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Alves SMDL, da Silva SB, Santos RCA, Feitosa SG, de Farias PHM, Júnior JADS, Rodrigues D, Potje SR, Tostes RC, Dos Anjos JV, Araújo AV. New morpholine-containing pyrimidinones act on α-adrenoceptors. Eur J Pharmacol 2024:176788. [PMID: 38977175 DOI: 10.1016/j.ejphar.2024.176788] [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: 10/11/2023] [Revised: 05/27/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
Drugs that act on α-adrenoceptors may contain morpholine and pyrimidinone heterocycles. The aim of this study was to synthesize a series of pyrimidinones (S6a-e and S8) and characterize their α-adrenoceptor activity. Cytotoxicity assays (MTT and LDH) were performed in A7r5 and HUVECs. Concentration-effect curves to phenylephrine (Phe) were performed in rat aortic rings in the presence of compounds S6a-e and S8 or vehicle. Nitric oxide (NO) production and NO stable metabolic products, nitrite and nitrate, expressed as total nitrogen oxides (NOx) were assessed in HUVECs by confocal microscopy with the DAF-2DA probe and by the Griess reaction, respectively. Molecular docking simulations were performed using the 6a compound and α2A-adrenoceptor. In the evaluated conditions, the percentage of viable cells and the release of LDH were similar between control cells and cells exposed to the tested pyrimidinones. S6d, S6e, S8, and the positive control prazosin (but not S6a, S6b, and S6c) decreased Phe-induced contractions in endothelium-denuded aortic rings. S6a, S6b, and S6c decreased Phe-induced contractions in endothelium-intact aortic rings. The effect of S6a was abolished by L-NAME. NO production and NOx levels were inhibited in the presence of the α2 receptor antagonist yohimbine and the NOS inhibitor L-NAME. The 6a docking simulation estimated that the mean binding free energy of the compound was lower than the estimated value for yohimbine. These data suggest that S6d, S6e, and S8 may be α1-adrenoceptor antagonists while S6a acts as an agonist of α2-adrenoceptors.
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Affiliation(s)
- Silvia Maria de Luna Alves
- Centro Acadêmico de Vitória, Universidade Federal de Pernambuco - UFPE, Vitória de Santo Antão-PE, Brasil
| | - Sidiane Barros da Silva
- Centro Acadêmico de Vitória, Universidade Federal de Pernambuco - UFPE, Vitória de Santo Antão-PE, Brasil
| | | | - Sidney Gustavo Feitosa
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco - UFPE, Recife-PE, Brasil
| | - Paulo Henrique Miranda de Farias
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco - UFPE, Recife-PE, Brasil
| | | | - Daniel Rodrigues
- Departamento de Farmacologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo - USP, Ribeirão Preto-SP, Brasil
| | - Simone Regina Potje
- Departamento de Ciências Médicas, Unidade Acadêmica de Passos, Universidade do Estado de Minas Gerais - UEMG, Passos-MG, Brasil
| | - Rita C Tostes
- Departamento de Farmacologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo - USP, Ribeirão Preto-SP, Brasil
| | - Janaína Vesiani Dos Anjos
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco - UFPE, Recife-PE, Brasil
| | - Alice Valença Araújo
- Centro Acadêmico de Vitória, Universidade Federal de Pernambuco - UFPE, Vitória de Santo Antão-PE, Brasil;.
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2
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Silva LDD, Pinheiro JLS, Rodrigues LHM, Santos VMRD, Borges JLF, Oliveira RRD, Maciel LG, Araújo TDSL, Martins CDS, Gomes DA, Lira EC, Souza MHLP, Medeiros JVR, Damasceno ROS. Crucial role of carbon monoxide as a regulator of diarrhea caused by cholera toxin: Evidence of direct interaction with toxin. Biochem Pharmacol 2023; 216:115791. [PMID: 37689274 DOI: 10.1016/j.bcp.2023.115791] [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: 07/04/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
The present study evaluated the role of heme oxygenase 1 (HO-1)/carbon monoxide (CO) pathway in the cholera toxin-induced diarrhea and its possible action mechanism. The pharmacological modulation with CORM-2 (a CO donor) or Hemin (a HO-1 inducer) decreased the intestinal fluid secretion and Cl- efflux, altered by cholera toxin. In contrast, ZnPP (a HO-1 inhibitor) reversed the antisecretory effect of Hemin and potentiated cholera toxin-induced intestinal secretion. Moreover, CORM-2 also prevented the alteration of intestinal epithelial architecture and local vascular permeability promoted by cholera toxin. The intestinal absorption was not altered by any of the pharmacological modulators. Cholera toxin inoculation also increased HO-1 immunoreactivity and bilirubin levels, a possible protective physiological response. Finally, using fluorometric technique, ELISA assay and molecular docking simulations, we show evidence that CO directly interacts with cholera toxin, forming a complex that affects its binding to GM1 receptor, which help explain the antisecretory effect. Thus, CO is an essential molecule for protection against choleric diarrhea and suggests its use as a possible therapeutic tool.
