1
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Singh Y, Cudic P, Cudic M. Exploring Glycan Binding Specificity of Odorranalectin by Alanine Scanning Library. European J Org Chem 2022; 2022. [PMID: 36120398 PMCID: PMC9479679 DOI: 10.1002/ejoc.202200302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescently labelled alanine scan analogues of odorranalectin (OL), a cyclic peptide that exhibits lectin like properties, were screened for binding BSA-conjugated monosaccharides using an enzyme-linked lectin assay (ELLA). Results revealed that Lys5, Phe7, Tyr9, Gly12, Leu14, and Thr17 were crucial for binding BSA-L-fucose, BSA-D-galactose and BSA-N-acetyl-D-galactosamine. Notably, Ala substitution of Ser3, Pro4, and Val13 resulted in higher binding affinities compared to the native OL. The obtained data also indicated that Arg8 plays an important role in differentiation of binding for BSA-L-fucose/D-galactose from BSA-N-acetyl-D-galactosamine. The thermodynamics of binding of the selected alanine analogues was evaluated by isothermal titration calorimetry. Low to moderate binding affinities were determined for the tetravalent MUC1 glycopeptide and asialofetuin, respectively, and high for the fucose rich polysaccharide, fucoidan. The thermodynamic profile of interactions with asialofetuin exhibits shift to an entropy-driven mechanism compared to the fucoidan, which displayed an enthalpyentropy compensation, typically associated with the carbohydratelectin recognition process.
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Affiliation(s)
- YashoNandini Singh
- Department of Chemistry and Biochemistry Florida Atlantic University 777 Glades Road Boca Raton Florida 33431 United States
| | - Predrag Cudic
- Department of Chemistry and Biochemistry Florida Atlantic University 777 Glades Road Boca Raton Florida 33431 United States
| | - Maré Cudic
- Department of Chemistry and Biochemistry Florida Atlantic University 777 Glades Road Boca Raton Florida 33431 United States
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2
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Liu L, Zhu R, Li J, Pei Y, Wang S, Xu P, Wang M, Wen Y, Zhang H, Du D, Ding H, Jiang H, Chen K, Zhou B, Yu L, Luo C. Computational and Structure-Based Development of High Potent Cell-Active Covalent Inhibitor Targeting the Peptidyl-Prolyl Isomerase NIMA-Interacting-1 (Pin1). J Med Chem 2022; 65:2174-2190. [PMID: 35089030 DOI: 10.1021/acs.jmedchem.1c01686] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The unique proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1 (Pin1) is reported to activate numerous cancer-driving pathways simultaneously, and aberrant Pin1 activation is present in many human cancers. Here, we identified a novel hit compound, ZL-Pin01, that covalently modified Pin1 at Cys113 with an half-maximal inhibitory concentration (IC50) of 1.33 ± 0.07 μM through screening an in-house library. Crystallographic study drove the process of structure-guided optimization and led to the potent inhibitor ZL-Pin13 with an IC50 of 0.067 ± 0.03 μM. We obtained four co-crystal structures of Pin1 complexed with inhibitors that elucidated the detailed binding mode of the derivatives with Pin1. Interestingly, the co-crystal of Pin1 with ZL-Pin13 obtained by co-crystallization revealed the conformational change of Gln129 induced by the inhibitor. Furthermore, ZL-Pin13 effectively inhibited the proliferation and downregulated the Pin1 substrates in MDA-MB-231 cells. Collectively, we developed a potent covalent inhibitor of Pin1, ZL-Pin13, which could be an effective probe for studying the functional roles of Pin1.
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Affiliation(s)
- Liping Liu
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Rui Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Jiacheng Li
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuan Pei
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Shuangshuang Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Pan Xu
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingyu Wang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yu Wen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Hao Zhang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Daohai Du
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hong Ding
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Bing Zhou
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lifang Yu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Cheng Luo
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
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3
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Domínguez SE, Kohn B, Ääritalo T, Damlin P, Scheler U, Kvarnström C. Cationic polythiophene-anionic fullerene pair in water and water-dioxane: studies on hydrogen bonding capabilities, kinetic and thermodynamic properties. Phys Chem Chem Phys 2021; 23:21013-21028. [PMID: 34522930 DOI: 10.1039/d0cp05748g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Despite the vast array of solution- and solid-state bio-analytical, bioelectronic and optoelectronic applications of cationic polythiophenes (CPTs), the number of studies focused on the role of hydrogen bonding (H-bonding) between these and other molecules is scarce, regardless of whether H-bonding is expected to play an important role in several such applications. Also, despite the advantages of using cosolvents to systematically examine the molecular interactions, there are no such studies for CPTs to our knowledge. This work presents a steady-state UV-vis/fluorescence spectroscopic, kinetic and thermodynamic study on the H-bonding interactions between a water-soluble, cationic-anionic (isothiouronium-tetraphosphonate), polythiophene-fullerene donor-acceptor pair with two-point, charge-assisted H-bonding (CAHB) capabilities, tuned using water or a 1,4-dioxane-water mixture (W-DI). Both solvents generate photoinduced electron transfer (PET), fluorescence resonance energy transfer (FRET), spontaneous binding, H-bonding, ground-state complexing via multiple site binding, formation of micelle-like aggregates and equivalence points at a similar concentration of the quencher. However, in comparison with water, W-DI promotes less-ordered, less packed micellar aggregates, due to hydrophobic desolvation of the H-bond and larger solvent displacement during the PT1-4Fo complexation. This would decrease the extent of charge-transfer and the size of the sphere-of-quenching, mainly by displacements or rotations of the H-bonds, instead of elongations, together with a possible larger extent of diffusion-controlled static quenching. At [4Fo] larger than the equivalence point the micelles formed in water do not have available binding sites due to a tighter aggregation, causing a decrease in the quenching efficiency, while the micelles formed in W-DI start showing larger quenching efficiencies, possibly due to an increase in entropy that overcomes the desolvation of the H-bonding. These results could be useful when analyzing outputs from systems including CPTs with H-bonding capabilities, operating in (or casted from) solvents with clear differences in polarity and/or H-bonding capacity.
