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Akinsiku OE, Soremekun OS, Soliman MES. Update and Potential Opportunities in CBP [Cyclic Adenosine Monophosphate (cAMP) Response Element-Binding Protein (CREB)-Binding Protein] Research Using Computational Techniques. Protein J 2021; 40:19-27. [PMID: 33394237 PMCID: PMC7868315 DOI: 10.1007/s10930-020-09951-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 11/29/2022]
Abstract
CBP [cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB)-binding protein] is one of the most researched proteins for its therapeutic function. Several studies have identified its vast functions and interactions with other transcription factors to initiate cellular signals of survival. In cancer and other diseases such as Alzheimer's, Rubinstein-taybi syndrome, and inflammatory diseases, CBP has been implicated and hence an attractive target in drug design and development. In this review, we explore the various computational techniques that have been used in CBP research, furthermore we identified computational gaps that could be explored to facilitate the development of highly therapeutic CBP inhibitors.
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Affiliation(s)
- Oluwayimika E Akinsiku
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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2
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Khalil R, Usmani S, Nur-E-Alam M, Ahmed S, Ul-Haq Z. Site-directed Fragnomics and MD Simulations Approaches to Identify Interleukin-2 Inhibitors. Med Chem 2020; 17:407-417. [PMID: 33191887 DOI: 10.2174/1573406416999201113104501] [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: 04/22/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION The aberrant expression of Interleukin-2 (IL2), the chief regulator of immunity, is associated with many auto-immune diseases. At present, there is no FDA approved drug targeting IL2, which puts forth the need for small molecular inhibitors to block IL2 and its receptor interaction. METHODOLOGY Herein, we used the contemporary fragnomics approach to design novel drug-like inhibitors targeting IL2. Briefly, the RECAP (Retrosynthetic Combinatorial Analysis Procedure) package implemented in MOE (Molecular Operating Environment check) software suite was utilised to obtain fragments fulfilling the 'rule of three' criteria for fragments. The binding site of IL2 was divided into three smaller grooves, and the fragments were docked to screen their affinity for a particular site, followed by site-directed RECAP synthesis. RESULTS A focused library of 10,000 compounds was prepared by re-combining the fragments according to their affinity for a particular site as observed in docking. Docking and subsequent analysis of newly synthesised compounds identified 40 privileged leads, presenting hydrogen bonding with basic residues of the pocket. A QSAR model was implied to predict the IC50 of the compounds and to analyse the electrostatic and hydrophobic contour maps. The resulting hits were found to be modest IL2 inhibitors with predicted inhibitory activity in the range of 5.17-4.40 nM. Further Dynamic simulation studies were carried out to determine the stability of the inhibitor-IL2 complex. CONCLUSION Our findings underline the potential of the novel compounds as valuable pharmacological agents in diseases characterised by IL2 overexpression.
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Affiliation(s)
- Ruqaiya Khalil
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Saman Usmani
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Jinnah Sindh Medical University, Karachi, Pakistan
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Saudi Arabia
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
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Prieto-Martínez FD, Medina-Franco JL. Current advances on the development of BET inhibitors: insights from computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:127-180. [PMID: 32951810 DOI: 10.1016/bs.apcsb.2020.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Epigenetics was coined almost 70 years ago for the description of heritable phenotype without altering DNA sequences. Research on the field has uncovered significant roles of such mechanisms, that account for the biogenesis of several diseases. Further studies have led the way for drug development which targets epi-enzymes, mainly for cancer treatment. Of the numerous epi-targets involved with histone acetylation, bromodomains have captured the spotlight of drug discovery focused on novel therapies. However, due to high sequence identity, the development of potent and selective inhibitors poses a significant challenge. Herein, we discuss recent computational developments on BET inhibitors and other methods that may be applied for drug discovery in general. As a proof-of-concept, we discuss a virtual screening to identify novel BET inhibitors based on coumarin derivatives. From public data, we identified putative structure-activity relationships of coumarin scaffold and propose R-group modifications for BET selectivity. Results showed that the optimization and design of novel coumarins could be further explored.