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Affiliation(s)
- Lorena Duarte da Silva
- Department of Physiology and Pharmacology, Federal University of Pernambuco, Recife, PE, Brazil
| | | | | | | | | | | | | | | | | | - Dayane Aparecida Gomes
- Department of Physiology and Pharmacology, Federal University of Pernambuco, Recife, PE, Brazil
| | - Eduardo Carvalho Lira
- Department of Physiology and Pharmacology, Federal University of Pernambuco, Recife, PE, Brazil
| | | | - Jand Venes Rolim Medeiros
- Biotechnology and Biodiversity Center Research, Parnaíba Delta Federal University, Parnaíba, PI, Brazil
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3
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Maciel LG, Barbosa ADS, de Alencar-Filho EB, Soares TA, Dos Anjos JV. A second generation of 1,2,4-oxadiazole derivatives with enhanced solubility for inhibition of 3-hydroxykynurenine transaminase (HKT) from Aedes aegypti. RSC Med Chem 2020; 12:222-236. [PMID: 34046611 DOI: 10.1039/d0md00305k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/17/2020] [Indexed: 12/30/2022] Open
Abstract
The most widely used method for the control of the Aedes aegypti mosquito population is the chemical control method. It represents a time- and cost-effective way to curb several diseases (e.g. dengue, Zika, chikungunya, yellow fever) through vector control. For this reason, the discovery of new compounds with a distinct mode of action from the available ones is essential in order to minimize the rise of insecticide resistance. Detoxification enzymes are an attractive target for the discovery of new insecticides. The kynurenine pathway is an important metabolic pathway, and it leads to the chemically stable xanthurenic acid, biosynthesized from 3-hydroxykynurenine, a precursor of reactive oxygen and nitrogen species, by the enzyme 3-hydroxykynurenine transaminase (HKT). Previously, we have reported the effectiveness of 1,2,4-oxadiazole derivatives acting as larvicides for A. aegypti and AeHKT inhibitors from in vitro and in silico studies. Here, we report the synthesis of new sodium 4-[3-(aryl)-1,2,4-oxadiazol-5-yl] propanoates and the cognate HKT-inhibitory activity. These new derivatives act as competitive inhibitors with IC50 values in the range of 42 to 339 μM. We further performed molecular docking simulations and QSAR analysis for the previously synthesized sodium 4-[3-(aryl)-1,2,4-oxadiazol-5-yl] butanoates reported earlier by our group and the data produced herein. Most of the 1,2,4-oxadiazole derivatives, including the canonical compounds for both series, showed a similar binding mode with HKT. The binding occurs similarly to the co-crystallized inhibitor via anchoring to Arg356 and positioning of the aromatic ring and its substituents outwards at the entry of the active site. QSAR analysis was performed in search of more than 770 molecular descriptors to establish a relationship between the lowest energy conformations and the IC50 values. The five best descriptors were selected to create and validate the model, which exhibited parameters that attested to its robustness and predictability. In summary, we observed that compounds with a para substitution and heavier groups (i.e. CF3 and NO2 substituents) had an enhanced HKT-inhibition profile. These compounds comprise a series described as AeHKT inhibitors via enzymatic inhibition experiments, opening the way to further the development of new substances with higher potency against HKT from Aedes aegypti.
