Design of protein–membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V

Segers, Kenneth; Spérandio, Olivier; Sack, Markus; Fischer, Rainer; Miteva, Maria A.; Rosing, Jan; Nicolaes, Gerry A. F.; Villoutreix, Bruno O.

doi:10.1073/pnas.0701051104

Cited by 57 publications

(71 citation statements)

References 45 publications

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“…Removal of TM may destabilize the protein-membrane interaction, thus affecting moenomycin or lipid II binding to TG. Indeed, stable proteinmembrane interaction has been reported recently to be crucial for the normal function of some membrane proteins, and hence it has been suggested to be a target for drug discovery (24).…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

Sung

Lai²,

Huang³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

161

180

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Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the development of new antibiotics. Here, we determined the X-ray crystal structure of the bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli in complex with its inhibitor moenomycin to 2.16-Å resolution. In addition to the transglycosylase and transpeptidase domains, our structure provides a complete visualization of this important antibacterial target, and reveals a domain for protein-protein interaction and a transmembrane helix domain essential for substrate binding, enzymatic activity, and membrane orientation.antibacterial development ͉ antibiotic resistance ͉ membrane protein structure ͉ peptidoglycan synthesis ͉ protein-protein interaction I n the last decade, the prevalence and occasional outbreaks of drug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE), have posed appalling hurdles in the treatment of bacterial infections (1, 2). New antibacterial agents are, as a result, in desperate demand to combat these pernicious antibiotic-resistant problems that can otherwise cause life-or-death struggles.Bacteria cell wall is a mesh-like structure of cross-linked peptidoglycan, which is essential to scaffold the cytoplasmic membrane and to maintain structural integrity of the cell (3). Cell wall synthesis at the membrane surface is mainly carried out by the membrane-bound enzymes, transpeptidases and transglycosylases, and inhibitors of the transpeptidase are among the most popular antibiotics in clinical use today (3).Escherichia coli PBP1b is a bifunctional transglycosylase, also known as peptidoglycan glycosyltransferase or murein synthase. It contains a transmembrane (TM) helix, 2 enzymatic domains [transglycosylase (TG) and transpeptidase (TP)] (4), and a domain composed of Ϸ100 aa residues between TM and TG with unknown structure and functionality (Fig. 1B). For Ͼ50 years, TP has been the main target for 2 most important classes of antibiotics: ␤-lactams (e.g., penicillin and methicillin) and glycopeptides (e.g., vancomycin). Not too long after they were introduced, resistant bacteria had emerged rapidly and caused serious medical problems. In contrast, resistant strains against moenomycin, the only natural inhibitor to TG from Streptomyces, have rarely been found. The development of new antibiotics against TG has been highly anticipated (5), and not until recently have the molecular structures of TG been available, even with the TM structure undefined.Two crystal structures of transglycosylase, a bifunctional transglycosylase from S. aureus (referred to as SaPBP2) and a transglycosylase domain from Aquifex aeolicus (referred to as AaPGT), have been determined recently with their TM domain or TM and TP domains removed, respectively (6-8). These structur...

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Section: Resultsmentioning

confidence: 99%

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

Sung

Lai²,

Huang³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

161

180

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“…Indeed, there are a number of cases where a disease is attributable to the abrogation of these properties (22) (23). Bioinformatics and computational biology have also begun to play a major role in lipid-binding domain studies, eliciting predictions of potential lipid-binding proteins (24), the role of electrostatics in lipid binding (25), and assembly of databases that compile lipid-binding domain data and predictions of membrane binding properties (26,27).…”

Section: : S299-s304mentioning

confidence: 99%

Lipid binding domains: more than simple lipid effectors

Stahelin

2009

Journal of Lipid Research

124

105

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The spatial and temporal regulation of lipid molecules in cell membranes is a hallmark of cellular signaling and membrane trafficking events. Lipid-mediated targeting provides for strict control and versatility, because cell membranes harbor a large number of lipid molecules with variation in head group and acyl chain structures. Signaling and trafficking proteins contain a large number of modular domains that exhibit specific lipid binding properties and play a critical role in their localization and function. Nearly 20 years of research including structural, computational, biochemical and biophysical studies have demonstrated how these lipid-binding domains recognize their target lipid and achieve subcellular localization. The integration of this individual lipid-binding domain data in the context of the fulllength proteins, macromolecular signaling complexes, and the lipidome is only beginning to be unraveled and represents a target of therapeutic development. This review brings together recent findings and classical concepts to concisely summarize the lipid-binding domain field while illustrating where the field is headed and how the gaps may be filled in with new technologies.-Stahelin, R. V. Lipid binding domains: more than simple lipid effectors. J. Lipid Res. 2009. 50: S299-S304.

