1
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Liang Y, Li Z, Zhang J, Li T, Lv C. Comparison of the Glucocorticoid Receptor Binding and Agonist Activities of Typical Glucocorticoids: Insights into Their Endocrine Disrupting Effects. Chem Biodivers 2024; 21:e202301525. [PMID: 38129310 DOI: 10.1002/cbdv.202301525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
Over the past decades, the synthetic glucocorticoids (GCs) have been widely used in clinical practice and animal husbandry. Given the health hazard of these toxic residues in food, it is necessary to explore the detailed interaction mechanisms of typical GCs and their main target glucocorticoid receptor (GR). Hence, this work compared the GR binding and agonist activities of typical GCs. Fluorescence polarization assay showed that these GCs were potent ligands of GR. Their GR binding affinities were in the order of methylprednisolone>betamethasone≈prednisolone>dexamethasone, with IC50 values of 1.67, 2.94, 2.95, and 5.58 nM. Additionally, the limits of detection of dexamethasone, betamethasone, prednisolone, and methylprednisolone were 0.32, 0.14, 0.19, and 0.09 μg/kg in fluorescence polarization assay. Reporter gene assay showed that these GCs induced GR transactivation in a dose-dependent manner, confirming their GR agonist activities. Among which, dexamethasone at the concentration of 100 nM produced a maximal induction of more than 11-fold over the blank control. Molecular docking and molecular dynamics simulations suggested that hydrogen-bonding and hydrophobic interactions played an important role in stabilizing the GC-GR-LBD complexes. In summary, this work might help to understand the GR-mediated endocrine disrupting effects of typical GCs.
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Affiliation(s)
- Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Zhuolin Li
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiezhu Li
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Chengyu Lv
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
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2
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Libouban PY, Aci-Sèche S, Gómez-Tamayo JC, Tresadern G, Bonnet P. The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks. Int J Mol Sci 2023; 24:16120. [PMID: 38003312 PMCID: PMC10671244 DOI: 10.3390/ijms242216120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Artificial intelligence (AI) has gained significant traction in the field of drug discovery, with deep learning (DL) algorithms playing a crucial role in predicting protein-ligand binding affinities. Despite advancements in neural network architectures, system representation, and training techniques, the performance of DL affinity prediction has reached a plateau, prompting the question of whether it is truly solved or if the current performance is overly optimistic and reliant on biased, easily predictable data. Like other DL-related problems, this issue seems to stem from the training and test sets used when building the models. In this work, we investigate the impact of several parameters related to the input data on the performance of neural network affinity prediction models. Notably, we identify the size of the binding pocket as a critical factor influencing the performance of our statistical models; furthermore, it is more important to train a model with as much data as possible than to restrict the training to only high-quality datasets. Finally, we also confirm the bias in the typically used current test sets. Therefore, several types of evaluation and benchmarking are required to understand models' decision-making processes and accurately compare the performance of models.
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Affiliation(s)
- Pierre-Yves Libouban
- Institute of Organic and Analytical Chemistry (ICOA), UMR7311, Université d’Orléans, CNRS, Pôle de Chimie rue de Chartres, 45067 Orléans, CEDEX 2, France; (P.-Y.L.); (S.A.-S.)
| | - Samia Aci-Sèche
- Institute of Organic and Analytical Chemistry (ICOA), UMR7311, Université d’Orléans, CNRS, Pôle de Chimie rue de Chartres, 45067 Orléans, CEDEX 2, France; (P.-Y.L.); (S.A.-S.)
| | - Jose Carlos Gómez-Tamayo
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., B-2340 Beerse, Belgium; (J.C.G.-T.); (G.T.)
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., B-2340 Beerse, Belgium; (J.C.G.-T.); (G.T.)
| | - Pascal Bonnet
- Institute of Organic and Analytical Chemistry (ICOA), UMR7311, Université d’Orléans, CNRS, Pôle de Chimie rue de Chartres, 45067 Orléans, CEDEX 2, France; (P.-Y.L.); (S.A.-S.)
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3
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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4
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Tahti EF, Blount JM, Jackson SN, Gao M, Gill NP, Smith SN, Pederson NJ, Rumph SN, Struyvenberg SA, Mackley IGP, Madden DR, Amacher JF. Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets. Protein Sci 2023; 32:e4611. [PMID: 36851847 PMCID: PMC10022582 DOI: 10.1002/pro.4611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Protein-protein interactions that involve recognition of short peptides are critical in cellular processes. Protein-peptide interaction surface areas are relatively small and shallow, and there are often overlapping specificities in families of peptide-binding domains. Therefore, dissecting selectivity determinants can be challenging. PDZ domains are a family of peptide-binding domains located in several intracellular signaling and trafficking pathways. These domains are also directly targeted by pathogens, and a hallmark of many oncogenic viral proteins is a PDZ-binding motif. However, amidst sequences that target PDZ domains, there is a wide spectrum in relative promiscuity. For example, the viral HPV16 E6 oncoprotein recognizes over double the number of PDZ domain-containing proteins as the cystic fibrosis transmembrane conductance regulator (CFTR) in the cell, despite similar PDZ targeting-sequences and identical motif residues. Here, we determine binding affinities for PDZ domains known to bind either HPV16 E6 alone or both CFTR and HPV16 E6, using peptides matching WT and hybrid sequences. We also use energy minimization to model PDZ-peptide complexes and use sequence analyses to investigate this difference. We find that while the majority of single mutations had marginal effects on overall affinity, the additive effect on the free energy of binding accurately describes the selectivity observed. Taken together, our results describe how complex and differing PDZ interactomes can be programmed in the cell.
