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Lin S, Liu C, Zhao X, Han X, Li X, Ye Y, Li Z. Recent Advances of Pyridinone in Medicinal Chemistry. Front Chem 2022; 10:869860. [PMID: 35402370 PMCID: PMC8984125 DOI: 10.3389/fchem.2022.869860] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
Pyridinones have been adopted as an important block in medicinal chemistry that could serve as hydrogen bond donors and acceptors. With the help of feasible synthesis routes via established condensation reactions, the physicochemical properties of such a scaffold could be manipulated by adjustment of polarity, lipophilicity, and hydrogen bonding, and eventually lead to its wide application in fragment-based drug design, biomolecular mimetics, and kinase hinge-binding motifs. In addition, most pyridinone derivatives exhibit various biological activities ranging from antitumor, antimicrobial, anti-inflammatory, and anticoagulant to cardiotonic effects. This review focuses on recent contributions of pyridinone cores to medicinal chemistry, and addresses the structural features and structure–activity relationships (SARs) of each drug-like molecule. These advancements contribute to an in-depth understanding of the potential of this biologically enriched scaffold and expedite the development of its new applications in drug discovery.
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Affiliation(s)
- Shibo Lin
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
- *Correspondence: Shibo Lin,
| | - Chun Liu
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xiaotian Zhao
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xiao Han
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Xuanhao Li
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Yongqin Ye
- Department of Pharmacy, Chengdu Second People’s Hospital, Chengdu, China
| | - Zheyu Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, China
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2
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Ilyina MG, Khamitov EM, Mustafin AG, Khursan SL. A theoretical quantitative estimation of acidity of uracil and its derivatives through the p
K
a
values. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Margarita G. Ilyina
- Department of ChemistryBashkir State University Ufa Russia
- Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and TechnologyInstitute of Petroleum Refining and Petrochemistry Ufa Russia
| | - Edward M. Khamitov
- Department of ChemistryBashkir State University Ufa Russia
- Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and TechnologyInstitute of Petroleum Refining and Petrochemistry Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
| | - Akhat G. Mustafin
- Department of ChemistryBashkir State University Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
| | - Sergey L. Khursan
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
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3
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El Kouni MH. Pyrimidine metabolism in schistosomes: A comparison with other parasites and the search for potential chemotherapeutic targets. Comp Biochem Physiol B Biochem Mol Biol 2017; 213:55-80. [PMID: 28735972 PMCID: PMC5593796 DOI: 10.1016/j.cbpb.2017.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/18/2022]
Abstract
Schistosomes are responsible for the parasitic disease schistosomiasis, an acute and chronic parasitic ailment that affects >240 million people in 70 countries worldwide. It is the second most devastating parasitic disease after malaria. At least 200,000 deaths per year are associated with the disease. In the absence of the availability of vaccines, chemotherapy is the main stay for combating schistosomiasis. The antischistosomal arsenal is currently limited to a single drug, Praziquantel, which is quite effective with a single-day treatment and virtually no host-toxicity. Recently, however, the question of reduced activity of Praziquantel has been raised. Therefore, the search for alternative antischistosomal drugs merits the study of new approaches of chemotherapy. The rational design of a drug is usually based on biochemical and physiological differences between pathogens and host. Pyrimidine metabolism is an excellent target for such studies. Schistosomes, unlike most of the host tissues, require a very active pyrimidine metabolism for the synthesis of DNA and RNA. This is essential for the production of the enormous numbers of eggs deposited daily by the parasite to which the granulomas response precipitates the pathogenesis of schistosomiasis. Furthermore, there are sufficient differences between corresponding enzymes of pyrimidine metabolism from the host and the parasite that can be exploited to design specific inhibitors or "subversive substrates" for the parasitic enzymes. Specificities of pyrimidine transport also diverge significantly between parasites and their mammalian host. This review deals with studies on pyrimidine metabolism in schistosomes and highlights the unique characteristic of this metabolism that could constitute excellent potential targets for the design of safe and effective antischistosomal drugs. In addition, pyrimidine metabolism in schistosomes is compared with that in other parasites where studies on pyrimidine metabolism have been more elaborate, in the hope of providing leads on how to identify likely chemotherapeutic targets which have not been looked at in schistosomes.
