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Paketurytė-Latvė V, Smirnov A, Manakova E, Baranauskiene L, Petrauskas V, Zubrienė A, Matulienė J, Dudutienė V, Čapkauskaitė E, Zakšauskas A, Leitans J, Gražulis S, Tars K, Matulis D. From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system. IUCRJ 2024; 11:556-569. [PMID: 38856178 PMCID: PMC11220870 DOI: 10.1107/s2052252524004627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.
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Affiliation(s)
- Vaida Paketurytė-Latvė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Jurgita Matulienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Edita Čapkauskaitė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Audrius Zakšauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Janis Leitans
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Saulius Gražulis
- Sector of Crystallography and Chemical Informatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, 1067 Riga, Latvia
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257 Vilnius, Lithuania
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2
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Schönbeck C, Kari J, Westh P. ITC analysis of polydisperse systems: Unravelling the impact of sample heterogeneity. Anal Biochem 2024; 687:115446. [PMID: 38147946 DOI: 10.1016/j.ab.2023.115446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Binding interactions often involve heterogeneous samples displaying a distribution of binding sites that vary in affinity and binding enthalpy. Examples include biological samples like proteins and chemically produced samples like modified cyclodextrins. Experimental studies often ignore sample heterogeneity and treat the system as an interaction of two homogeneous species, i.e. a chemically well-defined ligand binding to one type of site. The present study explores, by simulations and experiments, the impact of heterogeneity in isothermal titration calorimetry (ITC) setups where one of the binding components is heterogeneous. It is found that the standard single-site model, based on the assumption of two homogeneous binding components, provides excellent fits to simulated ITC data when the binding free energy is normally distributed and all sites have similar binding enthalpies. In such cases, heterogeneity can easily go undetected but leads to underestimated binding constants. Heterogeneity in the binding enthalpy is a bigger problem and may result in enthalpograms of increased complexity that are likely to be misinterpreted as two-site binding or other complex binding models. Finally, it is shown that heterogeneity can account for previously observed experimental anomalies. All simulations are accessible in Google Colab for readers to experiment with the simulation parameters.
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Affiliation(s)
| | - Jeppe Kari
- Department of Science and Environment, Roskilde University, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
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3
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Jamrozik E, Śmieja M, Podlewska S. ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation. J Chem Inf Model 2024; 64:1425-1432. [PMID: 38373602 DOI: 10.1021/acs.jcim.3c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Great progress in the development of computational strategies for drug design applications has revolutionized the process of searching for new drugs. Although the focus of in silico strategies is still put on the provision of the desired activity of a compound to the considered target, characterization of a compound in terms of its physicochemical and ADMET properties becomes an indispensable element of computer-aided drug design protocols. In the study, an online application ADMET-PrInt for in silico assessment of selected compound features: cardiotoxicity, solubility, genotoxicity, membrane permeability, and plasma protein binding was prepared. In addition to the prediction of particular property, ADMET-PrInt enables also the identification of compound features influencing this property thanks to the application of two explainability approaches: local interpretabile model-agnostic explanations and counterfactual analysis. It is an important factor for medicinal chemists, as it greatly facilitates the process of optimization of the compound structure in terms of the evaluated properties. The intuitive webpage, available at admet.if-pan.krakow.pl, allows making use of all predictive and interpretability models also by nonexperts and nonprogrammers.
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Affiliation(s)
- Ewelina Jamrozik
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348 Kraków, Poland
| | - Marek Śmieja
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348 Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
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4
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Biomarkers as predictors of treatment response to tricyclic antidepressants in major depressive disorder: A systematic review. J Psychiatr Res 2022; 150:202-213. [PMID: 35397333 DOI: 10.1016/j.jpsychires.2022.03.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/14/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022]
Abstract
Tricyclic antidepressants (TCAs) are frequently prescribed in case of non-response to first-line antidepressants in Major Depressive Disorder (MDD). Treatment of MDD often entails a trial-and-error process of finding a suitable antidepressant and its appropriate dose. Nowadays, a shift is seen towards a more personalized treatment strategy in MDD to increase treatment efficacy. One of these strategies involves the use of biomarkers for the prediction of antidepressant treatment response. We aimed to summarize biomarkers for prediction of TCA specific (i.e. per agent, not for the TCA as a drug class) treatment response in unipolar nonpsychotic MDD. We performed a systematic search in PubMed and MEDLINE. After full-text screening, 36 papers were included. Seven genetic biomarkers were identified for nortriptyline treatment response. For desipramine, we identified two biomarkers; one genetic and one nongenetic. Three nongenetic biomarkers were identified for imipramine. None of these biomarkers were replicated. Quality assessment demonstrated that biomarker studies vary in endpoint definitions and frequently lack power calculations. None of the biomarkers can be confirmed as a predictor for TCA treatment response. Despite the necessity for TCA treatment optimization, biomarker studies reporting drug-specific results for TCAs are limited and adequate replication studies are lacking. Moreover, biomarker studies generally use small sample sizes. To move forward, larger cohorts, pooled data or biomarkers combined with other clinical characteristics should be used to improve predictive power.