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Affiliation(s)
- Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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4
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He B, Wu FX, Yu LK, Wu L, Chen Q, Hao GF, Yang WC, Lin HY, Yang GF. Discovery of Novel Pyrazole-Quinazoline-2,4-dione Hybrids as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5059-5067. [PMID: 32286826 DOI: 10.1021/acs.jafc.0c00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) has been identified as one of the most significant targets in herbicide discovery for resistant weed control. In a continuing effort to discover potent novel HPPD inhibitors, we adopted a ring-expansion strategy to design a series of novel pyrazole-quinazoline-2,4-dione hybrids based on the previously discovered pyrazole-isoindoline-1,3-dione scaffold. One compound, 3-(2-chlorophenyl)-6-(5-hydroxy-1,3-dimethyl-1H-pyrazole-4-carbonyl)-1,5-dimethylquinazoline-2,4(1H,3H)-dione (9bj), displayed excellent potency against AtHPPD, with an IC50 value of 84 nM, which is approximately 16-fold more potent than pyrasulfotole (IC50 = 1359 nM) and 2.7-fold more potent than mesotrione (IC50 = 226 nM). Furthermore, the co-crystal structure of the AtHPPD-9bj complex (PDB ID 6LGT) was determined at a resolution of 1.75 Å. Similar to the existing HPPD inhibitors, compound 9bj formed a bidentate chelating interaction with the metal ion and a π-π stacking interaction with Phe381 and Phe424. In contrast, o-chlorophenyl at the N3 position of quinazoline-2,4-dione with a double conformation was surrounded by hydrophobic residues (Met335, Leu368, Leu427, Phe424, Phe392, and Phe381). Remarkably, the greenhouse assay indicated that most compounds displayed excellent herbicidal activity (complete inhibition) against at least one of the tested weeds at the application rate of 150 g of active ingredient (ai)/ha. Most promisingly, compounds 9aj and 9bi not only exhibited prominent weed control effects with a broad spectrum but also showed very good crop safety to cotton, peanuts, and corn at the dose of 150 g of ai/ha.
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Affiliation(s)
- Bo He
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Liang-Kun Yu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Lei Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, People's Republic of China
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Rodríguez Y, Gerona-Navarro G, Osman R, Zhou MM. In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4. Proteins 2020; 88:414-430. [PMID: 31587361 PMCID: PMC6982606 DOI: 10.1002/prot.25818] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/11/2023]
Abstract
Bromodomains (BrDs), a conserved structural module in chromatin-associated proteins, are well known for recognizing ε-N-acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD containing protein (BrD1 and BrD2) that plays a critical role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biological functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow-up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole-based compounds as BRD4 BrD1 inhibitors. Additionally, we investigated the molecular basis for Olinone's selective recognition by BrD1 over BrD2. Molecular dynamics simulations, free energy calculations, and conformational analyses of the apo-BRD4-BrD1|2 and BRD4-BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds number and in mobility of the ZA and BC loops of the acetyl-lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer-aided molecular design techniques can effectively guide the development of small-molecule BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivatives.
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Affiliation(s)
- Yoel Rodríguez
- Department of Natural Sciences, Hostos Community
College of CUNY, Bronx, NY 10451, USA,Department of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Corresponding Authors: Yoel Rodríguez.
Address: Department of Natural Sciences, Room A-507F, Hostos Community College
of CUNY, Bronx, NY 10451, USA. Phone: +1 (718) 518-4134, Fax: +1 (718) 518-1120.
- ; Ming-Ming Zhou. Address: Department
of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425
Madison Avenue, Box 1677, New York, NY 10029, USA. Phone: +1 (212) 659-8652.
Fax: +1 (212) 849-2456.
| | - Guillermo Gerona-Navarro
- Department of Chemistry, Brooklyn College, 2900
Bedford Avenue, Room 351 NE, Brooklyn, NY 11210, USA,Ph.D. Program in Chemistry. The Graduate Center of
The City University of New York, NY 10016, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA,Corresponding Authors: Yoel Rodríguez.