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Affiliation(s)
- Larissa G Maciel
- Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE) Recife - PE Brazil
| | - Andrey da S Barbosa
- Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE) Recife - PE Brazil
| | | | - Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE) Recife - PE Brazil
| | - Janaína V Dos Anjos
- Department of Fundamental Chemistry, Federal University of Pernambuco (UFPE) Recife - PE Brazil
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4
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Maciel LG, Oliveira AA, Romão TP, Leal LLL, Guido RVC, Silva-Filha MHNL, Dos Anjos JV, Soares TA. Discovery of 1,2,4-oxadiazole derivatives as a novel class of noncompetitive inhibitors of 3-hydroxykynurenine transaminase (HKT) from Aedes aegypti. Bioorg Med Chem 2019; 28:115252. [PMID: 31864777 DOI: 10.1016/j.bmc.2019.115252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]
Abstract
The mosquito Aedes aegypti is the vector of arboviruses such as Zika, Chikungunya, dengue and yellow fever. These infectious diseases have a major impact on public health. The unavailability of effective vaccines or drugs to prevent or treat most of these diseases makes vector control the main form of prevention. One strategy to promote mosquito population control is the use of synthetic insecticides to inhibit key enzymes in the metabolic pathway of these insects, particularly during larval stages. One of the main targets of the kynurenine detoxification pathway in mosquitoes is the enzyme 3-hydroxykynurenine transaminase (HKT), which catalyzes the conversion of 3-hydroxykynurenine (3-HK) into xanthurenic acid (XA). In this work, we report eleven newly synthesized oxadiazole derivatives and demonstrate that these compounds are potent noncompetitive inhibitors of HKT from Ae. aegypti. The present data provide direct evidence that HKT can be explored as a molecular target for the discovery of novel larvicides against Ae. aegypti. More importantly, it ensures that structural information derived from the HKT 3D-structure can be used to guide the development of more potent inhibitors.
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Affiliation(s)
- Larissa G Maciel
- Department of Fundamental Chemistry - Federal University of Pernambuco, Av. Jornalista Aníbal Fernandes, s/n°Cidade Universitária - Recife, PE 50740-560, Brazil
| | - Andrew A Oliveira
- Sao Carlos Institute of Physics - University of São Paulo, Av. Joao Dagnone, 1100 Jardim Santa Angelina, São Carlos, SP 13563-120, Brazil
| | - Tatiany P Romão
- Institute Aggeu Magalhães (IAM) - FIOCRUZ, Av. Professor Moraes Rego s/n°, Recife, PE 50740-560 Brazil
| | - Laylla L L Leal
- Department of Fundamental Chemistry - Federal University of Pernambuco, Av. Jornalista Aníbal Fernandes, s/n°Cidade Universitária - Recife, PE 50740-560, Brazil
| | - Rafael V C Guido
- Sao Carlos Institute of Physics - University of São Paulo, Av. Joao Dagnone, 1100 Jardim Santa Angelina, São Carlos, SP 13563-120, Brazil
| | | | - Janaína V Dos Anjos
- Department of Fundamental Chemistry - Federal University of Pernambuco, Av. Jornalista Aníbal Fernandes, s/n°Cidade Universitária - Recife, PE 50740-560, Brazil.
| | - Thereza A Soares
- Department of Fundamental Chemistry - Federal University of Pernambuco, Av. Jornalista Aníbal Fernandes, s/n°Cidade Universitária - Recife, PE 50740-560, Brazil.
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5
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Kong R, Wang F, Zhang J, Wang F, Chang S. CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking. J Chem Inf Model 2019; 59:3556-3564. [DOI: 10.1021/acs.jcim.9b00445] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Feng Wang
- School of Information Science & Engineering, Changzhou University, Changzhou 213164, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Fengfei Wang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
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6
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Duffy binding-like 1α adhesin from Plasmodium falciparum recognizes ABH histo-blood group saccharide in a type specific manner. Carbohydr Polym 2019; 207:266-275. [PMID: 30600009 DOI: 10.1016/j.carbpol.2018.11.082] [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: 06/21/2018] [Revised: 10/30/2018] [Accepted: 11/25/2018] [Indexed: 11/20/2022]
Abstract
The ability of erythrocytes, infected by Plasmodium falciparum, to adhere to endothelial cells (cytoadherence) and to capture uninfected erythrocyte (rosetting) is the leading cause of death by severe malaria. Evidences link the binding of the adhesin Duffy Binding Like1-α (DBL1α) domain to the ABH histo-blood antigens with formation of rosettes. Inspired by this very close relationship between the disease susceptibility and individual blood type, here we investigate the structural requirements involved in the interaction of DBL1α with A, B and H histo-blood determinants and their subtypes. Our results evidence the high preference of DBL1α to A epitopes, in comparison to B and H epitopes. DBL1α interacts with ABH epitopes in subtype specific manner, presenting a remarkable affinity for type 2 structures, Fucα1-2Galβ1-4GlcNAcβ1, particularly the A2 epitope. The contacts made by DBL1α binding pocket and the ABH histo-blood groups were mapped by theoretical methods and supported by NMR experiments.