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5
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Young DJ, Nguyen B, Li L, Higashimoto T, Levis MJ, Liu JO, Small D. A method for overcoming plasma protein inhibition of tyrosine kinase inhibitors. Blood Cancer Discov 2021; 2:532-547. [PMID: 34589716 PMCID: PMC8478262 DOI: 10.1158/2643-3230.bcd-20-0119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Plasma protein binding reduces potency of staurosporine-derived tyrosine kinase inhibitors against Flt3-mutant AML. “Decoy” drugs interfering with the binding, including mifepristone, can be harnessed to restore the antileukemia activity. FMS-like tyrosine kinase 3 (FLT3) is the most frequently mutated gene in acute myeloid leukemia and a target for tyrosine kinase inhibitors (TKI). FLT3 TKIs have yielded limited improvements to clinical outcomes. One reason for this is TKI inhibition by endogenous factors. We characterized plasma protein binding of FLT3 TKI, specifically staurosporine derivatives (STS-TKI) by alpha-1-acid glycoprotein (AGP), simulating its effects upon drug efficacy. Human AGP inhibits the antiproliferative activity of STS-TKI in FLT3/ITD-dependent cells, with IC50 shifts higher than clinically achievable. This is not seen with nonhuman plasma. Mifepristone cotreatment, with its higher AGP affinity, improves TKI activity despite AGP, yielding IC50s predicted to be clinically effective. In a mouse model of AGP drug inhibition, mifepristone restores midostaurin activity. This suggests combinatorial methods for overcoming plasma protein inhibition of existing TKIs for leukemia as well as providing a platform for investigating the drug–protein interaction space for developing more potent small-molecule agents.
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Affiliation(s)
- David J Young
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bao Nguyen
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Li Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tomoyasu Higashimoto
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mark J Levis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun O Liu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Donald Small
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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6
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Revisiting Chiral Recognition Mechanism on Chicken Alpha 1-Acid Glycoprotein: Location of Chiral Binding Sites and Insight into Chiral Binding Mechanism. SEPARATIONS 2021. [DOI: 10.3390/separations8060073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chiral stationary phases based on chicken alpha 1-acid glycoprotein (cAGP) have been used for enantioseparations of various compounds. However, the chiral binding sites and mechanism have not been clarified yet. Based on chromatographic properties of native and W26-modified cAGP columns and docking simulations of studied compounds into the generated model structure of cAGP, the chiral binding sites were located on cAGP and the chiral binding mechanism was discussed. On cAGP, there existed a binding cavity lined with H25, W26, Y47, R128, T129, D161 and E168, which contribute electrostatic or hydrogen bonding interactions. Benzoin and chlorpheniramine enantiomers interacted with cAGP at almost the same sites a little away from W26, while propranolol enantiomers docked, slightly shifting toward H25 and W26. Furthermore, in addition to hydrophobic interactions, ionic interactions between amino groups of chlorpheniramine enantiomers and a carboxy group of D161 or E168 played an important role in the chiral recognition, while hydrophobic interactions and hydrogen bonding interactions worked for the chiral recognition of benzoin and propranolol enantiomers.
