RESUMO
An integrated computational approach, based on molecular dynamics/mechanics, semi-empirical, and DFT calculations as well as dynamic docking studies, has been employed to gain insight into the mechanism of action of new antimalarial agents characterized by the scaffold of the marine compounds plakortin and aplidinone. The results of this approach show that these molecules, after interaction with Fe(II), likely coming from the heme molecule, give rise to the formation of radical species, that should represent the toxic intermediates responsible for subsequent reactions leading to plasmodium death. The three-dimensional structural requirements necessary for the activity of these new classes of antimalarial agents have been identified and discussed throughout the chapter.
Assuntos
Antimaláricos/química , Organismos Aquáticos/química , Produtos Biológicos/química , Desenho de Fármacos , Simulação de Acoplamento Molecular/tendências , Preparações Farmacêuticas/química , Animais , Sítios de Ligação , Produtos Biológicos/uso terapêutico , Química Farmacêutica/tendências , Simulação por Computador , Avaliação Pré-Clínica de Medicamentos/tendências , Modelos Químicos , Conformação Molecular , Conformação Proteica , Tecnologia Farmacêutica/tendênciasRESUMO
Computer-aided drug discovery plays a strategic role in the development of new potential therapeutic agents. Nevertheless, the modeling of biological systems still represents a challenge for computational chemists and at present a single computational method able to face such challenge is not available. This prompted us, as computational medicinal chemists, to develop in-house methodologies by mixing various bioinformatics and computational tools. Importantly, thanks to multi-disciplinary collaborations, our computational studies were integrated and validated by experimental data in an iterative process. In this review, we describe some recent applications of such integrated approaches and how they were successfully applied in i) the search of new allosteric inhibitors of protein-protein interactions and ii) the development of new redox-active antimalarials from natural leads.
Assuntos
Antimaláricos/química , Animais , Antimaláricos/farmacologia , Antimaláricos/uso terapêutico , Biologia Computacional/métodos , Desenho Assistido por Computador , Desenho de Fármacos , Descoberta de Drogas/métodos , Humanos , Oxirredução/efeitos dos fármacos , Mapas de Interação de Proteínas/efeitos dos fármacosRESUMO
The majority of functionally important biological processes are regulated by allosteric communication within individual proteins and across protein complexes. The proteins controlling these communication networks respond to changes in the cellular environment by switching between different conformational states. Targeting the interface residues mediating these processes through the rational identification of molecules modulating or mimicking their effects holds great therapeutic potential. Protein-protein interactions (PPIs) have shown to have a high degree of plasticity since they occur through small regions, called hot spots, which are included in binding surfaces or in binding clefts of the proteins and are characterized by a high degree of complementarity. This prompted several researchers to compare the protein structure to human grammar proposing terms like "protein language". The decoding of this language represent a new paradigm not only to clarify the dynamics of many biological processes but also to improve the opportunities in drug discovery. In this review, we try to give an overview on intra-molecular and inter-molecular protein communication mechanisms describing the protein interaction domains (PIDs) and short linear motifs (SLiMs), which delineate the authentic syntactic and semantic units in a protein. Moreover, we illustrate some novel approaches performed on natural compounds and on synthetic derivatives aimed at developing new classes of potential drugs able to interfere with intra-molecular and inter-molecular protein communication.
Assuntos
Produtos Biológicos/química , Descoberta de Drogas , Proteínas/química , Bibliotecas de Moléculas Pequenas/química , Regulação Alostérica , Desenho de Fármacos , Humanos , Ligantes , Modelos Moleculares , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Mapeamento de Interação de Proteínas , Proteínas/agonistas , Proteínas/antagonistas & inibidores , Bibliotecas de Moléculas Pequenas/síntese químicaRESUMO
GBP1 and PIM1 are known to interact with a molar ratio 1:1. GBP1:PIM1 binding initiates a signaling pathway that induces resistance to common chemotherapeutics such as paclitaxel. Since GBP1 is a large GTPase which undergoes conformational changes in a nucleotide-dependent manner, we investigated the effect of GTP/GDP binding on GBP1:PIM1 interaction by using computational and biological studies. It resulted that only GTP decreases the formation of the GBP1:PIM1 complex through an allosteric mechanism, putting the bases for the identification of new compounds potentially able to revert resistance to paclitaxel.
