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Engelhardt MU, Zimmermann MO, Dammann M, Stahlecker J, Poso A, Kronenberger T, Kunick C, Stehle T, Boeckler FM. Halogen Bonding on Water─A Drop in the Ocean? J Chem Theory Comput 2024. [PMID: 39291905 DOI: 10.1021/acs.jctc.4c00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Halogen bonding is a valuable interaction in drug design, offering an unconventional way to influence affinity and selectivity by leveraging the halogen atoms' ability to form directional bonds. The present study evaluates halogen-water interactions within protein binding sites, demonstrating that targeting a water molecule via halogen bonding can in specific cases contribute beneficially to ligand binding. In solving and examining the crystal structure of 2-cyclopentyl-7-iodo-1H-indole-3-carbonitrile bound to DYRK1a kinase, we identified a notable iodine-water interaction, where water accepts a halogen bond with good geometric and energetic features. This starting point triggered further investigations into the prevalence of such interactions across various halogen-bearing ligands (chlorine, bromine, iodine) in the PDB. Using QM calculations (MP2/TZVPP), we highlight the versatility and potential benefits of such halogen-water interactions, particularly when the water molecule is a stable part of the binding site's structured environment. While the interaction energies with water are lower compared to other typical halogen bond acceptors, we deem this different binding strength essential for reducing desolvation costs. We suggest that "interstitial" water molecules, as stable parts of the binding site engaging in multiple strong interactions, could be prime targets for halogen bonding. Further systematic studies, combining high-resolution crystal structures and quantum chemistry, are required to scrutinize whether halogen bonding on water is more than a "drop in the ocean".
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Affiliation(s)
- Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Markus O Zimmermann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Marcel Dammann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Jason Stahlecker
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Institute of Pharmaceutical Sciences, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Institute of Pharmaceutical Sciences, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076 Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany
- Partner-site Tübingen, German Center for Infection Research (DZIF), 72076 Tübingen, Germany
| | - Conrad Kunick
- Institute for Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
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2
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Moubayed NMS, Alsabbagh R, Smiline GAS, Gunasekaran S, Alshihri S, Sabour A. Evaluation of phyto-gallic acid as a potential inhibitor of Staphylococcus aureus efflux pump mediated tetracycline resistance: an in-vitro and in-silico study. Nat Prod Res 2024:1-8. [PMID: 38733626 DOI: 10.1080/14786419.2024.2349810] [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: 01/22/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
Plants contain many bioactive compounds with potent antibacterial and efflux pump inhibitory activity (EPI). In this study, gallic acid extracted from pomegranate molasses by analytical HPLC holds promise as an EPI drug for Staphylococcus aureus mediated tetracycline resistance, it lowered the bacterial resistance and reversed the mechanism via tet family efflux pump, using molecular technique and in-silico molecular docking analysis. Extracted gallic acid combined with tetracycline demonstrated a significant decrease in the minimal inhibitory concentration MIC compared to its single activity. Similarly, little growth and lower fluorescence of S. aureus were observed on ethidium bromide (2.5 mg/mL) agar plates, indicating a reversible efflux pump mechanism and a potent EPI activity. Molecular docking demonstrated a promising affinity binding energy between gallic acid and tet efflux genes, opening a new baseline in bacterial infection treatment. PCR for tetK and Qac A/B genes failed to show any relation between tet genes and gallic acid.
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Affiliation(s)
- Nadine M S Moubayed
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Ruba Alsabbagh
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Girija A S Smiline
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, Tamilnadu, India
| | - Shoba Gunasekaran
- Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous), University of Madras, Chennai, Tamil Nadu, India
| | - Sameeha Alshihri
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Amal Sabour
- Department of Botany and Microbiology, Science College, King Saud University, Riyadh, Saudi Arabia
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3
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Bakó I, Pusztai L, Pothoczki S. Outstanding Properties of the Hydration Shell around β-d-Glucose: A Computational Study. ACS OMEGA 2024; 9:20331-20337. [PMID: 38737074 PMCID: PMC11080014 DOI: 10.1021/acsomega.4c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Ab initio molecular dynamics (AIMD) simulations have been performed on aqueous solutions of four simple sugars, α-d-glucose, β-d-glucose, α-d-mannose, and α-d-galactose. Hydrogen-bonding (HB) properties, such as the number of donor- and acceptor-type HB-s, and the lengths and strengths of hydrogen bonds between sugar and water molecules, have been determined. Related electronic properties, such as the dipole moments of water molecules and partial charges of the sugar O atoms, have also been calculated. The hydrophilic and hydrophobic shells were characterized by means of spatial distribution functions. β-d-Glucose was found to form the highest number of hydrophilic and the smallest number of hydrophobic connections to neighboring water molecules. The average sugar-water H-bond length was the shortest for β-d-glucose, which suggests that these are the strongest such H-bonds. Furthermore, β-d-glucose appears to stand out in terms of the symmetry properties of both its hydrophilic and hydrophobic hydration shells. In summary, in all aspects considered here, there seems to be a correlation between the distinct characteristics of β-d-glucose reported here and its outstanding solubility in water. Admittedly, our findings represent only some of the important factors that influence the solubility.