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7
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Abstract
Computational docking can be used to predict bound conformations and free energies of binding for small-molecule ligands to macromolecular targets. Docking is widely used for the study of biomolecular interactions and mechanisms, and it is applied to structure-based drug design. The methods are fast enough to allow virtual screening of ligand libraries containing tens of thousands of compounds. This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. The entire protocol will require ∼5 h.
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8
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Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ. A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. J Chem Inf Model 2015; 55:645-59. [PMID: 25636146 DOI: 10.1021/ci500672v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Isoniazid (INH) is usually administered to treat latent Mycobacterium tuberculosis (Mtb) infections and is used in combination therapy to treat active tuberculosis (TB). Unfortunately, resistance to this drug is hampering its clinical effectiveness. INH is a prodrug that must be activated by Mtb catalase-peroxidase (KatG) before it can inhibit InhA (Mtb enoyl-acyl-carrier-protein reductase). Isoniazid-resistant cases of TB found in clinical settings usually involve mutations in or deletion of katG, which abrogate INH activation. Compounds that inhibit InhA without requiring prior activation by KatG would not be affected by this resistance mechanism and hence would display continued potency against these drug-resistant isolates of Mtb. Virtual screening experiments versus InhA in the GO Fight Against Malaria (GO FAM) project were designed to discover new scaffolds that display base-stacking interactions with the NAD cofactor. GO FAM experiments included targets from other pathogens, including Mtb, when they had structural similarity to a malaria target. Eight of the 16 soluble compounds identified by docking against InhA plus visual inspection were modest inhibitors and did not require prior activation by KatG. The best two inhibitors discovered are both fragment-sized compounds and displayed Ki values of 54 and 59 μM, respectively. Importantly, the novel inhibitors discovered have low structural similarity to known InhA inhibitors and thus help expand the number of chemotypes on which future medicinal chemistry efforts can be focused. These new fragment hits could eventually help advance the fight against INH-resistant Mtb strains, which pose a significant global health threat.
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Affiliation(s)
- Alexander L Perryman
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Sean Ekins
- ⊥Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States.,#Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Stefano Forli
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | | | - Arthur J Olson
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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Carvalho PHPR, Correa JR, Guido BC, Gatto CC, De Oliveira HCB, Soares TA, Neto BAD. Designed Benzothiadiazole Fluorophores for Selective Mitochondrial Imaging and Dynamics. Chemistry 2014; 20:15360-74. [DOI: 10.1002/chem.201404039] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Indexed: 11/06/2022]
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10
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Mota AAR, Carvalho PHPR, Guido BC, de Oliveira HCB, Soares TA, Corrêa JR, Neto BAD. Bioimaging, cellular uptake and dynamics in living cells of a lipophilic fluorescent benzothiadiazole at low temperature (4 °C). Chem Sci 2014. [DOI: 10.1039/c4sc01785d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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11
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Liu JQ, Wu J, Jia ZB, Chen HL, Li QL, Sakiyama H, Soares T, Ren Fei RF, Daiguebonne C, Guillou O, Ng SW. Two isoreticular metal–organic frameworks with CdSO4-like topology: selective gas sorption and drug delivery. Dalton Trans 2014; 43:17265-73. [DOI: 10.1039/c4dt01890g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we have also investigated the binding mode of 5-FU to these frameworks, which provides an atomic level view of host–guest interactions.