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Affiliation(s)
- Elise F. Tahti
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Jadon M. Blount
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Sophie N. Jackson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Melody Gao
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Nicholas P. Gill
- Department of BiochemistryGeisel School of Medicine at DartmouthHanoverNew HampshireUSA
| | - Sarah N. Smith
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Nick J. Pederson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | | | | | - Iain G. P. Mackley
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Dean R. Madden
- Department of BiochemistryGeisel School of Medicine at DartmouthHanoverNew HampshireUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
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5
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Kola-Mustapha AT, Raji MA, Adedeji O, Ambrose GO. Network Pharmacology and Molecular Modeling to Elucidate the Potential Mechanism of Neem Oil against Acne vulgaris. Molecules 2023; 28:molecules28062849. [PMID: 36985821 PMCID: PMC10056471 DOI: 10.3390/molecules28062849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Acne vulgaris is a common skin disorder with a complicated etiology. Papules, lesions, comedones, blackheads, and other skin lesions are common physical manifestations of Acne vulgaris, but the individual who has it also regularly has psychological repercussions. Natural oils are being utilized more and more to treat skin conditions since they have fewer negative effects and are expected to provide benefits. Using network pharmacology, this study aims to ascertain if neem oil has any anti-acne benefits and, if so, to speculate on probable mechanisms of action for such effects. The neem leaves (Azadirachta indica) were collected, verified, authenticated, and assigned a voucher number. After steam distillation was used to extract the neem oil, the phytochemical components of the oil were examined using gas chromatography-mass spectrometry (GC-MS). The components of the oil were computationally examined for drug-likeness using Lipinski's criteria. The Pharm Mapper service was used to anticipate the targets. Prior to pathway and protein-protein interaction investigations, molecular docking was performed to predict binding affinity. Neem oil was discovered to be a potential target for STAT1, CSK, CRABP2, and SYK genes in the treatment of Acne vulgaris. In conclusion, it was discovered that the neem oil components with PubChem IDs: ID_610088 (2-(1-adamantyl)-N-methylacetamide), ID_600826 (N-benzyl-2-(2-methyl-5-phenyl-3H-1,3,4-thiadiazol-2-yl)acetamide), and ID_16451547 (N-(3-methoxyphenyl)-2-(1-phenyltetrazol-5-yl)sulfanylpropanamide) have strong affinities for these drug targets and may thus be used as therapeutic agents in the treatment of acne.
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Affiliation(s)
- Adeola Tawakalitu Kola-Mustapha
- College of Pharmacy, Alfaisal University Riyadh, Riyadh 11461, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240101, Nigeria
| | - Muhabat Adeola Raji
- Department of Microbiology & Immunology, Alfaisal University, Riyadh 11461, Saudi Arabia
| | - Oluwakorede Adedeji
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240101, Nigeria
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6
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Yi SC, Wu YH, Yang RN, Li DZ, Abdelnabby H, Wang MQ. A Highly Expressed Antennae Odorant-Binding Protein Involved in Recognition of Herbivore-Induced Plant Volatiles in Dastarcus helophoroides. Int J Mol Sci 2023; 24. [PMID: 36834874 DOI: 10.3390/ijms24043464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Natural enemies such as parasitoids and parasites depend on sensitive olfactory to search for their specific hosts. Herbivore-induced plant volatiles (HIPVs) are vital components in providing host information for many natural enemies of herbivores. However, the olfactory-related proteins involved in the recognition of HIPVs are rarely reported. In this study, we established an exhaustive tissue and developmental expression profile of odorant-binding proteins (OBPs) from Dastarcus helophoroides, an essential natural enemy in the forestry ecosystem. Twenty DhelOBPs displayed various expression patterns in different organs and adult physiological states, suggesting a potential involvement in olfactory perception. In silico AlphaFold2-based modeling and molecular docking showed similar binding energies between six DhelOBPs (DhelOBP4, 5, 6, 14, 18, and 20) and HIPVs from Pinus massoniana. While in vitro fluorescence competitive binding assays showed only recombinant DhelOBP4, the most highly expressed in the antennae of emerging adults could bind to HIPVs with high binding affinities. RNAi-mediated behavioral assays indicated that DhelOBP4 was an essential functional protein for D. helophoroides adults recognizing two behaviorally attractive substances: p-cymene and γ-terpinene. Further binding conformation analyses revealed that Phe 54, Val 56, and Phe 71 might be the key binding sites for DhelOBP4 interacting with HIPVs. In conclusion, our results provide an essential molecular basis for the olfactory perception of D. helophoroides and reliable evidence for recognizing the HIPVs of natural enemies from insect OBPs' perspective.
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7
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Tahti EF, Blount JM, Jackson SN, Gao M, Gill NP, Smith SN, Pederson NJ, Rumph SN, Struyvenberg SA, Mackley IGP, Madden DR, Amacher JF. Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets. bioRxiv 2023:2022.12.31.522388. [PMID: 36711692 PMCID: PMC9881875 DOI: 10.1101/2022.12.31.522388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protein-protein interactions that include recognition of short sequences of amino acids, or peptides, are critical in cellular processes. Protein-peptide interaction surface areas are relatively small and shallow, and there are often overlapping specificities in families of peptide-binding domains. Therefore, dissecting selectivity determinants can be challenging. PDZ domains are an example of a peptide-binding domain located in several intracellular signaling and trafficking pathways, which form interactions critical for the regulation of receptor endocytic trafficking, tight junction formation, organization of supramolecular complexes in neurons, and other biological systems. These domains are also directly targeted by pathogens, and a hallmark of many oncogenic viral proteins is a PDZ-binding motif. However, amidst sequences that target PDZ domains, there is a wide spectrum in relative promiscuity. For example, the viral HPV16 E6 oncoprotein recognizes over double the number of PDZ domain-containing proteins as the cystic fibrosis transmembrane conductance regulator (CFTR) in the cell, despite similar PDZ targeting-sequences and identical motif residues. Here, we determine binding affinities for PDZ domains known to bind either HPV16 E6 alone or both CFTR and HPV16 E6, using peptides matching WT and hybrid sequences. We also use energy minimization to model PDZ-peptide complexes and use sequence analyses to investigate this difference. We find that while the majority of single mutations had a marginal effect on overall affinity, the additive effect on the free energy of binding accurately describes the selectivity observed. Taken together, our results describe how complex and differing PDZ interactomes can be programmed in the cell.