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Affiliation(s)
- Imre Bakó
- HUN-REN
Research Centre for Natural Sciences, Magyar tudósok körútja 2., H-1117 Budapest, Hungary
| | - László Pusztai
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
- International
Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Szilvia Pothoczki
- HUN-REN
Wigner Research Centre for Physics, Konkoly-Thege M. út 29-33., H-1121 Budapest, Hungary
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4
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Zamanos A, Ioannakis G, Emiris IZ. HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures. J Chem Inf Model 2024; 64:2594-2611. [PMID: 38552195 PMCID: PMC11005053 DOI: 10.1021/acs.jcim.3c01559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 04/09/2024]
Abstract
Water molecules are integral to the structural stability of proteins and vital for facilitating molecular interactions. However, accurately predicting their precise position around protein structures remains a significant challenge, making it a vibrant research area. In this paper, we introduce HydraProt (deep Hydration of Proteins), a novel methodology for predicting precise positions of water molecule oxygen atoms around protein structures, leveraging two interconnected deep learning architectures: a 3D U-net and a Multi-Layer Perceptron (MLP). Our approach starts by introducing a coarse voxel-based representation of the protein, which allows for rapid sampling of candidate water positions via the 3D U-net. These water positions are then assessed by embedding the water-protein relationship in the Euclidean space by means of an MLP. Finally, a postprocessing step is applied to further refine the MLP predictions. HydraProt surpasses existing state-of-the-art approaches in terms of precision and recall and has been validated on large data sets of protein structures. Notably, our method offers rapid inference runtime and should constitute the method of choice for protein structure studies and drug discovery applications. Our pretrained models, data, and the source code required to reproduce these results are accessible at https://github.com/azamanos/HydraProt.
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Affiliation(s)
- Andreas Zamanos
- Archimedes, Athena Research Center, Marousi 15125, Greece
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
| | - George Ioannakis
- Institute
for Language and Speech Processing, Athena
Research Center, Xanthi 67100, Greece
| | - Ioannis Z. Emiris
- Department
of Informatics and Telecommunications, National
and Kapodistrian University of Athens, Athens 16122, Greece
- Athena
Research Center, Marousi 15125, Greece
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5
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Bodoor K, El-Barghouthi MI, Alhamed DF, Assaf KI, Alrawashdeh L. Cucurbit[7]uril recognition of glucosamine anomers in water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Ibrahim E, Mahmoud A, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Kinetics and thermodynamics of thermal inactivation for recombinant Escherichia coli cellulases, cel12B, cel8C, and polygalacturonase, peh28; biocatalysts for biofuel precursor production. J Biochem 2021; 169:109-117. [PMID: 32810224 DOI: 10.1093/jb/mvaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/11/2020] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic biomass conversion using cellulases/polygalacturonases is a process that can be progressively influenced by several determinants involved in cellulose microfibril degradation. This article focuses on the kinetics and thermodynamics of thermal inactivation of recombinant Escherichia coli cellulases, cel12B, cel8C and a polygalacturonase, peh 28, derived from Pectobacterium carotovorum sub sp. carotovorum. Several consensus motifs conferring the enzymes' thermal stability in both cel12B and peh28 model structures have been detailed earlier, which were confirmed for the three enzymes through the current study of their thermal inactivation profiles over the 20-80°C range using the respective activities on carboxymethylcellulose and polygalacturonic acid. Kinetic constants and half-lives of thermal inactivation, inactivation energy, plus inactivation entropies, enthalpies and Gibbs free energies, revealed high stability, less conformational change and protein unfolding for cel12B and peh28 due to thermal denaturation compared to cel8C. The apparent thermal stability of peh28 and cel12B, along with their hydrolytic efficiency on a lignocellulosic biomass conversion as reported previously, makes these enzymes candidates for various industrial applications. Analysis of the Gibbs free energy values suggests that the thermal stabilities of cel12B and peh28 are entropy-controlled over the tested temperature range.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA.,Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Ahmed Mahmoud
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Kim D Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Keith E Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ebtesam N Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Patrick L Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363, USA
| | - Jean M Escudero
- Department of Basic Sciences, St. Louis College of Pharmacy, St. Louis, MO 63110-1088, USA
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7
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Ab initio investigation of the first hydration shell of glucose. Carbohydr Res 2020; 496:108114. [DOI: 10.1016/j.carres.2020.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/15/2020] [Accepted: 08/03/2020] [Indexed: 11/23/2022]
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8
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Tang M, Wang X, Gandhi NS, Foley BL, Burrage K, Woods RJ, Gu Y. Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study. Glycobiology 2020; 30:830-843. [PMID: 32188979 PMCID: PMC7526737 DOI: 10.1093/glycob/cwaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.
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Affiliation(s)
- Ming Tang
- School of Chemistry Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, 4001 Australia
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Neha S Gandhi
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4001, Australia
| | | | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4001, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane 4001, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - YuanTong Gu
- School of Chemistry Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, 4001 Australia
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Ramalingam AK, Selvi SGA, Jayaseelan VP. Targeting prolyl tripeptidyl peptidase from Porphyromonas gingivalis with the bioactive compounds from Rosmarinus officinalis. ASIAN BIOMED 2020. [DOI: 10.1515/abm-2019-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Complications in periodontitis and other systemic infections related to Porphyromonas gingivalis poses a serious impediment in the treatment process. This leads to the search of novel target proteins to develop newer drugs against P. gingivalis. Prolyl tripeptidyl peptidase (ptp-A) seem to be a vital protein in P. gingivalis virulence and can be a good target for the novel natural bioactive compounds.
Objectives
To explore the inhibitory potential of Rosmarinus officinalis biocompounds against the ptp-A of P. gingivalis.