Assuntos
Proteínas de Ligação ao GTP/química , Guanosina Difosfato/química , Simulação de Acoplamento Molecular , Proteínas de Neoplasias/química , Proteínas Proto-Oncogênicas c-pim-1/química , Regulação Alostérica , Sequência de Aminoácidos , Antineoplásicos Fitogênicos/química , Sítios de Ligação , Resistencia a Medicamentos Antineoplásicos , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Ligação ao GTP/genética , Expressão Gênica , Guanosina Trifosfato/química , Humanos , Cinética , Simulação de Dinâmica Molecular , Dados de Sequência Molecular , Proteínas de Neoplasias/genética , Paclitaxel/química , Ligação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Proto-Oncogênicas c-pim-1/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , TermodinâmicaRESUMO
Class III ß-tubulin plays a prominent role in the development of drug resistance to paclitaxel by allowing the incorporation of the GBP1 GTPase into microtubules. Once in the cytoskeleton, GBP1 binds to prosurvival kinases such as PIM1 and initiates a signaling pathway that induces resistance to paclitaxel. Therefore, the inhibition of the GBP1:PIM1 interaction could potentially revert resistance to paclitaxel. A panel of 44 4-azapodophyllotoxin derivatives was screened in the NCI-60 cell panel. The result is that 31 are active and the comparative analysis demonstrated specific activity in paclitaxel-resistant cells. Using surface plasmon resonance, we were able to prove that NSC756093 is a potent in vitro inhibitor of the GBP1:PIM1 interaction and that this property is maintained in vivo in ovarian cancer cells resistant to paclitaxel. Through bioinformatics, molecular modeling, and mutagenesis studies, we identified the putative NSC756093 binding site at the interface between the helical and the LG domain of GBP1. According to our results by binding to this site, the NSC756093 compound is able to stabilize a conformation of GBP1 not suitable for binding to PIM1.
Assuntos
Antineoplásicos/síntese química , Proteínas de Ligação ao GTP/antagonistas & inibidores , Paclitaxel/farmacologia , Proteínas Proto-Oncogênicas c-pim-1/antagonistas & inibidores , Antineoplásicos/farmacologia , Sítios de Ligação , Linhagem Celular Tumoral , Biologia Computacional , Descoberta de Drogas , Resistencia a Medicamentos Antineoplásicos , Proteínas de Ligação ao GTP/química , Humanos , Modelos Moleculares , Simulação de Acoplamento Molecular , Proteínas Proto-Oncogênicas c-pim-1/químicaRESUMO
The novel tetrasubstituted pyrrole derivatives 8g, 8h, and 8i showed selective cytotoxicity against M14 melanoma cells at low micromolar concentration. Structure-activity relationships (SARs) indicated the presence of three aromatic substituents on the pyrrole core as necessary for biological activity. Computational studies strongly suggest that the peculiar 3D orientation of these substituents is able to reproduce the hydrophobic side chains in LxxLL-like protein recognition motifs. Biological results showed altered p53 expression and nuclear translocation in cells sensitive to the compounds, suggesting p53 involvement in their anticancer mechanism of action. Unfortunately, because of poor solubility of the active analogues, it was not possible to perform further investigation by NMR techniques. Pharmacophore models were generated and used to perform 3D searches in molecular databases. Results indicated that two compounds share the same pharmacological profile and the same pharmacophoric features with our new derivatives, and one of them inhibited MDM2-MDM4 heterodimer formation.
Assuntos
Antineoplásicos/farmacologia , Mimetismo Molecular , Proteínas/química , Antineoplásicos/química , Apoptose/efeitos dos fármacos , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Humanos , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Relação Estrutura-AtividadeRESUMO
Bcl-2 plays a prominent role in regulating the function of mitochondria during respiration and in determining the threshold of apoptotic sensitivity. Despite its relevance, the mechanism through which these processes are achieved is still unknown. Using surface plasmon resonance technology to monitor Bcl-2 multimerisation we discovered that a simple dimeric model does not fit with experimental data. A molecular model of the experimentally observed Bcl-2 homomeric complex has been developed. Accordingly, using a panel of mutants we identified in the loop a critical region for the process of Bcl-2 multimerisation. Our results indicate that the Bcl-2 loop posttranscriptional changes can modulate its ability to make homo and hetero-complexes, ultimately leading to functional modulation, suggesting an intriguing relationship between the ability of Bcl-2 to form multimeric complexes and its multi-functional role as a membrane channel. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.
Assuntos
Proteínas Proto-Oncogênicas c-bcl-2/química , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Humanos , Immunoblotting , Cinética , Modelos Moleculares , Ligação Proteica , Multimerização Proteica , Relação Estrutura-Atividade , Ressonância de Plasmônio de SuperfícieRESUMO
As a continuation of our efforts to develop innovative ligands for D(3), 5-HT(1A), and 5-HT(2A) receptors with low propensity to block hERG channels, we propose a series bishetero(homo)arylpiperazines 5a-m as novel and potent multifunctional ligands characterized by low occupancy at D(2) and 5-HT(2C) receptors.