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Affiliation(s)
- Sergio E Domínguez
- Department of Chemistry, Turku University Centre for Materials and Surfaces (MatSurf), Vatselankatu 2, FI-20014 Turku, Finland.
| | - Benjamin Kohn
- Leibniz-Institut für, University of Turku, D-01069 Dresden, Germany
| | - Timo Ääritalo
- Department of Chemistry, Turku University Centre for Materials and Surfaces (MatSurf), Vatselankatu 2, FI-20014 Turku, Finland.
| | - Pia Damlin
- Department of Chemistry, Turku University Centre for Materials and Surfaces (MatSurf), Vatselankatu 2, FI-20014 Turku, Finland.
| | - Ulrich Scheler
- Leibniz-Institut für, University of Turku, D-01069 Dresden, Germany
| | - Carita Kvarnström
- Department of Chemistry, Turku University Centre for Materials and Surfaces (MatSurf), Vatselankatu 2, FI-20014 Turku, Finland.
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4
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Nonadditivity in public and inhouse data: implications for drug design. J Cheminform 2021; 13:47. [PMID: 34215341 PMCID: PMC8254291 DOI: 10.1186/s13321-021-00525-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
Numerous ligand-based drug discovery projects are based on structure-activity relationship (SAR) analysis, such as Free-Wilson (FW) or matched molecular pair (MMP) analysis. Intrinsically they assume linearity and additivity of substituent contributions. These techniques are challenged by nonadditivity (NA) in protein-ligand binding where the change of two functional groups in one molecule results in much higher or lower activity than expected from the respective single changes. Identifying nonlinear cases and possible underlying explanations is crucial for a drug design project since it might influence which lead to follow. By systematically analyzing all AstraZeneca (AZ) inhouse compound data and publicly available ChEMBL25 bioactivity data, we show significant NA events in almost every second assay among the inhouse and once in every third assay in public data sets. Furthermore, 9.4% of all compounds of the AZ database and 5.1% from public sources display significant additivity shifts indicating important SAR features or fundamental measurement errors. Using NA data in combination with machine learning showed that nonadditive data is challenging to predict and even the addition of nonadditive data into training did not result in an increase in predictivity. Overall, NA analysis should be applied on a regular basis in many areas of computational chemistry and can further improve rational drug design.
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5
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Ferrari E, Corsini R, Burastero SE, Tanfani F, Spisni A. The allergen Mus m 1.0102: Cysteine residues and molecular allergology. Mol Immunol 2020; 120:1-12. [PMID: 32044430 DOI: 10.1016/j.molimm.2020.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Mus m 1.0102 is a member of the mouse Major Urinary Protein family, belonging to the Lipocalins superfamily. Major Urinary Proteins (MUPs) are characterized by highly conserved structural motifs. These include a disulphide bond, involved in protein oxidative folding and protein structure stabilization, and a free cysteine residue, substituted by serine only in the pheromonal protein Darcin (MUP20). The free cysteine is recognized as responsible for the onset of inter- or intramolecular thiol/disulphide exchange, an event that favours protein aggregation. Here we show that the substitution of selected cysteine residues modulates Mus m 1.0102 protein folding, fold stability and unfolding reversibility, while maintaining its allergenic potency. Recombinant allergens used for immunotherapy or employed in allergy diagnostic kits require, as essential features, conformational stability, sample homogeneity and proper immunogenicity. In this perspective, recombinant Mus m 1.0102 might appear reasonably adequate as lead molecule because of its allergenic potential and thermal stability. However, its modest resistance to aggregation renders the protein unsuitable for pharmacological preparations. Point mutation is considered a winning strategy. We report that, among the tested mutants, C138A mutant acquires a structure more resistant to thermal stress and less prone to aggregation, two events that act positively on the protein shelf life. Those features make that MUP variant an attractive lead molecule for the development of a diagnostic kit and/or a vaccine.