Methods
Three-dimensional structure of ptp-A was retrieved from the Protein Data Bank with further optimization of both the protein and ligands. In silico inhibitory potential of the selected ligands against ptp-A was done by AutoDock 2.0 and was visualized with Biovia discovery studio visualizing tool with the assessment of the molecular properties of the ligands against ptp-A by molinspiration calculations and drug likeliness.
Results
High ptp-A inhibitory effect was observed using rosmarinic acid and luteolin with a bonding energy of −9.81 kcal/mol with 10 hydrogen bond interactions and −9.99 kcal/mol with 7 hydrogen bond interactions, respectively. Carnosic acid and p-coumaric acid showed a binding energy of −7.14 kcal/mol and −6.34 kcal/mol, respectively, with 5 hydrogen bond interactions. Molinspiration assessments showed R. officinalis compounds as the best drug candidates with the topological polar surface area scores <140 Å toward the best oral bioavailability.
Conclusion
The carnosic acid, rosmarinic acid, p-coumaric acid, and luteolin from R. officinalis seem to possess a promising inhibitory effect against ptp-A of Candida albicans suggesting ptp-A as the best target to combat P. gingivalis with further in vivo validation.
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Affiliation(s)
- Ashwin Kumar Ramalingam
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences , Saveetha University , Tamil Nadu 600077 , India
| | - Smiline Girija Aseervatham Selvi
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences , Saveetha University , Tamil Nadu 600077 , India
| | - Vijayashree Priyadharsini Jayaseelan
- Dental Research Cell (BRULAC-DRC), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences , Saveetha University , Tamil Nadu 600077 , India
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10
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The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations. J Comput Aided Mol Des 2019; 33:913-926. [PMID: 31686367 DOI: 10.1007/s10822-019-00239-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022]
Abstract
Misfolded Cu/Zn superoxide dismutase enzyme (SOD1) shows prion-like propagation in neuronal cells leading to neurotoxic aggregates that are implicated in amyotrophic lateral sclerosis (ALS). Tryptophan-32 (W32) in SOD1 is part of a potential site for templated conversion of wild type SOD1. This W32 binding site is located on a convex, solvent exposed surface of the SOD1 suggesting that hydration effects can play an important role in ligand recognition and binding. A recent X-ray crystal structure has revealed that 5-Fluorouridine (5-FUrd) binds at the W32 binding site and can act as a pharmacophore scaffold for the development of anti-ALS drugs. In this study, a new protocol is developed to account for structural (non-displaceable) water molecules in docking simulations and successfully applied to predict the correct docked conformation binding modes of 5-FUrd at the W32 binding site. The docked configuration is within 0.58 Å (RMSD) of the observed configuration. The docking protocol involved calculating a hydration structure around SOD1 using molecular theory of solvation (3D-RISM-KH, 3D-Reference Interaction Site Model-Kovalenko-Hirata) whereby, non-displaceable water molecules are identified for docking simulations. This protocol was also used to analyze the hydrated structure of the W32 binding site and to explain the role of solvation in ligand recognition and binding to SOD1. Structural water molecules mediate hydrogen bonds between 5-FUrd and the receptor, and create an environment favoring optimal placement of 5-FUrd in the W32 binding site.
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Sohaib Shahzan M, Smiline Girija AS, Vijayashree Priyadharsini J. A computational study targeting the mutated L321F of ERG11 gene in C. albicans, associated with fluconazole resistance with bioactive compounds from Acacianilotica. J Mycol Med 2019; 29:303-309. [PMID: 31570303 DOI: 10.1016/j.mycmed.2019.100899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/24/2019] [Accepted: 09/08/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Emergence of fluconazole resistance mediated by L321F mutation in the ERG11 gene poses a serious impediment in the candidal treatment process. This leads to the search of novel target proteins to develop newer drugs against fluconazole resistant C. albicans. The present investigation is thus aimed to explore the inhibitory potential of bioactive compounds from A. nilotica against the wild and mutated ERG11 gene of C. albicans. MATERIALS AND METHODS Homology modelling of the wild and mutated ERG11 target gene was done by Modeller 9.2, with SDM I-mutant form of ERG11 together with SAVES server and Ramachandran plot validation. 2D and 3D structures of the bioactive compounds from A. nilotica were optimized by ACD chemsketch. Molinspirational assessments for the molecular properties of the ligands and their drug likeliness were estimated. In silico inhibitory potential of the selected ligands against wild and mutated ERG11 was done by AutoDock 2.0 and was visualized with Accelrys discovery studio tool. RESULTS Apigenin proved to be the best candidate to target mutant ERG11 with a binding energy of -8.33 Kcal/mol followed by catechin with six hydrogen bonds with more drug likeliness. Molinspiration assessments showed zero violations for all the bioactive compounds from A. nilotica and the TPSA scores of the ligands showed the values<140Å towards the best oral bio-availability. CONCLUSION The findings of the study emphasize that kaempferol, apigenin and catechin from A. nilotica seem to possess a promising inhibitory effect against the wild and mutated ERG11 of C. albicans suggesting ERG11 as the best target to combat fluconazole resistant C. albicans with further in vivo validation targeting the same.
