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British Journal of Pharmacology Oct 2010An increasing number of examples in the literature suggest that the in vivo duration of drug action not only depends on macroscopic pharmacokinetic properties like... (Review)
Review
An increasing number of examples in the literature suggest that the in vivo duration of drug action not only depends on macroscopic pharmacokinetic properties like plasma half-life and the time needed to equilibrate between the plasma and the effect compartments, but is also influenced by long-lasting target binding and rebinding. The present review combines information from different research areas and simulations to explore the nature of these mechanisms and the conditions in which they are most prevalent. Simulations reveal that these latter phenomena become especially influential when there is no longer sufficient free drug around to maintain high levels of receptor occupancy. There is not always a direct link between slow dissociation and long-lasting in vivo target protection, as the rate of free drug elimination from the effect compartment is also a key influencing factor. Local phenomena that hinder the diffusion of free drug molecules away from their target may allow them to consecutively bind to the same target and/or targets nearby (denoted as 'rebinding') even when their concentration in the bulk phase has already dropped to insignificant levels. The micro-anatomic properties of many effect compartments are likely to intensify this phenomenon. By mimicking the complexity of tissues, intact cells offer the opportunity to investigate both mechanisms under the same, physiologically relevant conditions.
Topics: Animals; Humans; Models, Biological; Models, Statistical; Pharmaceutical Preparations; Pharmacokinetics; Protein Binding; Radioligand Assay
PubMed: 20880390
DOI: 10.1111/j.1476-5381.2010.00936.x -
Nature Communications Oct 2019Viral infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by...
Viral infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and their cell surface receptors. Despite recent progress, the molecular mechanisms underlying the multistep reovirus entry process are poorly understood. Using atomic force microscopy, we investigated how the reovirus σ1 attachment protein binds to both α-linked sialic acid (α-SA) and JAM-A cell-surface receptors. We discovered that initial σ1 binding to α-SA favors a strong multivalent anchorage to JAM-A. The enhanced JAM-A binding by virions following α-SA engagement is comparable to JAM-A binding by infectious subvirion particles (ISVPs) in the absence of α-SA. Since ISVPs have an extended σ1 conformer, this finding suggests that α-SA binding triggers a conformational change in σ1. These results provide new insights into the function of viral attachment proteins in the initiation of infection and open new avenues for the use of reoviruses as oncolytic agents.
Topics: Animals; CHO Cells; Cell Adhesion Molecules; Cell Line; Cricetulus; Host-Pathogen Interactions; Models, Molecular; Polysaccharides; Protein Binding; Receptors, Cell Surface; Receptors, Virus; Reoviridae; Viral Proteins; Virus Attachment; Virus Internalization
PubMed: 31575869
DOI: 10.1038/s41467-019-12411-2 -
Biophysical Journal Sep 2015Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank;...
Structures of protein complexes provide atomistic insights into protein interactions. Human proteins represent a quarter of all structures in the Protein Data Bank; however, available protein complexes cover less than 10% of the human proteome. Although it is theoretically possible to infer interactions in human proteins based on structures of homologous protein complexes, it is still unclear to what extent protein interactions and binding sites are conserved, and whether protein complexes from remotely related species can be used to infer interactions and binding sites. We considered biological units of protein complexes and clustered protein-protein binding sites into similarity groups based on their structure and sequence, which allowed us to identify unique binding sites. We showed that the growth rate of the number of unique binding sites in the Protein Data Bank was much slower than the growth rate of the number of structural complexes. Next, we investigated the evolutionary roots of unique binding sites and identified the major phyletic branches with the largest expansion in the number of novel binding sites. We found that many binding sites could be traced to the universal common ancestor of all cellular organisms, whereas relatively few binding sites emerged at the major evolutionary branching points. We analyzed the physicochemical properties of unique binding sites and found that the most ancient sites were the largest in size, involved many salt bridges, and were the most compact and least planar. In contrast, binding sites that appeared more recently in the evolution of eukaryotes were characterized by a larger fraction of polar and aromatic residues, and were less compact and more planar, possibly due to their more transient nature and roles in signaling processes.
Topics: Animals; Binding Sites; Evolution, Molecular; Humans; Models, Molecular; Protein Binding; Proteins
PubMed: 26213149
DOI: 10.1016/j.bpj.2015.06.056 -
Proceedings of the National Academy of... Oct 2018High-resolution structure-activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and...
High-resolution structure-activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids. We describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein. By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids can be exhaustively substituted into peptides, and single experiments can return all free energy changes of binding. We validate this approach by scanning two model protein-binding peptides with 21 diverse nonproteinogenic amino acids. Dense structure-activity maps were produced at the resolution of single aliphatic atom insertions and deletions. This permits rapid interrogation of interaction interfaces, as well as optimization of affinity, fine-tuning of physical properties, and systematic assessment of nonproteinogenic amino acids in binding and folding.
Topics: Amino Acid Sequence; Amino Acids; Genetic Code; Peptides, Cyclic; Protein Binding; Proteins; Structure-Activity Relationship; Thermodynamics
PubMed: 30301798
DOI: 10.1073/pnas.1809901115 -
Physical Chemistry Chemical Physics :... Apr 2020Interactions of proteins with functional groups are key to their biological functions, making it essential that they be accurately modeled. To investigate the impact of...
