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Pasupureddy R, Verma S, Goyal B, Pant A, Sharma R, Bhatt S, Vashisht K, Singh S, Saxena AK, Dixit R, Chakraborti S, Pandey KC. Understanding the complex formation of falstatin; an endogenous macromolecular inhibitor of falcipains. Int J Biol Macromol 2024; 265:130420. [PMID: 38460641 DOI: 10.1016/j.ijbiomac.2024.130420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Proteolytic activity constitutes a fundamental process essential for the survival of the malaria parasite and is thus highly regulated. Falstatin, a protease inhibitor of Plasmodium falciparum, tightly regulates the activity of cysteine hemoglobinases, falcipain-2 and 3 (FP2, FP3), by inhibiting FP2 through a single surface exposed loop. However, the multimeric nature of falstatin and its interaction with FP2 remained unexplored. Here we report that the N-terminal falstatin region is highly disordered, and needs chaperone activity (heat-shock protein 70, HSP70) for its folding. Protein-protein interaction assays showed a significant interaction between falstatin and HSP70. Further, characterization of the falstatin multimer through a series of biophysical techniques identified the formation of a falstatin decamer, which was extremely thermostable. Computational analysis of the falstatin decamer showed the presence of five falstatin dimers, with each dimer aligned in a head-to-tail orientation. Further, the falstatin C-terminal region was revealed to be primarily involved in the oligomerization process. Stoichiometric analysis of the FP2-falstatin multimer showed the formation of a heterooligomeric complex in a 1:1 ratio, with the participation of ten subunits of each protein. Taken together, our results report a novel protease-inhibitor complex and strengthens our understanding of the regulatory mechanisms of major plasmodium hemoglobinases.
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Affiliation(s)
- Rahul Pasupureddy
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India.
| | - Sonia Verma
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Department of Biotechnology, Noida Institute of Engineering & Technology, UP, India
| | - Bharti Goyal
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
| | - Akansha Pant
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India
| | - Ruby Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.
| | - Kapil Vashisht
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Ajay K Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Rajnikant Dixit
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Soumyananda Chakraborti
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Kailash C Pandey
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
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2
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da Silva DF, de Souza JL, da Costa DM, Costa DB, Moreira POL, Fonseca ALD, Varotti FDP, Cruz JN, Dos Santos CBR, Alves CQ, Leite FHA, Brandão HN. Antiplasmodial activity of coumarins isolated from Polygala boliviensis: in vitro and in silico studies. J Biomol Struct Dyn 2023; 41:13383-13403. [PMID: 36744465 DOI: 10.1080/07391102.2023.2173295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/21/2023] [Indexed: 02/07/2023]
Abstract
Polygala boliviensis is found in the Brazilian semiarid region. This specie is little chemically and biologically studied. Polygala spp. have different metabolites, especially coumarins. Studies indicate that coumarins have antimalarial potential, denoting the importance of researching new active compounds from plants, since the resistance of Plasmodium strains to conventional therapy has increased. The present study aimed to evaluate the antiplasmodial activity of auraptene and poligalen against a chloroquine-resistant strain of Plasmodium falciparum. Coumarins were isolated from P. boliviensis by open column chromatography and identified by Nuclear Magnetic Resonance Spectroscopy. A cytotoxicity assay was carried out using MTT test, and the in vitro antiplasmodial activity was evaluated using the W2 strain. The antiplasmodial activity results found were IC50=0.171 ± 0.016 for auraptene and 0.164 ± 0.012 for poligalen; the selectivity indexes were 78.71 and 609.76, respectively. Inverse virtual screening in the BRAMMT database by OCTOPUS 1.2 was applied to coumarins to find potential P. falciparum targets and showed higher affinity energy of auraptene for purine nucleoside phosphorylase (PfPNP) and of poligalen for dihydroorotate dehydrogenase (PfDHODH). Molecular Dynamics studies (MD and MM-GBSA) approach were applied to calculate binding energies against selected P. falciparum targets and showed that all coumarins were stable at the binding site during simulations. Furthermore, energies were favorable for complexation. This is the first report of auraptene in P. boliviensis species and of in vitro antiplasmodial activity of auraptene and poligalen. In silico studies indicated that the mechanism of action of coumarins is the inhibition of PfPNP and PfDHODH.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Danielle Figuerêdo da Silva
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Jéssica Lima de Souza
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Diego Mota da Costa
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - David Bacelar Costa