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Affiliation(s)
- M Sohaib Shahzan
- II year BDS student, Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. road, 600077 Chennai, Tamilnadu, India; Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. road, 600077 Chennai, Tamilnadu, India; BRULAC-DRC, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. road, 600077 Chennai, Tamilnadu, India
| | - A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. road, 600077 Chennai, Tamilnadu, India.
| | - J Vijayashree Priyadharsini
- BRULAC-DRC, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. road, 600077 Chennai, Tamilnadu, India
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12
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Madariaga-Mazón A, Osnaya-Hernández A, Chávez-Gómez A, García-Ramos JC, Cortés-Guzmán F, Castillo-Pazos DJ, Martínez-Mayorga K. Distribution of toxicity values across different species and modes of action of pesticides from PESTIMEP and PPDB databases. Toxicol Res (Camb) 2019; 8:146-156. [PMID: 30997018 PMCID: PMC6430098 DOI: 10.1039/c8tx00322j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/07/2019] [Indexed: 11/21/2022] Open
Abstract
The continuous use of compounds contained in commodities such as processed food, medicines, and pesticides, demands safety measures, in particular, for those in direct contact with humans and the environment. Safety measures have evolved and regulations are now in place around the globe. In the case of pesticides, attempts have been made to use toxicological data to inform of potentially harmful compounds either across species, on different routes of exposure, or entirely new chemicals. The generation of models, based on statistical and molecular modeling studies, allows for such predictions. However, the use of these models is framed by the available data, the experimental errors, the complexity of the measurement, and the available computational algorithms, among other factors. In this work, we present the methodologies used for extrapolation across different species and routes of administration and show the appropriateness of developing predictive models of pesticides based on their type and mode of action. The analyses include comparisons based on structural characteristics and physicochemical properties. Whenever possible, the scope and limitations of the methodologies are discussed. We expect that this work will serve as a useful introductory guide of the tools employed in the toxicity assessment of agrochemical compounds.
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Affiliation(s)
| | | | - Arni Chávez-Gómez
- Instituto de Química , Universidad Nacional Autónoma de México , Mexico City , Mexico .
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13
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Serratos IN, Millán-Pacheco C, Garza-Ramos G, Pérez-Hernández G, Zubillaga RA. Exploring interfacial water trapping in protein-ligand complexes with multithermal titration calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:488-495. [PMID: 29307720 DOI: 10.1016/j.bbapap.2018.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 12/02/2017] [Accepted: 01/03/2018] [Indexed: 11/18/2022]
Abstract
In this work, we examine the hypothesis about how trapped water molecules at the interface between triosephosphate isomerase (TIM) and either of two phosphorylated inhibitors, 2-phosphoglycolate (2PG) or phosphoglycolohydroxamate (PGH), can explain the anomalous highly negative binding heat capacities (ΔCp,b) of both complexes, TIM-2PG and TIM-PGH. We performed fluorimetric titrations of the enzyme with PGH inhibitor under osmotic stress conditions, using various concentrations of either osmolyte: sucrose, ethylene glycol or glycine betaine. We also analyze the binding processes under various stressor concentrations using a novel calorimetric methodology that allows ΔCp,b determinations in single experiments: Multithermal Titration Calorimetry. The binding constant of the TIM-PGH complex decreased gradually with the concentration of all osmolytes, but at diverse extents depending on the osmolyte nature. According to the osmotic stress theory, this decrease indicates that the number of water molecules associated with the enzyme increases with inhibitor binding, i.e. some solvent molecules became trapped. Additionally, the binding heat capacities became less negative at higher osmolyte concentrations, their final values depending on the osmolyte. These effects were also observed in the TIM-2PG complex using sucrose as stressor. Our results strongly suggest that some water molecules became immobilized when the TIM-inhibitor complexes were formed. A computational analysis of the hydration state of the binding site of TIM in both its free state and its complexed form with 2PG or PGH, based on molecular dynamics (MD) simulations in explicit solvent, showed that the binding site effectively immobilized additional water molecules after binding these inhibitors.
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Affiliation(s)
- Iris N Serratos
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México, C.P. 09340, Mexico.
| | - Cesar Millán-Pacheco
- Facultad de Farmacia. Universidad Autónoma del Estado de Morelos, Cuernavaca Mor. C.P. 62209, Mexico.
| | - Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico.
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Ciudad de México, C.P. 05348, Mexico.
| | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México, C.P. 09340, Mexico.
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14
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Chen D, Li Y, Zhao M, Tan W, Li X, Savidge T, Guo W, Fan X. Effective lead optimization targeting the displacement of bridging receptor–ligand water molecules. Phys Chem Chem Phys 2018; 20:24399-24407. [DOI: 10.1039/c8cp04118k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enhancing the binding affinities of ligands by means of lead modifications that displace bridging water molecules at protein–ligand interfaces is an important and widely studied lead optimization strategy.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Yibao Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Mingming Zhao
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Wen Tan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Xun Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Tor Savidge
- Department of Pathology & Immunology
- Baylor College of Medicine
- Houston
- USA
- Texas Children's Microbiome Center
| | - Wei Guo
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Xiaolin Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
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15
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Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
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16
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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17
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Testing the CP-correction procedure with different DFT methods on H-bonding complexes of κ-carrabiose with water molecules. J Mol Model 2017; 23:31. [PMID: 28091888 DOI: 10.1007/s00894-016-3199-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
Interaction of water molecules with κ-carrabiose disaccharide, within three H-bonding complexes, was investigated. Particular interest was focused on the way with which the BSSE correction has to be performed. Two strategies were used, either performing BSSE correction during or after optimization. For this aim, several DFT-functionals (hybrid GGA and hybrid meta-GGA) and 6-31 + G* basis set were considered. The results demonstrated the uselessness of including of BSSE-CP correction during optimization for all complexes. From a structural point of view, a proper H-bonding description was obtained using the PBE0 functional for all complexes. The basis set effect on the BSSE using B3LYP functional was also investigated. The reliability of B3LYP/6-31 + G** and B3LYP/6-31++G** models for the complexes involving one or two water molecules was reported while the use of B3LYP/6-311 + G** or B3LYP/6-311++G** levels was shown to be more appropriate for larger complexes equivalent to that involving three water molecules. CP-corrected interaction energies were demonstrated to be closer to CBS-4 M interaction energies than the uncorrected ones. Graphical abstract Functional and basis set effects on BSSE.
