1
|
Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
Collapse
Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| |
Collapse
|
2
|
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
|
3
|
Stasiak AC, Gogler K, Borisova M, Fink P, Mayer C, Stehle T, Zocher G. N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia. J Biol Chem 2023; 299:105076. [PMID: 37481208 PMCID: PMC10465942 DOI: 10.1016/j.jbc.2023.105076] [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: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023] Open
Abstract
The bacterial cell wall consists of a three-dimensional peptidoglycan layer, composed of peptides linked to the sugars N-acetylmuramic acid (MurNAc) and GlcNAc. Unlike other bacteria, the pathogenic Tannerella forsythia, a member of the red complex group of bacteria associated with the late stages of periodontitis, lacks biosynthetic pathways for MurNAc production and therefore obtains MurNAc from the environment. Sugar kinases play a crucial role in the MurNAc recycling process, activating the sugar molecules by phosphorylation. In this study, we present the first crystal structures of a MurNAc kinase, called murein sugar kinase (MurK), in its unbound state as well as in complexes with the ATP analog β-γ-methylene adenosine triphosphate (AMP-PCP) and with MurNAc. We also determined the crystal structures of K1058, a paralogous MurNAc kinase of T. forsythia, in its unbound state and in complex with MurNAc. We identified the active site and residues crucial for MurNAc specificity as the less bulky side chains of S133, P134, and L135, which enlarge the binding cavity for the lactyl ether group, unlike the glutamate or histidine residues present in structural homologs. In establishing the apparent kinetic parameters for both enzymes, we showed a comparable affinity for MurNAc (Km 180 μM and 30 μM for MurK and K1058, respectively), with MurK being over two hundred times faster than K1058 (Vmax 80 and 0.34 μmol min-1 mg-1, respectively). These data might support a structure-guided approach to development of inhibitory MurNAc analogs for pathogen MurK enzymes.
Collapse
Affiliation(s)
| | - Karolin Gogler
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Phillipp Fink
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, University of Tuebingen, Tuebingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany.
| |
Collapse
|
4
|
Green SB, Lanier RJ, Carey SM, Morgan DR, Gracz H, Sherman J, Rodriguez A, D'Antonio EL. Synthesis, biochemical, and biological evaluation of C2 linkage derivatives of amino sugars, inhibitors of glucokinase from Trypanosoma cruzi. Bioorg Med Chem Lett 2021; 47:128227. [PMID: 34174398 DOI: 10.1016/j.bmcl.2021.128227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 11/25/2022]
Abstract
Eighteen amino sugar analogues were screened against Trypanosoma cruzi glucokinase (TcGlcK), a potential drug-target of the protozoan parasite in order to assess for viable enzyme inhibition. The analogues were divided into three amino sugar scaffolds that included d-glucosamine (d-GlcN), d-mannosamine (d-ManN), and d-galactosamine (d-GalN); moreover, all but one of these compounds were novel. TcGlcK is an important metabolic enzyme that has a role in producing G6P for glycolysis and the pentose phosphate pathway (PPP). The inhibition of these pathways via glucose kinases (i.e., glucokinase and hexokinase) appears to be a strategic approach for drug discovery. Glucose kinases phosphorylate d-glucose with co-substrate ATP to yield G6P and the formed G6P enters both pathways for catabolism. The compound screen revealed five on-target confirmed inhibitors that were all from the d-GlcN series, such as compounds 1, 2, 4, 5, and 6. Four of these compounds were strong TcGlcK inhibitors (1, 2, 4, and 6) since they were found to have micromolar inhibitory constant (Ki) values around 20 μM. Three of the on-target confirmed inhibitors (1, 5, and 6) revealed notable in vitro anti-T. cruzi activity with IC50 values being less than 50 μM. Compound 1 was benzoyl glucosamine (BENZ-GlcN), a known TcGlcK inhibitor that was the starting point for the design of the compounds in this study; in addition, TcGlcK - compound 1 inhibition properties were previously determined [D'Antonio, E. L. et al. (2015) Mol. Biochem. Parasitol. 204, 64-76]. As such, compounds 5 and 6 were further evaluated biochemically, where formal Ki values were determined as well as their mode of TcGlcK inhibition. The Ki values determined for compounds 5 and 6 were 107 ± 4 μM and 15.2 ± 3.3 μM, respectively, and both of these compounds exhibited the competitive inhibition mode.
Collapse
Affiliation(s)
- Scott B Green
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA
| | - Robert J Lanier
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA
| | - Shane M Carey
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA
| | | | - Hanna Gracz
- NMRService LLC, Raleigh, NC 27612, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695, USA
| | - Julian Sherman
- Department of Microbiology, New York University School of Medicine, 430 East 29(th) Street, New York, NY 10016, USA
| | - Ana Rodriguez
- Department of Microbiology, New York University School of Medicine, 430 East 29(th) Street, New York, NY 10016, USA
| | - Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA.
| |
Collapse
|
5
|
Mercaldi GF, D'Antonio EL, Aguessi A, Rodriguez A, Cordeiro AT. Discovery of antichagasic inhibitors by high-throughput screening with Trypanosoma cruzi glucokinase. Bioorg Med Chem Lett 2019; 29:1948-1953. [PMID: 31133533 DOI: 10.1016/j.bmcl.2019.05.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 12/14/2022]
Abstract
A high-throughput screening (HTS) campaign was carried out for Trypanosoma cruzi glucokinase (TcGlcK), a potential drug-target of the pathogenic protozoan parasite. Glycolysis and the pentose phosphate pathway (PPP) are important metabolic pathways for T. cruzi and the inhibition of the glucose kinases (i.e. glucokinase and hexokinase) may be a strategic approach for drug discovery. Glucose kinases phosphorylate d-glucose with co-substrate ATP to yield G6P, and moreover, the produced G6P enters both pathways for catabolism. The TcGlcK - HTS campaign revealed 25 novel enzyme inhibitors that were distributed in nine chemical classes and were discovered from a primary screen of 13,040 compounds. Thirteen of these compounds were found to have low micromolar IC50 enzyme - inhibition values; strikingly, four of those compounds exhibited low toxicity towards NIH-3T3 murine host cells and notable in vitro trypanocidal activity. These compounds were of three chemical classes: (a) the 3-nitro-2-phenyl-2H-chromene scaffold, (b) the N-phenyl-benzenesulfonamide scaffold, and (c) the gossypol scaffold. Two compounds from the 3-nitro-2-phenyl-2H-chromene scaffold were determined to be hit-to-lead candidates that can proceed further down the early-stage drug discovery process.
Collapse
Affiliation(s)
- Gustavo F Mercaldi
- Brazilian Center for Research in Energy and Materials, Brazilian Biosciences National Laboratory, Campinas, SP 13083-970, Brazil
| | - Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA.
| | - Annelie Aguessi
- Department of Microbiology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA
| | - Ana Rodriguez
- Department of Microbiology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA
| | - Artur T Cordeiro
- Brazilian Center for Research in Energy and Materials, Brazilian Biosciences National Laboratory, Campinas, SP 13083-970, Brazil
| |
Collapse
|