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Affiliation(s)
- Jian-Qiang Liu
- School of Pharmacy
- Guangdong Medical College
- Dongguan, P. R. China
| | - Jian Wu
- Guangxi Key Laboratory of Chemistry and Engineering of Forest Products
- Guangxi University for Nationalities
- College of Chemistry and Chemical Engineering
- Nanning, China
| | - Zhen-Bin Jia
- School of Pharmacy
- Guangdong Medical College
- Dongguan, P. R. China
| | - Hong-Lang Chen
- School of Pharmacy
- Guangdong Medical College
- Dongguan, P. R. China
| | - Qing-Lin Li
- School of Pharmacy
- Guangdong Medical College
- Dongguan, P. R. China
| | - Hiroshi Sakiyama
- Department of Material and Biological Chemistry
- Faculty of Science
- Yamagata University
- Kojirakawa, Japan
| | - Thereza Soares
- Departament de Fundamental Chemistry
- Universidade Federal de Pernambuco
- Recife 50740-560, Brazil
| | - Ren Fei Ren Fei
- Department of Pharmacy
- Nanfang Hospital
- Southern Medical University
- Guangzhou 510515, China
| | - Carole Daiguebonne
- INSA
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- F-35708 Rennes, France
| | - Olivier Guillou
- INSA
- UMR 6226 “Institut des Sciences Chimiques de Rennes”
- F-35708 Rennes, France
| | - Seik Weng Ng
- Department of Chemistry
- University of Malaya
- 50603 Kuala Lumpur, Malaysia
- Chemistry Department
- King Abdulaziz University
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The enzyme 3-hydroxykynurenine transaminase as potential target for 1,2,4-oxadiazoles with larvicide activity against the dengue vector Aedes aegypti. Bioorg Med Chem 2013; 21:6996-7003. [PMID: 24095017 DOI: 10.1016/j.bmc.2013.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/30/2013] [Accepted: 09/07/2013] [Indexed: 11/21/2022]
Abstract
The mosquito Aedes aegypti is the vector agent responsible for the transmission of yellow fever and dengue fever viruses to over 80 million people in tropical and subtropical regions of the world. Exhaustive efforts have lead to a vaccine candidate with only 30% effectiveness against the dengue virus and failure to protect patients against the serotype 2. Hence, vector control remains the most viable route to dengue fever control programs. We have synthesized a class of 1,2,4-oxadiazole derivatives whose most biologically active compounds exhibit potent activity against Aedes aegypti larvae (ca. of 15 ppm) and low toxicity in mammals. Exposure to these larvicides results in larvae pigmentation in a manner correlated with the LC50 measurements. Structural comparisons of the 1,2,4-oxadiazole nucleus against known inhibitors of insect enzymes allowed the identification of 3-hydroxykynurenine transaminase as a potential target for these synthetic larvicides. Molecular docking calculations indicate that 1,2,4-oxadiazole compounds can bind to 3-hydroxykynurenine transaminase with similar conformation and binding energies as its crystallographic inhibitor 4-(2-aminophenyl)-4-oxobutanoic acid.
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13
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Vasconcelos IB, Silva TGD, Militão GCG, Soares TA, Rodrigues NM, Rodrigues MO, Costa NBD, Freire RO, Junior SA. Cytotoxicity and slow release of the anti-cancer drug doxorubicin from ZIF-8. RSC Adv 2012. [DOI: 10.1039/c2ra21087h] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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14
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Chen LTL, Yao Q, Soares TA, Squier TC, Bigelow DJ. Phospholamban modulates the functional coupling between nucleotide domains in Ca-ATPase oligomeric complexes in cardiac sarcoplasmic reticulum. Biochemistry 2010; 48:2411-21. [PMID: 19191503 DOI: 10.1021/bi8021526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligomeric interactions between Ca-ATPase polypeptide chains and their modulation by phospholamban (PLB) were measured in native cardiac sarcoplasmic reticulum (SR) microsomes. Progressive modification of Lys(514) with fluorescein 5-isothiocyanate (FITC), which physically blocks access to the nucleotide binding site by ATP, demonstrates that Ca-ATPase active sites function independently of one another prior to the phosphorylation of PLB. However, upon cAMP-dependent protein kinase (PKA) phosphorylation of PLB, a second-order dependence between residual enzyme activity and the fraction of active sites is observed, consistent with a dimeric functional complex. Complementary distance measurements were made using FITC or 5-iodoacetamidofluorescein (IAF) bound to Cys(674) within the N- or P-domains, respectively, to detect structural coupling within oligomeric complexes. Accompanying the phosphorylation of PLB, neighboring Ca-ATPase polypeptide chains exhibit a 4 +/- 2 A decrease in the proximity between FITC sites within the N-domain and a 9 +/- 3 A increase in the proximity between IAF sites within P-domains. Thus, the phosphorylation of PLB induces spatial rearrangements between the N- and P-domain elements of proximal Ca-ATPase polypeptide chains which restore functional interactions between neighboring polypeptide chains and, in turn, result in increased rates of catalytic turnover. These results are interpreted in terms of a structural model, calculated through optimization of shape complementarity, desolvation, and electrostatic energies, which suggests a dimeric arrangement of Ca-ATPase polypeptide chains through the proximal association of N-domains that accommodates interaction with PLB. We suggest that the phosphorylation of PLB acts to release constraints involving interdomain subunit interactions that enhance catalytically important N-domain motions.