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18
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Liu W, Jia X, Wang M, Li P, Wang X, Hu W, Zheng J, Mei Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv 2017. [DOI: 10.1039/c7ra06215j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Meiting Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Wenxin Hu
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Jun Zheng
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
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19
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Zeng Z, Bernstein ER. Photoelectron spectroscopy and density functional theory studies of (fructose + (H 2O) n) − ( n = 1–5) anionic clusters. Phys Chem Chem Phys 2017; 19:31121-31137. [DOI: 10.1039/c7cp06625b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
(Fructose + (H2O)n)− (n = 1–5) cluster anions mainly exist as open chain structures. Some cyclic structures of (fructose + (H2O)n)− (n = 3, 4) are present too.
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Affiliation(s)
- Zhen Zeng
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
| | - Elliot R. Bernstein
- Department of Chemistry
- NSF ERC for Extreme Ultraviolet Science and Technology
- Colorado State University
- Fort Collins
- USA
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20
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Arai S, Shibazaki C, Adachi M, Honjo E, Tamada T, Maeda Y, Tahara T, Kato T, Miyazaki H, Blaber M, Kuroki R. An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody. Protein Sci 2016; 25:1786-96. [PMID: 27419667 PMCID: PMC5029525 DOI: 10.1002/pro.2985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022]
Abstract
Human thrombopoietin (hTPO) primarily stimulates megakaryocytopoiesis and platelet production and is neutralized by the mouse TN1 antibody. The thermodynamic characteristics of TN1 antibody-hTPO complexation were analyzed by isothermal titration calorimetry (ITC) using an antigen-binding fragment (Fab) derived from the TN1 antibody (TN1-Fab). To clarify the mechanism by which hTPO is recognized by TN1-Fab the conformation of free TN1-Fab was determined to a resolution of 2.0 Å using X-ray crystallography and compared with the hTPO-bound form of TN1-Fab determined by a previous study. This structural comparison revealed that the conformation of TN1-Fab does not substantially change after hTPO binding and a set of 15 water molecules is released from the antigen-binding site (paratope) of TN1-Fab upon hTPO complexation. Interestingly, the heat capacity change (ΔCp) measured by ITC (-1.52 ± 0.05 kJ mol(-1) K(-1) ) differed significantly from calculations based upon the X-ray structure data of the hTPO-bound and unbound forms of TN1-Fab (-1.02 ∼ 0.25 kJ mol(-1) K(-1) ) suggesting that hTPO undergoes an induced-fit conformational change combined with significant desolvation upon TN1-Fab binding. The results shed light on the structural biology associated with neutralizing antibody recognition.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan.
| | - Chie Shibazaki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Eijiro Honjo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Taro Tamada
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
| | - Yoshitake Maeda
- Kyowa Hakko Kirin Co. Ltd, 3-6-6 Asahi-Cho, Machida, Tokyo, 194-8533, Japan
| | - Tomoyuki Tahara
- Kyowa Hakko Kirin Co. Ltd, 3-6-6 Asahi-Cho, Machida, Tokyo, 194-8533, Japan
| | - Takashi Kato
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Hiroshi Miyazaki
- Department of Innovative Drug Discovery and Development, Japan Agency for Medical Research and Development, 1-5-5 Nihonbashi-muromachi, Chuo, Tokyo, 103-0022, Japan
| | - Michael Blaber
- College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida, 32306-4300, USA
| | - Ryota Kuroki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki, 319-1106, Japan
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21
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Wang J, Jang Y, Khedkar JK, Koo JY, Kim Y, Lee CJ, Rhee YM, Kim K. How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity? Chemistry 2016; 22:15791-15799. [PMID: 27632939 DOI: 10.1002/chem.201602810] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 01/06/2023]
Abstract
Cucurbit[7]uril (CB[7]) is known to bind strongly to hydrophilic amino saccharide guests with exceptional α-anomer selectivities under aqueous conditions. Single-crystal X-ray crystallography and computational methods were used to elucidate the reason behind this interesting phenomenon. The crystal structures of protonated galactosamine (GalN) and glucosamine (GluN) complexes confirm the inclusion of α anomers inside CB[7] and disclose the details of the host-guest binding. Whereas computed gas-phase structures agree with these crystal structures, gas-phase binding free energies show preferences for the β-anomer complexes over their α counterparts, in striking contrast to the experimental results under aqueous conditions. However, when the solvation effect is considered, the binding structures drastically change and the preference for the α anomers is recovered. The α anomers also tend to bind more tightly and leave less space in the CB[7] cavity toward inclusion of only one water molecule, whereas loosely bound β anomers leave more space toward accommodating two water molecules, with markedly different hydrogen-bonding natures. Surprisingly, entropy seems to contribute significantly to both anomeric discrimination and binding. This suggests that of all the driving factors for the strong complexation of the hydrophilic amino saccharide guests, water mediation plays a crucial role in the anomer discrimination.