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Affiliation(s)
- Elise F. Tahti
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Jadon M. Blount
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Sophie N. Jackson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Melody Gao
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Nicholas P. Gill
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Sarah N. Smith
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Nick J. Pederson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Simone N. Rumph
- Department of Biochemistry, Bowdoin College, Brunswick, ME, USA
| | | | - Iain G. P. Mackley
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Dean R. Madden
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jeanine F. Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
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8
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Wu S, Hassan FU, Luo Y, Fatima I, Ahmed I, Ihsan A, Safdar W, Liu Q, Rehman SU. Comparative Genomic Characterization of Buffalo Fibronectin Type III Domain Proteins: Exploring the Novel Role of FNDC5/Irisin as a Ligand of Gonadal Receptors. Biology (Basel) 2021; 10:1207. [PMID: 34827201 PMCID: PMC8615036 DOI: 10.3390/biology10111207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/29/2022]
Abstract
FN-III proteins are widely distributed in mammals and are usually involved in cellular growth, differentiation, and adhesion. The FNDC5/irisin regulates energy metabolism and is present in different tissues (liver, brain, etc.). The present study aimed to investigate the physiochemical characteristics and the evolution of FN-III proteins and FNDC5/irisin as a ligand targeting the gonadal receptors including androgen (AR), DDB1 and CUL4 associated factor 6 (DCAF6), estrogen-related receptor β (ERR-β), estrogen-related receptor γ (ERR-γ), Krüppel-like factor 15 (KLF15), and nuclear receptor subfamily 3 group C member 1 (NR3C1). Moreover, the putative role of irisin in folliculogenesis and spermatogenesis was also elucidated. We presented the molecular structure and function of 29 FN-III genes widely distributed in the buffalo genome. Phylogenetic analysis, motif, and conserved domain pattern demonstrated the evolutionary well-conserved nature of FN-III proteins with a variety of stable to unstable, hydrophobic to hydrophilic, and thermostable to thermo-unstable properties. The comparative structural configuration of FNDC5 revealed amino acid variations but still the FNDC5 structure of humans, buffalo, and cattle was quite similar to each other. For the first time, we predicted the binding scores and interface residues of FNDC5/irisin as a ligand for six representative receptors having a functional role in energy homeostasis, and a significant involvement in folliculogenesis and spermatogenesis in buffalo.
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Affiliation(s)
- Siwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.W.); (Y.L.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Yuhong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.W.); (Y.L.)
| | - Israr Fatima
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad 38000, Pakistan;
| | - Ishtiaq Ahmed
- School of Medical Science, Gold Coast Campus, Griffith University, Southport, QLD 4222, Australia;
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal 57000, Pakistan;
| | - Warda Safdar
- Department of Biochemistry, Bahauddin Zakariya University, Multan 60000, Pakistan;
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.W.); (Y.L.)
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.W.); (Y.L.)
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9
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Abstract
Signal transduction pathways rely on dynamic interactions between protein globular domains and short linear motifs (SLiMs). The weak affinities of these interactions are essential to allow fast rewiring of signaling pathways and downstream responses but also pose technical challenges for interaction detection and measurement. We recently developed a technique (MRBLE-pep) that leverages spectrally encoded hydrogel beads to measure binding affinities between a single protein of interest and 48 different peptide sequences in a single small volume. In prior work, we applied it to map the binding specificity landscape between calcineurin and the PxIxIT SLiM (Nguyen, H. Q. et al. Elife 2019, 8). Here, using peptide sequences known to bind the PP2A regulatory subunit B56α, we systematically compare affinities measured by MRBLE-pep or isothermal calorimetry (ITC) and confirm that MRBLE-pep accurately quantifies relative affinity over a wide dynamic range while using a fraction of the material required for traditional methods such as ITC.
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Affiliation(s)
- Jamin
B. Hein
- Department
of Biology, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- The
Novo Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Martha S. Cyert
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Polly M. Fordyce
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg
Biohub, San Francisco, California 94110, United States
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10
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Sursyakova VV, Rubaylo AI. Boundary values of binding constants determined by affinity capillary electrophoresis. J Sep Sci 2021; 44:4200-4203. [PMID: 34510741 DOI: 10.1002/jssc.202100507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/14/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022]
Abstract
This study shows that the upper limit of binding (stability) constants determined by mobility shift affinity capillary electrophoresis can be increased from 104 to 106 -109 L/mol if the lowest possible analyte concentration in samples is used (for example, the concentration that gives electrophoretic peaks with a signal-to-noise ratio of 10) and the effective electrophoretic mobility of the analyte is calculated via the parameter a1 of the Haarhoff-Van der Linde function. The equation to calculate the boundary values of binding constants for 1:1 complexes was derived for the case when the constants cannot be calculated in the usual way. These values are obtained from the inequality: the difference between the ionic mobility of the analyte-ligand complex and the effective electrophoretic mobility of the analyte determined at the lowest ligand concentration in the background electrolyte at which the analyte appears as an undistorted peak in electropherograms is less than or equal to the absolute error in mobility measurements. The application of the equation was illustrated by the example of electrophoretic data for a complex between betulin 3,28-diphthalate and (2-hydroxypropyl)-γ-cyclodextrin. An algorithm to determine the binding constants for strong complexation by mobility shift affinity capillary electrophoresis was suggested.
