group of BIMU8. We were surprised that the Trp6.48 toggle switch was not necessary for receptor activation by the natural agonist 5-HT. R(*)-5-HT is probably attained through other routes of activation. Thus, different conformational arrangements occur during stabilization of R(*)basal, R(*)-5-HT, R(*)-benzamides, and R(*)-BIMU8.


Assuntos
Receptores 5-HT4 de Serotonina/química , Agonistas do Receptor 5-HT4 de Serotonina , Agonistas do Receptor de Serotonina/farmacologia , Sequência de Aminoácidos/genética , Animais , Células COS , Chlorocebus aethiops , Relação Dose-Resposta a Droga , Camundongos , Dados de Sequência Molecular , Conformação Proteica/efeitos dos fármacos , Estrutura Secundária de Proteína , Receptores 5-HT4 de Serotonina/fisiologia
8.
ChemistryOpen ; 8(1): 114-125, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30697513

RESUMO

We here report on our continued studies of ligands binding to the promising drug target angiotensin II type 2 receptor (AT2R). Two series of compounds were synthesized and investigated. The first series explored the effects of adding small substituents to the phenyl ring of the known selective nonpeptide AT2R antagonist C38, generating small but significant shifts in AT2R affinity. One compound in the first series was equipotent to C38 and showed similar kinetic solubility, and stability in both human and mouse liver microsomes. The second series was comprised of new bicyclic derivatives, amongst which one ligand exhibited a five-fold improved affinity to AT2R as compared to C38. The majority of the compounds in the second series, including the most potent ligand, were inferior to C38 with regard to stability in both human and mouse microsomes. In contrast to our previously reported findings, ligands with shorter carbamate alkyl chains only demonstrated slightly improved stability in microsomes. Based on data presented herein, a more adequate, tentative model of the binding modes of ligand analogues to the prototype AT2R antagonist C38 is proposed, as deduced from docking redefined by molecular dynamic simulations.

9.
Methods Mol Biol ; 1705: 23-44, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29188557

RESUMO

The recent increase in available G protein-coupled receptor structures now contributes decisively to the structure-based ligand design. In this context, computational approaches in combination with medicinal chemistry and pharmacology are extremely helpful. Here, we provide an update on our structure-based computational protocols, used to answer key questions related to GPCR-ligand binding. All combined, these techniques can shed light on ligand binding modes, determine the molecular basis of conformational selection, for agonists and antagonists, as well as of subtype selectivity. To illustrate each of these questions, we will consider examples from existing projects on three families of class A (rhodopsin-like) GPCRs: one small-molecule (nucleotide-like) family, i.e., the adenosine receptors, and two peptide-binding receptors: neuropeptide-Y and angiotensin II receptors. The successful application of the same computational protocols to investigate this diverse group of receptor families gives an idea of the general applicability of our methodology in the characterization of GPCR-ligand binding.


Assuntos
Ligantes , Modelos Moleculares , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Algoritmos , Sítios de Ligação , Desenho de Fármacos , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade
10.
Curr Top Med Chem ; 17(1): 40-58, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-27448653

RESUMO

The family of adenosine receptors (ARs) is focus of several medicinal chemistry programs aimed to find new potent and selective drugs. Each receptor subtype has been proposed as a relevant drug target in the treatment of, e.g., cardiovascular or inflammatory diseases, asthma or Parkinson's disease. Until recently, most of these efforts have been dominated by ligand-based or empirical approaches. However, the latest advances in G protein-coupled receptor (GPCR) crystallography allowed for a thorough structural characterization of the A2AAR subtype, which has been crystalized with a number of agonists and antagonists. Consequently, the ligand discovery of AR ligands has been enriched with a number of structure-based approaches. These include the generation of higher-confident homology models for the remaining AR subtypes, virtual screening identification of novel chemotypes, structure-based lead-optimization programs, rationalization of selectivity profiles, or the structural characterization of novel binding sites that enable the design of novel allosteric modulators. Computational methodologies have importantly contributed to the success of these structure-based approaches, and the recent advances in the field are also analyzed in this review. We conclude that the design of adenosine receptor ligands has improved dramatically with the consideration of structure- based approaches, which is paving the way to a better understanding of the biology and pharmacological modulation of this relevant family of receptors.