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Affiliation(s)
- Jianping Wang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Yoonjung Jang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Jayshree K Khedkar
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Jin Young Koo
- Division of Advanced Materials Science, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Yonghwi Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Chang Jun Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Young Min Rhee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Division of Advanced Materials Science, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.
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22
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Morozenko A, Stuchebrukhov AA. Dowser++, a new method of hydrating protein structures. Proteins 2016; 84:1347-57. [PMID: 27273373 DOI: 10.1002/prot.25081] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/19/2016] [Accepted: 05/30/2016] [Indexed: 12/30/2022]
Abstract
A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi-empirical modification of a popular program for protein hydration Dowser, and the usage of protocols AutoDock Vina, and WaterDock. The positions of water molecules predicted by Dowser++ were compared with experimental data for a set of 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules, as well as for the D- and K-channels of cytochrome c oxidase, and the recent data on PSII. Comparison is also made with the predictions of the original Dowser, and its improved version, Dowser+, described in our previous publication. We also present a model for quantitative estimation of the quality of water molecules placement made by a program, which includes an assumption of possible false negative data from the crystallographic analysis. The comparison of predictions made by Dowser++, Dowser and Dowser+ demonstrates significant improvement of predictive power of the new method. Proteins 2016; 84:1347-1357. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- A Morozenko
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616.
| | - A A Stuchebrukhov
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California, 95616.
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23
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Cui X, Cai W, Shao X. Glucose induced variation of water structure from temperature dependent near infrared spectra. RSC Adv 2016. [DOI: 10.1039/c6ra18912a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The different effects of glucose on water species provide evidence to explain the bioprotective function of carbohydrates in aqueous solutions.
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Affiliation(s)
- Xiaoyu Cui
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Wensheng Cai
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Xueguang Shao
- Research Center for Analytical Sciences
- College of Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
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24
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Biggin PC, Aldeghi M, Bodkin MJ, Heifetz A. Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:161-181. [PMID: 27553242 DOI: 10.1007/978-3-319-35072-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.
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Affiliation(s)
- Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael J Bodkin
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Alexander Heifetz
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
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25
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Feng T, Li M, Zhou J, Zhuang H, Chen F, Ye R, Campanella O, Fang Z. Application of molecular dynamics simulation in food carbohydrate research—a review. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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27
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. J Mol Recognit 2015; 27:482-92. [PMID: 24984865 DOI: 10.1002/jmr.2369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 02/06/2023]
Abstract
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
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Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India
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28
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Force fields and scoring functions for carbohydrate simulation. Carbohydr Res 2015; 401:73-81. [DOI: 10.1016/j.carres.2014.10.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
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29
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Hadden JA, Tessier MB, Fadda E, Woods RJ. Calculating binding free energies for protein-carbohydrate complexes. Methods Mol Biol 2015; 1273:431-65. [PMID: 25753724 DOI: 10.1007/978-1-4939-2343-4_26] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.
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Affiliation(s)
- Jodi A Hadden
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
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30
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Barandun LJ, Ehrmann FR, Zimmerli D, Immekus F, Giroud M, Grünenfelder C, Schweizer WB, Bernet B, Betz M, Heine A, Klebe G, Diederich F. Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Chemistry 2014; 21:126-35. [DOI: 10.1002/chem.201405764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/09/2022]
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31
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Yuan G, Gedeon NG, Jankins TC, Jones GB. Novel approaches for targeting the adenosine A2Areceptor. Expert Opin Drug Discov 2014; 10:63-80. [DOI: 10.1517/17460441.2015.971006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Yang Y, Hu B, Lill MA. Analysis of factors influencing hydration site prediction based on molecular dynamics simulations. J Chem Inf Model 2014; 54:2987-95. [PMID: 25252619 PMCID: PMC4210176 DOI: 10.1021/ci500426q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Water
contributes significantly to the binding of small molecules
to proteins in biochemical systems. Molecular dynamics (MD) simulation
based programs such as WaterMap and WATsite have been used to probe
the locations and thermodynamic properties of hydration sites at the
surface or in the binding site of proteins generating important information
for structure-based drug design. However, questions associated with
the influence of the simulation protocol on hydration site analysis
remain. In this study, we use WATsite to investigate the influence
of factors such as simulation length and variations in initial protein
conformations on hydration site prediction. We find that 4 ns MD simulation
is appropriate to obtain a reliable prediction of the locations and
thermodynamic properties of hydration sites. In addition, hydration
site prediction can be largely affected by the initial protein conformations
used for MD simulations. Here, we provide a first quantification of
this effect and further indicate that similar conformations of binding
site residues (RMSD < 0.5 Å) are required to obtain consistent
hydration site predictions.
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Affiliation(s)
- Ying Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University , 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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33
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Morozenko A, Leontyev IV, Stuchebrukhov AA. Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis. J Chem Theory Comput 2014; 10:4618-4623. [PMID: 25328496 PMCID: PMC4196742 DOI: 10.1021/ct500358r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 12/26/2022]
Abstract
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The
energetics of water molecules in proteins is studied using
the water placement software Dowser. We compared the water position
predictions for 14 high-resolution crystal structures of oligopeptide-binding
protein (OppA) containing a large number of resolved internal water
molecules. From the analysis of the outputs of Dowser with variable
parameters and comparison with experimental X-ray data, we derived
an estimate of the average dipole moment of water molecules located
in the internal cavities of the protein and their binding energies.