- Departamento de Saúde, Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Paulo Otávio Lourenço Moreira
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Amanda Luisa da Fonseca
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Fernando de Pilla Varotti
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Jorddy Neves Cruz
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Modelagem e Química Computacional, Universidade Federal do Amapá, Macapá, Amapá, Brazil
| | - Cleydson Breno Rodrigues Dos Santos
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Modelagem e Química Computacional, Universidade Federal do Amapá, Macapá, Amapá, Brazil
| | - Clayton Queiroz Alves
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Franco Henrique Andrade Leite
- Departamento de Saúde, Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Hugo Neves Brandão
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
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Rajaram K, Tewari SG, Wallqvist A, Prigge ST. Metabolic changes accompanying the loss of fumarate hydratase and malate-quinone oxidoreductase in the asexual blood stage of Plasmodium falciparum. J Biol Chem 2022; 298:101897. [PMID: 35398098 PMCID: PMC9118666 DOI: 10.1016/j.jbc.2022.101897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
In the glucose-rich milieu of red blood cells, asexually replicating malarial parasites mainly rely on glycolysis for ATP production, with limited carbon flux through the mitochondrial tricarboxylic acid (TCA) cycle. By contrast, gametocytes and mosquito-stage parasites exhibit an increased dependence on the TCA cycle and oxidative phosphorylation for more economical energy generation. Prior genetic studies supported these stage-specific metabolic preferences by revealing that six of eight TCA cycle enzymes are completely dispensable during the asexual blood stages of Plasmodium falciparum, with only fumarate hydratase (FH) and malate-quinone oxidoreductase (MQO) being refractory to deletion. Several hypotheses have been put forth to explain the possible essentiality of FH and MQO, including their participation in a malate shuttle between the mitochondrial matrix and the cytosol. However, using newer genetic techniques like CRISPR and dimerizable Cre, we were able to generate deletion strains of FH and MQO in P. falciparum. We employed metabolomic analyses to characterize a double knockout mutant of FH and MQO (ΔFM) and identified changes in purine salvage and urea cycle metabolism that may help to limit fumarate accumulation. Correspondingly, we found that the ΔFM mutant was more sensitive to exogenous fumarate, which is known to cause toxicity by modifying and inactivating proteins and metabolites. Overall, our data indicate that P. falciparum is able to adequately compensate for the loss of FH and MQO, rendering them unsuitable targets for drug development.
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Affiliation(s)
- Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shivendra G Tewari
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, Maryland, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, Maryland, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, Maryland, USA.
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4
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Brochier-Armanet C, Madern D. Phylogenetics and biochemistry elucidate the evolutionary link between l-malate and l-lactate dehydrogenases and disclose an intermediate group of sequences with mix functional properties. Biochimie 2021; 191:140-153. [PMID: 34418486 DOI: 10.1016/j.biochi.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/19/2021] [Accepted: 08/15/2021] [Indexed: 01/23/2023]
Abstract
The NAD(P)-dependent malate dehydrogenases (MDH) (EC 1.1.1.37) and NAD-dependent lactate dehydrogenases (LDH) (EC. 1.1.1.27) form a large superfamily that has been characterized in organisms belonging to the three Domains of Life. MDH catalyzes the reversible conversion of the oxaloacetate into malate, while LDH operates at the late stage of glycolysis by converting pyruvate into lactate. Phylogenetic studies proposed that the LDH/MDH superfamily encompasses five main groups of enzymes. Here, starting from 16,052 reference proteomes, we reinvestigated the relationships between MDH and LDH. We showed that the LDH/MDH superfamily encompasses three main families: MDH1, MDH2, and a large family encompassing MDH3, LDH, and L-2-hydroxyisocaproate dehydrogenases (HicDH) sequences. An in-depth analysis of the phylogeny of the MDH3/LDH/HicDH family and of the nature of three important amino acids, located within the catalytic site and involved in binding and substrate discrimination, revealed a large group of sequences displaying unexpected combinations of amino acids at these three critical positions. This group branched in-between canonical MDH3 and LDH sequences. The functional characterization of several enzymes from this intermediate group disclosed a mix of functional properties, indicating that the MDH3/LDH/HicDH family is much more diverse than previously thought, and blurred the frontier between MDH3 and LDH enzymes. Present-days enzymes of the intermediate group are a valuable material to study the evolutionary steps that led to functional diversity and emergence of allosteric regulation within the LDH/MDH superfamily.