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Affiliation(s)
- Viktoria V Sursyakova
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
| | - Anatoly I Rubaylo
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,School of Non-Ferrous Metals and Material Science, Siberian Federal University, Krasnoyarsk, Russia.,Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
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11
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Gao M, Mackley IGP, Mesbahi-Vasey S, Bamonte HA, Struyvenberg SA, Landolt L, Pederson NJ, Williams LI, Bahl CD, Brooks L, Amacher JF. Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. Protein Sci 2020; 29:2226-2244. [PMID: 32914530 DOI: 10.1002/pro.3947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022]
Abstract
Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular-like "rosette" state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide-binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high-resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG-3 PDZ domains from M. brevicollis. Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG-3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.
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Affiliation(s)
- Melody Gao
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Iain G P Mackley
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Samaneh Mesbahi-Vasey
- Institute for Protein Innovation, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Haley A Bamonte
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Sarah A Struyvenberg
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Louisa Landolt
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Nick J Pederson
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Lucy I Williams
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Lionel Brooks
- Department of Biology, Western Washington University, Bellingham, Washington, USA
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington, USA
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12
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Yang H, Zu G, Liu Y, Xie D, Gan X, Song B. Tomato Chlorosis Virus Minor Coat Protein as a Novel Target To Screen Antiviral Drugs. J Agric Food Chem 2020; 68:3425-3433. [PMID: 32091891 DOI: 10.1021/acs.jafc.9b08215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Minor coat protein (mCP), an important component of tomato chlorosis virus (ToCV), plays a significant role in the process of virus assembly and movement and is directly related to the virus-insect transmission. Therefore, ToCV mCP could be considered as a potent target for anti-ToCV drugs. In this study, ToCV mCP was first cloned, expressed, purified, and a novel target to screen the antiviral agents. The results showed that some antiviral compounds bound to ToCV mCP with strongly affinities in vitro, including quinazoline derivatives 4a and 4b, Ningnanmycin, and Ribavirin. Subsequently, three-dimensional-quantitative structure-activity relationship (3D-QSAR) analysis was performed based on the binding affinities, and the model indicated that 4a and 4b had indeed stronger binding effects on ToCV mCP than other quinazoline derivatives. Finally, the anti-ToCV activities of compounds 4a and 4b were evaluated by quantitative real-time polymerase chain reaction in vivo. Compounds 4a and 4b inhibited infection of ToCV in the host and as well as reduced the level of ToCV mCP gene expression. Thus, ToCV mCP can be used as a novel drug target for screening anti-ToCV agents, and the ligand-based 3D-QSAR analysis of quinazoline derivatives provided new insights into the design and optimization of novel anti-ToCV drug molecules based on ToCV mCP.
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Affiliation(s)
- Huanyu Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Guangcheng Zu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Yuewen Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Dandan Xie
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Xiuhai Gan
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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13
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Smith RD, Clark JJ, Ahmed A, Orban ZJ, Dunbar JB Jr, Carlson HA. Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. J Mol Biol 2019; 431:2423-33. [PMID: 31125569 DOI: 10.1016/j.jmb.2019.05.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 01/02/2023]
Abstract
The goal of Binding MOAD is to provide users with a data set focused on high-quality x-ray crystal structures that have been solved with biologically relevant ligands bound. Where available, experimental binding affinities (Ka, Kd, Ki, IC50) are provided from the primary literature of the crystal structure. The database has been updated regularly since 2005, and this most recent update has added nearly 7000 new structures (growth of 21%). MOAD currently contains 32,747 structures, composed of 9117 protein families and 16,044 unique ligands. The data are freely available on www.BindingMOAD.org. This paper outlines updates to the data in Binding MOAD as well as improvements made to both the website and its contents. The NGL viewer has been added to improve visualization of the ligands and protein structures. MarvinJS has been implemented, over the outdated MarvinView, to work with JChem for small molecule searching in the database. To add tools for predicting polypharmacology, we have added information about sequence, binding-site, and ligand similarity between entries in the database. A main premise behind polypharmacology is that similar binding sites will bind similar ligands. The large amount of protein-ligand information available in Binding MOAD allows us to compute pairwise ligand and binding-site similarities. Lists of similar ligands and similar binding sites have been added to allow users to identify potential polypharmacology pairs. To show the utility of the polypharmacology data, we detail a few examples from Binding MOAD of drug repurposing targets with their respective similarities.
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14
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Dempsey CE, Bigotti MG, Adams JC, Brancaccio A. Analysis of α-Dystroglycan/LG Domain Binding Modes: Investigating Protein Motifs That Regulate the Affinity of Isolated LG Domains. Front Mol Biosci 2019; 6:18. [PMID: 30984766 PMCID: PMC6450144 DOI: 10.3389/fmolb.2019.00018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
Dystroglycan (DG) is an adhesion complex that links the cytoskeleton to the surrounding extracellular matrix in skeletal muscle and a wide variety of other tissues. It is composed of a highly glycosylated extracellular α-DG associated noncovalently with a transmembrane β-DG whose cytodomain interacts with dystrophin and its isoforms. Alpha-dystroglycan (α-DG) binds tightly and in a calcium-dependent fashion to multiple extracellular proteins and proteoglycans, each of which harbors at least one, or, more frequently, tandem arrays of laminin-globular (LG) domains. Considerable biochemical and structural work has accumulated on the α-DG-binding LG domains, highlighting a significant heterogeneity in ligand-binding properties of domains from different proteins as well as between single and multiple LG domains within the same protein. Here we review biochemical, structural, and functional information on the LG domains reported to bind α-dystroglycan. In addition, we have incorporated bioinformatics and modeling to explore whether specific motifs responsible for α-dystroglycan recognition can be identified within isolated LG domains. In particular, we analyzed the LG domains of slits and agrin as well as those of paradigmatic α-DG non-binders such as laminin-α3. While some stretches of basic residues may be important, no universally conserved motifs could be identified. However, the data confirm that the coordinated calcium atom within the LG domain is needed to establish an interaction with the sugars of α-DG, although it appears that this alone is insufficient to mediate significant α-DG binding. We develop a scenario involving different binding modes of a single LG domain unit, or tandemly repeated units, with α-DG. A variability of binding modes might be important to generate a range of affinities to allow physiological regulation of this interaction, reflecting its crucial biological importance.
