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Júnior MA, Silva LC, Rocha OB, Oliveira AA, Portis IG, Alonso A, Alonso L, Silva KS, Gomes MN, Andrade CH, Soares CM, Pereira M. Proteomic identification of metabolic changes in Paracoccidioides brasiliensis induced by a nitroheteroarylchalcone. Future Microbiol 2023; 18:1077-1093. [PMID: 37424510 DOI: 10.2217/fmb-2022-0150] [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] [Indexed: 07/11/2023] Open
Abstract
Aim: To access the metabolic changes caused by a chalcone derivative (LabMol-75) through a proteomic approach. Methods: Proteomic analysis was performed after 9 h of Paracoccidioides brasiliensis yeast (Pb18) cell incubation with the LabMol-75 at MIC. The proteomic findings were validated through in vitro and in silico assays. Results: Exposure to the compound led to the downregulation of proteins associated with glycolysis and gluconeogenesis, β-oxidation, the citrate cycle and the electron transport chain. Conclusion: LabMol-75 caused an energetic imbalance in the fungus metabolism and deep oxidative stress. Additionally, the in silico molecular docking approach pointed to this molecule as a putative competitive inhibitor of DHPS.
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Affiliation(s)
- Marcos Abc Júnior
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lívia C Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Olivia B Rocha
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Amanda A Oliveira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Igor G Portis
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Antonio Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lais Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kleber Sf Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Marcelo N Gomes
- InsiChem, Goiás State University, Anápolis, Goiás, Brazil
- Faculdade Metropolitana de Anápolis, Anápolis, Goiás, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Célia Ma Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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Arputharaj DS, Rajasekaran M, Nidhin P. Sulfamethoxazole: Molecular docking and crystal structure prediction. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2022.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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3
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Adhikari N, Choudhury AAK, Shakya A, Ghosh SK, Patgiri SJ, Singh UP, Bhat HR. Design and development of novel
N
‐(4‐aminobenzoyl)‐
l
‐glutamic acid conjugated 1,3,5‐triazine derivatives as
Pf
‐DHFR inhibitor: An
in‐silico
and
in‐vitro
study. J Biochem Mol Toxicol 2022; 37:e23290. [PMID: 36541419 DOI: 10.1002/jbt.23290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
In the present work, a library of 120 compounds was prepared using various aliphatic and aromatic amines. Finally, 10 compounds were selected through in silico screening carrying 4-aminobenzoyl-l-glutamic acid and 1,3,5-triazine moiety. The docking results of compounds 4d16 and 4d38 revealed higher binding interaction with amino acids Asp54 (-537.96 kcal/mol) and Asp54, Phe116 (-618.22 kcal/mol) against wild (1J3I) and quadruple mutant (1J3K) type of Pf-DHFR inhibitors and were comparable to standard WR99210. These compounds were developed by facile and microwave-assisted synthesis via nucleophilic substitution reaction and characterized by different spectroscopic methods. In vitro antimalarial assay results also suggested that these two compounds were having higher antimalarial activity against chloroquine-sensitive (3D7) and chloroquine-resistant (Dd2) strain out of the ten synthesized compounds with IC50 13.25 μM and 14.72 μM, respectively. These hybrid scaffolds might be useful in the lead discovery of a new class of Pf-DHFR inhibitors.