Address: Department of Natural Sciences, Room A-507F, Hostos Community College
of CUNY, Bronx, NY 10451, USA. Phone: +1 (718) 518-4134, Fax: +1 (718) 518-1120.
- ; Ming-Ming Zhou. Address: Department
of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425
Madison Avenue, Box 1677, New York, NY 10029, USA. Phone: +1 (212) 659-8652.
Fax: +1 (212) 849-2456.
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Elshan NGRD, Rettig MB, Jung ME. Molecules targeting the androgen receptor (AR) signaling axis beyond the AR-Ligand binding domain. Med Res Rev 2019; 39:910-960. [PMID: 30565725 PMCID: PMC6608750 DOI: 10.1002/med.21548] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/21/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Prostate cancer (PCa) is the second most common cause of cancer-related mortality in men in the United States. The androgen receptor (AR) and the physiological pathways it regulates are central to the initiation and progression of PCa. As a member of the nuclear steroid receptor family, it is a transcription factor with three distinct functional domains (ligand-binding domain [LBD], DNA-binding domain [DBD], and transactivation domain [TAD]) in its structure. All clinically approved drugs for PCa ultimately target the AR-LBD. Clinically active drugs that target the DBD and TAD have not yet been developed due to multiple factors. Despite these limitations, the last several years have seen a rise in the discovery of molecules that could successfully target these domains. This review aims to present and comprehensively discuss such molecules that affect AR signaling through direct or indirect interactions with the AR-TAD or the DBD. The compounds discussed here include hairpin polyamides, niclosamide, marine sponge-derived small molecules (eg, EPI compounds), mahanine, VPC compounds, JN compounds, and bromodomain and extraterminal domain inhibitors. We highlight the significant in vitro and in vivo data found for each compound and the apparent limitations and/or potential for further development of these agents as PCa therapies.
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Affiliation(s)
| | - Matthew B. Rettig
- . Division of Hematology/Oncology, VA Greater Los Angeles Healthcare System West LA, Los Angeles, CA, United States
- . Departments of Medicine and Urology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Michael E. Jung
- . Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, United States
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7
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E-pharmacophore-based screening of mGluR5 negative allosteric modulators for central nervous system disorder. Comput Biol Chem 2019; 78:414-423. [DOI: 10.1016/j.compbiolchem.2018.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/25/2018] [Indexed: 01/01/2023]
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8
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NMR-Fragment Based Virtual Screening: A Brief Overview. Molecules 2018; 23:molecules23020233. [PMID: 29370102 PMCID: PMC6017141 DOI: 10.3390/molecules23020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.
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Śledź P, Caflisch A. Protein structure-based drug design: from docking to molecular dynamics. Curr Opin Struct Biol 2017; 48:93-102. [PMID: 29149726 DOI: 10.1016/j.sbi.2017.10.010] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 01/24/2023]
Abstract
Recent years have witnessed rapid developments of computer-aided drug design methods, which have reached accuracy that allows their routine practical applications in drug discovery campaigns. Protein structure-based methods are useful for the prediction of binding modes of small molecules and their relative affinity. The high-throughput docking of up to 106 small molecules followed by scoring based on implicit-solvent force field can robustly identify micromolar binders using a rigid protein target. Molecular dynamics with explicit solvent is a low-throughput technique for the characterization of flexible binding sites and accurate evaluation of binding pathways, kinetics, and thermodynamics. In this review we highlight recent advancements in applications of ligand docking tools and molecular dynamics simulations to ligand identification and optimization.
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Affiliation(s)
- Paweł Śledź
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zürich, Switzerland.
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10
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W Young D. Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.15406/mojbb.2017.04.00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, González-Bello C. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem 2017; 12:1512-1524. [DOI: 10.1002/cmdc.201700396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Adrián Robles
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marino Convertino
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
- Current address: Department of Biochemistry and Biophysics; University of North Carolina, School of Medicine; Chapel Hill NC 27599 USA
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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