Identification and characterization of cruzain allosteric inhibitors: a computer-aided approach
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Data
2017-09-29
Autores
Hernández Alvarez, Lilian [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
Trypanosoma cruzi é o agente causal da doença de Chagas, uma infecção negligenciada que afeta milhões de pessoas nas regiões tropicais. A maioria dos fármacos empregados no tratamento desta doença são altamente tóxicos e geram resistência. Na atualidade, o descobrimento de inibidores alostéricos é um tópico emergente dentro da área de desenho computacional de fármacos, pois promove a acessibilidade a medicamentos mais seletivos e menos tóxicos. Neste trabalho foi desenvolvida uma estratégia para a descoberta computacional de inibidores alostéricos a qual foi aplicada à cruzaína, a principal cisteíno protease do T. cruzi. A caracterização molecular da forma livre e ligada da cruzaína foi investigada através do ancoramento molecular, simulações de dinâmica molecular, cálculos de energia livre de ligação e construção de redes de interações entre resíduos. A partir da análise baseada na geometria das estruturas geradas na dinâmica molecular, foram detectados dois potenciais sítios alostéricos na cruzaína. Os resultados sugerem a existência de diferentes mecanismos de regulação exercidos pela ligação de inibidores diferentes no mesmo sítio alostérico. Além disso, foram identificados os resíduos que estabelecem os caminhos de transmissão de informação entre um dos sítios alostéricos identificado e o sítio ativo da enzima. O presente estudo é a primeira aproximação de desenho de inibidores alostéricos da cruzaína e serve para futuras intervenções farmacológicas. Esses resultados constituem uma base para o desenho de inibidores específicos de cisteíno proteases homólogas da papaína.
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it may improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied for or cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based detection on trajectory snapshots we determined the existence of two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanism exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation for designing cruzain allosteric inhibitors and may serve for future pharmacological intervention. These findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it may improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied for or cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based detection on trajectory snapshots we determined the existence of two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanism exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation for designing cruzain allosteric inhibitors and may serve for future pharmacological intervention. These findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
Descrição
Palavras-chave
Cruzaína, Alosteria, Triagem virtual, Energia livre de ligação, Correlação generalizada, Redes de proteínas, Comunidades, Caminho subótimo, Cruzain, Allostery, Virtual screening, Binding free energy, Generalize correlation, Protein network, Communities, Suboptimal pathway