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Anchau Wegermann C, Santana Bezerra E, Gomes de Macedo Sant'Anna I, Ortega De Oliveira PC, da Costa Silva R, Rocco Machado T, Wanderley Tinoco L, Vieira de Souza MCB, Pascutti P, Santos Boechat FDC, de Moraes MC. Insights into nucleoside hydrolase from Leishmania donovani inhibition: A new bioaffinity chromatography-based screening assay and docking studies. Bioorg Chem 2024; 146:107302. [PMID: 38521010 DOI: 10.1016/j.bioorg.2024.107302] [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: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
Leishmaniasis, a group of neglected infectious diseases, encompasses a serious health concern, particularly with visceral leishmaniasis exhibiting potentially fatal outcomes. Nucleoside hydrolase (NH) has a fundamental role in the purine salvage pathway, crucial for Leishmania donovani survival, and presents a promising target for developing new drugs for visceral leishmaniasis treatment. In this study, LdNH was immobilized into fused silica capillaries, resulting in immobilized enzyme reactors (IMERs). The LdNH-IMER activity was monitored on-flow in a multidimensional liquid chromatography system, with the IMER in the first dimension. A C18 analytical column in the second dimension furnished the rapid separation of the substrate (inosine) and product (hypoxanthine), enabling direct enzyme activity monitoring through product quantification. LdNH-IMER exhibited high stability and was characterized by determining the Michaelis-Menten constant. A known inhibitor (1-(β-d-Ribofuranosyl)-4-quinolone derivative) was used as a model to validate the established method in inhibitor recognition. Screening of three additional derivatives of 1-(β-d-Ribofuranosyl)-4-quinolone led to the discovery of novel inhibitors, with compound 2a exhibiting superior inhibitory activity (Ki = 23.37 ± 3.64 µmol/L) compared to the employed model inhibitor. Docking and Molecular Dynamics studies provided crucial insights into inhibitor interactions at the enzyme active site, offering valuable information for developing new LdNH inhibitors. Therefore, this study presents a novel screening assay and contributes to the development of potent LdNH inhibitors.
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Affiliation(s)
- Camila Anchau Wegermann
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil; Laboratório GQCBio, Grupo de Química de Coordenação Biológica, Departamento de Química Geral e Inorgânica, Instituto de Química, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Evelyn Santana Bezerra
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Isabella Gomes de Macedo Sant'Anna
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Pamella Christina Ortega De Oliveira
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil
| | - Rodrigo da Costa Silva
- Laboratório LNHC, Instituto de Química, Departamento de Química Orgânica, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Thamires Rocco Machado
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luzineide Wanderley Tinoco
- Núcleo de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, 21941-902 Rio de Janeiro, RJ, Brazil
| | | | - Pedro Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda da Costa Santos Boechat
- Laboratório LNHC, Instituto de Química, Departamento de Química Orgânica, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Marcela Cristina de Moraes
- BioCrom, Laboratório de Cromatografia de Bioafinidade e Química Ambiental, Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Brazil.
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2
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de Oliveira PCO, Ceroullo MS, Dos Santos MB, Medeiros PRC, Marques BCB, Tinoco LW, de Souza MCBV, da Costa Santos Boechat F, de Moraes MC. Nucleoside hydrolase immobilized on magnetic particles as a tool for onflow screening and characterization of inhibitors. J Pharm Biomed Anal 2023; 235:115589. [PMID: 37531732 DOI: 10.1016/j.jpba.2023.115589] [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: 04/28/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
Nucleoside Hydrolases (NH) are considered a target for the development of new antiprotozoal agents. The development of new and automated screening assays for the identification of NH inhibitors can accelerate the first stages of the drug discovery process. In this work, NH from Leishmania donovani (LdNH) was covalently immobilized onto magnetic particles (LdNH-MPs) and trapped by magnets into a TFE tube to yield an immobilized enzyme reactor (IMER). For an automated assay, the LdNH-MP-IMER was connected in-line to an analytical column in an HPLC-DAD system to monitor the enzyme activity through quantification of the product hypoxanthine. Kinetic studies provided a KM value of 2079 ± 87 µmol.L-1 for the inosine substrate. Validation of the LdNH-MP-IMER for onflow screening purposes was performed with a library containing 12 quinolone ribonucleosides. Among them, three were identified as new competitive LdNH inhibitors, with Ki values between 83.5 and 169.4 µmol.L-1. This novel in-line screening assay has proven to be reliable, fast, low cost, and applicable to large libraries of compounds.