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Affiliation(s)
- Nayana Adhikari
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | | | - Anshul Shakya
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | - Surajit K. Ghosh
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
| | - Saurav J. Patgiri
- Regional Medical Research Centre, Indian Council of Medical Research (ICMR) Dibrugarh Assam India
| | - Udaya P. Singh
- Drug Design & Discovery Laboratory, Department of Pharmaceutical Sciences Sam Higginbottom University of Agriculture, Technology & Sciences Prayagraj Uttar Pradesh India
| | - Hans R. Bhat
- Department of Pharmaceutical Sciences Dibrugarh University Dibrugarh Assam India
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4
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Zhong CJ, Hu XL, Yang XL, Gan HQ, Yan KC, Shu FT, Wei P, Gong T, Luo PF, James TD, Chen ZH, Zheng YJ, He XP, Xia ZF. Metabolically Specific In Situ Fluorescent Visualization of Bacterial Infection on Wound Tissues. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39808-39818. [PMID: 36005548 DOI: 10.1021/acsami.2c10115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ability to effectively detect bacterial infection in human tissues is important for the timely treatment of the infection. However, traditional techniques fail to visualize bacterial species adhered to host cells in situ in a target-specific manner. Dihydropteroate synthase (DHPS) exclusively exists in bacterial species and metabolically converts p-aminobenzoic acid (PABA) to folic acid (FA). By targeting this bacterium-specific metabolism, we have developed a fluorescent imaging probe, PABA-DCM, based on the conjugation of PABA with a long-wavelength fluorophore, dicyanomethylene 4H-pyran (DCM). We confirmed that the probe can be used in the synthetic pathway of a broad spectrum of Gram-positive and negative bacteria, resulting in a significantly extended retention time in bacterial over mammalian cells. We validated that DHPS catalytically introduces a dihydropteridine group to the amino end of the PABA motif of PABA-DCM, and the resulting adduct leads to an increase in the FA levels of bacteria. We also constructed a hydrogel dressing containing PABA-DCM and graphene oxide (GO), termed PABA-DCM@GO, that achieves target-specific fluorescence visualization of bacterial infection on the wounded tissues of mice. Our research paves the way for the development of fluorescent imaging agents that target species-conserved metabolic pathways of microorganisms for the in situ monitoring of infections in human tissues.
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Affiliation(s)
- Chen-Jian Zhong
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
| | - Xi-Le Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Xiao-Lan Yang
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
- Department of Burn Surgery and Wound Repair, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362001, Fujian, China
| | - Hui-Qi Gan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Kai-Cheng Yan
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Fu-Ting Shu
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
| | - Pei Wei
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
| | - Teng Gong
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
| | - Peng-Fei Luo
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA27AY, United Kingdom
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, PR China
| | - Zhao-Hong Chen
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
| | - Yong-Jun Zheng
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 200438, China
| | - Zhao-Fan Xia
- Department of Burn Surgery and Wound Repair, Fujian Burn Medical Center, Fujian Provincial Key Laboratory of Burn and Trauma, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, PR China
- Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai 200433, China
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5
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Structure based design, synthesis, and biological evaluation of imidazole derivatives targeting dihydropteroate synthase enzyme. Bioorg Med Chem Lett 2021; 36:127819. [PMID: 33513385 DOI: 10.1016/j.bmcl.2021.127819] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 12/16/2022]
Abstract
In this study, we have designed and synthesized 2-((5-acetyl-1-(phenyl)-4-methyl-1H-imidazol-2-yl)thio)-N-(4-((benzyl)oxy)phenyl) acetamide derivatives. Antimicrobial activities of all the imidazole derivatives have been examined against Gram-positive and Gram-negative bacteria and results showed that the conjugates have appreciable antibacterial activity. Besides, several analogous were evaluated for their in vitro antiresistant bacterial strains such as Extended-spectrum beta-lactamases (ESBL), Vancomycin-resistant Enterococcus (VRE), and Methicillin-resistant Staphylococcus aureus (MRSA). The SAR revealed that the 12l compound resulted in potency against all bacterial strains as well as ESBL, VRE, and MRSA strains. Lipinski's rule of five, and ADME studies were preformed for all the synthesized compounds with Staphylococcus aureus dihydropteroate synthase (saDHPS) protein (PDB ID: 6CLV) and were found standard drug-likeness properties of conjugates. Moreover, the binding mode of the ligands with the protein study has been examined by molecular docking and results are quite promising. Besides, all the analogous were tested for their in vitro antituberculosis, antimalarial, and antioxidant activity.
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6
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Chitnumsub P, Jaruwat A, Talawanich Y, Noytanom K, Liwnaree B, Poen S, Yuthavong Y. The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance. FEBS J 2020; 287:3273-3297. [PMID: 31883412 DOI: 10.1111/febs.15196] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/04/2019] [Accepted: 12/27/2019] [Indexed: 11/28/2022]
Abstract
The clinical efficacy of sulfa drugs as antimalarials has declined owing to the evolution of resistance in Plasmodium falciparum (Pf) malaria parasites. In order to understand the basis of this resistance and to design more effective antimalarials, we have solved 13 structures of the bifunctional enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK)-dihydropteroate synthase (DHPS) from wild-type (WT) P. falciparum and sulfa-resistant mutants, both as apoenzyme and as complexes with pteroate (PTA) and sulfa derivatives. The structures of these complexes show that PTA, which effectively inhibits both the WT and mutants, stays in active sites without steric constraint. In contrast, parts of the sulfa compounds situated outside of the substrate envelope are in the vicinity of the resistance mutations. Steric conflict between compound and mutant residue along with increased flexibility of loop D2 in the mutants can account for the reduced compound binding affinity to the mutants. Kinetic data show that the mutants have enhanced enzyme activity compared with the WT. These PfDHPS structural insights are critical for the design of novel, substrate envelope-compliant DHPS inhibitors that are less vulnerable to resistance mutations. DATABASES: The data reported in this paper have been deposited in the Protein Data Bank, www.wwpdb.org. PDB ID codes: 6JWQ for apoWT; 6JWR, 6JWS, and 6JWT for PTA complexes of WT, A437G (3D7), and V1/S; 6JWU, 6JWV, and 6JWW for STZ-DHP complexes of WT, 3D7, and V1/S; 6JWX, 6JWY, and 6JWZ for SDX-DHP complexes of WT, 3D7, and W2; 6KCK, 6KCL, and 6KCM for Pterin/pHBA complexes of WT, TN1, and W2.
