In silico structural studies on protein targets for drug discovery against neglected tropical diseases

Author(s)

Lilian Hernández Alvarez

• Document type: Doctoral Thesis
• Press: São José do Rio Preto. 2022-06-22.
• Institution: Universidade Estadual Paulista (Unesp). Instituto de Biociências Letras e Ciências Exatas. São José do Rio Preto
• Defense date: 2022-05-31
• Advisor: Fátima Pereira de Souza

Abstract

Neglected tropical diseases (NTDs) are a group of infections that are prevalent in remote and rural areas of low-income countries in Sub-Saharan Africa, Asia, and the Americas. These diseases do not receive enough attention, representing the lowest priority markets for the big pharmaceutical manufacturers. NTDs caused by protozoan parasites are responsible for significant morbidity and mortality and current drug treatments are toxic and prolonged. Here, experimental and computational approaches were employed to contribute to the knowledge of the molecular bases of several targets and the development of future drugs against these diseases. A computational strategy was employed to predict novel competitive inhibitors against the papain-like cysteine protease cruzain. The experimental evaluation of the predicted compounds allowed us to identify a novel competitive inhibitor of this protease with an IC50 under 15 μM. In addition, the X-ray structures of the cruzain complexes with gallinamide A and analogs were also determined, and two series of synthetic gallinamide A analogs (23 compounds) were evaluated against cruzain and intracellular Trypanosoma cruzi amastigotes. The employed computational techniques allowed us to identify the hot spots and structural determinates underlying the selective inhibition of this compound series. Moreover, in silico strategy was developed to elucidate the molecular bases of the previously-reported allosteric modulation in Leishmania major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Here, the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems were described. This study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E IP1, providing an understanding of trypanosomatids’ gene expression and gaining insight into the allostery of eIF4Es. Finally, the computational modeling of full-length sterol 14alpha-demethylase (AcCYP51) homodimer of Acanthamoeba castellani inserted in a lipid bilayer was performed. Our model revealed that AcCYP51 dimer interacts with the membrane lipids and remains stable within the bilayer along the simulation time. These results also provided us the insights into the superior potency of isavuconazole against this parasite. (AU)

• FAPESP's process: 18/03911-8 - Structure-based design of competitive and allosteric inhibitors of cruzain
• Grantee: Lilian Hernández Alvarez
• Support Opportunities: Scholarships in Brazil - Doctorate