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Affiliation(s)
- Elena Ferrari
- Dept. Medicine and Surgery, University of Parma, via Gramsci 14, 43126, Parma, Italy.
| | - Romina Corsini
- Dept. Medicine and Surgery, University of Parma, via Gramsci 14, 43126, Parma, Italy.
| | - Samuele E Burastero
- Div. Immunology, IRCCS San Raffaele, Via Olgettina 60, 20132, Milano, Italy.
| | - Fabio Tanfani
- Dept. Life and Environmental Sciences, Marche Polytechnic University, via Brecce Bianche, 60131, Ancona, Italy.
| | - Alberto Spisni
- Dept. Medicine and Surgery, University of Parma, via Gramsci 14, 43126, Parma, Italy.
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6
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Ricatti J, Acquasaliente L, Ribaudo G, De Filippis V, Bellini M, Llovera RE, Barollo S, Pezzani R, Zagotto G, Persaud KC, Mucignat-Caretta C. Effects of point mutations in the binding pocket of the mouse major urinary protein MUP20 on ligand affinity and specificity. Sci Rep 2019; 9:300. [PMID: 30670733 PMCID: PMC6342991 DOI: 10.1038/s41598-018-36391-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022] Open
Abstract
The mouse Major Urinary Proteins (MUPs) contain a conserved β-barrel structure with a characteristic central hydrophobic pocket that binds a variety of volatile compounds. After release of urine, these molecules are slowly emitted in the environment where they play an important role in chemical communication. MUPs are highly polymorphic and conformationally stable. They may be of interest in the construction of biosensor arrays capable of detection of a broad range of analytes. In this work, 14 critical amino acids in the binding pocket involved in ligand interactions were identified in MUP20 using in silico techniques and 7 MUP20 mutants were synthesised and characterised to produce a set of proteins with diverse ligand binding profiles to structurally different ligands. A single amino acid substitution in the binding pocket can dramatically change the MUPs binding affinity and ligand specificity. These results have great potential for the design of new biosensor and gas-sensor recognition elements.
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Affiliation(s)
- Jimena Ricatti
- Department of Molecular Medicine, University of Padua, Padua, Italy.,Cell Biology and Neuroscience Institute, University of Buenos Aires-National Scientific and Technical Council (UBA-CONICET), Buenos Aires, Argentina
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Marino Bellini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Ramiro Esteban Llovera
- Multidisciplinary Institute of Cell Biology, National Scientific and Technical Council (CONICET) and Department of Science and Technology, National University of Quilmes, Buenos Aires, Argentina
| | - Susi Barollo
- Department of Medicine, University of Padua, Padua, Italy
| | | | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Krishna C Persaud
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, UK
| | - Carla Mucignat-Caretta
- Department of Molecular Medicine, University of Padua, Padua, Italy. .,National Institute of Biostructures and Biosystems, Rome, Italy.
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7
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Sagatova AA, Keniya MV, Wilson RK, Sabherwal M, Tyndall JDA, Monk BC. Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14α-demethylase. Sci Rep 2016; 6:26213. [PMID: 27188873 PMCID: PMC4870556 DOI: 10.1038/srep26213] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/25/2016] [Indexed: 12/27/2022] Open
Abstract
Emergence of fungal strains showing resistance to triazole drugs can make treatment of fungal disease problematic. Triazole resistance can arise due to single mutations in the drug target lanosterol 14α-demethylase (Erg11p/CYP51). We have determined how commonly occurring single site mutations in pathogenic fungi affect triazole binding using Saccharomyces cerevisiae Erg11p (ScErg11p) as a target surrogate. The mutations Y140F/H were introduced into full-length hexahistidine-tagged ScErg11p. Phenotypes and high-resolution X-ray crystal structures were determined for the mutant enzymes complexed with short-tailed (fluconazole and voriconazole) or long-tailed (itraconazole and posaconazole) triazoles and wild type enzyme complexed with voriconazole. The mutations disrupted a water-mediated hydrogen bond network involved in binding of short-tailed triazoles, which contain a tertiary hydroxyl not present in long-tailed triazoles. This appears to be the mechanism by which resistance to these short chain azoles occurs. Understanding how these mutations affect drug affinity will aid the design of azoles that overcome resistance.
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Affiliation(s)
- Alia A Sagatova
- Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
| | - Mikhail V Keniya
- Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
| | - Rajni K Wilson
- Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
| | - Manya Sabherwal
- Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand
| | - Joel D A Tyndall
- New Zealand's National School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Brian C Monk
- Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand.,Department of Oral Sciences, University of Otago, Dunedin, New Zealand
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8
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Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity. Sci Rep 2015; 5:14836. [PMID: 26443076 PMCID: PMC4595849 DOI: 10.1038/srep14836] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/09/2015] [Indexed: 12/14/2022] Open
Abstract
Human dihydroorotate dehydrogenase (hDHODH) is an attractive therapeutic target for the treatment of rheumatoid arthritis, transplant rejection and other autoimmune diseases. Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range. Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo. Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold. This work not only elucidates promising scaffolds targeting hDHODH for the treatment of rheumatoid arthritis, but also demonstrates that the water-mediated hydrogen bond interaction is an important factor in molecular design and optimization.