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Affiliation(s)
- Mahmoud H El Kouni
- Department of Pharmacology and Toxicology, Center for AIDS Research, Comprehensive Cancer Center, General Clinical Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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4
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Structural investigations on orotate phosphoribosyltransferase from Mycobacterium tuberculosis, a key enzyme of the de novo pyrimidine biosynthesis. Sci Rep 2017; 7:1180. [PMID: 28446777 PMCID: PMC5430920 DOI: 10.1038/s41598-017-01057-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 03/20/2017] [Indexed: 02/02/2023] Open
Abstract
The Mycobacterium tuberculosis orotate phosphoribosyltransferase (MtOPRT) catalyses the conversion of α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate (OA) in pyrophosphate and orotidine 5'-monophosphate (OMP), in presence of Mg2+. This enzyme is the only responsible for the synthesis of orotidine 5'-monophosphate, a key precursor in the de novo pyrimidine biosynthesis pathway, making MtOPRT an attractive drug target for the development of antitubercular agents. We report the crystal structures of MtOPRT in complex with PRPP (2.25 Å resolution), inorganic phosphate (1.90 Å resolution) and the exogenous compound Fe(III) dicitrate (2.40 Å resolution). The overall structure of the mycobacterial enzyme is highly similar to those described for other OPRTases, with the "flexible loop" assuming a well define conformation and making specific contacts with the Fe(III)-dicitrate complex. The structures here reported add to the knowledge of a potential drug target for tuberculosis, and will provide a useful tool for the structure-based drug design of potent enzyme inhibitors.
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5
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Orotic Acid, More Than Just an Intermediate of Pyrimidine de novo Synthesis. J Genet Genomics 2015; 42:207-19. [DOI: 10.1016/j.jgg.2015.04.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/04/2015] [Accepted: 04/09/2015] [Indexed: 01/21/2023]
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6
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Trithiocyanurate complexes of iron, manganese and nickel and their anticholinesterase activity. Molecules 2014; 19:4338-54. [PMID: 24717551 PMCID: PMC6272027 DOI: 10.3390/molecules19044338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/31/2014] [Accepted: 04/01/2014] [Indexed: 11/23/2022] Open
Abstract
The complexes of Fe(II), Mn(II) and Ni(II) with a combination of a Schiff base, nitrogen-donor ligand or macrocyclic ligand and trithiocyanuric acid (ttcH3) were prepared and characterized by elemental analysis and spectroscopies. Crystal and molecular structures of the iron complex of composition [Fe(L1)](ttcH2)(ClO4)·EtOH·H2O (1), where L1 is Schiff base derived from tris(2-aminoethyl)amine and 2-pyridinecarboxaldehyde, were solved. It was found that the Schiff base is coordinated to the central iron atom by six nitrogens forming deformed octahedral arrangement, whereas trithiocyanurate(1-) anion, perchlorate and solvent molecules are not coordinated. The X-ray structure of the Schiff base sodium salt is also presented and compared with the iron complex. The anticholinesterase activity of the complexes was also studied.