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Affiliation(s)
| | | | - Josephine C Adams
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Andrea Brancaccio
- School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Istituto di Chimica del Riconoscimento Molecolare - CNR, Università Cattolica del Sacro Cuore, Rome, Italy
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15
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Abdelkhalek AS, Alley GS, Alwassil OI, Khatri S, Mosier PD, Nyce HL, White MM, Schulte MK, Dukat M. "Methylene Bridge" to 5-HT 3 Receptor Antagonists: Conformationally Constrained Phenylguanidines. ACS Chem Neurosci 2019; 10:1380-1389. [PMID: 30375852 DOI: 10.1021/acschemneuro.8b00431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Arylguanidines, depending upon their aromatic substitution pattern, display varying actions at 5-HT3 receptors (e.g., partial agonist, agonist, superagonist). Here, we demonstrate that conformational constraint of these agents as dihydroquinazolines (such as A6CDQ; 1) results in their conversion to 5-HT3 receptor antagonists. We examined the structure-activity relationships of 1. Replacement/removal of any of the guanidinium nitrogen atoms of 1 resulted in decreased affinity. All three nitrogen atoms of 1 are necessary for optimal binding affinity at 5-HT3 receptors. Introduction of substituents as small as an N2-methyl group abolishes affinity. The results are consistent with homology modeling/docking studies and binding data from site-directed mutagenesis studies. Introducing a "methylene bridge" to the arylguanidine structure, regardless of its functional activity, results in a 5-HT3 receptor antagonist.
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Affiliation(s)
- Ahmed S. Abdelkhalek
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Genevieve S. Alley
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Osama I. Alwassil
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Shailesh Khatri
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Philip D. Mosier
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Heather L. Nyce
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania 19102, United States
| | - Michael M. White
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania 19102, United States
| | - Marvin K. Schulte
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Małgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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16
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Pallesen J, Møllerud S, Frydenvang K, Pickering DS, Bornholdt J, Nielsen B, Pasini D, Han L, Marconi L, Kastrup JS, Johansen TN. N1-Substituted Quinoxaline-2,3-diones as Kainate Receptor Antagonists: X-ray Crystallography, Structure-Affinity Relationships, and in Vitro Pharmacology. ACS Chem Neurosci 2019; 10:1841-1853. [PMID: 30620174 DOI: 10.1021/acschemneuro.8b00726] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Among the ionotropic glutamate receptors, the physiological role of kainate receptors is less well understood. Although ligands with selectivity toward the kainate receptor subtype GluK1 are available, tool compounds with selectivity at the remaining kainate receptor subtypes are sparse. Here, we have synthesized a series of quinoxaline-2,3-diones with substitutions in the N1-, 6-, and 7-position to investigate the structure-activity relationship (SAR) at GluK1-3 and GluK5. Pharmacological characterization at native and recombinant kainate and AMPA receptors revealed that compound 37 had a GluK3-binding affinity ( Ki) of 0.142 μM and 8-fold preference for GluK3 over GluK1. Despite lower binding affinity of 22 at GluK3 ( Ki = 2.91 μM), its preference for GluK3 over GluK1 and GluK2 was >30-fold. Compound 37 was crystallized with the GluK1 ligand-binding domain to understand the SAR. The X-ray structure showed that 37 stabilized the protein in an open conformation, consistent with an antagonist binding mode.
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Affiliation(s)
- Jakob Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stine Møllerud
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Darryl S. Pickering
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jan Bornholdt
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Birgitte Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Diletta Pasini
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Liwei Han
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Laura Marconi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Tommy N. Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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17
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Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J. Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Chemphyschem 2018; 19:873-879. [PMID: 29316128 DOI: 10.1002/cphc.201701104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/11/2022]
Abstract
Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (Ki ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Magdalena Hořejší
- Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
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18
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Zhang X, Liu S, Xing J, Pi Z, Liu Z, Song F. Systematic study on metabolism and activity evaluation of Radix Scutellaria extract in rat plasma using UHPLC with quadrupole time-of-flight mass spectrometry and microdialysis intensity-fading mass spectrometry. J Sep Sci 2018; 41:1704-1710. [PMID: 29293286 DOI: 10.1002/jssc.201700666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
Radix Scutellaria is a widely used traditional Chinese medicine in the treatment of various diseases. However, the activities of the absorbed components and metabolites of its main flavones in rat plasma need further investigation. In this study, a systematic method based on ultra-high performance liquid chromatography with quadruple time-of-flight mass spectrometry was developed to speculate the absorbed components and metabolites of the main flavonoids in Radix Scutellaria extract in rat plasma sample after oral administration of the extract. Twelve compounds, including four prototype components and eight metabolites, were confirmed in drug-containing plasma. In these metabolites, five were originally detected in rat plasma. The possible metabolic pathways of these polyhydroxy flavones in vivo were described and clarified. Microdialysis with intensity-fading mass spectrometry was originally employed to investigate the binding affinities of the absorbed components and metabolites with α-glucosidase. The order of their binding affinities was P4 > P3 > P2 > P1≥M5 > M3 > M1. The research result is helpful to deepen the understanding of the absorbed components and metabolic pathways of main flavones from Radix Scutellaria, and provide a new approach to screen potential inhibitors from in vivo components originated from Chinese herb.