The water parameters thus obtained from the experimental data are
then analyzed within the framework of charge-scaling theory developed
recently by this group; the parameters are shown to be in good agreement
with the predictions that the theory makes for the dipole moment in
a protein environment. The water dipole in the protein environment
is found to be much different from that in the bulk and in such models
as SPC or TIPnP. The role of charge scaling due to electronic polarizability
of the protein is discussed.
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Affiliation(s)
- A Morozenko
- Department of Chemistry, University of California Davis , One Shields Avenue, Davis, California 95616, United States
| | - I V Leontyev
- Department of Chemistry, University of California Davis , One Shields Avenue, Davis, California 95616, United States
| | - A A Stuchebrukhov
- Department of Chemistry, University of California Davis , One Shields Avenue, Davis, California 95616, United States
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34
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Grant OC, Woods RJ. Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol 2014; 28:47-55. [PMID: 25108191 DOI: 10.1016/j.sbi.2014.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023]
Abstract
Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States; School of Chemistry, University Road, National University of Ireland, Galway, Ireland.
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35
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Sun H, Zhao L, Peng S, Huang N. Incorporating replacement free energy of binding-site waters in molecular docking. Proteins 2014; 82:1765-76. [DOI: 10.1002/prot.24530] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Hanzi Sun
- College of Life Sciences; Beijing Normal University; Beijing 100875 China
- National Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park; Beijing 102206 China
| | - Lifeng Zhao
- National Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park; Beijing 102206 China
| | - Shiming Peng
- National Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park; Beijing 102206 China
| | - Niu Huang
- College of Life Sciences; Beijing Normal University; Beijing 100875 China
- National Institute of Biological Sciences, Beijing, Zhongguancun Life Science Park; Beijing 102206 China
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36
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Kabiri M, Bushnak I, McDermot MT, Unsworth LD. Toward a Mechanistic Understanding of Ionic Self-Complementary Peptide Self-Assembly: Role of Water Molecules and Ions. Biomacromolecules 2013; 14:3943-50. [DOI: 10.1021/bm401077b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | - Mark T. McDermot
- NanoLife
Group, National Institute for Nanotechnology, National Research Council (Canada), Edmonton, Alberta, Canada
| | - Larry D. Unsworth
- NanoLife
Group, National Institute for Nanotechnology, National Research Council (Canada), Edmonton, Alberta, Canada
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37
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Moore CJ, Auzanneau FI. Understanding the Recognition of Lewis X by Anti-Lex Monoclonal Antibodies. J Med Chem 2013; 56:8183-90. [DOI: 10.1021/jm401304h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
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39
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Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. J Biomol Struct Dyn 2013; 31:630-48. [DOI: 10.1080/07391102.2012.706081] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Abstract
Glycans are key participants in biological processes ranging from reproduction to cellular communication to infection. Revealing glycan roles and the underlying molecular mechanisms by which glycans manifest their function requires access to glycan derivatives that vary systematically. To this end, glycopolymers (polymers bearing pendant carbohydrates) have emerged as valuable glycan analogs. Because glycopolymers can readily be synthesized, their overall shape can be varied, and they can be altered systematically to dissect the structural features that underpin their activities. This review provides examples in which glycopolymers have been used to effect carbohydrate-mediated signal transduction. Our objective is to illustrate how these powerful tools can reveal the molecular mechanisms that underlie carbohydrate-mediated signal transduction.
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Affiliation(s)
- Laura L Kiessling
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA.
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41
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Kumar A, Zhang KYJ. Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. J Chem Inf Model 2013; 53:1880-92. [DOI: 10.1021/ci400052w] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ashutosh Kumar
- Zhang Initiative
Research Unit, RIKEN, 2-1 Hirosawa,
Wako, Saitama 351-0198, Japan
| | - Kam Y. J. Zhang
- Zhang Initiative
Research Unit, RIKEN, 2-1 Hirosawa,
Wako, Saitama 351-0198, Japan
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42
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43
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Jana M, Bandyopadhyay S. Restricted dynamics of water around a protein-carbohydrate complex: computer simulation studies. J Chem Phys 2012; 137:055102. [PMID: 22894384 DOI: 10.1063/1.4739421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Water-mediated protein-carbohydrate interaction is a complex phenomenon responsible for different biological processes in cellular environment. One of the unexplored but important issues in this area is the role played by water during the recognition process and also in controlling the microscopic properties of the complex. In this study, we have carried out atomistic molecular dynamics simulations of a protein-carbohydrate complex formed between the hyaluronan binding domain of the murine Cd44 protein and the octasaccharide hyaluronan in explicit water. Efforts have been made to explore the heterogeneous influence of the complex on the dynamic properties of water present in different regions around it. It is revealed from our analyses that the heterogeneous dynamics of water around the complex are coupled with differential time scales of formation and breaking of hydrogen bonds at the interface. Presence of a highly rigid thin layer of motionally restricted water molecules bridging the protein and the carbohydrate in the common region of the complex has been identified. Such water molecules are expected to play a crucial role in controlling properties of the complex. Importantly, it is demonstrated that the formation of the protein-carbohydrate complex affects the transverse and longitudinal degrees of freedom of the interfacial water molecules in a heterogeneous manner.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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44