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Affiliation(s)
- Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622, Villeurbanne, France.
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5
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Reyes Romero A, Lunev S, Popowicz GM, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak TA, Dömling ASS, Groves MR. A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity. Commun Biol 2021; 4:949. [PMID: 34376783 PMCID: PMC8355244 DOI: 10.1038/s42003-021-02442-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/09/2021] [Indexed: 11/14/2022] Open
Abstract
Malate dehydrogenases (MDHs) sustain tumor growth and carbon metabolism by pathogens including Plasmodium falciparum. However, clinical success of MDH inhibitors is absent, as current small molecule approaches targeting the active site are unselective. The presence of an allosteric binding site at oligomeric interface allows the development of more specific inhibitors. To this end we performed a differential NMR-based screening of 1500 fragments to identify fragments that bind at the oligomeric interface. Subsequent biophysical and biochemical experiments of an identified fragment indicate an allosteric mechanism of 4-(3,4-difluorophenyl) thiazol-2-amine (4DT) inhibition by impacting the formation of the active site loop, located >30 Å from the 4DT binding site. Further characterization of the more tractable homolog 4-phenylthiazol-2-amine (4PA) and 16 other derivatives are also reported. These data pave the way for downstream development of more selective molecules by utilizing the oligomeric interfaces showing higher species sequence divergence than the MDH active site. Romero et al. perform NMR-based screening of 1500 fragments to identify fragments that bind at the oligomeric interface of malate dehydrogenase (MDH). Their study indicates an allosteric mechanism impacting enzymatic activity, paving the way for development of more selective molecules and a starting point for the future development of specific MDH inhibitors.
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Affiliation(s)
- Atilio Reyes Romero
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands
| | - Serjey Lunev
- EV Biotech, Zernikelaan 8, Groningen, the Netherlands
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Vito Calderone
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Alexander S S Dömling
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands
| | - Matthew R Groves
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands.
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6
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Sonani RR, Kurpiewska K, Lewiński K, Dubin G. Distinct sequence and structural feature of trypanosoma malate dehydrogenase. Biochem Biophys Res Commun 2021; 557:288-293. [PMID: 33894416 DOI: 10.1016/j.bbrc.2021.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Glycosomal malate dehydrogenase from Trypanosoma cruzi (tcgMDH) catalyzes the oxidation/reduction of malate/oxaloacetate, a crucial step of the glycolytic process occurring in the glycosome of the human parasite. Inhibition of tcgMDH is considered a druggable trait for the development of trypanocidal drugs. Sequence comparison of MDHs from different organisms revealed a distinct insertion of a prolin rich 9-mer (62-KLPPVPRDP-70) in tcgMDH as compared to other eukaryotic MDHs. Crystal structure of tcgMDH is solved here at 2.6 Å resolution with Rwork/Rfree values of 0.206/0.216. The tcgMDH forms homo-dimer with the solvation free energy (ΔGo) gain of -9.77 kcal/mol. The dimeric form is also confirmed in solution by biochemical assays, chemical-crosslinking and dynamic light scattering. The inserted 9-mer adopts a structure of a solvent accessible loop in the vicinity of NAD+ binding site. The distinct sequence and structural feature of tcgMDH, revealed in the present report, provides an anchor point for the development of inhibitors specific for tcgMDH, possible trypanocidal agents of the future.
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Affiliation(s)
- Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.