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9
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Said AM, Hangauer DG. Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors. Eur J Med Chem 2015; 96:405-24. [DOI: 10.1016/j.ejmech.2015.03.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 01/07/2023]
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10
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Molecular dynamics study of the conformations of glycosidic linkages in sialic acid modified ganglioside GM3 analogues. Glycoconj J 2014; 31:365-86. [PMID: 24909815 DOI: 10.1007/s10719-014-9532-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/25/2014] [Accepted: 05/21/2014] [Indexed: 10/25/2022]
Abstract
The objective of the present study is to model the analogues of monosialoganglioside (GM3) by making modifications in its sialic acid residue with different substitutions in aqueous environment and to determine their structural stability based upon computational molecular dynamics. Molecular mechanics and molecular dynamics investigation was carried out to study the conformational preferences of the analogues of GM3. Dynamic simulations were carried out on the analogues of GM3 varying in the substituents at C-1, C-4, C-5, C-8 and C-9 positions of their sialic acid or Neuraminic acid (NeuAc) residue. The analogues are soaked in a periodic box of TIP3P water as solvent and subjected to a 10 ns molecular dynamics (MD) simulation using AMBER ff03 and gaff force fields with 30 ps equilibration. The analogue of GM3 with 9-N-succNeuAc (analogue5, C9 substitution) was observed to have the lowest energy of -6112.5 kcal/mol. Graphical analysis made on the MD trajectory reveals the direct and water mediated hydrogen bonds existing in these sialic acid analogues. The preferable conformations for glycosidic linkages of GM3 analogues found in different minimum energy regions in the conformational maps were identified. This study sheds light on the conformational preferences of GM3 analogues which may be essential for the design of GM3 analogues as inhibitors for different ganglioside specific pathogenic proteins such as bacterial toxins, influenza toxins and neuraminidases.
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11
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Bello M, García-Hernández E. Ligand entry into the calyx of β-lactoglobulin. Biopolymers 2014; 101:744-57. [DOI: 10.1002/bip.22454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/06/2013] [Accepted: 12/17/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina; Instituto Politécnico Nacional, México. Plan de San Luis Y Diaz Mirón S/N; Col. Casco de Santo Tomas, 11340 México, D. F. México
| | - Enrique García-Hernández
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; 04360 México, D. F. México
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12
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Katti S, Lokhande N, González D, Cassill A, Renthal R. Quantitative analysis of pheromone-binding protein specificity. INSECT MOLECULAR BIOLOGY 2013; 22:31-40. [PMID: 23121132 PMCID: PMC3552018 DOI: 10.1111/j.1365-2583.2012.01167.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins, using β-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila odorant-binding protein that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in Escherichia coli was assessed by measuring N-phenyl-1-naphthylamine (NPN) binding and Förster resonance energy transfer between LUSH tryptophan 123 (W123) and NPN. Binding of cVA was measured from quenching of W123 fluorescence as a function of cVA concentration. The equilibrium constant for transfer of cVA between β-cyclodextrin and LUSH was determined from a linked equilibria model. This constant, multiplied by the β-cyclodextrin-cVA dissociation constant, gives the LUSH-cVA dissociation constant: ∼100 nM. It was also found that other ligands quench W123 fluorescence. The LUSH-ligand dissociation constants were determined to be ∼200 nM for the silk moth pheromone bombykol and ∼90 nM for methyl oleate. The results indicate that the ligand-binding cavity of LUSH can accommodate a variety ligands with strong binding interactions. Implications of this for the Laughlin, Ha, Jones and Smith model of pheromone reception are discussed.
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Affiliation(s)
- S Katti
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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13
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Nasief NN, Tan H, Kong J, Hangauer D. Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes. J Med Chem 2012; 55:8283-302. [PMID: 22894131 DOI: 10.1021/jm300472k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.
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Affiliation(s)
- Nader N Nasief
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
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14
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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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15
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Bello M, Gutiérrez G, García-Hernández E. Structure and dynamics of β-lactoglobulin in complex with dodecyl sulfate and laurate: A molecular dynamics study. Biophys Chem 2012; 165-166:79-86. [DOI: 10.1016/j.bpc.2012.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/16/2012] [Accepted: 03/17/2012] [Indexed: 11/25/2022]
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16
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Ferrari E, Breda D, Longhi R, Vangelista L, Nakaie CR, Elviri L, Casali E, Pertinhez TA, Spisni A, Burastero SE. In search of a vaccine for mouse allergy: significant reduction of Mus m 1 allergenicity by structure-guided single-point mutations. Int Arch Allergy Immunol 2011; 157:226-37. [PMID: 22041937 DOI: 10.1159/000327551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 03/14/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mouse urinary proteins are relevant allergens from mice urine. We used the recombinant protein Mus m 1 as an allergen model to identify if, by altering Mus m 1 architecture via single-point mutations, we could effectively modify its allergenicity. METHODS Based on structural considerations, we synthesized two single-point mutants, Mus m 1-Y120A and Mus m 1-Y120F, which were expected to harbor large structural alterations. Circular dichroism and fluorescence analysis showed significant conformational rearrangements of the aromatic side chains in the internal cavity of Mus m 1-Y120A when compared to Mus m 1-Y120F and Mus m 1. Evaluation of the allergenic potential of the recombinant molecules was performed in vitro with both immunochemical approaches and assays based on the measurement of basophil degranulation. Moreover, to assess the integrity of the T cell epitopes and as an in vitro measure of immunogenicity, we tested the reactivity of T lymphocytes from subjects allergic to mouse urine against proteins and synthetic peptides encompassing the immunodominant linear epitope containing the mutation. RESULTS We found that the selected point mutation was able to modulate the protein allergenicity, and to severely impair the recognition of Mus m 1 by IgE, while T cell reactivity was fully maintained. CONCLUSIONS In silico predicted, minimum selected structural modifications allowed to design one protein with reduced allergenicity and preserved immunogenicity. Structurally guided mutations can direct the design of proteins with reduced allergenicity which can be used as vaccines for a safer and more effective immunotherapy of allergic disorders.