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Tschampel SM, Woods RJ. Quantifying the role of water in protein-carbohydrate interactions. J Phys Chem A 2012; 107:9175-81. [PMID: 16906231 PMCID: PMC1538976 DOI: 10.1021/jp035027u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water-mediated interactions play a key role in carbohydrate-lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d) level in which either a methanol molecule was bound to the conserved water (liganded state) or in which a water molecule replaces the methanol (unliganded state). Not surprisingly, the binding of a water to clusters containing charged amino acid side chains was more favorable by 1.55 to 7.23 kcal/mol than that for the binding of a water to the corresponding pure water clusters. In contrast, the binding energy of water to clusters containing polar-uncharged amino acid side chains ranged from 4.35 kcal/mol less favorable to 4.72 kcal/mol more favorable than for binding to the analogous pure water clusters. The overall trend for the binding of methanol versus water, in any of the clusters, favored methanol by an average value of 1.05 kcal/mol. To extend these studies to a complex between a protein (Concanavalin A) and its carbohydrate ligand, a cluster was examined that contained the side chains of three key amino acids, namely asparagine, aspartate, and arginine, as well as a key water molecule, arranged as in the X-ray diffraction structure of Con A. Again, using methanol as a model for the endogenous carbohydrate ligand, energies of -5.94 kcal/mol and -5.70 kcal/mol were obtained for the binding of methanol and water, respectively, to the Con A-water cluster. The extent to which cooperativity enhanced the binding energies has been quantified in terms of nonadditive three-body contributions. In general, the binding of water or methanol to neutral dimers formed cooperative clusters; in contrast, the cooperativity in charged clusters depended on the overall geometry as well as the charge.
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Affiliation(s)
| | - Robert J. Woods
- * Corresponding author. Phone: 706-542-4454. Fax: 706-542-4412. E-mail:
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45
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Moore CJ, Auzanneau FI. Synthesis of 4" manipulated Lewis X trisaccharide analogues. Beilstein J Org Chem 2012; 8:1134-43. [PMID: 23019441 PMCID: PMC3458731 DOI: 10.3762/bjoc.8.126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/29/2012] [Indexed: 11/25/2022] Open
Abstract
Three analogues of the Lex trisaccharide antigen (β-D-Galp(1→4)[α-L-Fucp(1→3)]-D-GlcNAcp) in which the galactosyl residue is modified at O-4 as a methyloxy, deoxychloro or deoxyfluoro, were synthesized. We first report the preparation of the modified 4-OMe, 4-Cl and 4-F trichloroacetimidate galactosyl donors and then report their use in the glycosylation of an N-acetylglucosamine glycosyl acceptor. Thus, we observed that the reactivity of these donors towards the BF3·OEt2-promoted glycosylation at O-4 of the N-acetylglucosamine glycosyl acceptors followed the ranking 4-F > 4-OAc ≈ 4-OMe > 4-Cl. The resulting disaccharides were deprotected at O-3 of the glucosamine residue and fucosylated, giving access to the desired protected Lex analogues. One-step global deprotection (Na/NH3) of the protected 4”-methoxy analogue, and two-step deprotections (removal of a p-methoxybenzyl with DDQ, then Zemplén deacylation) of the 4”-deoxychloro and 4”-deoxyfluoro protected Lex analogues gave the desired compounds in good yields.
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Affiliation(s)
- Christopher J Moore
- Department of Chemistry, University of Guelph, 50 Stone Rd. East, Guelph, Ontario, N1G 2W1, Canada
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46
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Son I, Shek YL, Dubins DN, Chalikian TV. Volumetric Characterization of Tri-N-acetylglucosamine Binding to Lysozyme. Biochemistry 2012; 51:5784-90. [DOI: 10.1021/bi3006994] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ikbae Son
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S
3M2, Canada
| | - Yuen Lai Shek
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S
3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S
3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S
3M2, Canada
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47
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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48
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Ponader D, Wojcik F, Beceren-Braun F, Dernedde J, Hartmann L. Sequence-Defined Glycopolymer Segments Presenting Mannose: Synthesis and Lectin Binding Affinity. Biomacromolecules 2012; 13:1845-52. [DOI: 10.1021/bm300331z] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Daniela Ponader
- MPI of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam-Golm,
Germany
| | - Felix Wojcik
- MPI of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam-Golm,
Germany
| | - Figen Beceren-Braun
- Institut für
Laboratoriumsmedizin,
Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin, 12203 Berlin, Germany
| | - Jens Dernedde
- Institut für
Laboratoriumsmedizin,
Klinische Chemie und Pathobiochemie, Charité-Universitätsmedizin, 12203 Berlin, Germany
| | - Laura Hartmann
- MPI of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam-Golm,
Germany
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49
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Jana M, Bandyopadhyay S. Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water. Phys Chem Chem Phys 2012; 14:6628-38. [PMID: 22460826 DOI: 10.1039/c2cp24104h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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50
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von Schantz L, Håkansson M, Logan DT, Walse B, Österlin J, Nordberg-Karlsson E, Ohlin M. Structural basis for carbohydrate-binding specificity—A comparative assessment of two engineered carbohydrate-binding modules. Glycobiology 2012; 22:948-61. [DOI: 10.1093/glycob/cws063] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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