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      Evaluation of the Interactions between Human Serum Albumin (HSA) and Non-Steroidal Anti-Inflammatory (NSAIDs) Drugs by Multiwavelength Molecular Fluorescence, Structural and Computational Analysis

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          Abstract

          The interaction between drugs and transport proteins, such as albumins, is a key factor in drug bioavailability. One of the techniques commonly used for the evaluation of the drug-protein complex formation is fluorescence. This work studies the interaction of human serum albumin (HSA) with four non-steroidal anti-inflammatory drugs (NSAIDs)—ibuprofen, flurbiprofen, naproxen, and diflunisal—by monitoring the fluorescence quenching when the drug-albumin complex is formed. Two approaches—the double logarithm Stern-Volmer equation and the STAR program—are used to evaluate the binding parameters. The results are analyzed considering the binding properties, determined by using other complementary techniques and the available structural information of albumin complexes with NSAID-related compounds. Finally, this combined analysis has been synergistically used to interpret the binding of flurbiprofen to HSA.

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          Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

          Richard A Friesner, Jay L. Banks, Robert B Murphy … (2004)
          Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 A in nearly half of the cases and are greater than 2 A in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
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            Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

            Richard A Friesner, Robert B Murphy, Matthew P Repasky … (2006)
            A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included: (1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce experimental binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, respectively) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.
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              Structural basis of the drug-binding specificity of human serum albumin.

              Jamie Ghuman, Patricia A Zunszain, Isabelle Petitpas … (2005)
              Human serum albumin (HSA) is an abundant plasma protein that binds a remarkably wide range of drugs, thereby restricting their free, active concentrations. The problem of overcoming the binding affinity of lead compounds for HSA represents a major challenge in drug development. Crystallographic analysis of 17 different complexes of HSA with a wide variety of drugs and small-molecule toxins reveals the precise architecture of the two primary drug-binding sites on the protein, identifying residues that are key determinants of binding specificity and illuminating the capacity of both pockets for flexible accommodation. Numerous secondary binding sites for drugs distributed across the protein have also been identified. The binding of fatty acids, the primary physiological ligand for the protein, is shown to alter the polarity and increase the volume of drug site 1. These results clarify the interpretation of accumulated drug binding data and provide a valuable template for design efforts to modulate the interaction with HSA.
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                Author and article information

                Contributors
                Osvaldo Andrade Santos-Filho: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Pharmaceuticals (Basel)
                Journal ID (iso-abbrev): Pharmaceuticals (Basel)
                Journal ID (publisher-id): pharmaceuticals
                Title: Pharmaceuticals
                Publisher: MDPI
                ISSN (Electronic): 1424-8247
                Publication date (Electronic): 04 March 2021
                Publication date Collection: March 2021
                Volume: 14
                Issue: 3
                Electronic Location Identifier: 214
                Affiliations
                [1 ]Department of Chemical Engineering and Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain; jlbeltran@ 123456ub.edu (J.L.B.); annamariaboliolire@ 123456gmail.com (A.M.B.); crafols@ 123456ub.edu (C.R.)
                [2 ]Institute of Biomedicine (IBUB), University of Barcelona, 08028 Barcelona, Spain; fjluque@ 123456ub.edu
                [3 ]Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, University of Barcelona, Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain; lluis.campos@ 123456pharmacelera.com
                [4 ]Pharmacelera, Torre R, 4a planta, Despatx A05, Parc Científic de Barcelona, Baldiri Reixac 8, 08028 Barcelona, Spain
                [5 ]Institut of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain
                Author notes
                [* ]Correspondence: samezqueta@ 123456ub.edu ; Tel.: +34-93-402-1277
                Author information
                https://orcid.org/0000-0001-8976-467X
                https://orcid.org/0000-0002-1555-399X
                https://orcid.org/0000-0003-0751-2247
                https://orcid.org/0000-0002-8049-3567
                https://orcid.org/0000-0001-7811-986X
                Article
                Publisher ID: pharmaceuticals-14-00214
                DOI: 10.3390/ph14030214
                PMC ID: 8000696
                PubMed ID: 33806467
                SO-VID: c8f33354-c9eb-46a4-9ece-58997fa70d01
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 02 February 2021
                Date accepted : 26 February 2021
                Categories
                Subject: Article

                Keywords: non-steroidal anti-inflammatory drugs,drug-protein interactions,human serum albumin,fluorescence multiwavelength data treatment,fluorescence quenching,molecular modeling
                Data availability:
                Keywords: non-steroidal anti-inflammatory drugs, drug-protein interactions, human serum albumin, fluorescence multiwavelength data treatment, fluorescence quenching, molecular modeling

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