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Affiliation(s)
- Elena Ferrari
- Department of Experimental Medicine, University of Parma, Parma, Italy
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17
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Hu G, Zhang Q, Chen LY. Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation. J Mol Model 2011; 17:1919-26. [PMID: 21110054 PMCID: PMC3144287 DOI: 10.1007/s00894-010-0892-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Accepted: 10/29/2010] [Indexed: 01/16/2023]
Abstract
Molecular dynamics simulations and free energy calculation have been performed to study how the single-chain variable fragment (scFv) binds methamphetamine (METH) and amphetamine (AMP). The structures of the scFv:METH and the scFv:AMP complexes are analyzed by examining the time-dependence of their RMSDs, by analyzing the distance between some key atoms of the selected residues, and by comparing the averaged structures with their corresponding crystallographic structures. It is observed that binding an AMP to the scFv does not cause significant changes to the binding pocket of the scFv:ligand complex. The binding free energy of scFv:AMP without introducing an extra water into the binding pocket is much stronger than scFv:METH. This is against the first of the two scenarios postulated in the experimental work of Celikel et al. (Protein Science 18, 2336 (2009)). However, adding a water to the AMP (at the position of the methyl group of METH), the binding free energy of the scFv:AMP-H2O complex, is found to be significantly weaker than scFv:METH. This is consistent with the second of the two scenarios given by Celikel et al. Decomposition of the binding energy into ligand-residue pair interactions shows that two residues (Tyr175 and Tyr177) have nearly-zero interactions with AMP in the scFv:AMP-H2O complex, whereas their interactions with METH in the scFv:METH complex are as large as -0.8 and -0.74 kcal mol(-1). The insights gained from this study may be helpful in designing more potent antibodies in treating METH abuse.
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Affiliation(s)
- Guodong Hu
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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18
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Bello M, Portillo-Téllez MDC, García-Hernández E. Energetics of Ligand Recognition and Self-Association of Bovine β-Lactoglobulin: Differences between Variants A and B. Biochemistry 2010; 50:151-61. [DOI: 10.1021/bi1016155] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martiniano Bello
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, D.F., México
| | - María del Carmen Portillo-Téllez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, D.F., México
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04510, D.F., México
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19
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Perez-Miller S, Zou Q, Novotny MV, Hurley TD. High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones. Protein Sci 2010; 19:1469-79. [PMID: 20509168 DOI: 10.1002/pro.426] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP-IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP-IV is highly specific for the male mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X-ray crystal structure of MUP-IV bound to three mouse pheromones: SBT, 2,5-dimethylpyrazine, and 2-heptanone. We also obtained the structure of MUP-IV with 2-ethylhexanol bound in the cavity. These four structures show that relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water-mediated hydrogen bond network in the MUP-I and MUP-II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP-IV.
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Affiliation(s)
- Samantha Perez-Miller
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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20
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Roy J, Laughton CA. Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding. Biophys J 2010; 99:218-26. [PMID: 20655850 DOI: 10.1016/j.bpj.2010.03.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 11/27/2022] Open
Abstract
The mouse major urinary protein (MUP) has proved to be an intriguing test bed for detailed studies on protein-ligand recognition. NMR, calorimetric, and modeling investigations have revealed that the thermodynamics of ligand binding involve a complex interplay between competing enthalpic and entropic terms. We performed six independent, 1.2 micros molecular-dynamics simulations on MUP--three replicates on the apo-protein, and three on the complex with the pheromone isobutylmethoxypyrazine. Our findings provide the most comprehensive picture to date of the structure and dynamics of MUP, and how they are modulated by ligand binding. The mechanical pathways by which amino acid side chains can transmit information regarding ligand binding to surface loops and either increase or decrease their flexibility (entropy-entropy compensation) are identified. Dewetting of the highly hydrophobic binding cavity is confirmed, and the results reveal an aspect of ligand binding that was not observed in earlier, shorter simulations: bound ligand retains extensive rotational freedom. Both of these features have significant implications for interpretations of the entropic component of binding. More generally, these simulations test the ability of current molecular simulation methods to produce a reliable and reproducible picture of protein dynamics on the microsecond timescale.
