Phage display screening against a set of targets to establish peptide-based sugar mimetics and molecular docking to predict binding site

Yu, Limin.; Yu, Peggy Shuang; Mui, Elizabeth Yee Yen; McKelvie, Jennifer C.; Pham, Thi Phuong Tu; Yap, Yan Wen; Wong, Wan Qing; Wu, Jiawen; Deng, Wei; Orner, Brendan P.

doi:10.1016/j.bmc.2009.03.054

Cited by 26 publications

(20 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Consequently, peptide mimetics of sugars are gaining interest as substitutes. 26 We questioned whether short peptides would mimic sugar components of natural ligands of receptors that function to stimulate phagocytosis. Peptide mimetics of sugars have potential advantages over glycans and glycoproteins because of chemical synthesis and ease of purification.…”

Section: Introductionmentioning

confidence: 99%

Peptide Sugar Mimetics Prevent HIV Type 1 Replication in Peripheral Blood Mononuclear Cells in the Presence of HIV-Positive Antiserum

Eggink

Salas

Hanson

et al. 2010

AIDS Research and Human Retroviruses

View full text Add to dashboard Cite

Cells of the immune system express a number of receptors that bind carbohydrate ligands. We questioned whether peptide mimetics of these ligands will activate phagocytic cells and thereby enhance an antiviral response. Short peptide sequences were identified by computational modeling of docking to glycan-specific lectins, selected as receptor analogs, and incorporated into quadravalent structures by peptide synthesis. A peptide with the sequence HPSLK bound to several lectins specific for monosaccharides and to lectins specific for Neu5Ac-Gal-containing complex glycans, whereas a longer sequence, NPSHPLSG, bound only lectins specific for the more complex glycans. In cultures of peripheral blood mononuclear cells (PBMCs) these peptides stimulated phagocytosis of opsonized microspheres. The peptides inhibited replication of HIV-1 in PBMC cultures by 20-80% at concentrations between 1 nM and 1 muM but inhibited replication 100% in the presence of diluted HIV-positive antiserum that alone inhibited replication by 30%. HPSLK caused about 50% loss of viability of cells at 1 mM, a concentration 10(6)-fold higher than an effective inhibitory concentration, but no toxicity was observed with NPSHPLSG. These results demonstrated that peptidomimetics of glycan ligands of cellular receptors are effective in activating phagocytosis, which may be a factor in providing complete inhibition of HIV-1 replication in vitro.

show abstract

Section: Introductionmentioning

confidence: 99%

Peptide Sugar Mimetics Prevent HIV Type 1 Replication in Peripheral Blood Mononuclear Cells in the Presence of HIV-Positive Antiserum

Eggink

Salas

Hanson

et al. 2010

AIDS Research and Human Retroviruses

View full text Add to dashboard Cite

show abstract

“…Most frequently, the characterization of natural peptides still relies on cycles of purification and sequencing that prevent large scale exploration. Alternative routes rely on the use of phage display techniques [see for instance (11, 12)] or combinatorial chemical methods (13, 14) that have led to success in the identification of peptides targeting specific protein–protein interactions [e.g. (15)].…”

Section: Introductionmentioning

confidence: 99%

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

2014

View full text Add to dashboard Cite

With the recent progress in complete genome sequencing, mining the increasing amount of genomic information available should in theory provide the means to discover new classes of peptides. However, annotation pipelines often do not consider small reading frames likely to be expressed. BactPepDB, available online at http://bactpepdb.rpbs.univ-paris-diderot.fr, is a database that aims at providing an exhaustive re-annotation of all complete prokaryotic genomes—chromosomal and plasmid DNA—available in RefSeq for coding sequences ranging between 10 and 80 amino acids. The identified peptides are classified as (i) previously identified in RefSeq, (ii) entity-overlapping (intragenic) or intergenic, and (iii) potential pseudogenes—intergenic sequences corresponding to a portion of a previously annotated larger gene. Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides, and provides information about their conservation, together with some of their expected biological/structural features. The BactPepDB interface allows to search for candidate peptides in the database, or to search for peptides similar to a query, according to the multiple properties predicted or related to genomic localization.Database URL: http://www.yeastgenome.org/

show abstract

“…In one example, active ˇ-lactamase was displayed on a filamentous bacteriophage and enriched from a population of inactive phage-displayed ˇ-lactamase by using bifunctional "suicide" inhibitors (Soumillion et al, 1994). Approaches such as this, however, require efficient removal of the inhibitors prior to panning, a step that is accomplished typically via polyethylene glycol (PEG) precipitation (Vanwetswinkel et al, 1996) or dialysis (Yu et al, 2009). Such methods are laborious and result in significant phage loss (Ling et al, 2004).…”

mentioning

confidence: 97%

Purification and quantitation of bacteriophage M13 using desalting spin columns and digital PCR

Reitinger

Petriv

Mehr

et al. 2012

Journal of Virological Methods

View full text Add to dashboard Cite

Phage display screening against a set of targets to establish peptide-based sugar mimetics and molecular docking to predict binding site

Cited by 26 publications

References 32 publications

Peptide Sugar Mimetics Prevent HIV Type 1 Replication in Peripheral Blood Mononuclear Cells in the Presence of HIV-Positive Antiserum

Peptide Sugar Mimetics Prevent HIV Type 1 Replication in Peripheral Blood Mononuclear Cells in the Presence of HIV-Positive Antiserum

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

Purification and quantitation of bacteriophage M13 using desalting spin columns and digital PCR

Contact Info

Product

Resources

About