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Sacquin-Mora S. Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins. J R Soc Interface 2019; 16:20190075. [PMID: 31288649 DOI: 10.1098/rsif.2019.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein's internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all-atom classic molecular dynamics simulations and coarse-grain calculations of the resulting conformational ensemble mechanical properties. Here, we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris , France
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Gabel SA, Duff MR, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. A Structural Basis for Biguanide Activity. Biochemistry 2017; 56:4786-4798. [PMID: 28766937 PMCID: PMC5740485 DOI: 10.1021/acs.biochem.7b00619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metformin is the most commonly prescribed treatment for type II diabetes and related disorders; however, molecular insights into its mode(s) of action have been limited by an absence of structural data. Structural considerations along with a growing body of literature demonstrating its effects on one-carbon metabolism suggest the possibility of folate mimicry and anti-folate activity. Motivated by the growing recognition that anti-diabetic biguanides may act directly upon the gut microbiome, we have determined structures of the complexes formed between the anti-diabetic biguanides (phenformin, buformin, and metformin) and Escherichia coli dihydrofolate reductase (ecDHFR) based on nuclear magnetic resonance, crystallographic, and molecular modeling studies. Interligand Overhauser effects indicate that metformin can form ternary complexes with p-aminobenzoyl-l-glutamate (pABG) as well as other ligands that occupy the region of the folate-binding site that interacts with pABG; however, DHFR inhibition is not cooperative. The biguanides competitively inhibit the activity of ecDHFR, with the phenformin inhibition constant being 100-fold lower than that of metformin. This inhibition may be significant at concentrations present in the gut of treated individuals, and inhibition of DHFR in intestinal mucosal cells may also occur if accumulation levels are sufficient. Perturbation of folate homeostasis can alter the pyridine nucleotide redox ratios that are important regulators of cellular metabolism.
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Affiliation(s)
- Scott A. Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Michael R. Duff
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Eugene F. DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | | | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Robert E. London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
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Dihydrofolate reductase inhibitors: a quantitative structure–activity relationship study using 2D-QSAR and 3D-QSAR methods. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1742-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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de Souza FR, Guimarães AP, Cuya T, de Freitas MP, Gonçalves ADS, Forgione P, Costa França TC. Analysis of Coxiela burnetti dihydrofolate reductase via in silico docking with inhibitors and molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:2975-2986. [PMID: 27726597 DOI: 10.1080/07391102.2016.1239550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Coxiella burnetii is a gram-negative bacterium able to infect several eukaryotic cells, mainly monocytes and macrophages. It is found widely in nature with ticks, birds, and mammals as major hosts. C. burnetii is also the biological warfare agent that causes Q fever, a disease that has no vaccine or proven chemotherapy available. Considering the current geopolitical context, this fact reinforces the need for discovering new treatments and molecular targets for drug design against C. burnetii. Among the main molecular targets against bacterial diseases reported, the enzyme dihydrofolate reductase (DHFR) has been investigated for several infectious diseases. In the present work, we applied molecular modeling techniques to evaluate the interactions of known DHFR inhibitors in the active sites of human and C. burnetii DHFR (HssDHFR and CbDHFR) in order to investigate their potential as selective inhibitors of CbDHFR. Results showed that most of the ligands studied compete for the binding site of the substrate more effectively than the reference drug trimethoprim. Also the most promising compounds were proposed as leads for the drug design of potential CbDHFR inhibitors.
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Affiliation(s)
- Felipe Rodrigues de Souza
- a Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD) , Military Institute of Engineering , Rio de Janeiro , RJ , Brazil
| | - Ana Paula Guimarães
- b Department of Chemistry , Federal University of Viçosa , Viçosa , MG , Brazil
| | - Teobaldo Cuya
- c Faculty of Technology , University of the State of Rio de Janeiro , Resende , RJ , Brazil
| | | | | | - Pat Forgione
- f Department of Chemistry and Biochemistry , Concordia University , Montreal , Canada
| | - Tanos Celmar Costa França
- a Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMCBD) , Military Institute of Engineering , Rio de Janeiro , RJ , Brazil.,f Department of Chemistry and Biochemistry , Concordia University , Montreal , Canada.,g Faculty of Management and Informatics , University Hradec Kralove , Hradec Kralove , Czech Republic
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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Giacoppo JOS, Mancini DT, Guimarães AP, Gonçalves AS, da Cunha EFF, França TCC, Ramalho TC. Molecular modeling toward selective inhibitors of dihydrofolate reductase from the biological warfare agent Bacillus anthracis. Eur J Med Chem 2014; 91:63-71. [PMID: 24985033 DOI: 10.1016/j.ejmech.2014.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
In the present work, we applied docking and molecular dynamics techniques to study 11 compounds inside the enzymes dihydrofolate reductase (DHFR) from the biological warfare agent Bacillus anthracis (BaDHFR) and Homo sapiens sapiens (HssDHFR). Six of these compounds were selected for a study with the mutant BaF96IDHFR. Our results corroborated with experimental data and allowed the proposition of a new molecule with potential activity and better selectivity for BaDHFR.
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Affiliation(s)
- Juliana O S Giacoppo
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Daiana T Mancini
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Ana P Guimarães
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education Science and Technology of Espirito Santo (IFES), Avenida Ministro Salgado Filho S/N°, 29106-010, Vila Velha, ES, Brazil
| | - Elaine F F da Cunha
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, 22290-270, Rio de Janeiro, RJ, Brazil
| | - Teodorico C Ramalho
- Laboratory of Computational Chemistry, Department of Chemistry, Federal University of Lavras (UFLA), Campus Universitário, PO Box 3037, 37200-000, Lavras, MG, Brazil.