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Affiliation(s)
- Julie Roy
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
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21
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Pertinhez TA, Ferrari E, Casali E, Patel JA, Spisni A, Smith LJ. The binding cavity of mouse major urinary protein is optimised for a variety of ligand binding modes. Biochem Biophys Res Commun 2009; 390:1266-71. [DOI: 10.1016/j.bbrc.2009.10.133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 10/24/2009] [Indexed: 11/16/2022]
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22
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Palencia A, Camara-Artigas A, Pisabarro MT, Martinez JC, Luque I. Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl. J Biol Chem 2009; 285:2823-33. [PMID: 19906645 DOI: 10.1074/jbc.m109.048033] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.
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Affiliation(s)
- Andres Palencia
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
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23
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Novikov SN, Churakov GA, Philimonenko AA, Ermakova II, Fedorova EM, Burkot IA. The pattern of major urinary proteins (MUPS) expression during postnatal ontogenesis of the laboratory mouse depends on genotype and sex. Russ J Dev Biol 2009. [DOI: 10.1134/s1062360409040031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Wong S, Amaro RE, McCammon JA. MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. J Chem Theory Comput 2009; 5:422-429. [PMID: 19461869 PMCID: PMC2651627 DOI: 10.1021/ct8003707] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Indexed: 11/28/2022]
Abstract
The calculation of protein interaction energetics is of fundamental interest, yet accurate quantities are difficult to obtain due to the complex and dynamic nature of protein interfaces. This is further complicated by the presence of water molecules, which can exhibit transient interactions of variable duration and strength with the protein surface. The T-cell receptor (TCR) and its staphylococcal enterotoxin 3 (SEC3) binding partner are well-characterized examples of a protein−protein interaction system exhibiting interfacial plasticity, cooperativity, and additivity among mutants. Specifically engineered mutants induce intercalating interfacial water molecules, which subsequently enhance protein−protein binding affinity. In this work, we perform a set of molecular mechanics (MM) Poisson−Boltzmann (PB) surface area (SA) calculations on the wild type and two mutant TCR-SEC3 systems and show that the method is able to discriminate between weak and strong binders only when key explicit water molecules are included in the analysis. The results presented here point to the promise of MM-PBSA toward rationalizing molecular recognition at protein−protein interfaces, while establishing a general approach to handle explicit interfacial water molecules in such calculations.
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Affiliation(s)
- Sergio Wong
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365
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25
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Kadirvelraj R, Foley BL, Dyekjær JD, Woods RJ. Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J Am Chem Soc 2008; 130:16933-42. [PMID: 19053475 PMCID: PMC2626182 DOI: 10.1021/ja8039663] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ordered water molecules bound to protein surfaces, or in protein-ligand interfaces, are frequently observed by crystallography. The investigation of the impact of such conserved water molecules on protein stability and ligand affinity requires detailed structural, dynamic, and thermodynamic analyses. Several crystal structures of the legume lectin concanavalin A (Con A) bound to closely related carbohydrate ligands show the presence of a conserved water molecule that mediates ligand binding. Experimental thermodynamic and theoretical studies have examined the role of this conserved water in the complexation of Con A with a synthetic analog of the natural trisaccharide, in which a hydroxyethyl side chain replaces the hydroxyl group at the C-2 position in the central mannosyl residue. Molecular modeling earlier indicated (Clarke, C.; Woods, R. J.; Glushka, J.; Cooper, A.; Nutley, M. A.; Boons, G.-J. J. Am. Chem. Soc. 2001, 123, 12238-12247) that the hydroxyl group in this synthetic side chain could occupy a position equivalent to that of the conserved water, and thus might displace it. An interpretation of the experimental thermodynamic data, which was consistent with the displacement of the conserved water, was also presented. The current work reports the crystal structure of Con A with this synthetic ligand and shows that even though the position and interactions of the conserved water are distorted, this key water is not displaced by the hydroxyethyl moiety. This new structural data provides a firm basis for molecular dynamics simulations and thermodynamic integration calculations whose results indicate that differences in van der Waals contacts (insertion energy), rather than electrostatic interactions (charging energy) are fundamentally responsible for the lower affinity of the synthetic ligand. When combined with the new crystallographic data, this study provides a straightforward interpretation for the lower affinity of the synthetic analog; specifically, that it arises primarily from weaker interactions with the protein via the positionally perturbed conserved water. This interpretation is fully consistent with the experimental observations that the free energy of binding is enthalpy driven, that there is both less enthalpic gain and less entropic penalty for binding the synthetic ligand, relative to the natural trisaccharide, and that the entropic component does not arise from releasing an ordered water molecule from the protein surface to the bulk solvent.