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Affiliation(s)
| | - Millena Santana Ceroullo
- BioCrom, Organic Chemistry Department, Chemistry Institute, Fluminense Federal University, Niterói, RJ, Brazil
| | - Mayane Barbosa Dos Santos
- LNHC, Organic Chemistry Department, Chemistry Institute, Fluminense Federal University, Niterói, RJ, Brazil
| | | | - Bruno Clemente Brandão Marques
- Laboratory for Analysis and Development of Enzyme Inhibitors, Natural Products Research Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luzineide Wanderley Tinoco
- Laboratory for Analysis and Development of Enzyme Inhibitors, Natural Products Research Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | | | - Marcela Cristina de Moraes
- BioCrom, Organic Chemistry Department, Chemistry Institute, Fluminense Federal University, Niterói, RJ, Brazil.
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3
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Patrone M, Galasyn GS, Kerin F, Nyitray MM, Parkin DW, Stockman BJ, Degano M. A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis. J Biol Chem 2023; 299:105077. [PMID: 37482279 PMCID: PMC10474468 DOI: 10.1016/j.jbc.2023.105077] [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: 04/11/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023] Open
Abstract
Pathogenic parasites of the Trichomonas genus are causative agents of sexually transmitted diseases affecting millions of individuals worldwide and whose outcome may include stillbirths and enhanced cancer risks and susceptibility to HIV infection. Trichomonas vaginalis relies on imported purine and pyrimidine nucleosides and nucleobases for survival, since it lacks the enzymatic activities necessary for de novo biosynthesis. Here we show that T. vaginalis additionally lacks homologues of the bacterial or mammalian enzymes required for the synthesis of the nicotinamide ring, a crucial component in the redox cofactors NAD+ and NADP. Moreover, we show that a yet fully uncharacterized T. vaginalis protein homologous to bacterial and protozoan nucleoside hydrolases is active as a pyrimidine nucleosidase but shows the highest specificity toward the NAD+ metabolite nicotinamide riboside. Crystal structures of the trichomonal riboside hydrolase in different states reveals novel intermediates along the nucleoside hydrolase-catalyzed hydrolytic reaction, including an unexpected asymmetry in the homotetrameric assembly. The active site structure explains the broad specificity toward different ribosides and offers precise insights for the engineering of specific inhibitors that may simultaneously target different essential pathways in the parasite.
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Affiliation(s)
- Marco Patrone
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy; Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy
| | - Gregory S Galasyn
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Fiona Kerin
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Mattias M Nyitray
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - David W Parkin
- Department of Chemistry, Adelphi University, Garden City, New York, USA
| | - Brian J Stockman
- Department of Chemistry, Adelphi University, Garden City, New York, USA.
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy; Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy.
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4
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Degano M. Structure, Oligomerization and Activity Modulation in N-Ribohydrolases. Int J Mol Sci 2022; 23:ijms23052576. [PMID: 35269719 PMCID: PMC8910321 DOI: 10.3390/ijms23052576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Enzymes catalyzing the hydrolysis of the N-glycosidic bond in nucleosides and other ribosides (N-ribohydrolases, NHs) with diverse substrate specificities are found in all kingdoms of life. While the overall NH fold is highly conserved, limited substitutions and insertions can account for differences in substrate selection, catalytic efficiency, and distinct structural features. The NH structural module is also employed in monomeric proteins devoid of enzymatic activity with different physiological roles. The homo-oligomeric quaternary structure of active NHs parallels the different catalytic strategies used by each isozyme, while providing a buttressing effect to maintain the active site geometry and allow the conformational changes required for catalysis. The unique features of the NH catalytic strategy and structure make these proteins attractive targets for diverse therapeutic goals in different diseases.