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7
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Breda A, Machado P, Rosado LA, Souto AA, Santos DS, Basso LA. Pyrimidin-2(1H)-ones based inhibitors of Mycobacterium tuberculosis orotate phosphoribosyltransferase. Eur J Med Chem 2012; 54:113-22. [PMID: 22608674 DOI: 10.1016/j.ejmech.2012.04.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/20/2012] [Accepted: 04/24/2012] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) is an ancient human chronic infectious disease caused mainly by Mycobacterium tuberculosis. The emergence of strains resistant to first and second line anti-TB drugs, associated with the increasing number of TB cases among HIV positive subjects, and the large number of individuals infected with latent bacilli have urged the development of new strategies to treat TB. Enzymes of nucleotide metabolism pathways provide promising molecular targets for the development of drugs, aiming at both active and latent TB. The orotate phosphoribosyltransferase (OPRT) enzyme catalyzes the synthesis of orotidine 5'-monophosphate from 5'-phospho-α-d-ribose 1'-diphosphate and orotic acid, in the de novo pyrimidine synthesis pathway. Based on the kinetic mechanism and molecular properties, here we describe the design, selection and synthesis of substrate analogs with inhibitory activity of M. tuberculosis OPRT (MtOPRT) enzyme. Steady-state kinetic measurements were employed to determine the mode of inhibition of commercially available and chemically derived compounds. The 6-Hydroxy-2-oxo-1,2-dihydropyridine-4-carboxylic acid (6) chemical compound and its derivative, 3-Benzylidene-2,6-dioxo-1,2,3,6-tetrahydropyridine-4-carboxylic acid (13), showed enzyme inhibition constants in the submicromolar range. Isothermal titration calorimetry data indicated that binding of both compounds to MtOPRT have negative enthalpy and favorable Gibbs free energy probably due to their high complementarity to the enzyme's binding pocket. Improvement of compound 13 hydrophobic character by addition of an aromatic ring substituent resulted in entropic optimization, reflected on a thermodynamic discrimination profile characteristic of high affinity ligands. These inhibitors represent lead compounds for further development of MtOPRT inhibitors with increased potency, which may be tested as anti-TB agents.
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Affiliation(s)
- Ardala Breda
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga 6900, Prédio 92A - TECNOPUC, 90619-900 Porto Alegre, Rio Grande do Sul, Brazil.
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8
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Amorati R, Valgimigli L, Pedulli GF, Grabovskiy SA, Kabal’nova NN, Chatgilialoglu C. Base-Promoted Reaction of 5-Hydroxyuracil Derivatives with Peroxyl Radicals. Org Lett 2010; 12:4130-3. [DOI: 10.1021/ol1017245] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Riccardo Amorati
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
| | - Luca Valgimigli
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
| | - Gian Franco Pedulli
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
| | - Stanislav A. Grabovskiy
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
| | - Natalia N. Kabal’nova
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Department of Organic Chemistry “A. Mangini”, University of Bologna, Via S. Giacomo 11, I-40126 Bologna, Italy, and ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobbetti 101, I-40129 Bologna, Italy
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9
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Kopel P, Doležal K, Machala L, Langer V. Synthesis, characterization and screening of biological activity of Zn(II), Fe(II) and Mn(II) complexes with trithiocyanuric acid. Polyhedron 2007. [DOI: 10.1016/j.poly.2006.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Abstract
Synthesis de novo, acquisition by salvage and interconversion of purines and pyrimidines represent the fundamental requirements for their eventual assembly into nucleic acids as nucleotides and the deployment of their derivatives in other biochemical pathways. A small number of drugs targeted to nucleotide metabolism, by virtue of their effect on folate biosynthesis and recycling, have been successfully used against apicomplexan parasites such as Plasmodium and Toxoplasma for many years, although resistance is now a major problem in the prevention and treatment of malaria. Many targets not involving folate metabolism have also been explored at the experimental level. However, the unravelling of the genome sequences of these eukaryotic unicellular organisms, together with increasingly sophisticated molecular analyses, opens up possibilities of introducing new drugs that could interfere with these processes. This review examines the status of established drugs of this type and the potential for further exploiting the vulnerability of apicomplexan human pathogens to inhibition of this key area of metabolism.
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Affiliation(s)
- John E Hyde
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK.