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Affiliation(s)
- Renuka Kadirvelraj
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA
| | - B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA
| | | | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA
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26
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Conserved water molecules stabilize the Omega-loop in class A beta-lactamases. Antimicrob Agents Chemother 2008; 52:1072-9. [PMID: 18195065 DOI: 10.1128/aac.01035-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A set of 49 high-resolution (<or=2.2 A) structures of the TEM, SHV, and CTX-M class A beta-lactamase families was systematically analyzed to investigate the role of conserved water molecules in the stabilization of the Omega-loop. Overall, 13 water molecules were found to be conserved in at least 45 structures, including two water positions which were found to be conserved in all structures. Of the 13 conserved water molecules, 6 are located at the Omega-loop, forming a dense cluster with hydrogen bonds to residues at the Omega-loop as well as to the rest of the protein. This layer of conserved water molecules is packed between the Omega-loop and the rest of the protein and acts as structural glue, which could reduce the flexibility of the Omega-loop. A correlation between conserved water molecules and conserved protein residues could in general not be detected, with the exception of the conserved water molecules at the Omega-loop. Furthermore, the evolutionary relationship between the three families, derived from the number of conserved water molecules, is similar to the relationship derived from phylogenetic analysis.
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27
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Askew EB, Gampe RT, Stanley TB, Faggart JL, Wilson EM. Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone. J Biol Chem 2007; 282:25801-16. [PMID: 17591767 PMCID: PMC4075031 DOI: 10.1074/jbc.m703268200] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The androgen receptor (AR) is transcriptionally activated by high affinity binding of testosterone (T) or its 5alpha-reduced metabolite, dihydrotestosterone (DHT), a more potent androgen required for male reproductive tract development. The molecular basis for the weaker activity of T was investigated by determining T-bound ligand binding domain crystal structures of wild-type AR and a prostate cancer somatic mutant complexed with the AR FXXLF or coactivator LXXLL peptide. Nearly identical interactions of T and DHT in the AR ligand binding pocket correlate with similar rates of dissociation from an AR fragment containing the ligand binding domain. However, T induces weaker AR FXXLF and coactivator LXXLL motif interactions at activation function 2 (AF2). Less effective FXXLF motif binding to AF2 accounts for faster T dissociation from full-length AR. T can nevertheless acquire DHT-like activity through an AR helix-10 H874Y prostate cancer mutation. The Tyr-874 mutant side chain mediates a new hydrogen bonding scheme from exterior helix-10 to backbone protein core helix-4 residue Tyr-739 to rescue T-induced AR activity by improving AF2 binding of FXXLF and LXXLL motifs. Greater AR AF2 activity by improved core helix interactions is supported by the effects of melanoma antigen gene protein-11, an AR coregulator that binds the AR FXXLF motif and targets AF2 for activation. We conclude that T is a weaker androgen than DHT because of less favorable T-dependent AR FXXLF and coactivator LXXLL motif interactions at AF2.
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Affiliation(s)
- Emily B. Askew
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599
- Laboratories for Reproductive Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert T. Gampe
- Computational and Structural Sciences, Division of Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27709
| | - Thomas B. Stanley
- Computational and Structural Sciences, Division of Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, North Carolina 27709
| | - Jonathan L. Faggart
- Laboratories for Reproductive Biology, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Elizabeth M. Wilson
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599
- Laboratories for Reproductive Biology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
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28
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Ababou A, Ladbury JE. Survey of the year 2005: literature on applications of isothermal titration calorimetry. J Mol Recognit 2007; 20:4-14. [PMID: 17006876 DOI: 10.1002/jmr.803] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isothermal titration calorimetry (ITC) can provide a full thermodynamic characterization of an interaction. Its usage does not suffer from constraints of molecular size, shape or chemical constitution. Neither is there any need for chemical modification or attachment to solid support. This ease of use has made it an invaluable instrumental resource and led to its appearance in many laboratories. Despite this, the value of the thermodynamic parameterization has, only quite recently, become widely appreciated. Although our understanding of the correlation between thermodynamic data and structural details continues to be somewhat naïve, a large number of publications have begun to improve the situation. In this overview of the literature for 2005, we have attempted to highlight works of interest and novelty. Furthermore, we draw attention to those works which we feel have provided a route to better analysis and increased our ability to understand the meaning of thermodynamic change on binding.
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Affiliation(s)
- Adessamad Ababou
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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29
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Bellapadrona G, Chiaraluce R, Consalvi V, Ilari A, Stefanini S, Chiancone E. The mutations Lys 114 → Gln and Asp 126 → Asn disrupt an intersubunit salt bridge and convert Listeria innocua Dps into its natural mutant Listeria monocytogenes Dps. Effects on protein stability at Low pH. Proteins 2006; 66:975-83. [PMID: 17186524 DOI: 10.1002/prot.21305] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The stability of the dodecameric Listeria monocytogenes Dps has been compared with that of the Listeria innocua protein. The two proteins differ only in two amino acid residues that form an intersubunit salt-bridge in L. innocua Dps. This salt-bridge is replaced by a hydrogen bonding network in L. monocytogenes Dps as revealed by the X-ray crystal structure. The resistance to low pH and high temperature was assayed for both Dps proteins under equilibrium conditions and kinetically. Despite the identical equilibrium behavior, significant differences in the kinetic stability and activation energy of the unfolding process are apparent at pH 1.5. The higher stability of L. monocytogenes Dps has been accounted for in terms of the persistence of the hydrogen bonding network at this low pH value. In contrast, the salt-bridge between Lys 114 and Asp 126 characteristic of L. innocua Dps is most likely abolished due to protonation of Asp 126.