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Affiliation(s)
- Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, via Olgettina 60, 20132 Milano, Italy;
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy
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5
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An aza-nucleoside, fragment-like inhibitor of the DNA repair enzyme alkyladenine glycosylase (AAG). Bioorg Med Chem 2020; 28:115507. [PMID: 32327352 DOI: 10.1016/j.bmc.2020.115507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 11/21/2022]
Abstract
The DNA repair enzyme AAG has been shown in mice to promote tissue necrosis in response to ischaemic reperfusion or treatment with alkylating agents. A chemical probe inhibitor is required for investigations of the biological mechanism causing this phenomenon and as a lead for drugs that are potentially protective against tissue damage from organ failure and transplantation, and alkylative chemotherapy. Herein, we describe the rationale behind the choice of arylmethylpyrrolidines as appropriate aza-nucleoside mimics for an inhibitor followed by their synthesis and the first use of a microplate-based assay for quantification of their inhibition of AAG. We finally report the discovery of an imidazol-4-ylmethylpyrrolidine as a fragment-sized, weak inhibitor of AAG.
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6
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Nuñez C, Horenstein NA. Functional Analysis of a Gene Cluster from Chitinophaga pinensis Involved in Biosynthesis of the Pyrrolidine Azasugar DAB-1. JOURNAL OF NATURAL PRODUCTS 2019; 82:3401-3409. [PMID: 31793783 DOI: 10.1021/acs.jnatprod.9b00758] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Azasugars, "nitrogen in the ring" analogues of monosaccharides, are known to be distributed in select plant, fungal. and bacterial species. We identify Chitinophaga pinensis DSM 2588 as the first bacterial source of the plant pyrrolidine azasugar 1,4-dideoxy-1,4-aminoarabinitol (DAB-1). Comparative sequence analyses identified C. pinensis as a putative azasugar producer, via observation of a three-gene cluster coding for putative aminotransferase, alcohol dehydrogenase, and sugar phosphatase enzymes, similar to the previously reported azasugar biosynthetic signature identified in Bacillus amyloliquefaciens FZB42. Multistep fractionation of C. pinensis culture media guided by a maltase inhibition assay yielded a component with a mass consistent with the structure of DAB-1. Heterologous expression of the three-gene cluster in E. coli, a non-azasugar producer, led to the isolation of nectrisine, a biosynthetic precursor to DAB-1, which displayed potent slow tight binding inhibition of maltase. Reduction of nectrisine with NaBH4 removed the slow tight binding inhibition kinetics, and MS analysis provided evidence for the production of a compound matching that of the isolated DAB-1 from C. pinensis. 1H NMR analysis of the nectrisine produced in E. coli after NaBD4 reduction produced a spectrum consistent with DAB-1 deuterated at C-1, primarily at the pro-S position. These results support the idea that the azasugar three-gene cluster represents a general biosynthetic path leading to several different compounds, which may prove useful for the identification of other azasugar-producing organisms.
