1
|
Carey SM, Kearns SP, Millington ME, Buechner GS, Alvarez BE, Daneshian L, Abiskaroon B, Chruszcz M, D'Antonio EL. At the outer part of the active site in Trypanosoma cruzi glucokinase: The role of phenylalanine 337. Biochimie 2024; 218:8-19. [PMID: 37741546 DOI: 10.1016/j.biochi.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/10/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
The hole mutagenesis approach was used to interrogate the importance of F337 in Trypanosoma cruzi glucokinase (TcGlcK) in order to understand the complete set of binding interactions that are made by d-glucosamine analogue inhibitors containing aromatic tail groups that can extend to the outer part of the active site. An interesting inhibitor of this analogue class includes 2-N-carboxybenzyl-2-deoxy-d-glucosamine (CBZ-GlcN), which exhibits strong TcGlcK binding with a Ki of 710 nM. The residue F337 is found at the outer part of the active site that stems from the second protein subunit of the homodimeric assembly. In this study, F337 was changed to leucine and alanine so as to diminish phenylalanine's side chain size and attenuate intermolecular interactions in this region of the binding cavity. Results from enzyme - inhibitor assays revealed that the phenyl group of F337 made dominant hydrophobic interactions with the phenyl group of CBZ-GlcN as opposed to π - π stacking interactions. Moreover, enzymatic activity assays and X-ray crystallographic experiments indicated that each of these site-directed mutants primarily retained their activity and had high structural similarity of their protein fold. A computed structure model of T. cruzi hexokinase (TcHxK), which was produced by the artificial intelligence system AlphaFold, was compared to an X-ray crystal structure of TcGlcK. Our structural analysis revealed that TcHxK lacked an F337 counterpart residue and probably exists in the monomeric form. We proposed that the d-glucosamine analogue inhibitors that are structurally similar to CBZ-GlcN may not bind as strongly in TcHxK as they do in TcGlcK because of absent van der Waals contact from residue side chains.
Collapse
Affiliation(s)
- Shane M Carey
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA
| | - Sean P Kearns
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA
| | - Matthew E Millington
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA
| | - Gregory S Buechner
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA
| | - Beda E Alvarez
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Brendan Abiskaroon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, Bluffton, SC 29909, USA.
| |
Collapse
|
2
|
de Azevedo SLC, Catanho M, Guimarães ACR, Galvão TC. Genomic surveillance: a potential shortcut for effective Chagas disease management. Mem Inst Oswaldo Cruz 2023; 117:e220164. [PMID: 36700581 PMCID: PMC9870261 DOI: 10.1590/0074-02760220164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/29/2022] [Indexed: 01/27/2023] Open
Abstract
Chagas disease is an enduring public health issue in many Latin American countries, receiving insufficient investment in research and development. Strategies for disease control and management currently lack efficient pharmaceuticals, commercial diagnostic kits with improved sensitivity, and vaccines. Genetic heterogeneity of Trypanosoma cruzi is a key aspect for novel drug design since pharmacological technologies rely on the degree of conservation of parasite target proteins. Therefore, there is a need to expand the knowledge regarding parasite genetics which, if fulfilled, could leverage Chagas disease research and development, and improve disease control strategies. The growing capacity of whole-genome sequencing technology and its adoption as disease surveillance routine may be key for solving this long-lasting problem.
Collapse
Affiliation(s)
- Sophia Lincoln Cardoso de Azevedo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil,Universidade Federal Fluminense, Niterói, RJ, Brasil
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina Ramos Guimarães
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil
| | - Teca Calcagno Galvão
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil,+ Corresponding author:
| |
Collapse
|
3
|
Narsimulu B, Qureshi R, Jakkula P, Are S, Qureshi IA. Biophysical and Structural Characterization of Ribulose-5-phosphate Epimerase from Leishmania donovani. ACS OMEGA 2022; 7:548-564. [PMID: 35036723 PMCID: PMC8756792 DOI: 10.1021/acsomega.1c04967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Pentose phosphate pathway (PPP) plays a crucial role in the maintenance of NADPH/NADP+ homeostasis and provides protection against oxidative stress through detoxification of the reactive oxygen species. Ribulose-5-phosphate epimerase (RPE) participates in catalysis of the interconversion of ribulose-5-phosphate (Ru5P) to xylulose-5-phosphate (Xu5P) during PPP, however the structural attributes of this enzyme are still underexplored in many human pathogens including leishmanial parasites. The present study focuses upon cloning, purification and characterization of RPE of Leishmania donovani (LdRPE) using various biophysical and structural approaches. Sequence analysis has shown the presence of trypanosomatid-specific insertions at the N-terminus that are absent in humans and other eukaryotes. Gel filtration chromatography indicated recombinant LdRPE to exist as a dimer in the solution. Circular dichroism studies revealed a higher alpha helical content at physiological pH and temperature that comparatively varies with changing these parameters. Additionally, intrinsic fluorescence and quenching studies of LdRPE have depicted that tryptophan residues are mainly buried in the hydrophobic regions, and the recombinant enzyme is moderately tolerant to urea. Moreover, homology modeling was employed to generate the three-dimensional structure of LdRPE followed by molecular docking with the substrate, product, and substrate analogues. The modeled structure of LdRPE unravelled the presence of conserved active site residues as well as a single binding pocket for the substrate and product, while an in silico study suggested binding of substrate analogues into a similar pocket with more affinity than the substrate. Additionally, molecular dynamics simulation analysis has deciphered complexes of LdRPE with most of the ligands exhibiting more stability than its apo form and lesser fluctuations in active site residues in the presence of ligands. Altogether, our study presents structural insights into leishmanial RPE that could provide the basis for its implication to develop potent antileishmanials.
Collapse
Affiliation(s)
- Bandigi Narsimulu
- Department
of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Hyderabad 500046, India
| | | | - Pranay Jakkula
- Department
of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Hyderabad 500046, India
| | - Sayanna Are
- Department
of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Hyderabad 500046, India
| | - Insaf Ahmed Qureshi
- Department
of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Hyderabad 500046, India
| |
Collapse
|