Interactions of proteins with functional groups are key to their biological functions, making it essential that they be accurately modeled. To investigate the impact of the inclusion of explicit treatment of electronic polarizability in force fields on protein-functional group interactions, the additive CHARMM and Drude polarizable force field are compared in the context of the Site-Identification by Ligand Competitive Saturation (SILCS) simulation methodology from which functional group interaction patterns with five proteins for which experimental binding affinities of multiple ligands are available, were obtained. The explicit treatment of polarizability produces significant differences in the functional group interactions in the ligand binding sites including overall enhanced binding of functional groups to the proteins. This is associated with variations of the dipole moments of solutes representative of functional groups in the binding sites relative to aqueous solution with higher dipole moments systematically occurring in the latter, though exceptions occur with positively charged methylammonium. Such variation indicates the complex, heterogeneous nature of the electronic environments of ligand binding sites and emphasizes the inherent limitation of fixed charged, additive force fields for modeling ligand-protein interactions. These effects yield more defined orientation of the functional groups in the binding pockets and a small, but systematic improvement in the ability of the SILCS method to predict the binding orientation and relative affinities of ligands to their target proteins. Overall, these results indicate that the physical model associated with the explicit treatment of polarizability along with the presence of lone pairs in a force field leads to changes in the nature of the interactions of functional groups with proteins versus that occurring with additive force fields, suggesting the utility of polarizable force fields in obtaining a more realistic understanding of protein-ligand interactions.
Topics: Binding Sites; Electrophysiological Phenomena; Ligands; Protein Binding; Proteins
PubMed: 32195493
DOI: 10.1039/d0cp00088d -
Biochemistry Sep 2011In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional... (Review)
Review
In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings.
Topics: Animals; Biochemical Phenomena; Crystallography, X-Ray; Galectins; Humans; Polysaccharides; Protein Binding
PubMed: 21848324
DOI: 10.1021/bi201121m -
Drug Metabolism and Pharmacokinetics 2009Human serum albumin (HSA) is an abundant and highly soluble plasma protein with the capacity to bind a remarkably diverse set of lipophilic anionic compounds so that it... (Review)
Review
Human serum albumin (HSA) is an abundant and highly soluble plasma protein with the capacity to bind a remarkably diverse set of lipophilic anionic compounds so that it fulfils important roles in the transport of nutrients, hormones and toxins. The protein attracts great interest from the pharmaceutical industry since it can also bind a variety of drug molecules, impacting their delivery and efficacy. Our understanding of the binding and transport properties of albumin has been transformed by structural studies of the protein, in which crystallographic analysis has played a leading role. This review summarises the main insights to have accrued from this work, highlighting the significant advances that have been made but also pointing out some of the challenges ahead. Since further progress is likely to benefit from increased structural scrutiny of HSA, methodological developments instrumental to the success of crystallographic analysis of the protein are discussed in some detail.
Topics: Binding Sites; Clinical Laboratory Techniques; Crystallography; Crystallography, X-Ray; Humans; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Binding; Protein Conformation; Serum Albumin
PubMed: 19745561
DOI: 10.2133/dmpk.24.342 -
ACS Chemical Biology Nov 2008Induction of protein--protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein... (Review)
Review
Induction of protein--protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein molecules together for enhanced or novel biological effect. The first such bifunctional molecules were the rapamycin- and FK506-based "chemical inducers of dimerization", but the field has since expanded with new molecules and new applications in chemical genetics and cell biology. Examples include coumermycin-mediated gyrase B dimerization, proteolysis targeting chimeric molecules (PROTACs), drug hybrids, and strategies for exploiting multivalency in toxin binding and antibody recruitment. This Review discusses these and other advances in the design and use of bifunctional small molecules and potential strategies for future systems.
Topics: Dimerization; Drug Design; Ligands; Protein Binding; Proteins
PubMed: 19112665
DOI: 10.1021/cb8001792 -
Biochemistry Feb 2020Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we...
Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).
Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site. Only two of these are exploited by Nrf2, which alanine scanning of both proteins shows to bind primarily through E79 and E82 interacting with KEAP1 residues S363, R380, R415, R483, and S508. We identify fragment hits and obtain X-ray complex structures for three fragments via crystal soaking using a new crystal form of KEAP1. Combining these results provides a comprehensive and quantitative picture of the origins of binding energy at the interface. Our findings additionally reveal non-native interactions that might be exploited in the design of uncharged synthetic ligands to occupy the same site on KEAP1 that has evolved to bind the highly charged DEETGE binding loop of Nrf2. These include π-stacking with KEAP1 Y525 and interactions at an FTMap-identified hot spot deep in the binding site. Finally, we discuss how the complementary information provided by alanine-scanning mutagenesis, fragment screening, and computational hot spot mapping can be integrated to more comprehensively evaluate PPI druggability.
Topics: Binding Sites; Drug Discovery; Humans; Kelch-Like ECH-Associated Protein 1; Ligands; NF-E2-Related Factor 2; Protein Binding; Protein Domains; Protein Interaction Domains and Motifs; Small Molecule Libraries
PubMed: 31851823
DOI: 10.1021/acs.biochem.9b00943 -
Structure (London, England : 1993) Sep 2019In this issue of Structure, Li et al. (2019) describe the structure of the MORN4-Myo3a complex, revealing that the MORN repeats in MORN4 form a single-layer...
In this issue of Structure, Li et al. (2019) describe the structure of the MORN4-Myo3a complex, revealing that the MORN repeats in MORN4 form a single-layer antiparallel β sheet and employs an extensive surface area in binding Myo3a. Their findings suggest that single-layer β sheets are versatile protein-binding modules.
Topics: Protein Binding; Protein Conformation, beta-Strand; Protein Structure, Secondary; Proteins
PubMed: 31484049
DOI: 10.1016/j.str.2019.08.007