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Affiliation(s)
- Claribel Nuñez
- Department of Chemistry , University of Florida , Gainesville , Florida 32611-7200 , United States
| | - Nicole A Horenstein
- Department of Chemistry , University of Florida , Gainesville , Florida 32611-7200 , United States
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7
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Lenz SAP, Wetmore SD. Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations. J Comput Aided Mol Des 2018; 32:1375-1388. [PMID: 30478756 DOI: 10.1007/s10822-018-0178-y] [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: 07/20/2018] [Accepted: 11/21/2018] [Indexed: 11/25/2022]
Abstract
Parasitic protozoa rely on nucleoside hydrolases that play key roles in the purine salvage pathway by catalyzing the hydrolytic cleavage of the N-glycosidic bond that connects nucleobases to ribose sugars. Cytidine-uridine nucleoside hydrolase (CU-NH) is generally specific toward pyrimidine nucleosides; however, previous work has shown that replacing two active site residues with Tyr, specifically the Thr223Tyr and Gln227Tyr mutations, allows CU-NH to process inosine. The current study uses molecular dynamics (MD) simulations to gain atomic-level insight into the activity of wild-type and mutant E. coli CU-NH toward inosine. By examining systems that differ in the identity and protonation states of active site catalytic residues, key enzyme-substrate interactions that dictate the substrate specificity of CU-NH are identified. Regardless of the wild-type or mutant CU-NH considered, our calculations suggest that inosine binding is facilitated by interactions of the ribose moiety with active site residues and Ca2+, and π-interactions between two His residues (His82 and His239) and the nucleobase. However, the lack of observed activity toward inosine for wild-type CU-NH is explained by no residue being correctly aligned to stabilize the departing nucleobase. In contrast, a hydrogen-bonding network between hypoxanthine and a newly identified general acid (Asp15) is present when the two Tyr mutations are engineered into the active site. Investigation of the single CU-NH mutants reveals that this hydrogen-bonding network is only maintained when both Tyr mutations are present due to a π-interaction between the residues. These results rationalize previous experiments that show the single Tyr mutants are unable to efficiently hydrolyze inosine and explain how the Tyr residues work synergistically in the double mutant to stabilize the nucleobase leaving group during hydrolysis. Overall, our simulations provide a structural explanation for the substrate specificity of nucleoside hydrolases, which may be used to rationally develop new treatments for kinetoplastid diseases.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada.
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8
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Karami M, Jalali C, Mirzaie S. Combined virtual screening, MMPBSA, molecular docking and dynamics studies against deadly anthrax: An in silico effort to inhibit Bacillus anthracis nucleoside hydrolase. J Theor Biol 2017; 420:180-189. [DOI: 10.1016/j.jtbi.2017.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/03/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
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9
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Singh RK, Steyaert J, Versées W. Structural and biochemical characterization of the nucleoside hydrolase from C. elegans reveals the role of two active site cysteine residues in catalysis. Protein Sci 2017; 26:985-996. [PMID: 28218438 DOI: 10.1002/pro.3141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/28/2022]
Abstract
Nucleoside hydrolases (NHs) catalyze the hydrolysis of the N-glycoside bond in ribonucleosides and are found in all three domains of life. Although in parasitic protozoa a role in purine salvage has been well established, their precise function in bacteria and higher eukaryotes is still largely unknown. NHs have been classified into three homology groups based on the conservation of active site residues. While many structures are available of representatives of group I and II, structural information for group III NHs is lacking. Here, we report the first crystal structure of a purine-specific nucleoside hydrolase belonging to homology group III from the nematode Caenorhabditis elegans (CeNH) to 1.65Å resolution. In contrast to dimeric purine-specific NHs from group II, CeNH is a homotetramer. A cysteine residue that characterizes group III NHs (Cys253) structurally aligns with the catalytic histidine and tryptophan residues of group I and group II enzymes, respectively. Moreover, a second cysteine (Cys42) points into the active site of CeNH. Substrate docking shows that both cysteine residues are appropriately positioned to interact with the purine ring. Site-directed mutagenesis and kinetic analysis proposes a catalytic role for both cysteines residues, with Cys253 playing the most prominent role in leaving group activation.
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Affiliation(s)
- Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.,VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels, 1050, Belgium
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10
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Evans GB, Cameron SA, Luxenburger A, Guan R, Suarez J, Thomas K, Schramm VL, Tyler PC. Tight binding enantiomers of pre-clinical drug candidates. Bioorg Med Chem 2015; 23:5326-33. [PMID: 26260335 PMCID: PMC4567382 DOI: 10.1016/j.bmc.2015.07.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
MTDIA is a picomolar transition state analogue inhibitor of human methylthioadenosine phosphorylase and a femtomolar inhibitor of Escherichia coli methylthioadenosine nucleosidase. MTDIA has proven to be a non-toxic, orally available pre-clinical drug candidate with remarkable anti-tumour activity against a variety of human cancers in mouse xenografts. The structurally similar compound MTDIH is a potent inhibitor of human and malarial purine nucleoside phosphorylase (PNP) as well as the newly discovered enzyme, methylthioinosine phosphorylase, isolated from Pseudomonas aeruginosa. Since the enantiomers of some pharmaceuticals have revealed surprising biological activities, the enantiomers of MTDIH and MTDIA, compounds 1 and 2, respectively, were prepared and their enzyme binding properties studied. Despite binding less tightly to their target enzymes than their enantiomers compounds 1 and 2 are nanomolar inhibitors.