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7
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Li Z, Lei L, Huo M, Liu Z, Yang X, Wang Y, Yuan Y. Interactions and complex stabilities of grape seed procyanidins with zein hydrolysate. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.14628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zi‐Zi Li
- School of Chemistry and Chemical Engineering Guangzhou University Guangzhou 510006 China
| | - Lei Lei
- School of Chemistry and Chemical Engineering Guangzhou University Guangzhou 510006 China
| | - Min‐Xi Huo
- Guangzhou Inspection Testing and Certification Group Co., Ltd Guangzhou 511447 China
| | - Zi‐Rui Liu
- Guangdong Science and Technology Cooperation Center Guangzhou 510033 China
| | - Xin‐Quan Yang
- School of Life Sciences Guangzhou University Guangzhou 510006 China
- Office of Science and Research Guangzhou University Guangzhou 510006 China
| | - Yu‐Lin Wang
- Office of Science and Research Guangzhou University Guangzhou 510006 China
| | - Yang Yuan
- School of Chemistry and Chemical Engineering Guangzhou University Guangzhou 510006 China
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8
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Zhang X, Liu R. Advances in BPA-induced Oxidative Stress and Related Effects and Mechanisms in Liver, 1991-2017. Mini Rev Med Chem 2020; 20:432-443. [PMID: 30207228 DOI: 10.2174/1389557518666180912105345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022]
Abstract
Bisphenol A (BPA) is a widely spreading environmental endocrine disruptor . Its characteristics, including small doses and frequent contact, make it easy to enter human body through drinking water, food, air and other pathways, leading to tumors, infertility, and liver damage. The present review summarizes the underlying mechanism of oxidative stress and its related effects induced by BPA in the liver. The progress of the mechanism for oxidative stress induced by BPA is summarized, including mitochondrial dysfunction, lipid peroxidation and inflammation reaction, liver dyslipidemia, apoptosis, and cell death mechanism. In the future, it is necessary to elucidate the molecular mechanisms and timing of oxidative stress to clarify the effects on different exposures to different genders and growth stages. Besides, studying the toxic effects on BPA surrogates, BPA metabolites and BPA combined with other pollutants in the environment is beneficial to clarify the environmental and human health effects of BPA and provide technical reference for the development of practical control measures.
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Affiliation(s)
- Xun Zhang
- School of Environmental Science and Engineering, Shandong University, China -America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China -America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, China.,Department of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, China
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9
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AlAjmi MF, Rehman MT, Khan RA, Khan MA, Muteeb G, Khan MS, Noman OM, Alsalme A, Hussain A. Understanding the interaction between α-1-acid glycoprotein (AGP) and potential Cu/Zn metallo-drugs of benzimidazole derived organic motifs: A multi-spectroscopic and molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 225:117457. [PMID: 31450223 DOI: 10.1016/j.saa.2019.117457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Drug-binding and interactions with plasma proteins strongly affect their efficiency of delivery, hence considered as a key factor in determining the overall pharmacological action. Alpha-1-acid glycoprotein (AGP), a second most abundant plasma protein in blood circulation, has unique drug binding ability and involved in the transportation of various compounds. Here, we have investigated the mechanism of interaction between AGP and potential Cu/Zn metallo-drugs of benzimidazole derived organic motifs (CuL2 and ZnL2, where L is Schiff base ligand) by applying integrated spectroscopic, biophysical techniques and computational molecular docking analyses. We found that both the metallo-drugs (CuL2 and ZnL2) were bound at the central cavity of AGP interacting with the residues of lobe I, lobe II as well as lobe III. The binding of metallo-drugs to AGP occurs in 1:1 M ratios. Hydrogen bonding, electrostatic and hydrophobic interactions played a significant role in stabilizing the AGP-metallo-drug complexes. Binding affinities of both the metallo-drugs towards AGP at 298 K were of the order of 104-105 M-1, corresponding to Gibbs free energy of stabilization of approximately -5.50 to -6.62 kcal mol-1. Furthermore, the spectroscopic investigation by circular dichroism and synchronous fluorescence analyses suggest conformational changes in AGP upon the binding of metallic compounds.