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Affiliation(s)
- Linda T L Chen
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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15
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Sevastik R, Himo F. Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase. Bioorg Chem 2007; 35:444-57. [PMID: 17904194 DOI: 10.1016/j.bioorg.2007.08.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Accepted: 08/07/2007] [Indexed: 11/22/2022]
Abstract
The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.
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Affiliation(s)
- Robin Sevastik
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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16
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Tuttle T, Thiel W. Substrate Orientation in 4-Oxalocrotonate Tautomerase and Its Effect on QM/MM Energy Profiles. J Phys Chem B 2007; 111:7665-74. [PMID: 17567166 DOI: 10.1021/jp0685986] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tautomerization of 2-oxo-4E-hexendioate by 4-oxalocrotonate tautomerase has been studied by quantum mechanical/molecular mechanical (QM/MM) methods using three models, A-C, with different substrate orientations. The computed QM/MM energy profiles are rather different. Various energy partitioning analyses indicate the origin of these differences and the role of the active site residues for different substrate orientations. The proposed new model C is preferred over the previously used models A and B because it combines favorable substrate binding geometries with reasonable barriers and is consistent with the experimental evidence from mutation studies concerning the catalytic ability of specific residues in the binding site, especially R11'.
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Affiliation(s)
- Tell Tuttle
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany.
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17
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Tuttle T, Keinan E, Thiel W. Understanding the Enzymatic Activity of 4-Oxalocrotonate Tautomerase and Its Mutant Analogues: A Computational Study. J Phys Chem B 2006; 110:19685-95. [PMID: 17004838 DOI: 10.1021/jp0634858] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of replacing arginine residues (Arg) with citrulline residues (Cit) in the binding site of 4-oxalocrotonate tautomerase (4-OT) was investigated with force field molecular dynamics and hybrid quantum mechanics/molecular mechanics studies. It is found that the Arg61Cit mutation has only minor effects on the k(cat) and K(M) values determined experimentally because of the flexibility of this residue. The decrease in k(cat) and increase in K(M) for the Arg11Cit and Arg39Cit mutations are due to the disruption of the binding site, which arises from repulsive interactions with neighboring residues. The results of this investigation shed new light on the effects of mutations in the binding site of 4-OT and consequently on how the enzyme binds the active substrate.
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Affiliation(s)
- Tell Tuttle
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany.
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18
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Cisneros GA, Liu H, Zhang Y, Yang W. Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase. J Am Chem Soc 2003; 125:10384-93. [PMID: 12926963 DOI: 10.1021/ja029672a] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism for the reaction catalyzed by the 4-oxalocrotonate tautomerase (4-OT) enzyme has been studied using a quantum mechanical/molecular mechanical (QM/MM) method developed in our laboratory. Total free energy barriers were obtained for the two steps involved in this reaction. In the first step, Pro-1 acts as a general base to abstract a proton from the third carbon of the substrate, 2-oxo-4-hexenedioate, creating a negative charge on the oxygen at C-2 of this substrate. In the second step, the same hydrogen abstracted by the N-terminal Pro-1 is shuttled back to the fifth carbon of the substrate to form the product, 2-oxo-3-hexenedioate. The calculated total free energy barriers are 14.54 and 16.45 kcal/mol for the first and second steps, respectively. Our calculations clearly show that there is no general acid in the reaction. Arg-39' ', which is hydrogen bonded to the carboxylate group of the substrate, and an ordered water, which moves closer to the site of the charge formed in the transition state and intermediate, play the main role in transition state/intermediate stabilization without acting as general acids in the reaction.