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Affiliation(s)
- Gary B Evans
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Scott A Cameron
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand; Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Andreas Luxenburger
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - Rong Guan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Javier Suarez
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Peter C Tyler
- Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
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11
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Chen N, Zhao Y, Lu J, Wu R, Cao Z. Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase. J Chem Theory Comput 2015; 11:3180-8. [DOI: 10.1021/acs.jctc.5b00045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People’s Republic of China
| | - Yuan Zhao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
| | - Jianing Lu
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People’s Republic of China
| | - Zexing Cao
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 360015, People’s Republic of China
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12
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Chirke SS, Rajender A, Lakshmi JK, Rao BV. A divergent, short, and stereoselective approach to pyrrolidine iminosugars: synthesis of 1,4-dideoxy-1,4-imino-derivatives of d-allitol, d-ribitol, ethyl-erythritol, and (−)-2,3-trans-3-4-cis-dihydroxyproline. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.01.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Roman G. Mannich bases in medicinal chemistry and drug design. Eur J Med Chem 2015; 89:743-816. [PMID: 25462280 PMCID: PMC7115492 DOI: 10.1016/j.ejmech.2014.10.076] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/18/2023]
Abstract
The biological activity of Mannich bases, a structurally heterogeneous class of chemical compounds that are generated from various substrates through the introduction of an aminomethyl function by means of the Mannich reaction, is surveyed, with emphasis on the relationship between structure and biological activity. The review covers extensively the literature reports that have disclosed Mannich bases as anticancer and cytotoxic agents, or compounds with potential antibacterial and antifungal activity in the last decade. The most relevant studies on the activity of Mannich bases as antimycobacterial agents, antimalarials, or antiviral candidates have been included as well. The review contains also a thorough coverage of anticonvulsant, anti-inflammatory, analgesic and antioxidant activities of Mannich bases. In addition, several minor biological activities of Mannich bases, such as their ability to regulate blood pressure or inhibit platelet aggregation, their antiparasitic and anti-ulcer effects, as well as their use as agents for the treatment of mental disorders have been presented. The review gives in the end a brief overview of the potential of Mannich bases as inhibitors of various enzymes or ligands for several receptors.
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Affiliation(s)
- Gheorghe Roman
- Petru Poni Institute of Macromolecular Chemistry, Department of Inorganic Polymers, 41A Aleea Gr. Ghica Vodă, Iaşi 700487, Romania.
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14
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Hernández D, Boto A. Nucleoside Analogues: Synthesis and Biological Properties of Azanucleoside Derivatives. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301731] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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Chirke SS, Rajender A, Rao BV. A divergent approach for the synthesis of some polyhydroxy pyrrolidines and piperidines from ribosylamine. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Giannese F, Berg M, Van der Veken P, Castagna V, Tornaghi P, Augustyns K, Degano M. Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1553-66. [PMID: 23897478 DOI: 10.1107/s0907444913010792] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 04/20/2013] [Indexed: 11/11/2022]
Abstract
Sleeping sickness is a deadly disease that primarily affects sub-Saharan Africa and is caused by protozoan parasites of the Trypanosoma genus. Trypanosomes are purine auxotrophs and their uptake pathway has long been appreciated as an attractive target for drug design. Recently, one tight-binding competitive inhibitor of the trypanosomal purine-specific nucleoside hydrolase (IAGNH) showed remarkable trypanocidal activity in a murine model of infection. Here, the enzymatic characterization of T. brucei brucei IAGNH is presented, together with its high-resolution structures in the unliganded form and in complexes with different inhibitors, including the trypanocidal compound UAMC-00363. A description of the crucial contacts that account for the high-affinity inhibition of IAGNH by iminoribitol-based compounds is provided and the molecular mechanism underlying the conformational change necessary for enzymatic catalysis is identified. It is demonstrated for the first time that metalorganic complexes can compete for binding at the active site of nucleoside hydrolase enzymes, mimicking the positively charged transition state of the enzymatic reaction. Moreover, we show that divalent metal ions can act as noncompetitive IAGNH inhibitors, stabilizing a nonproductive conformation of the catalytic loop. These results open a path for rational improvement of the potency and the selectivity of existing compounds and suggest new scaffolds that may be used as blueprints for the design of novel antitrypanosomal compounds.