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Affiliation(s)
- Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Rais Ahmad Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Meraj A Khan
- Program in Translational Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ghazala Muteeb
- Department of Nursing, College of Applied Medical Sciences, King Faisal University, Hofuf-400-Al-Ahsa-31982, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar Mohammed Noman
- Medicinal, Aromatic and Poisonous Plants Research Center, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
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10
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Orofino F, Truglio GI, Fiorucci D, D'Agostino I, Borgini M, Poggialini F, Zamperini C, Dreassi E, Maccari L, Torelli R, Martini C, Bernabei M, Meis JF, Khandelwal NK, Prasad R, Sanguinetti M, Bugli F, Botta M. In vitro characterization, ADME analysis, and histological and toxicological evaluation of BM1, a macrocyclic amidinourea active against azole-resistant Candida strains. Int J Antimicrob Agents 2019; 55:105865. [PMID: 31866465 DOI: 10.1016/j.ijantimicag.2019.105865] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/08/2019] [Accepted: 12/14/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Candida species are one of the most common causes of nosocomial bloodstream infections among the opportunistic fungi. Extensive use of antifungal agents, most of which were launched on the market more than 20 years ago, led to the selection of drug-resistant or even multidrug-resistant fungi. We recently described a novel class of antifungal macrocyclic compounds with an amidinourea moiety that is highly active against azole-resistant Candida strains. OBJECTIVE A compound from this family, BM1, was investigated in terms of in vitro activity against various Candida species, including C. auris isolates, interaction with the ABC transporter, CDR6, and in vivo distribution and safety. METHODS In vitro assays (CYP inhibition, microsomal stability, permeability, spot assays) were used to collect chemical and biological data; animal models (rat) paired with LC-MS analysis were utilised to evaluate in vivo toxicology, pharmacokinetics, and distribution. RESULTS The current research shows BM1 has a low in vivo toxicity profile, affinity for the renal system in rats, and good absorption, distribution, metabolism, and excretion (ADME). BM1 also has potent activity against azole-resistant fungal strains, including C. auris isolates and CDR6-overexpressing strains. CONCLUSIONS The results confirmed low minimum inhibitory concentrations (MICs) against several Candida species, including preliminary data vs. C. auris. BM1 has good ADME and biochemical characteristics, is suitable and safe for daily administration and is particularly indicated for renal infections. These data indicate BM1 and its derivatives form a novel, promising antifungal class.
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Affiliation(s)
- Francesco Orofino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Giuseppina I Truglio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Ilaria D'Agostino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Matteo Borgini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Claudio Zamperini
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Elena Dreassi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Laura Maccari
- Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Riccardo Torelli
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Cecilia Martini
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Micaela Bernabei
- Istituto di Anatomia Patologica, Fondazione Policlinico Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands; Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Rajendra Prasad
- Amity Institute of Integrative Sciences and Health, Amity University, Gurgaon 122413, Haryana, India
| | - Maurizio Sanguinetti
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy; Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy; Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy; Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Philadelphia, PA 19122, USA
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11
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Interaction of antitubercular drug candidates with α 1-acid glycoprotein produced in pulmonary granulomas. Int J Biol Macromol 2019; 147:1318-1327. [PMID: 31759028 DOI: 10.1016/j.ijbiomac.2019.10.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/09/2019] [Accepted: 10/09/2019] [Indexed: 11/24/2022]
Abstract
The intracellular pathogen Mycobacterium tuberculosis can survive and replicate within host macrophages. Among various immunomodulatory substances, macrophages also produce α1-acid glycoprotein (AAG) which is secreted into the extracellular matrix of tuberculosis granulomas that represents a specific binding environment. Employing circular dichroism (CD) and UV/VIS absorption spectroscopic methods, we demonstrated and evaluated the AAG binding properties of novel antitubercular drug candidates developed against sensitive and multidrug-resistant strains of M. tuberculosis. As inferred from the CD spectroscopic data, these chemically diverse organic molecules are engulfed within the β-barrel of the protein either in a monomeric or dimeric form. Molecular docking simulations suggested the importance of H-bonds and ligand-aromatic residue π-π stacking interactions in stabilizing the drug molecules at the protein binding site. Based on the estimated Kd values (7-20 μM), AAG could be considered as the significant binding partner of the antitubercular agents studied herein. As such, it may affect the drug distribution and bioavailability not only in serum but also in macrophages and in the extracellular matrix of tuberculosis granulomas.