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Affiliation(s)
- Xueju Zhang
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu Liu
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Junpeng Xing
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Zifeng Pi
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Zhiqiang Liu
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fengrui Song
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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19
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Møllerud S, Pinto A, Marconi L, Frydenvang K, Thorsen TS, Laulumaa S, Venskutonytė R, Winther S, Moral AMC, Tamborini L, Conti P, Pickering DS, Kastrup JS. Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors. ACS Chem Neurosci 2017; 8:2056-2064. [PMID: 28691798 DOI: 10.1021/acschemneuro.7b00201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are involved in most of the fast excitatory synaptic transmission in the central nervous system. These receptors are important for learning and memory formation, but are also involved in the development of diseases such as Alzheimer's disease, epilepsy and depression. To understand the function of different types of iGluRs, selective agonists are invaluable as pharmacological tool compounds. Here, we report binding affinities of two bicyclic, conformationally restricted analogues of glutamate (CIP-AS and LM-12b) at AMPA (GluA2 and GluA3) and kainate receptor subunits (GluK1-3 and GluK5). Both CIP-AS and LM-12b were found to be GluK3-preferring agonists, with Ki of 6 and 22 nM, respectively, at recombinant GluK3 receptors. The detailed binding mode of CIP-AS and LM-12b in the ligand-binding domains of the AMPA receptor subunit GluA2 (GluA2-LBD) and the kainate receptor subunits GluK1 (GluK1-LBD) and GluK3 (GluK3-LBD) was investigated by X-ray crystallography. CIP-AS stabilized all three receptor constructs in conformations similar to those with kainate. Remarkably, whereas LM-12b bound in a similar manner to CIP-AS in GluA2-LBD and GluK3-LBD, it introduced full closure of the ligand-binding domain in GluK1-LBD and formation of a D1-D2 interlobe hydrogen bond between Glu441 and Ser721, as also observed with glutamate. As the binding affinity of LM-12b at GluK1 is ∼8-fold better than that for CIP-AS (Ki of 85 and 656 nM, respectively), it shows that small changes in agonist structure can lead to prominent differences in structure and function.
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Affiliation(s)
- Stine Møllerud
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milano, Italy
| | - Laura Marconi
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, 20133 Milano, Italy
| | - Karla Frydenvang
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Saara Laulumaa
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Raminta Venskutonytė
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Sebastian Winther
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ana Maria Cuñado Moral
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lucia Tamborini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, 20133 Milano, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, 20133 Milano, Italy
| | - Darryl S. Pickering
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jette Sandholm Kastrup
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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20
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Alix K, Khatri S, Mosier PD, Casterlow S, Yan D, Nyce HL, White MM, Schulte MK, Dukat M. Superagonist, Full Agonist, Partial Agonist, and Antagonist Actions of Arylguanidines at 5-Hydroxytryptamine-3 (5-HT 3) Subunit A Receptors. ACS Chem Neurosci 2016; 7:1565-1574. [PMID: 27533595 DOI: 10.1021/acschemneuro.6b00196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Introduction of minor variations to the substitution pattern of arylguanidine 5-hydroxytryptamine-3 (5-HT3) receptor ligands resulted in a broad spectrum of functionally-active ligands from antagonist to superagonist. For example, (i) introduction of an additional Cl-substituent(s) to our lead full agonist N-(3-chlorophenyl)guanidine (mCPG, 2; efficacy % = 106) yielded superagonists 7-9 (efficacy % = 186, 139, and 129, respectively), (ii) a positional isomer of 2, p-Cl analog 11, displayed partial agonist actions (efficacy % = 12), and (iii) replacing the halogen atom at the meta or para position with an electron donating OCH3 group or a stronger electron withdrawing (i.e., CF3) group resulted in antagonists 13-16. We posit based on combined mutagenesis, crystallographic, and computational analyses that for the 5-HT3 receptor, the arylguanidines that are better able to simultaneously engage the primary and complementary subunits, thus keeping them in close proximity, have greater agonist character while those that are deficient in this ability are antagonists.
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Affiliation(s)
- Katie Alix
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Shailesh Khatri
- Department
of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Philip D. Mosier
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Samantha Casterlow
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Dong Yan
- Department
of Biochemistry and Molecular Biology Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Heather L. Nyce
- Department
of Biochemistry and Molecular Biology Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Michael M. White
- Department
of Biochemistry and Molecular Biology Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Marvin K. Schulte
- Department
of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Małgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Ramírez D, Caballero J. Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target? Int J Mol Sci 2016; 17:ijms17040525. [PMID: 27104528 PMCID: PMC4848981 DOI: 10.3390/ijms17040525] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/22/2016] [Accepted: 04/01/2016] [Indexed: 12/05/2022] Open
Abstract
Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand–receptor interaction modes, and for the exploration of large chemical datasets through virtual screening experiments. Despite their unquestionable merits, docking methods are not reliable for predicting binding energies due to the simple scoring functions they use. However, comparisons between two or three complexes using the predicted binding energies as a criterion are commonly found in the literature. In the present work we tested how wise is it to trust the docking energies when two complexes between a target protein and enantiomer pairs are compared. For this purpose, a ligand library composed by 141 enantiomeric pairs was used, including compounds with biological activities reported against seven protein targets. Docking results using the software Glide (considering extra precision (XP), standard precision (SP), and high-throughput virtual screening (HTVS) modes) and AutoDock Vina were compared with the reported biological activities using a classification scheme. Our test failed for all modes and targets, demonstrating that an accurate prediction when binding energies of enantiomers are compared using docking may be due to chance. We also compared pairs of compounds with different molecular weights and found the same results.
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Affiliation(s)
- David Ramírez
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 2 Norte 685, Casilla 721, Talca, Chile.
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 2 Norte 685, Casilla 721, Talca, Chile.
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Seo S, Rebehmed J, de Brevern AG, Karboune S. Enzymatic Synthesis of Galactosylated Serine/Threonine Derivatives by β-Galactosidase from Escherichia coli. Int J Mol Sci 2015; 16:13714-28. [PMID: 26084049 DOI: 10.3390/ijms160613714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/11/2015] [Indexed: 01/08/2023] Open
Abstract
The transgalactosylations of serine/threonine derivatives were investigated using β-galactosidase from Escherichia coli as biocatalyst. Using ortho-nitrophenyl-β-d-galactoside as donor, the highest bioconversion yield of transgalactosylated N-carboxy benzyl l-serine benzyl ester (23.2%) was achieved in heptane:buffer medium (70:30), whereas with the lactose, the highest bioconversion yield (3.94%) was obtained in the buffer reaction system. The structures of most abundant galactosylated serine products were characterized by MS/MS. The molecular docking simulation revealed that the binding of serine/threonine derivatives to the enzyme’s active site was stronger (−4.6~−7.9 kcal/mol) than that of the natural acceptor, glucose, and mainly occurred through interactions with aromatic residues. For N-tert-butoxycarbonyl serine methyl ester (6.8%) and N-carboxybenzyl serine benzyl ester (3.4%), their binding affinities and the distances between their hydroxyl side chain and the 1′-OH group of galactose moiety were in good accordance with the quantified bioconversion yields. Despite its lower predicted bioconversion yield, the high experimental bioconversion yield obtained with N-carboxybenzyl serine methyl ester (23.2%) demonstrated the importance of the thermodynamically-driven nature of the transgalactosylation reaction.
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Abstract
Measuring binding affinities and association/dissociation rates of molecular interactions is important for a quantitative understanding of cellular mechanisms. Many low-throughput methods have been developed throughout the years to obtain these parameters. Acquiring data with higher accuracy and throughput is, however, necessary to characterize complex biological networks. Here, we provide an overview of a high-throughput microfluidic method based on mechanically induced trapping of molecular interactions (MITOMI). MITOMI can be used to obtain affinity constants and kinetic rates of hundreds of protein-ligand interactions in parallel. It has been used in dozens of studies to measure binding affinities of transcription factors, map protein interaction networks, identify pharmacological inhibitors, and perform high-throughput, low-cost molecular diagnostics. This article covers the technological aspects of MITOMI and its applications.
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Affiliation(s)
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Abstract
Anticholinergics, or antimuscarinic drugs, are drugs that competitively inhibit the action of acetylcholine at muscarinic receptors, leading to a blockade of the actions of the parasympathetic nervous system at sites where overactivity can lead to increased symptom burden. Successful blockade of the parasympathetic nervous system ultimately leads to decreased production of secretions in the salivary, bronchial, and gastrointestinal tracts. These effects are often used for several symptoms that originate due to parasympathetic nervous system overactivity, such as the "death rattle" and malignant bowel obstruction. Anticholinergic agents are divided into either tertiary amines or quaternary ammonium compounds, which differ in their ability to cross into the central nervous system. Quaternary compounds do not cross into the central nervous system and have a different adverse effect profile than the tertiary amines. The purpose of this review is to highlight anticholinergic agents, their pharmacology, and an evidence-based assessment of their role in palliative care.
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Affiliation(s)
- Eric Prommer
- Division of Hematology/Oncology, Mayo Clinic College of Medicine Mayo Clinic Hospital, Scottsdale, AZ 85054, USA.
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Correia AR, Wang T, Craig EA, Gomes CM. Iron-binding activity in yeast frataxin entails a trade off with stability in the alpha1/beta1 acidic ridge region. Biochem J 2010; 426:197-203. [PMID: 20001966 PMCID: PMC2819628 DOI: 10.1042/bj20091612] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Frataxin is a highly conserved mitochondrial protein whose deficiency in humans results in Friedreich's ataxia (FRDA), an autosomal recessive disorder characterized by progressive ataxia and cardiomyopathy. Although its cellular function is still not fully clear, the fact that frataxin plays a crucial role in Fe-S assembly on the scaffold protein Isu is well accepted. In the present paper, we report the characterization of eight frataxin variants having alterations on two putative functional regions: the alpha1/beta1 acidic ridge and the conserved beta-sheet surface. We report that frataxin iron-binding capacity is quite robust: even when five of the most conserved residues from the putative iron-binding region are altered, at least two iron atoms per monomer can be bound, although with decreased affinity. Furthermore, we conclude that the acidic ridge is designed to favour function over stability. The negative charges have a functional role, but at the same time significantly impair frataxin's stability. Removing five of those charges results in a thermal stabilization of approximately 24 degrees C and reduces the inherent conformational plasticity. Alterations on the conserved beta-sheet residues have only a modest impact on the protein stability, highlighting the functional importance of residues 122-124.
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Affiliation(s)
- Ana R. Correia
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tao Wang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Elizabeth A. Craig
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Cláudio M. Gomes
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Serna DD, Moore JL, Rayson GD. Site-specific Eu(III) binding affinities to a Datura innoxia biosorbent. J Hazard Mater 2010; 173:409-414. [PMID: 19836885 PMCID: PMC3837531 DOI: 10.1016/j.jhazmat.2009.08.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 08/21/2009] [Accepted: 08/21/2009] [Indexed: 05/28/2023]
Abstract
The binding of Eu(III) to a biosorbent derived from cultured cells of the plant Datura innoxia, have been investigated through elucidation of apparent affinity constants associated with different chemical environments present on the cell wall. Adsorption isotherms for separate types of binding sites were generated using metal ion luminescence measurements. Application of regularized regression analysis to these isotherm data for four chemically distinguishable sites revealed the presence of sites exhibiting both low (mean log K(app)=-0.3 to 0.6) and higher (mean log K(app)=3.2-3.5) apparent affinities for pH conditions of 2.0, 4.0, and 5.0. Low affinity sites were observed for all pH conditions and attributed to non-specific binding of the metal ions to the negatively charged biomaterial. The pH-dependent higher affinity sites are ascribed to specific sites involving either an ion-exchange mechanism or formation of weak surface-metal ion complexes. These results differed significantly from a similar analysis of total metal binding isotherms that indicated mean log K(app) values of -0.5 to 0.25 (low affinity) and 5.6-6.0 (high affinity).
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Affiliation(s)
| | | | - Gary D. Rayson
- Corresponding author. Tel.: +1 575 646 5839; fax: +1 575 646 2649. (G.D. Rayson)
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Thode AB, Kruse SW, Nix JC, Jones DNM. The role of multiple hydrogen-bonding groups in specific alcohol binding sites in proteins: insights from structural studies of LUSH. J Mol Biol 2008; 376:1360-76. [PMID: 18234222 PMCID: PMC2293277 DOI: 10.1016/j.jmb.2007.12.063] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/16/2022]
Abstract
It is now generally accepted that many of the physiological effects of alcohol consumption are a direct result of binding to specific sites in neuronal proteins such as ion channels or other components of neuronal signaling cascades. Binding to these targets generally occurs in water-filled pockets and leads to alterations in protein structure and dynamics. However, the precise interactions required to confer alcohol sensitivity to a particular protein remain undefined. Using information from the previously solved crystal structures of the Drosophila melanogaster protein LUSH in complexes with short-chain alcohols, we have designed and tested the effects of specific amino acid substitutions on alcohol binding. The effects of these substitutions, specifically S52A, T57S, and T57A, were examined using a combination of molecular dynamics, X-ray crystallography, fluorescence spectroscopy, and thermal unfolding. These studies reveal that the binding of ethanol is highly sensitive to small changes in the composition of the alcohol binding site. We find that T57 is the most critical residue for binding alcohols; the T57A substitution completely abolishes binding, while the T57S substitution differentially affects ethanol binding compared to longer-chain alcohols. The additional requirement for a potential hydrogen-bond acceptor at position 52 suggests that both the presence of multiple hydrogen-bonding groups and the identity of the hydrogen-bonding residues are critical for defining an ethanol binding site. These results provide new insights into the detailed chemistry of alcohol's interactions with proteins.
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Affiliation(s)
- Anna B. Thode
- Program in Biomolecular Structure, University of Colorado, Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
| | - Schoen W Kruse
- Department of Pharmacology, University of Colorado Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source Beamline 4.2.2, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - David N. M. Jones
- Department of Pharmacology, University of Colorado Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
- Program in Biomolecular Structure, University of Colorado, Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
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Tan YY, Wade JD, Tregear GW, Summers RJ. Quantitative autoradiographic studies of relaxin binding in rat atria, uterus and cerebral cortex: characterization and effects of oestrogen treatment. Br J Pharmacol 1999; 127:91-8. [PMID: 10369460 PMCID: PMC1565996 DOI: 10.1038/sj.bjp.0702517] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The binding characteristics of the relaxin receptor in rat atria, uterus and cortex were studied using a [33P]-labelled human gene 2 relaxin (B33) and quantitative receptor autoradiography. The binding kinetics of [33P]-human gene 2 relaxin (B33) were investigated in slide-mounted rat atrial sections. The binding achieved equilibrium after 60 min incubation at room temperature (23+/-1 degrees C) and dissociated slowly. The association and dissociation rate constants were 4.31+/-0.34x10(8) M(-1) x min(-1) and 1.55+/-0.38x10(-3) min(-1) respectively. Thus, the kinetic dissociation constant was 3.46+/-0.59 pM. Binding was saturable to a single population of non-interacting sites throughout atria, in uterine myometrium and the 5th layer of cerebral cortex. The binding affinities (pK(D)) of [33P]-human gene 2 relaxin (B33) were 8.92+/-0.09 in atrial myocardium and 8.79+/-0.04 in cerebral cortex of male rats, and 8.79+/-0.10 in uterine myometrium. Receptor densities in the cerebral cortex and atria were higher than in uterine myometrium, indicating that relaxin also has important roles in non-reproductive tissues. In male rats, treatment with 17beta-oestradiol (20 microg in 0.1 ml sesame oil s.c., 18-24 h) significantly decreased the density of relaxin receptors in atria and cerebral cortex. Identical treatment in female rats had no significant effect in atria and cerebral cortex, but it significantly increased the density of relaxin receptors in uterine myometrium. Relaxin binding was competitively displaced by porcine and rat native relaxins. Porcine native relaxin binds to the relaxin receptor in male rat atria (8.90+/-0.02), and cerebral cortex (8.90+/-0.03) and uterine myometrium (8.89+/-0.03) with affinities not significantly different from human gene 2 (B33) relaxin. Nevertheless, rat relaxin binds to the receptors with affinities (8.35+/-0.09 in atria, 8.22+/-0.07 in cerebral cortex and 8.48+/-0.06 in uterine myometrium) significantly less than human gene 2 (B33) and porcine relaxins. Quantitative receptor autoradiography is the method of choice for measurement of affinities and densities of relaxin receptor in atria, uterine myometrium and cerebral cortex. High densities were found in all these tissues. 17beta-oestradiol treatment produced complex effects where it increased the densities of relaxin receptors in uterus but decreased those in atria and cerebral cortex of the male rats, and had no effect on the atria and cerebral cortex of the female rats.
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Affiliation(s)
- Y Y Tan
- Department of Pharmaceutical Science, Universiti Sains Malaysia, Minden 11800, Penang, Malaysia
- Howard Florey Institute, Parkville 3052, Victoria, Australia
| | - J D Wade
- Howard Florey Institute, Parkville 3052, Victoria, Australia
| | - G W Tregear
- Howard Florey Institute, Parkville 3052, Victoria, Australia
| | - R J Summers
- Department of Pharmacology, Monash University, Clayton 3168, Victoria, Australia
- Author for correspondence:
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