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Affiliation(s)
- Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yuwadee Talawanich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Krittikar Noytanom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Benjamas Liwnaree
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sinothai Poen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
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7
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Firestone RS, Schramm VL. The Transition-State Structure for Human MAT2A from Isotope Effects. J Am Chem Soc 2017; 139:13754-13760. [PMID: 28880543 DOI: 10.1021/jacs.7b05803] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human methionine S-adenosyltransferase (MAT2A) catalyzes the formation of S-adenosylmethionine (SAM) from ATP and methionine. Synthetic lethal genetic analysis has identified MAT2A as an anticancer target in tumor cells lacking expression of 5'-methylthioadenosine phosphorylase (MTAP). Approximately 15% of human cancers are MTAP-/-. The remainder can be rendered MTAP- through MTAP inhibitors. We used kinetic isotope effect (KIE), commitment factor (Cf), and binding isotope effect (BIE) measurements combined with quantum mechanical (QM) calculations to solve the transition state structure of human MAT2A. The reaction is characterized by an advanced SN2 transition state. The bond forming from the nucleophilic methionine sulfur to the 5'-C of ATP is 2.03 Å at the transition state (bond order of 0.67). Departure of the leaving group triphosphate of ATP is well advanced and forms a 2.32 Å bond between the 5'-C of ATP and the oxygen of the triphosphate (bond order of 0.23). Interaction of MAT2A with its MAT2B regulatory subunit causes no change in the intrinsic KIEs, indicating the same transition state structure. The transition state for MAT2A is more advanced along the reaction coordinate (more product-like) than that from the near-symmetrical transition state of methionine adenosyltransferase from E. coli.
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Affiliation(s)
- Ross S Firestone
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York, New York 10461, United States
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9
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Poulin MB, Schneck JL, Matico RE, Hou W, McDevitt PJ, Holbert M, Schramm VL. Nucleosome Binding Alters the Substrate Bonding Environment of Histone H3 Lysine 36 Methyltransferase NSD2. J Am Chem Soc 2016; 138:6699-702. [PMID: 27183271 PMCID: PMC6702673 DOI: 10.1021/jacs.6b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear receptor-binding SET domain protein 2 (NSD2) is a histone H3 lysine 36 (H3K36)-specific methyltransferase enzyme that is overexpressed in a number of cancers, including multiple myeloma. NSD2 binds to S-adenosyl-l-methionine (SAM) and nucleosome substrates to catalyze the transfer of a methyl group from SAM to the ε-amino group of histone H3K36. Equilibrium binding isotope effects and density functional theory calculations indicate that the SAM methyl group is sterically constrained in complex with NSD2, and that this steric constraint is released upon nucleosome binding. Together, these results show that nucleosome binding to NSD2 induces a significant change in the chemical environment of enzyme-bound SAM.
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Affiliation(s)
- Myles B. Poulin
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jessica L. Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Rosalie E. Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Patrick J. McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Marc Holbert
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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Krzemińska A, Świderek KP, Paneth P. Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase. Phys Chem Chem Phys 2016; 18:310-7. [DOI: 10.1039/c5cp06050h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 18O binding isotope effect allows us to distinguish the actual binding site of an inhibitor in HIV-1 reverse transcriptase.
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Affiliation(s)
- A. Krzemińska
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | - K. P. Świderek
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
- Department de Quimica Fisica i Analitica
| | - P. Paneth
- Institute of Applied Radiation Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
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