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Affiliation(s)
- G Andrés Cisneros
- Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708-0346, USA
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19
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Brik A, Dawson PE, Keinan E. The product of the natural reaction catalyzed by 4-oxalocrotonate tautomerase becomes an affinity label of its mutant. Bioorg Med Chem 2002; 10:3891-7. [PMID: 12413840 DOI: 10.1016/s0968-0896(02)00385-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerization of 4-oxalocrotonate, 1, to 2-oxo-3E-hexenedioate, 3, using a general acid/base mechanism that involves a conserved N-terminal proline residue. The P1A and P1G mutants have been shown to catalyze this isomerization but at reduced rates. Analysis of these mutants by mass spectrometry demonstrated that P1A is susceptible to a 1,4-addition of the N-terminal primary amine across the double bond of enone 3 to form a covalent adduct. Although slower than the isomerization reaction, the addition is fast, with 50% of the active sites being alkylated within 12 min. By contrast, the wt4-OT shows no detectable modification over 24 h. These results support the hypothesis that avoidance of nucleophilic reactions, such as the irreversible Michael addition to the product, could be a contributing factor in the evolutionary conservation of N-terminal proline residues in 4OT.
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Affiliation(s)
- Ashraf Brik
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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20
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Soares TA, Lins RD, Straatsma TP, Briggs JM. Internal dynamics and ionization states of the macrophage migration inhibitory factor: comparison between wild-type and mutant forms. Biopolymers 2002; 65:313-23. [PMID: 12382291 DOI: 10.1002/bip.10252] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The macrophage migration inhibitory factor (MIF) is a cytokine that shares a common structural architecture and catalytic strategy with three isomerases: 4-oxalocrotonate tautomerase, 5-carboxymethyl-2-hydroxymuconate isomerase, and D-dopachrome tautomerase. A highly conserved N-terminal proline acts as a base-acid during the proton transfer reaction catalyzed by these enzymes. Such unusual catalytic strategy appears to be possible only due to the N-terminal proline pK(a) shifted to 5.0-6.0 units. Mutations of this residue result in a significant decrease of the catalytic activity of MIF. Two hypotheses have been proposed to explain the catalytic inefficiency of MIF: the lower basicity of primary amines with regard to secondary ones and the increased flexibility resulting from the replacement of a proline by residues like glycine. To investigate that, we have performed molecular dynamics simulations of MIF wild-type and its mutant P1G, as well as calculated the protonation properties of several mutant forms. It was found that the N-terminal glycine does not show larger fluctuations compared to proline, but the former residue is more exposed to the solvent throughout the simulations. The apparent pK(a) of these residues displays very little change (as expected from the structural rigidity of MIF) and is not significantly affected by the surrounding ionizable residues. Instead, the hydrophobic character of the active site seems to be the main factor in determining the pKa of the N-terminal residue and the catalytic efficiency of MIF.
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Affiliation(s)
- T A Soares
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
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21
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Soares T, Goodsell D, Ferreira R, Olson AJ, Briggs JM. Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism. J Mol Recognit 2000; 13:146-56. [PMID: 10867710 DOI: 10.1002/1099-1352(200005/06)13:3<146::aid-jmr497>3.0.co;2-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The macrophage migration inhibitory factor (MIF) is a cytokine that is structurally similar to certain isomerases and for which multiple immune and catalytic roles have been proposed. Different catalytic activities have been reported for MIF, yet the exact mechanism by which MIF acts is not completely known. As a tautomerase, the enzyme uses a general acid-base mechanism of proton transfer in which the amino-terminal proline has been shown to function as the catalytic base. We report the results of molecular docking simulations of macrophage migration inhibitory factor with three substrates, D-dopachrome, L-dopachrome methyl ester and p-(hydroxyphenyl)pyruvate. Electrostatic pK(a) predictions were also performed for the free and complexed forms of the enzyme. The predicted binding mode of p-(hydroxyphenyl)pyruvate is in agreement with the recently published X-ray structure. A model for the binding mode of D-dopachrome and L-dopachrome methyl ester to MIF is proposed which offers insights into the catalytic mechanism of D-dopachrome tautomerase activity of MIF. The proposed catalytic mechanism is further supported by the pK(a) predictions, which suggest that residue Lys32 acts as the general acid for the enzymatic catalysis of D-dopachrome.
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Affiliation(s)
- T Soares
- Department of Biology and Biochemistry, University of Houston, TX 77204-5513, USA
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