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Affiliation(s)
- Francesca Giannese
- Biocrystallography Unit, Department of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, via Olgettina 58, 20132 Milano, Italy
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Chen N, Ge H, Xu J, Cao Z, Wu R. Loop motion and base release in purine-specific nucleoside hydrolase: A molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1117-24. [DOI: 10.1016/j.bbapap.2013.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/25/2022]
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18
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Convenient Synthesis of 1,4-Dideoxy-1,4-imino-D-ribitol from D-Ribose. J CHEM-NY 2013. [DOI: 10.1155/2013/519415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a convenient synthesis of 1,4-dideoxy-1,4-imino-D-ribitol (DRB) from D-ribose. L-Lyxonolactone, a key intermediate in this synthesis, was prepared by base-promoted hydrolysis of a 5-chlorinated D-ribonolactone derivative with inversion of configuration at the C-4 position. Cyclization of the generated dimesylated L-lyxitol with benzylamine proceeded with another configurational inversion at C-4 to afford the D-ribo-configured pyrrolidine system, which upon deprotection gave DRB.
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19
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A flexible enantioselective approach to 3,4-dihydroxyprolinol derivatives by SmI2-mediated reductive coupling of chiral nitrone with ketones/aldehydes. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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20
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Mancini DT, Matos KS, da Cunha EF, Assis TM, Guimarães AP, França TC, Ramalho TC. Molecular modeling studies on nucleoside hydrolase from the biological warfare agentBrucella suis. J Biomol Struct Dyn 2012; 30:125-36. [DOI: 10.1080/07391102.2012.674293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B 2012; 116:1984-91. [DOI: 10.1021/jp211403j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruibo Wu
- School of
Pharmaceutical Sciences,
East Campus, Sun Yat-sen University, Guangzhou
510006, China
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Wengjin Gong
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Ting, Liu
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Zexing Cao
- State Key
Laboratory of Physical
Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of
Theoretical and Computational Chemistry, College of Chemistry and
Chemical Engineering, Xiamen University, Xiamen 361005, China
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22
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Guimarães AP, Oliveira AA, da Cunha EFF, Ramalho TC, França TCC. Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation. J Mol Model 2011; 17:2939-51. [DOI: 10.1007/s00894-011-0968-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 01/11/2011] [Indexed: 10/18/2022]
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23
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Guimarães AP, Oliveira AA, da Cunha EFF, Ramalho TC, França TCC. Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase fromBacillus anthracis. J Biomol Struct Dyn 2011; 28:455-69. [DOI: 10.1080/07391102.2011.10508588] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Boto A, Hernández D, Hernández R. One-Pot Conversion of Proline Derivatives into Iodinated Iminosugar-Based Nucleosides, Useful Precursors of Highly Functionalized Nucleoside Analogues. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Vandemeulebroucke A, Minici C, Bruno I, Muzzolini L, Tornaghi P, Parkin DW, Versées W, Steyaert J, Degano M. Structure and Mechanism of the 6-Oxopurine Nucleosidase from Trypanosoma brucei brucei,. Biochemistry 2010; 49:8999-9010. [DOI: 10.1021/bi100697d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- An Vandemeulebroucke
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Claudia Minici
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Ilaria Bruno
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Laura Muzzolini
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - Paola Tornaghi
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
| | - David W. Parkin
- Department of Chemistry, Adelphi University, Garden City, New York 11530-0701
| | - Wim Versées
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Jan Steyaert
- Department of Molecular and Cellular Interactions (VIB) and Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Massimo Degano
- Division of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, Milan, Italy