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Beierlein JM, Anderson AC. New developments in vaccines, inhibitors of anthrax toxins, and antibiotic therapeutics for Bacillus anthracis. Curr Med Chem 2012; 18:5083-94. [PMID: 22050756 DOI: 10.2174/092986711797636036] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/07/2011] [Accepted: 09/09/2011] [Indexed: 01/28/2023]
Abstract
Bacillus anthracis, the causative agent responsible for anthrax infections, poses a significant biodefense threat. There is a high mortality rate associated with untreated anthrax infections; specifically, inhalation anthrax is a particularly virulent form of infection with mortality rates close to 100%, even with aggressive treatment. Currently, a vaccine is not available to the general public and few antibiotics have been approved by the FDA for the treatment of inhalation anthrax. With the threat of natural or engineered bacterial resistance to antibiotics and the limited population for whom the current drugs are approved, there is a clear need for more effective treatments against this deadly infection. A comprehensive review of current research in drug discovery is presented in this article, including efforts to improve the purity and stability of vaccines, design inhibitors targeting the anthrax toxins, and identify inhibitors of novel enzyme targets. High resolution structural information for the anthrax toxins and several essential metabolic enzymes has played a significant role in aiding the structure-based design of potent and selective antibiotics.
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Affiliation(s)
- J M Beierlein
- Dept. Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, USA
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Abstract
INTRODUCTION For > 50 years, drugs targeting the folate pathway have significantly impacted disease treatment as anticancer, antimicrobial and immunomodulatory agents. The discovery of novel antifolate agents with improved properties and superior activities remains an attractive strategy, both in academia and the pharmaceutical industry. AREAS COVERED This review surveys the patent literature from 2006 to 2010 for small molecule inhibitors of enzymatic targets in the folate biosynthetic pathway. EXPERT OPINION The pursuit of antifolates as anticancer and antimicrobial agents continues to be an active area of research. New patent disclosures reveal novel antifolate scaffolds, antifolates with improved drug-like properties and new strategies to effectively target cancer cells. The continued use of high resolution structural information has guided the discovery of several compounds. Owing to the need for high levels of potency and selectivity, especially in targeting pathogenic species, the use of high resolution crystal structures remains an important tool to guide the design of novel antifolates. Interestingly, the patents disclosing novel compounds were ones where X-ray crystallography was an integral component of the design process. Finally, a variety of new structures have been reported that may play an important role in the future development of therapeutic antifolates.
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Affiliation(s)
- Dennis L Wright
- University of Connecticut, Department of Pharmaceutical Sciences , 69 N. Eagleville Rd. Storrs, CT, USA
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Beierlein JM, Karri NG, Anderson AC. Targeted mutations of Bacillus anthracis dihydrofolate reductase condense complex structure−activity relationships. J Med Chem 2010; 53:7327-36. [PMID: 20882962 DOI: 10.1021/jm100727t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several antifolates, including trimethoprim (TMP) and a series of propargyl-linked analogues, bind dihydrofolate reductase from Bacillus anthracis (BaDHFR) with lower affinity than is typical in other bacterial species. To guide lead optimization for BaDHFR, we explored a new approach to determine structure-activity relationships whereby the enzyme is altered and the analogues remain constant, essentially reversing the standard experimental design. Active site mutants of the enzyme, Ba(F96I)DHFR and Ba(Y102F)DHFR, were created and evaluated with enzyme inhibition assays and crystal structures. The affinities of the antifolates increase up to 60-fold with the Y102F mutant, suggesting that interactions with Tyr 102 are critical for affinity. Crystal structures of the enzymes bound to TMP and propargyl-linked inhibitors reveal the basis of TMP resistance and illuminate the influence of Tyr 102 on the lipophilic linker between the pyrimidine and aryl rings. Two new inhibitors test and validate these conclusions and show the value of the technique for providing new directions during lead optimization.
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Affiliation(s)
- Jennifer M Beierlein
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Road, Storrs, Connecticut 06269, USA
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Reddy T, Rainey JK. Interpretation of biomolecular NMR spin relaxation parameters. Biochem Cell Biol 2010; 88:131-42. [PMID: 20453916 DOI: 10.1139/o09-152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Biomolecular nuclear magnetic resonance (NMR) spin relaxation experiments provide exquisite information on the picosecond to nanosecond timescale motions of bond vectors. Spin-lattice (T1) and spin-spin (T2) relaxation times and the steady-state nuclear Overhauser effect (NOE) are the first set of parameters extracted from typical 15N or 13C NMR relaxation experiments. Therefore, verifying that T1, T2, and NOE are consistent with theoretical predictions is an important step before carrying out the more detailed model-free and reduced spectral density mapping analyses commonly employed. In this mini-review, we discuss the essential motional parameters used to describe biomolecular dynamics in the context of a variety of examples of folded and intrinsically disordered proteins and peptides in aqueous and membrane mimetic environments. Estimates of these parameters can be used as input for an online interface, introduced herein, allowing plotting of trends of T1, T2, and NOE with magnetic field strength. The plots may serve as a first-check to the spectroscopist preparing to embark on a detailed NMR relaxation analysis.
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Affiliation(s)
- Tyler Reddy
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 1X5 Canada
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