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Mangiagalli M, Barbiroli A, Santambrogio C, Ferrari C, Nardini M, Lotti M, Brocca S. The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping. Int J Biol Macromol 2021; 181:263-274. [PMID: 33775759 DOI: 10.1016/j.ijbiomac.2021.03.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Cristian Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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8
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Ferraris DM, Gelardi ELM, Garavaglia S, Miggiano R, Rizzi M. Targeting NAD-dependent dehydrogenases in drug discovery against infectious diseases and cancer. Biochem Soc Trans 2020; 48:693-707. [PMID: 32311017 DOI: 10.1042/BST20191261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/10/2020] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
Dehydrogenases are oxidoreductase enzymes that play a variety of fundamental functions in the living organisms and have primary roles in pathogen survival and infection processes as well as in cancer development. We review here a sub-set of NAD-dependent dehydrogenases involved in human diseases and the recent advancements in drug development targeting pathogen-associated NAD-dependent dehydrogenases. We focus also on the molecular aspects of the inhibition process listing the structures of the most relevant molecules targeting this enzyme family. Our aim is to review the most impacting findings regarding the discovery of novel inhibitory compounds targeting the selected NAD-dependent dehydrogenases involved in cancer and infectious diseases.
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9
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Thabault L, Liberelle M, Frédérick R. Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-63. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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10
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Gorki V, Walter NS, Singh R, Chauhan M, Dhingra N, Salunke DB, Kaur S. β-Carboline Derivatives Tackling Malaria: Biological Evaluation and Docking Analysis. ACS Omega 2020; 5:17993-18006. [PMID: 32743172 PMCID: PMC7391373 DOI: 10.1021/acsomega.0c01256] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/15/2020] [Indexed: 05/12/2023]
Abstract
Increasing resistance to presently available antimalarial drugs urges the need to look for new promising compounds. The β-carboline moiety, present in several biologically active natural products and drugs, is an important scaffold for antimalarial drug discovery. The present study explores the antimalarial activity of a β-carboline derivative (1R,3S)-methyl 1-(benzo[d][1,3]dioxol-5-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate (9a) alone in vitro against Plasmodium falciparum and in vivo in combination therapy with the standard drug artesunate against Plasmodium berghei. Compound 9a inhibited both 3D7 and RKL-9 strains of P. falciparum with half-maximal inhibitory concentration (IC50) < 1 μg/mL, respectively. The compound was nontoxic (50% cytotoxic concentration (CC50) > 640 μg/mL) to normal dermal fibroblasts. Selectivity index was >10 against both the strains. The compound exhibited considerable in vivo antimalarial activity (median effective dose (ED50) = 27.74 mg/kg) in monotherapy. The combination of 9a (100 mg/kg) and artesunate (50 mg/kg) resulted in 99.69% chemosuppression on day 5 along with a mean survival time of 25.8 ± 4.91 days with complete parasite clearance. Biochemical studies indicated the safety of the HIT compound to hepatic and renal functions of mice. Molecular docking also highlighted the suitability of 9a as a potential antimalarial candidate.
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Affiliation(s)
- Varun Gorki
- Parasitology
Laboratory, Department of Zoology, Panjab
University, Chandigarh 160014, India
| | - Neha Sylvia Walter
- Parasitology
Laboratory, Department of Zoology, Panjab
University, Chandigarh 160014, India
| | - Rahul Singh
- Department
of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Monika Chauhan
- University
Institute of Pharmaceutical Sciences, Panjab
University, Chandigarh 160014, India
| | - Neelima Dhingra
- University
Institute of Pharmaceutical Sciences, Panjab
University, Chandigarh 160014, India
| | - Deepak B. Salunke
- Department
of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Sukhbir Kaur
- Parasitology
Laboratory, Department of Zoology, Panjab
University, Chandigarh 160014, India
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11
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Bosch SS, Lunev S, Batista FA, Linzke M, Kronenberger T, Dömling ASS, Groves MR, Wrenger C. Molecular Target Validation of Aspartate Transcarbamoylase from Plasmodium falciparum by Torin 2. ACS Infect Dis 2020; 6:986-999. [PMID: 32129597 DOI: 10.1021/acsinfecdis.9b00411] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Malaria is a tropical disease that kills about half a million people around the world annually. Enzymatic reactions within pyrimidine biosynthesis have been proven to be essential for Plasmodium proliferation. Here we report on the essentiality of the second enzymatic step of the pyrimidine biosynthesis pathway, catalyzed by aspartate transcarbamoylase (ATC). Crystallization experiments using a double mutant ofPlasmodium falciparum ATC (PfATC) revealed the importance of the mutated residues for enzyme catalysis. Subsequently, this mutant was employed in protein interference assays (PIAs), which resulted in inhibition of parasite proliferation when parasites transfected with the double mutant were cultivated in medium lacking an excess of nutrients, including aspartate. Addition of 5 or 10 mg/L of aspartate to the minimal medium restored the parasites' normal growth rate. In vitro and whole-cell assays in the presence of the compound Torin 2 showed inhibition of specific activity and parasite growth, respectively. In silico analyses revealed the potential binding mode of Torin 2 to PfATC. Furthermore, a transgenic ATC-overexpressing cell line exhibited a 10-fold increased tolerance to Torin 2 compared with control cultures. Taken together, our results confirm the antimalarial activity of Torin 2, suggesting PfATC as a target of this drug and a promising target for the development of novel antimalarials.