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12
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Pasero C, D'Agostino I, De Luca F, Zamperini C, Deodato D, Truglio GI, Sannio F, Del Prete R, Ferraro T, Visaggio D, Mancini A, Guglielmi MB, Visca P, Docquier JD, Botta M. Alkyl-guanidine Compounds as Potent Broad-Spectrum Antibacterial Agents: Chemical Library Extension and Biological Characterization. J Med Chem 2018; 61:9162-9176. [PMID: 30265809 DOI: 10.1021/acs.jmedchem.8b00619] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nowadays, the increasing of multidrug-resistant pathogenic bacteria represents a serious threat to public health, and the lack of new antibiotics is becoming a global emergency. Therefore, research in antibacterial fields is urgently needed to expand the currently available arsenal of drugs. We have recently reported an alkyl-guanidine derivative (2), characterized by a symmetrical dimeric structure, as a good candidate for further developments, with a high antibacterial activity against both Gram-positive and Gram-negative strains. In this study, starting from its chemical scaffold, we synthesized a small library of analogues. Moreover, biological and in vitro pharmacokinetic characterizations were conducted on some selected derivatives, revealing notable properties: broad-spectrum profile, activity against resistant clinical isolates, and appreciable aqueous solubility. Interestingly, 2 seems neither to select for resistant strains nor to macroscopically alter the membranes, but further studies are required to determine the mode of action.
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Affiliation(s)
- Carolina Pasero
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy
| | - Ilaria D'Agostino
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy
| | - Filomena De Luca
- Department of Medical Biotechnology , University of Siena , I-53100 Siena , Italy
| | - Claudio Zamperini
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy.,Lead Discovery Siena s.r.l. , Via Vittorio Alfieri 31 , I-53019 Castelnuovo Berardenga , Italy
| | - Davide Deodato
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy
| | - Giuseppina I Truglio
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy
| | - Filomena Sannio
- Department of Medical Biotechnology , University of Siena , I-53100 Siena , Italy
| | - Rosita Del Prete
- Department of Medical Biotechnology , University of Siena , I-53100 Siena , Italy
| | - Teresa Ferraro
- Lead Discovery Siena s.r.l. , Via Vittorio Alfieri 31 , I-53019 Castelnuovo Berardenga , Italy
| | - Daniela Visaggio
- Department of Sciences , Roma Tre University , Rome 00146 , Italy
| | - Arianna Mancini
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy
| | | | - Paolo Visca
- Department of Sciences , Roma Tre University , Rome 00146 , Italy
| | - Jean-Denis Docquier
- Department of Medical Biotechnology , University of Siena , I-53100 Siena , Italy.,Lead Discovery Siena s.r.l. , Via Vittorio Alfieri 31 , I-53019 Castelnuovo Berardenga , Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry, and Pharmacy , University of Siena , I-53100 Siena , Italy.,Lead Discovery Siena s.r.l. , Via Vittorio Alfieri 31 , I-53019 Castelnuovo Berardenga , Italy.,Sbarro Institute for Cancer Research and Molecular Medicine , Temple University , BioLife Science Building, Suite 333, 1900 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
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13
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The engineered β-lactoglobulin with complementarity to the chlorpromazine chiral conformers. Int J Biol Macromol 2018; 114:85-96. [DOI: 10.1016/j.ijbiomac.2018.03.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 12/19/2022]
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14
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Binding interactions between enantiomeric α-aminophosphonate derivatives and tobacco mosaic virus coat protein. Int J Biol Macromol 2017; 94:603-610. [DOI: 10.1016/j.ijbiomac.2016.10.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
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15
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Abdelhameed AS, Ajmal MR, Ponnusamy K, Subbarao N, Khan RH. Interaction of the recently approved anticancer drug nintedanib with human acute phase reactant α 1-acid glycoprotein. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Okabe T, Yakushiji T, Igawa W, Ono M, Kido T, Ebara S, Yamashita K, Yamamoto MH, Saito S, Hoshimoto K, Amemiya K, Isomura N, Araki H, Ochiai M. The Efficacy of Tolvaptan in Congestive Heart Failure Patients with and Without Hypoalbuminemia: A Pilot Study. Cardiovasc Ther 2016; 33:275-81. [PMID: 26122275 DOI: 10.1111/1755-5922.12142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Heart failure (HF) with hypoalbuminemia is associated with poor response to conventional therapy. We investigated whether tolvaptan, a potent aquaretic agent, might be of benefit in HF patients with hypoalbuminemia. METHODS We prospectively enrolled 40 patients hospitalized for HF. Patients received conventional therapy including loop diuretics. We subsequently added tolvaptan in the range of 3.75-15 mg daily and it was discontinued after improvement of HF symptoms. We compared clinical and laboratory data in HF patients with and without hypoalbuminemia (defined as serum albumin <3.0 g/dL). RESULTS Tolvaptan was administered in 18 HF patients with hypoalbuminemia (Group A) and 22 HF patients without hypoalbuminemia (Group B). The mean serum albumin was 2.63 ± 0.27 and 3.46 ± 0.25 g/dL, respectively. The average urine output on tolvaptan increased significantly in both groups (1644.4 ± 797.6-3011.6 ± 1453.8 mL/day, P = 0.004; 1459 ± 612.7-2112.2 ± 724.5 mL/day, P = 0.008; respectively). In addition, we observed higher urine output on therapy in Group A than in Group B (P = 0.015). There was a moderate negative correlation between serum albumin and average urine output on tolvaptan (r = -0.42, P = 0.007). CONCLUSIONS The addition of tolvaptan to low dose loop diuretics might be an effective strategy for treatment of HF patients with hypoalbuminemia.
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Affiliation(s)
- Toshitaka Okabe
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Tadayuki Yakushiji
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Wataru Igawa
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Morio Ono
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Takehiko Kido
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Seitaro Ebara
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Kennosuke Yamashita
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Myong Hwa Yamamoto
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Shigeo Saito
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Koichi Hoshimoto
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Kisaki Amemiya
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Naoei Isomura
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Hiroshi Araki
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
| | - Masahiko Ochiai
- Division of Cardiology and Cardiac Catheterization Laboratories, Showa University Northern Yokohama Hospital, Tsuzuki, Yokohama, Japan
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17
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Ajmal MR, Abdelhameed AS, Alam P, Khan RH. Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 159:199-208. [PMID: 26851488 DOI: 10.1016/j.saa.2016.01.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/15/2016] [Accepted: 01/23/2016] [Indexed: 06/05/2023]
Abstract
In the current study we have investigated the interaction of newly approved kinase inhibitors namely Cabozantinib (CBZ) and Tofacitinib (TFB) with human Alpha-1 acid glycoprotein (AAG) under simulated physiological conditions using fluorescence quenching measurements, circular dichroism, dynamic light scattering and molecular docking methods. CBZ and TFB binds to AAG with significant affinity and the calculated binding constant for the drugs lie in the order of 10(4). With the increase in temperature the binding constant values decreased for both CBZ and TFB. The fluorescence resonance energy transfer (FRET) from AAG to CBZ and TFB suggested the fluorescence intensity of AAG was quenched by the two studied drugs via the formation of a non-fluorescent complex in the static manner. The molecular distance r value calculated from FRET is around 2 nm for both drugs, fluorescence spectroscopy data was employed for the study of thermodynamic parameters, standard Gibbs free energy change at 300 K was calculated as -5.234 kcal mol(-1) for CBZ-AAG interaction and -6.237 kcal mol(-1) for TFB-AAG interaction, standard enthalpy change and standard entropy change for CBZ-AAG interaction are -9.553 kcal mol(-1) and -14.618 cal mol(-1) K(-1) respectively while for AAG-TFB interaction, standard enthalpy and standard entropy change was calculated as 4.019 kcal mol(-1) and 7.206 cal mol(-1) K(-1) respectively. Protein binding of the two drugs caused the tertiary structure alterations. Dynamic light scattering measurements demonstrated the reduction in the hydrodynamic radii of the protein. Furthermore molecular docking results suggested the Hydrophobic interaction and hydrogen bonding were the interactive forces in the binding process of CBZ to AAG while in case of TFB only hydrophobic interactions were found to be involved, overlap of the binding site for two studied drugs on the AAG molecule was revealed by docking results.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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Lambrinidis G, Vallianatou T, Tsantili-Kakoulidou A. In vitro, in silico and integrated strategies for the estimation of plasma protein binding. A review. Adv Drug Deliv Rev 2015; 86:27-45. [PMID: 25819487 DOI: 10.1016/j.addr.2015.03.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 02/11/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022]
Abstract
Plasma protein binding (PPB) strongly affects drug distribution and pharmacokinetic behavior with consequences in overall pharmacological action. Extended plasma protein binding may be associated with drug safety issues and several adverse effects, like low clearance, low brain penetration, drug-drug interactions, loss of efficacy, while influencing the fate of enantiomers and diastereoisomers by stereoselective binding within the body. Therefore in holistic drug design approaches, where ADME(T) properties are considered in parallel with target affinity, considerable efforts are focused in early estimation of PPB mainly in regard to human serum albumin (HSA), which is the most abundant and most important plasma protein. The second critical serum protein α1-acid glycoprotein (AGP), although often underscored, plays also an important and complicated role in clinical therapy and thus the last years it has been studied thoroughly too. In the present review, after an overview of the principles of HSA and AGP binding as well as the structure topology of the proteins, the current trends and perspectives in the field of PPB predictions are presented and discussed considering both HSA and AGP binding. Since however for the latter protein systematic studies have started only the last years, the review focuses mainly to HSA. One part of the review highlights the challenge to develop rapid techniques for HSA and AGP binding simulation and their performance in assessment of PPB. The second part focuses on in silico approaches to predict HSA and AGP binding, analyzing and evaluating structure-based and ligand-based methods, as well as combination of both methods in the aim to exploit the different information and overcome the limitations of each individual approach. Ligand-based methods use the Quantitative Structure-Activity Relationships (QSAR) methodology to establish quantitate models for the prediction of binding constants from molecular descriptors, while they provide only indirect information on binding mechanism. Efforts for the establishment of global models, automated workflows and web-based platforms for PPB predictions are presented and discussed. Structure-based methods relying on the crystal structures of drug-protein complexes provide detailed information on the underlying mechanism but are usually restricted to specific compounds. They are useful to identify the specific binding site while they may be important in investigating drug-drug interactions, related to PPB. Moreover, chemometrics or structure-based modeling may be supported by experimental data a promising integrated alternative strategy for ADME(T) properties optimization. In the case of PPB the use of molecular modeling combined with bioanalytical techniques is frequently used for the investigation of AGP binding.
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Yao C, Na N, Huang L, He D, Ouyang J. High-throughput detection of drugs binding to proteins using desorption electrospray ionization mass spectrometry. Anal Chim Acta 2013; 794:60-6. [DOI: 10.1016/j.aca.2013.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/31/2013] [Accepted: 07/05/2013] [Indexed: 01/24/2023]
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Sivertsen A, Brandsdal BO, Svendsen JS, Andersen JH, Svenson J. Short cationic antimicrobial peptides bind to human alpha-1 acid glycoprotein with no implications for thein vitrobioactivity. J Mol Recognit 2013; 26:461-9. [DOI: 10.1002/jmr.2288] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/14/2013] [Accepted: 05/23/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Annfrid Sivertsen
- The Norwegian Structural Biology Centre, Department of Chemistry, Faculty of Science and Technology; University of Tromsø; NO-9037; Tromsø; Norway
| | | | - John Sigurd Svendsen
- Department of Chemistry, Faculty of Science and Technology; University of Tromsø; NO-9037; Tromsø; Norway
| | - Jeanette Hammer Andersen
- Centre for Research-based Innovation on Marine Bioactivities and Drug Discovery (MABCENT); University of Tromsø; NO-9037; Tromsø; Norway
| | - Johan Svenson
- Department of Chemistry, Faculty of Science and Technology; University of Tromsø; NO-9037; Tromsø; Norway
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Greige-Gerges H, Kaissi R, Magdalou J, Jraij A. Reviewing the binding of a series of parabens to human serum albumin. Biopharm Drug Dispos 2013; 34:186-94. [DOI: 10.1002/bdd.1836] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/14/2012] [Accepted: 01/05/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Hélène Greige-Gerges
- Bioactive Molecules Research Group, Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE, Hadath); Lebanese University; Lebanon
| | - Rana Kaissi
- Bioactive Molecules Research Group, Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE, Hadath); Lebanese University; Lebanon
| | - Jacques Magdalou
- UMR 7561 CNRS-Université de Lorraine, Faculté de Médecine; 54500; Vandoeuvre-les-Nancy; France
| | - Alia Jraij
- Bioactive Molecules Research Group, Doctoral School of Science and Technology, Research Platform for Environmental Science (PRASE, Hadath); Lebanese University; Lebanon
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