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Affiliation(s)
- Giuliano Bellapadrona
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università La Sapienza, Rome, Italy
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30
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Abstract
Water molecules are often found at the binding interface of biomolecular complexes mediating the interaction between polar groups via hydrogen bonds, or simply filling space providing van der Waals interactions. Recent studies have demonstrated the importance of taking such water molecules into account in docking and binding affinity prediction. Here, we review the recent experimental and theoretical work aimed at quantifying the influence of interfacial water on the thermodynamic properties of binding. We highlight especially our recent results obtained by inhomogeneous fluid solvation theory in several systems and the prediction of the thermodynamic consequences of displacement of the bound water molecule by ligand modification. Finally, we discuss possible directions for further progress in this field.
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Affiliation(s)
- Zheng Li
- Department of Chemistry, City College of New York/CUNY, New York, NY 10031, USA
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31
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Cerutti DS, Jain T, McCammon JA. CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci 2006; 15:1579-96. [PMID: 16815913 PMCID: PMC2242569 DOI: 10.1110/ps.051985106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951+/-0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8+/-9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0365, USA.
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32
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Shimokhina N, Bronowska A, Homans SW. Contribution of Ligand Desolvation to Binding Thermodynamics in a Ligand–Protein Interaction. Angew Chem Int Ed Engl 2006; 45:6374-6. [PMID: 16906619 DOI: 10.1002/anie.200602227] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Natalia Shimokhina
- Institute of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
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33
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Shimokhina N, Bronowska A, Homans SW. Contribution of Ligand Desolvation to Binding Thermodynamics in a Ligand–Protein Interaction. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Yonkunas MJ, Xu Y, Tang P. Anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations. Biophys J 2005; 89:2350-6. [PMID: 16040747 PMCID: PMC1366735 DOI: 10.1529/biophysj.105.063396] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nature and the sites of interactions between anesthetic halothane and homodimeric Delta5-3-ketosteroid isomerase (KSI) are characterized by flexible ligand docking and confirmed by 1H-15N NMR. The dynamics consequence of halothane interaction and the implication of the dynamic changes to KSI function are studied by multiple 5-ns molecular dynamics simulations in the presence and absence of halothane. Both docking and MD simulations show that halothane prefer the amphiphilic dimeric interface to the hydrophobic active site of KSI. Halothane occupancy at the dimer interface disrupted the intersubunit hydrogen bonding formed either directly through side chains of polar residues or indirectly through the mediation of the interfacial water molecules. Moreover, in the presence of halothane, the exchange rate of the bound waters with bulk water was increased. Halothane perturbation to the dimer interface affected the overall flexibility of the active site. This action is likely to contribute to the halothane-induced reduction of the KSI activity. The allosteric halothane modulation of the dynamics-function relationship of KSI without direct competition at the enzymatic active sites may be generalized to offer a unifying explanation of anesthetic action on a diverse range of multidomain neuronal proteins that are potentially relevant to clinical general anesthesia.
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Affiliation(s)
- Michael J Yonkunas
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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McGavin RS, Gagne RA, Chervenak MC, Bundle DR. The design, synthesis and evaluation of high affinity macrocyclic carbohydrate inhibitors. Org Biomol Chem 2005; 3:2723-32. [PMID: 16032350 DOI: 10.1039/b416105j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbohydrate-protein interactions have been investigated for a model system of a monoclonal antibody, SYA/J6, which binds a trisaccharide epitope of the O-polysaccharide of the Shigella flexneri variant Y lipopolysaccharide. The thermodynamics of binding for the methyl glycoside of the native trisaccharide epitope, Rha-Rha-GlcNAc () to SYA/J6 over a range of temperatures exhibits strong, linear enthalpy-entropy compensation and a negative heat capacity change (DeltaC(p)=-152 cal mol(-1) degree(-1)). At 293 K the free energy of association is the sum of favourable enthalpy and entropy contributions (DeltaH=-3.9 kcal mol(-1) and -TDeltaS=-2.9 kcal mol(-1)). Crystal structures for SYA/J6 Fab detailed the position of the native trisaccharide epitope, Rha-Rha-GlcNAc, and facilitated a strategy to design a tighter binding, low molecular weight ligand. This involved pre-organization of the native trisaccharide in its bound conformation by addition of intramolecular constraints (a beta-alanyl or glycinyl tether). ELISA measurements indicated that the glycinyl tethered trisaccharide was not an optimal candidate for further analysis, while microcalorimetry provided data showing that the beta-alanyl tethered trisaccharide displayed a 15-fold increase in affinity for SYA/J6. Tethering resulted in a favourable entropic contribution to binding, relative to the native trisaccharide (-TDeltaDeltaS=-1.2 kcal mol(-1)). Potential energy and dynamics calculations using the AMBER Plus force fields indicated that trisaccharide adopted a rigid conformation similar to that of the bound conformation of the native trisaccharide epitope. While this strategy resulted in modest free energy gains by minimizing losses due to conformational entropy, thermodynamic data are consistent with significant contributions from solvent reorganization.
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Affiliation(s)
- Robert S McGavin
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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