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Affiliation(s)
- Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Fernando A. Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Alexander S. S. Dömling
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Matthew R. Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
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Abstract
Introduction: Malaria is one of the most prevalent human infections worldwide with over 40% of the world's population living in malaria-endemic areas. In the absence of an effective vaccine, emergence of drug-resistant strains requires urgent drug development. Current methods applied to drug target validation, a crucial step in drug discovery, possess limitations in malaria. These constraints require the development of techniques capable of simplifying the validation of Plasmodial targets.Areas covered: The authors review the current state of the art in techniques used to validate drug targets in malaria, including our contribution - the protein interference assay (PIA) - as an additional tool in rapid in vivo target validation.Expert opinion: Each technique in this review has advantages and disadvantages, implying that future validation efforts should not focus on a single approach, but integrate multiple approaches. PIA is a significant addition to the current toolset of antimalarial validation. Validation of aspartate metabolism as a druggable pathway provided proof of concept of how oligomeric interfaces can be exploited to control specific activity in vivo. PIA has the potential to be applied not only to other enzymes/pathways of the malaria parasite but could, in principle, be extrapolated to other infectious diseases.
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Affiliation(s)
- Fernando A Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.,Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Benjamin Gyau
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Juliana F Vilacha
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Soraya S Bosch
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.,Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matthew R Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
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Batista FA, Bosch SS, Butzloff S, Lunev S, Meissner KA, Linzke M, Romero AR, Wang C, Müller IB, Dömling ASS, Groves MR, Wrenger C. Oligomeric protein interference validates druggability of aspartate interconversion in Plasmodium falciparum. Microbiologyopen 2019; 8:e00779. [PMID: 30821109 PMCID: PMC6612543 DOI: 10.1002/mbo3.779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
The appearance of multi-drug resistant strains of malaria poses a major challenge to human health and validated drug targets are urgently required. To define a protein's function in vivo and thereby validate it as a drug target, highly specific tools are required that modify protein function with minimal cross-reactivity. While modern genetic approaches often offer the desired level of target specificity, applying these techniques is frequently challenging-particularly in the most dangerous malaria parasite, Plasmodium falciparum. Our hypothesis is that such challenges can be addressed by incorporating mutant proteins within oligomeric protein complexes of the target organism in vivo. In this manuscript, we provide data to support our hypothesis by demonstrating that recombinant expression of mutant proteins within P. falciparum leverages the native protein oligomeric state to influence protein function in vivo, thereby providing a rapid validation of potential drug targets. Our data show that interference with aspartate metabolism in vivo leads to a significant hindrance in parasite survival and strongly suggest that enzymes integral to aspartate metabolism are promising targets for the discovery of novel antimalarials.
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Affiliation(s)
- Fernando A. Batista
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Sabine Butzloff
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Sergey Lunev
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Kamila A. Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Atilio R. Romero
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Chao Wang
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Ingrid B. Müller
- LG MüllerBernhard Nocht Institute for Tropical MedicineHamburgGermany
| | - Alexander S. S. Dömling
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Matthew R. Groves
- Department of Pharmacy, Structural Biology Unit, XB20 Drug DesignUniversity of GroningenGroningenThe Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
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Lee D, Hong J, Kim K. Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula. Biochem Biophys Res Commun 2019; 509:833-8. [DOI: 10.1016/j.bbrc.2019.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/04/2019] [Indexed: 11/22/2022]
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