Assuntos
Desenho de Fármacos , Receptores Purinérgicos P1/química , Sequência de Aminoácidos , Biologia Computacional , Humanos , Ligantes , Estrutura Molecular , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade
11.
J Med Chem ; 53(3): 1357-69, 2010 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-20078106

RESUMO

On the basis of our previously described pharmacophore model for serotonin 5-HT(6) receptor (5-HT(6)R) antagonists, we have designed, synthesized, and pharmacologically characterized a series of benzimidazole derivatives 1-20 that represent a new family of potent antagonists at the human 5-HT(6)R. Site-directed mutagenesis and a beta(2)-adrenoceptor-based homology model of the 5-HT(6)R were used to predict the mode of binding of antagonist SB-258585 and the new synthesized ligands. Substitution of W6.48, F6.52, or N6.55 by Ala fully impedes compound 4 to block 5-HT-induced activation. Thus, we propose that D3.32 in TM 3 anchors the protonated piperazine ring, the benzimidazole ring expands parallel to EL 2 to hydrogen bond N6.55 in TM 6, and the aromatic ring is placed between TMs 3 and 5 in CH(2)-containing compounds and between TMs 3 and 6 in CO-containing compounds. This combined experimental and computational study has permitted to propose the molecular mechanisms by which the new benzimidazole derivatives act as 5-HT(6)R antagonists.


Assuntos
Benzimidazóis/química , Benzimidazóis/farmacologia , Receptores de Serotonina/química , Receptores de Serotonina/metabolismo , Antagonistas da Serotonina/síntese química , Animais , Benzimidazóis/síntese química , Ligação Competitiva , Células COS , Células Cultivadas , Chlorocebus aethiops , Simulação por Computador , AMP Cíclico/metabolismo , Ensaio de Imunoadsorção Enzimática , Humanos , Rim/citologia , Rim/efeitos dos fármacos , Estrutura Molecular , Mutagênese Sítio-Dirigida , Conformação Proteica , Ensaio Radioligante , Receptores de Serotonina/genética , Antagonistas da Serotonina/química , Antagonistas da Serotonina/farmacologia , Relação Estrutura-Atividade
12.
J Med Chem ; 52(8): 2384-92, 2009 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-19326916

RESUMO

We report the synthesis of a new set of compounds of general structure I (1-20) with structural modifications in the pharmacophoric elements of the previously reported lead UCM-5600. The new derivatives have been evaluated for binding affinity at 5-HT(7) and 5-HT(1A) receptors. The influence of the different structural features in terms of 5-HT(7)/5-HT(1A) receptor affinity and selectivity was analyzed by computational simulations of the complexes between compounds I and beta(2)-based 3-D models of these receptors. Compound 18 (HYD(1) = 1,3-dihydro-2H-indol-2-one; spacer = -(CH(2))(4)-; HYD(2) + HYD(3) = 3,4-dihydroisoquinolin-2(1H)-yl) exhibits high 5-HT(7)R affinity (K(i) = 7 nM) and selectivity over the 5-HT(1A)R (31-fold), and has been characterized as a partial agonist of the human 5-HT(7)R.


Assuntos
Indóis/síntese química , Isoquinolinas/síntese química , Receptor 5-HT1A de Serotonina/metabolismo , Receptores de Serotonina/metabolismo , Antagonistas da Serotonina/síntese química , Agonistas do Receptor de Serotonina/síntese química , Sequência de Aminoácidos , Animais , Linhagem Celular , Cricetinae , Cricetulus , Agonismo Parcial de Drogas , Humanos , Indóis/química , Indóis/farmacologia , Isoquinolinas/química , Isoquinolinas/farmacologia , Ligantes , Modelos Moleculares , Dados de Sequência Molecular , Ensaio Radioligante , Agonistas do Receptor 5-HT1 de Serotonina , Antagonistas do Receptor 5-HT1 de Serotonina , Antagonistas da Serotonina/química , Antagonistas da Serotonina/farmacologia , Agonistas do Receptor de Serotonina/química , Agonistas do Receptor de Serotonina/farmacologia , Relação Estrutura-Atividade
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA