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Kumar N, Bajiya N, Patiyal S, Raghava GPS. Multi-perspectives and challenges in identifying B-cell epitopes. Protein Sci 2023; 32:e4785. [PMID: 37733481 PMCID: PMC10578127 DOI: 10.1002/pro.4785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/23/2023]
Abstract
The identification of B-cell epitopes (BCEs) in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predicting BCEs. However, existing reviews have only covered specific aspects, such as the progress in predicting conformational or linear BCEs. Therefore, in this paper, we have undertaken a systematic approach to provide a comprehensive review covering all aspects associated with the identification of BCEs. First, we have covered the experimental techniques developed over the years for identifying linear and conformational epitopes, including the limitations and challenges associated with these techniques. Second, we have briefly described the historical perspectives and resources that maintain experimentally validated information on BCEs. Third, we have extensively reviewed the computational methods developed for predicting conformational BCEs from the structure of the antigen, as well as the methods for predicting conformational epitopes from the sequence. Fourth, we have systematically reviewed the in silico methods developed in the last four decades for predicting linear or continuous BCEs. Finally, we have discussed the overall challenge of identifying continuous or conformational BCEs. In this review, we only listed major computational resources; a complete list with the URL is available from the BCinfo website (https://webs.iiitd.edu.in/raghava/bcinfo/).
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Affiliation(s)
- Nishant Kumar
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Nisha Bajiya
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Sumeet Patiyal
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
| | - Gajendra P. S. Raghava
- Department of Computational BiologyIndraprastha Institute of Information TechnologyNew DelhiIndia
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2
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Galy R, Ballereau S, Génisson Y, Mourey L, Plaquevent JC, Maveyraud L. Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis: A Crystallographic and Molecular Modelling Study. Pharmaceuticals (Basel) 2021; 14:ph14121282. [PMID: 34959681 PMCID: PMC8708032 DOI: 10.3390/ph14121282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
The mycolic acid biosynthetic pathway represents a promising source of pharmacological targets in the fight against tuberculosis. In Mycobacterium tuberculosis, mycolic acids are subject to specific chemical modifications introduced by a set of eight S-adenosylmethionine dependent methyltransferases. Among these, Hma (MmaA4) is responsible for the introduction of oxygenated modifications. Crystallographic screening of a library of fragments allowed the identification of seven ligands of Hma. Two mutually exclusive binding modes were identified, depending on the conformation of residues 147–154. These residues are disordered in apo-Hma but fold upon binding of the S-adenosylmethionine (SAM) cofactor as well as of analogues, resulting in the formation of the short η1-helix. One of the observed conformations would be incompatible with the presence of the cofactor, suggesting that allosteric inhibitors could be designed against Hma. Chimeric compounds were designed by fusing some of the bound fragments, and the relative binding affinities of initial fragments and evolved compounds were investigated using molecular dynamics simulation and generalised Born and Poisson–Boltzmann calculations coupled to the surface area continuum solvation method. Molecular dynamics simulations were also performed on apo-Hma to assess the structural plasticity of the unliganded protein. Our results indicate a significant improvement in the binding properties of the designed compounds, suggesting that they could be further optimised to inhibit Hma activity.
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Affiliation(s)
- Romain Galy
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France; (R.G.); (L.M.)
| | - Stéphanie Ballereau
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31062 Toulouse, France; (S.B.); (Y.G.); (J.-C.P.)
| | - Yves Génisson
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31062 Toulouse, France; (S.B.); (Y.G.); (J.-C.P.)
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France; (R.G.); (L.M.)
| | - Jean-Christophe Plaquevent
- Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt Biologique, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31062 Toulouse, France; (S.B.); (Y.G.); (J.-C.P.)
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France; (R.G.); (L.M.)
- Correspondence: ; Tel.: +33-561-17-54-35
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Thorpe JH, Wall ID, Sinnamon RH, Taylor AN, Stavenger RA. Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2020; 76:40-46. [PMID: 31929185 PMCID: PMC6957112 DOI: 10.1107/s2053230x19017199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.
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Affiliation(s)
- James H. Thorpe
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Ian D. Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England
| | - Robert H. Sinnamon
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Amy N. Taylor
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
| | - Robert A. Stavenger
- GlaxoSmithKline, Upper Providence, 1250 South Collegeville Road, PO Box 5089, Collegeville, PA 19426-0989, USA
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4
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Yoou MS, Cho S, Choi Y. Molecular Docking-assisted Protein Chip Screening of Inhibitors for Bcl-2 Family Protein-protein Interaction to Discover Anticancer Agents by Fragment-based Approach. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3306-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Marchand JR, Caflisch A. In silico fragment-based drug design with SEED. Eur J Med Chem 2018; 156:907-917. [PMID: 30064119 DOI: 10.1016/j.ejmech.2018.07.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/13/2022]
Abstract
We report on two fragment-based drug design protocols, SEED2XR and ALTA, which start by high-throughput docking. SEED2XR is a two-stage protocol for fragment-based drug design. The first stage is in silico and consists of the automatic docking of 103-104 fragments using SEED, which requires about 1 s per fragment. SEED is a docking software developed specifically for fragment docking and binding energy evaluation by a force field with implicit solvent. In the second stage of SEED2XR, the 10-102 fragments with the most favorable predicted binding energies are validated by protein X-ray crystallography. The recent applications of SEED2XR to bromodomains demonstrate that the whole SEED2XR protocol can be carried out in about a week of working time, with hit rates ranging from 10% to 40%. Information on fragment-target interactions generated by the SEED2XR protocol or directly from SEED docking has been used for the discovery of hundreds of hits. ALTA is a computational protocol for screening which identifies candidate ligands that preserve the interactions between the optimal SEED fragments and the protein target. Medicinal chemistry optimization of ligands predicted by ALTA has resulted in pre-clinical candidates for protein kinases and bromodomains. The high-throughput, very low cost, sustainability, and high hit rate of the SEED-based protocols, unreachable by purely experimental techniques, make them perfectly suitable for both academic and industrial drug discovery research.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland.
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6
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Grixti JM, O'Hagan S, Day PJ, Kell DB. Enhancing Drug Efficacy and Therapeutic Index through Cheminformatics-Based Selection of Small Molecule Binary Weapons That Improve Transporter-Mediated Targeting: A Cytotoxicity System Based on Gemcitabine. Front Pharmacol 2017; 8:155. [PMID: 28396636 PMCID: PMC5366350 DOI: 10.3389/fphar.2017.00155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/10/2017] [Indexed: 12/23/2022] Open
Abstract
The transport of drug molecules is mainly determined by the distribution of influx and efflux transporters for which they are substrates. To enable tissue targeting, we sought to develop the idea that we might affect the transporter-mediated disposition of small-molecule drugs via the addition of a second small molecule that of itself had no inhibitory pharmacological effect but that influenced the expression of transporters for the primary drug. We refer to this as a “binary weapon” strategy. The experimental system tested the ability of a molecule that on its own had no cytotoxic effect to increase the toxicity of the nucleoside analog gemcitabine to Panc1 pancreatic cancer cells. An initial phenotypic screen of a 500-member polar drug (fragment) library yielded three “hits.” The structures of 20 of the other 2,000 members of this library suite had a Tanimoto similarity greater than 0.7 to those of the initial hits, and each was itself a hit (the cheminformatics thus providing for a massive enrichment). We chose the top six representatives for further study. They fell into three clusters whose members bore reasonable structural similarities to each other (two were in fact isomers), lending strength to the self-consistency of both our conceptual and experimental strategies. Existing literature had suggested that indole-3-carbinol might play a similar role to that of our fragments, but in our hands it was without effect; nor was it structurally similar to any of our hits. As there was no evidence that the fragments could affect toxicity directly, we looked for effects on transporter transcript levels. In our hands, only the ENT1-3 uptake and ABCC2,3,4,5, and 10 efflux transporters displayed measurable transcripts in Panc1 cultures, along with a ribonucleoside reductase RRM1 known to affect gemcitabine toxicity. Very strikingly, the addition of gemcitabine alone increased the expression of the transcript for ABCC2 (MRP2) by more than 12-fold, and that of RRM1 by more than fourfold, and each of the fragment “hits” served to reverse this. However, an inhibitor of ABCC2 was without significant effect, implying that RRM1 was possibly the more significant player. These effects were somewhat selective for Panc cells. It seems, therefore, that while the effects we measured were here mediated more by efflux than influx transporters, and potentially by other means, the binary weapon idea is hereby fully confirmed: it is indeed possible to find molecules that manipulate the expression of transporters that are involved in the bioactivity of a pharmaceutical drug. This opens up an entirely new area, that of chemical genomics-based drug targeting.
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Affiliation(s)
- Justine M Grixti
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Steve O'Hagan
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
| | - Philip J Day
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Douglas B Kell
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
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Miller MS, Maheshwari S, McRobb FM, Kinzler KW, Amzel LM, Vogelstein B, Gabelli SB. Identification of allosteric binding sites for PI3Kα oncogenic mutant specific inhibitor design. Bioorg Med Chem 2017; 25:1481-1486. [PMID: 28129991 DOI: 10.1016/j.bmc.2017.01.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
PIK3CA, the gene that encodes the catalytic subunit of phosphatidylinositol 3-kinase α (PI3Kα), is frequently mutated in breast and other types of cancer. A specific inhibitor that targets the mutant forms of PI3Kα could maximize treatment efficiency while minimizing side-effects. Herein we describe the identification of novel binding pockets that may provide an opportunity for the design of mutant selective inhibitors. Using a fragment-based approach, we screened a library of 352 fragments (MW<300Da) for binding to PI3Kα by X-ray crystallography. Five novel binding pockets were identified, each providing potential opportunities for inhibitor design. Of particular interest was a binding pocket near Glu542, which is located in one of the two most frequently mutated domains.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Sweta Maheshwari
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Fiona M McRobb
- Schrödinger, Inc., 120 West 45th Street, New York, NY 10036, United States
| | - Kenneth W Kinzler
- Ludwig Center and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - L Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Bert Vogelstein
- Ludwig Center and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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8
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Potocnakova L, Bhide M, Pulzova LB. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res 2016; 2016:6760830. [PMID: 28127568 PMCID: PMC5227168 DOI: 10.1155/2016/6760830] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/21/2016] [Accepted: 12/13/2016] [Indexed: 01/09/2023] Open
Abstract
Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.
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Affiliation(s)
- Lenka Potocnakova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
- Institute of Neuroimmunology of Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Lucia Borszekova Pulzova
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia
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9
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Ma R, Wang P, Wu J, Ruan K. Process of Fragment-Based Lead Discovery-A Perspective from NMR. Molecules 2016; 21:molecules21070854. [PMID: 27438813 PMCID: PMC6273320 DOI: 10.3390/molecules21070854] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 11/23/2022] Open
Abstract
Fragment-based lead discovery (FBLD) has proven fruitful during the past two decades for a variety of targets, even challenging protein–protein interaction (PPI) systems. Nuclear magnetic resonance (NMR) spectroscopy plays a vital role, from initial fragment-based screening to lead generation, because of its power to probe the intrinsically weak interactions between targets and low-molecular-weight fragments. Here, we review the NMR FBLD process from initial library construction to lead generation. We describe technical aspects regarding fragment library design, ligand- and protein-observed screening, and protein–ligand structure model generation. For weak binders, the initial hit-to-lead evolution can be guided by structural information retrieved from NMR spectroscopy, including chemical shift perturbation, transferred pseudocontact shifts, and paramagnetic relaxation enhancement. This perspective examines structure-guided optimization from weak fragment screening hits to potent leads for challenging PPI targets.
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Affiliation(s)
- Rongsheng Ma
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China.
| | - Pengchao Wang
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China.
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China.
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, Anhui, China.
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10
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Villoutreix B. Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation. ANNALES PHARMACEUTIQUES FRANÇAISES 2016; 74:253-66. [DOI: 10.1016/j.pharma.2016.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022]
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Lau EC, Mason DJ, Eichhorst N, Engelder P, Mesa C, Kithsiri Wijeratne EM, Gunaherath GMKB, Leslie Gunatilaka AA, La Clair JJ, Chapman E. Functional chromatographic technique for natural product isolation. Org Biomol Chem 2015; 13:2255-9. [PMID: 25588099 PMCID: PMC4576851 DOI: 10.1039/c4ob02292k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Natural product discovery arises through a unique interplay between chromatographic purification and biological assays. Currently, most techniques used for natural product purification deliver leads without a defined biological action. We now describe a technique, referred to herein as functional chromatography, that deploys biological affinity as the matrix for compound isolation.
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Affiliation(s)
- Eric C. Lau
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
| | - Damian J. Mason
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
| | - Nicole Eichhorst
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
| | - Pearce Engelder
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
| | - Celestina Mesa
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
| | - E. M. Kithsiri Wijeratne
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, AZ 85706-6800, USA
| | - G. M. Kamal B. Gunaherath
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, AZ 85706-6800, USA
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research and Commercialization, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, AZ 85706-6800, USA
| | - James J. La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA 92163-1052, USA
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721-0207, USA
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12
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Chen H, Zhou X, Wang A, Zheng Y, Gao Y, Zhou J. Evolutions in fragment-based drug design: the deconstruction-reconstruction approach. Drug Discov Today 2015; 20:105-13. [PMID: 25263697 PMCID: PMC4305461 DOI: 10.1016/j.drudis.2014.09.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/18/2014] [Accepted: 09/17/2014] [Indexed: 12/21/2022]
Abstract
Recent advances in the understanding of molecular recognition and protein-ligand interactions have facilitated rapid development of potent and selective ligands for therapeutically relevant targets. Over the past two decades, a variety of useful approaches and emerging techniques have been developed to promote the identification and optimization of leads that have high potential for generating new therapeutic agents. Intriguingly, the innovation of a fragment-based drug design (FBDD) approach has enabled rapid and efficient progress in drug discovery. In this critical review, we focus on the construction of fragment libraries and the advantages and disadvantages of various fragment-based screening (FBS) for constructing such libraries. We also highlight the deconstruction-reconstruction strategy by utilizing privileged fragments of reported ligands.
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Affiliation(s)
- Haijun Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China; Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xiaobin Zhou
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Ailan Wang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Yunquan Zheng
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Yu Gao
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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13
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Chen Y, Tang H. High-throughput screening assays to identify small molecules preventing photoreceptor degeneration caused by the rhodopsin P23H mutation. Methods Mol Biol 2015; 1271:369-90. [PMID: 25697536 DOI: 10.1007/978-1-4939-2330-4_24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput screening (HTS) is one of the major techniques for discovering promising molecules for drug development. Rhodopsin mutations cause the most common autosomal dominant form of retinitis pigmentosa, an inherited retinal degenerative disease that currently has no effective treatment. To find an optimal pharmacological treatment for rhodopsin-associated retinitis pigmentosa, we performed two cell-based HTSs with mammalian cells expressing the P23H rod opsin mutant and identified two sets of novel compounds for further validation and characterization. The first HTS screen identified pharmacological chaperones of P23H opsin that increased its translocation from the endoplasmic reticulum to the plasma membrane. The second HTS screen selected small molecules that enhanced the clearance of the mutant opsin while vision could be sustained by the healthy gene allele expressing wild-type rhodopsin. Here we describe the methodology of these two HTS assays in detail.
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Affiliation(s)
- Yuanyuan Chen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106-4965, USA,
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14
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Aguirre C, ten Brink T, Cala O, Guichou JF, Krimm I. Protein-ligand structure guided by backbone and side-chain proton chemical shift perturbations. JOURNAL OF BIOMOLECULAR NMR 2014; 60:147-156. [PMID: 25256941 DOI: 10.1007/s10858-014-9864-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/19/2014] [Indexed: 06/03/2023]
Abstract
The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity (100 μM-5 mM). The determination of the protein-fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for the protein-ligand recognition, and for growing the initial fragment into potent active compounds. The vast majority of fragments are aromatic compounds that induce chemical shift perturbations (CSP) on protein NMR spectra. These experimental CSPs can be quantitatively used to guide the ligand docking, through the comparison between experimental CSPs and CSP back-calculation based on the ring current effect. Here we implemented the CSP back-calculation into the scoring function of the program PLANTS. We compare the results obtained with CSPs measured either on amide or aliphatic protons of the human peroxiredoxin 5. We show that the different kinds of protons lead to different results for resolving the 3D structures of protein-fragment complexes, with the best results obtained with the Hα protons.
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Affiliation(s)
- Clémentine Aguirre
- UMR5280 CNRS, Institut des Sciences Analytiques, Ecole Normale Supérieure de Lyon, Université Lyon 1, Villeurbanne, France
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Ten Brink T, Aguirre C, Exner TE, Krimm I. Performance of protein-ligand docking with simulated chemical shift perturbations. J Chem Inf Model 2014; 55:275-83. [PMID: 25357133 DOI: 10.1021/ci500446s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein chemical shift perturbations (CSPs) that result from the binding of a ligand to the protein contain structural information about the complex. Therefore, the CSP data, typically obtained during library screening from two-dimensional (2D) nuclear magnetic resonance (NMR) spectra, are often available before attempts to solve the experimental structure of the complex are started, and can be used to solve the complex structure with CSP-based docking. Here, we compare the performance of the post-docking filter and the guided-docking approaches using either amide or α-proton CSPs with 10 protein-ligand complexes. We show that the comparison of experimental CSPs with CSPs simulated for virtual ligand positions can be used to evidence protein conformational change upon binding and possibly improve the CSP-based docking.
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Affiliation(s)
- Tim Ten Brink
- Institut des Sciences Analytiques, UMR CNRS 5280, Université Lyon 1 , F-69100 Villeurbanne, France
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Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5. PLoS One 2014; 9:e102300. [PMID: 25025339 PMCID: PMC4099364 DOI: 10.1371/journal.pone.0102300] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/16/2014] [Indexed: 02/02/2023] Open
Abstract
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.
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Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Tim ten Brink
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Jean-François Guichou
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, Université Montpellier 1 et 2, Montpellier, France
| | - Olivier Cala
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
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Wang E, Chinni S, Bhore SJ. Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling. Bioinformation 2014; 10:130-7. [PMID: 24748752 PMCID: PMC3974239 DOI: 10.6026/97320630010130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. OBJECTIVE The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. MATERIALS AND METHODS The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. RESULTS The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. CONCLUSION The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.
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Affiliation(s)
- Edina Wang
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
| | - Suresh Chinni
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
| | - Subhash Janardhan Bhore
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
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Calderone R, Sun N, Gay-Andrieu F, Groutas W, Weerawarna P, Prasad S, Alex D, Li D. Antifungal drug discovery: the process and outcomes. Future Microbiol 2014; 9:791-805. [PMID: 25046525 PMCID: PMC4144029 DOI: 10.2217/fmb.14.32] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
New data suggest that the global incidence of several types of fungal diseases have traditionally been under-documented. Of these, mortality caused by invasive fungal infections remains disturbingly high, equal to or exceeding deaths caused by drug-resistant tuberculosis and malaria. It is clear that basic research on new antifungal drugs, vaccines and diagnostic tools is needed. In this review, we focus upon antifungal drug discovery including in vitro assays, compound libraries and approaches to target identification. Genome mining has made it possible to identify fungal-specific targets; however, new compounds to these targets are apparently not in the antimicrobial pipeline. We suggest that 'repurposing' compounds (off patent) might be a more immediate starting point. Furthermore, we examine the dogma on antifungal discovery and suggest that a major thrust in technologies such as structural biology, homology modeling and virtual imaging is needed to drive discovery.
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Affiliation(s)
| | - Nuo Sun
- National Institutes of Health, Bethesda, MD, USA
| | | | - William Groutas
- Department of Chemistry, Wichita State University, Wichita, KS, USA
| | | | | | - Deepu Alex
- Department of Pathology, MedStar, Georgetown University Medical Center, Washington, DC, USA
| | - Dongmei Li
- Georgetown University Medical Center, Washington, DC, USA
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