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Boto A, Hernández D, Hernández R. One-Pot Synthesis of Azanucleosides from Proline Derivatives - Stereoselectivity in Sequential Processes. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000360] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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27
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Evaluation of nucleoside hydrolase inhibitors for treatment of African trypanosomiasis. Antimicrob Agents Chemother 2010; 54:1900-8. [PMID: 20194690 DOI: 10.1128/aac.01787-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this paper, we present the biochemical and biological evaluation of N-arylmethyl-substituted iminoribitol derivatives as potential chemotherapeutic agents against trypanosomiasis. Previously, a library of 52 compounds was designed and synthesized as potent and selective inhibitors of Trypanosoma vivax inosine-adenosine-guanosine nucleoside hydrolase (IAG-NH). However, when the compounds were tested against bloodstream-form Trypanosoma brucei brucei, only one inhibitor, N-(9-deaza-adenin-9-yl)methyl-1,4-dideoxy-1,4-imino-d-ribitol (UAMC-00363), displayed significant activity (mean 50% inhibitory concentration [IC(50)] +/- standard error, 0.49 +/- 0.31 microM). Validation in an in vivo model of African trypanosomiasis showed promising results for this compound. Several experiments were performed to investigate why only UAMC-00363 showed antiparasitic activity. First, the compound library was screened against T. b. brucei IAG-NH and inosine-guanosine nucleoside hydrolase (IG-NH) to confirm the previously demonstrated inhibitory effects of the compounds on T. vivax IAG-NH. Second, to verify the uptake of these compounds by T. b. brucei, their affinities for the nucleoside P1 and nucleoside/nucleobase P2 transporters of T. b. brucei were tested. Only UAMC-00363 displayed significant affinity for the P2 transporter. It was also shown that UAMC-00363 is concentrated in the cell via at least one additional transporter, since P2 knockout mutants of T. b. brucei displayed no resistance to the compound. Consequently, no cross-resistance to the diamidine or the melaminophenyl arsenical classes of trypanocides is expected. Third, three enzymes of the purine salvage pathway of procyclic T. b. brucei (IAG-NH, IG-NH, and methylthioadenosine phosphorylase [MTAP]) were investigated using RNA interference. The findings from all these studies showed that it is probably not sufficient to target only the nucleoside hydrolase activity to block the purine salvage pathway of T. b. brucei and that, therefore, it is possible that UAMC-00363 acts on an additional target.
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Borrmann T, Abdelrahman A, Volpini R, Lambertucci C, Alksnis E, Gorzalka S, Knospe M, Schiedel AC, Cristalli G, Müller CE. Structure−Activity Relationships of Adenine and Deazaadenine Derivatives as Ligands for Adenine Receptors, a New Purinergic Receptor Family. J Med Chem 2009; 52:5974-89. [DOI: 10.1021/jm9006356] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Borrmann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Aliaa Abdelrahman
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Rosaria Volpini
- Dipartimento di Scienze Chimiche, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Catia Lambertucci
- Dipartimento di Scienze Chimiche, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Edgars Alksnis
- Latvian Institute of Organic Synthesis, Aizkraukles iela 21, Riga LV-1006, Latvia
| | - Simone Gorzalka
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Melanie Knospe
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Anke C. Schiedel
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Gloria Cristalli
- Dipartimento di Scienze Chimiche, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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Versées W, Goeminne A, Berg M, Vandemeulebroucke A, Haemers A, Augustyns K, Steyaert J. Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:953-60. [DOI: 10.1016/j.bbapap.2009.02.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 02/02/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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30
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Berg M, Bal G, Goeminne A, Van der Veken P, Versées W, Steyaert J, Haemers A, Augustyns K. Synthesis of BicyclicN-Arylmethyl-Substituted Iminoribitol Derivatives as Selective Nucleoside Hydrolase Inhibitors. ChemMedChem 2009; 4:249-60. [DOI: 10.1002/cmdc.200800231] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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