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11
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Reversible dehydration process in a novel three-dimensional covalent network based on pyrimidine-4,6-dionato bridging ligand. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2006.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Krungkrai SR, Aoki S, Palacpac NMQ, Sato D, Mitamura T, Krungkrai J, Horii T. Human malaria parasite orotate phosphoribosyltransferase: functional expression, characterization of kinetic reaction mechanism and inhibition profile. Mol Biochem Parasitol 2004; 134:245-55. [PMID: 15003844 DOI: 10.1016/j.molbiopara.2003.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 11/04/2003] [Accepted: 12/19/2003] [Indexed: 11/22/2022]
Abstract
Plasmodium falciparum, the causative agent of the most lethal form of human malaria, relies on de novo pyrimidine biosynthesis. A gene encoding orotate phosphoribosyltransferase (OPRT), the fifth enzyme of the de novo pathway catalyzing formation of orotidine 5'-monophosphate (OMP) and pyrophosphate (PP(i)) from 5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate, was identified from P. falciparum (pfOPRT). The deduced amino acid sequence for pfOPRT was compared with OPRTs from other organisms and found to be most similar to that of Escherichia coli. The catalytic residues and consensus sequences for substrate binding in the enzyme were conserved among other organisms. The pfOPRT was exceptional in that it contained a unique insertion of 20 amino acids and an amino-terminal extension of 66 amino acids, making the longest amino acid sequence (281 amino acids with a predicted molecular mass of 33kDa). The cDNA of the pfOPRT gene was cloned, sequenced and functionally expressed in soluble form. The recombinant pfOPRT was purified from the E. coli lysate by two steps, nickel metal-affinity and gel-filtration chromatography. From 1l E. coli culture, 1.2-1.5mg of pure pfOPRT was obtained. SDS-PAGE revealed that the pfOPRT had a molecular mass of 33kDa and analytical gel-filtration chromatography showed that the enzyme activity eluted at approximately 67kDa. Using dimethyl suberimidate to cross-link neighboring subunits of the pfOPRT, it was confirmed that the native enzyme exists in a dimeric form. The steady state kinetics of initial velocity and product inhibition studies indicate that the enzyme pfOPRT follows a random sequential kinetic mechanism. Compounds aimed at the pfOPRT nexus may act against the parasite through at least two mechanisms: by directly inhibiting the enzyme activity, or be processed to an inhibitor of thymidylate synthase. This study provides a working system with which to investigate new antimalarial agents targeted against P. falciparum OPRT.
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Affiliation(s)
- Sudaratana R Krungkrai
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
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13
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Mejias-Torres IA, Zimmermann BH. Molecular cloning, recombinant expression and partial characterization of the aspartate transcarbamoylase from Toxoplasma gondii. Mol Biochem Parasitol 2002; 119:191-201. [PMID: 11814571 DOI: 10.1016/s0166-6851(01)00415-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A cDNA coding for a monofunctional aspartate transcarbamoylase (ATCase) was isolated from a Toxoplasma gondii tachyzoite cDNA library using a complementation method. The calculated molecular mass of the deduced amino acid sequence was 46.8 kDa, with a predicted pI of 7.1. Size exclusion chromatography/laser-light scattering showed a single, monodisperse peak with molecular mass of 144 kDa. Amino acid sequence alignments revealed that active site residues of the Escherichia coli ATCase catalytic chain were conserved in the T. gondii sequence, and the latter shared 26-33% overall sequence identity with other ATCases. A recombinant enzyme was overexpressed in E. coli, and was purified with a yield of approximately 0.8 mg l(-1) culture. The temperature dependence of the recombinant enzyme was similar to that of native ATCase in T. gondii extracts. The K(m)'s for aspartate and carbamoyl phosphate were 7.82 mM, and 67.6 microM, respectively. The V(max) was 23900 micromol h(-1) mg(-1). Pyrimidine nucleotides had no significant effect on the enzyme's activity. N-phosphonoacetyl-L-aspartate (PALA) inhibited the enzyme with K(i)=0.38 microM. The T. gondii ATCases contained two additional sequences of approximately 24 residues each, which are not found in other ATCases. One of these sequences was susceptible to proteolysis by elastase.
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Affiliation(s)
- Ida A Mejias-Torres
- Department of Biochemistry, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, PR 00935, USA
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