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“…A number of small organic molecules were identified that disrupt C2 domain membrane anchoring of FVIII (14) and FV (15). One of these inhibitors, 005B10, identified from in silico screening, was found to inhibit FVIII interaction with negatively charged phospholipids (15).…”

Section: Blood Coagulation Factor VIII (Fviii)mentioning

confidence: 99%

“…, that interferes with C2 domain membrane binding was identified by Segers et al (15) using a computational approach. This compound inhibited membrane binding of FVIII with an IC 50 of 7.8 M, as measured by surface plasmon resonance (Fig.…”

Section: The Structure Of the C2 Domain-inhibitor Complex And The Inhmentioning

confidence: 99%

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Trp2313-His2315 of Factor VIII C2 Domain Is Involved in Membrane Binding

Liu

Lin

Yuan

et al. 2010

Journal of Biological Chemistry

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Factor VIII (FVIII) plays a critical role in blood coagulation by forming the tenase complex with factor IXa and calcium ions on a membrane surface containing negatively charged phospholipids. The tenase complex activates factor X during blood coagulation. Blood coagulation factor VIII (FVIII)2 is synthesized as a single polypeptide chain, including a 19-residue signal peptide.The mature FVIII contains 2,332 amino acid residues arranged within five domains organized as A1-A2-B-A3-C1-C2 (1, 2). FVIII circulates in the blood as a heterodimer: the A1, A2, and variable portions of the B domain forming the heavy chain with a molecular weight varying between 90,000 and 200,000; and the A3, C1 and C2 domains forming the light chain with a molecular weight of 80,000. The noncovalent assembly of the heterodimer is facilitated by divalent metal ions, as revealed by recent crystallographic studies (3, 4). In plasma, FVIII circulates as a complex with von Willebrand factor which stabilizes FVIII by preventing its rapid clearance from the blood circulation (5). During blood coagulation, FVIII is cleaved by thrombin at Arg 372 , Arg 740 , and Arg 1689 (6), which converts it to a fully active cofactor, FVIIIa. FVIIIa dissociates from von Willebrand factor and binds to membrane surfaces where it assembles with the serine protease factor IXa. The presence of FVIIIa enhances the V max for factor X activation by FIXa by 200,000-fold (7). This large amplification requires that the FVIII level in blood be controlled. Mutations of FVIII cause hemophilia A, an X-linked bleeding disorder (8). The molecular mechanisms of FVIII binding to membranes are not fully understood.Several lines of evidence suggest that the light chain of FVIII, in particular the C2 domain, is responsible for the specific binding to membrane surfaces (9, 10). A 1.5-Å x-ray crystal structure of the FVIII C2 domain and a mutagenesis study suggested that two hydrophobic loops formed by Met 2199 -Phe 2200 and Leu 2251 -Leu 2255 play an important role (11,12). Two additional loops formed by Trp 2313 -His 2315 and Gln 2222 -Lys 2227 ) were also proposed to be involved in membrane binding based on an electron microscopy study (13).C2 domain membrane-binding sites were proposed as a drug target to regulate the functional concentrations of coagulation factors, FVIII and FV, that contain a C2 domain (14). A number of small organic molecules were identified that disrupt C2 domain membrane anchoring of FVIII (14) and FV (15). One of these inhibitors, 005B10, identified from in silico screening, was found to inhibit FVIII interaction with negatively charged phospholipids (15). In this study, we report the high resolution crystal structure (1.15 Å) of the human FVIII C2 domain in * This work was supported, in whole or in part, by National Institutes of Health Grant HL086584. This work was also supported by grants from the Natural Science Foundation of China (30811130467 and 30625011), the Ministry of Science and Technology (2006AA02A313 and 2007CB914304), the Chinese Academy ...

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Design of protein–membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V

Cited by 57 publications

References 45 publications

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli

Lipid binding domains: more than simple lipid effectors

Trp2313-His2315 of Factor VIII C2 Domain Is Involved in Membrane Binding

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