Solution Structures and Integrin Binding Activities of an RGD Peptide with Two Isomers

Assa‐Munt, Nuria; Jia, Xu; Laakkonen, Pirjo; Ruoslahti, Erkki

doi:10.1021/bi002101f

Cited by 136 publications

(109 citation statements)

References 32 publications

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“…Turning our attention to polypeptide systems, six protein conformations (1PLW [45], 1FUL [46], 1RVS [47], 1EDW [48], 1FDF [49] and 1UBQ [50]) from the Brookhaven National Laboratory Protein Data Bank (PDB) [51] were used as starting configurations for our calculations. Table 1 shows the computed HOMO-LUMO gaps for these structures in vacuo, using the PBE functional.…”

Section: Protein Systemsmentioning

confidence: 99%

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

Lever¹,

Cole

Hine

et al. 2013

J. Phys.: Condens. Matter

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A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (Rudberg 2012 J. Phys.: Condens. Matter 24 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.S Online supplementary data available from stacks.iop.org/JPhysCM/25/152101/mmedia

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Section: Protein Systemsmentioning

confidence: 99%

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

Lever¹,

Cole

Hine

et al. 2013

J. Phys.: Condens. Matter

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“…Also in this case, structure-activity relationship studies showed that a folded structure is necessary for activity. Although theoretical and NMR-based experimental studies showed the presence of turn geometry also in the RGD sequence, centered on the glycine residue, the extreme conformational freedom of RGD makes, in this case, the open structure more favorable (24,25). For this reason, the presence of conformational constraints is necessary to obtain the optimal geometry for receptor recognition, e.g.…”

Section: Figmentioning

confidence: 99%

Structure-Activity Relationships of Linear and Cyclic Peptides Containing the NGR Tumor-homing Motif

Colombo

Curnis

Mori

et al. 2002

Journal of Biological Chemistry

175

136

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Cyclic and linear peptides containing the Asn-Gly-Arg (NGR) motif have proven useful for delivering various anti-tumor compounds and viral particles to tumor vessels. We have investigated the role of cyclic constraints on the structure and tumor-homing properties of NGR peptides using tumor necrosis factor-␣ (TNF) derivatives containing disulfide-bridged (CNGRC-TNF) and linear (GNGRG-TNF) NGR domains. Experiments carried out in animal models showed that both GNGRG and CNGRC can target TNF to tumors. However, the antitumor activity of CNGRC-TNF was >10-fold higher than that of GNGRG-TNF. Molecular dynamic simulation of cyclic CNGRC showed the presence of a bend geometry involving residues Gly 3 -Arg 4 . Molecular dynamic simulation of the same peptide without disulfide constraints showed that the most populated and thermodynamically favored configuration is characterized by the presence of a ␤-turn involving residues Gly 3 -Arg 4 and hydrogen bonding interactions between the backbone atoms of Asn 2 and Cys 5 . These results suggest that the NGR motif has a strong propensity to form ␤-turn in linear peptides and may explain the finding that GNGRG peptide can target TNF to tumors, albeit to a lower extent than CNGRC. The disulfide bridge constraint is critical for stabilizing the bent conformation and for increasing the tumor targeting efficiency.Phage display peptide libraries are commonly used to obtain peptide sequences interacting with proteins differentially expressed in normal and pathological tissues (1, 2). For instance, in vivo panning of phage libraries in tumor-bearing animals have proven useful for selecting peptides able to interact with proteins expressed within tumor-associated vessels and to home to neoplastic tissues (3). Among the various tumor targeting ligands identified so far, the CNGRC peptide have proven useful for delivering various anti-tumor compounds, like chemotherapeutic drugs, apoptotic peptides and cytokines, to tumor vessels (3-5). For example, we have recently shown that targeted delivery of tumor necrosis factor-␣ (TNF) 1 to tumor vasculature can be obtained by coupling its N terminus to the C terminus of the CNGRC peptide, by genetic engineering technology (5). This approach markedly improved the therapeutic index of TNF in animal models, either when used alone (5) or in combination with chemotherapeutic agents (6). Studies on the mechanism of action showed that the targeting domain of this TNF derivative (called NGR-TNF) binds an aminopeptidase (CD13) isoform expressed in tumor vessels, and not other isoforms expressed in normal epithelia or myeloid cells (7). Besides CNGRC, other tumor vasculature targeting peptides containing the NGR motif have been identified, such as linear NGRAHA and cyclic CVLNGRMEC (3). These and other linear and cyclic NGR peptides have been used for targeting viral particles to endothelial cells (8, 9). Although these findings may suggest that peptide cyclization is not necessary for the targeting properties of NGR peptides, the role of cysteines and th...

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“…RGD binds to five ␣V integrins (␣v␤1, ␣V␤3, ␣v␤5 ␣v␤6, and ␣v␤8), two ␤1 integrins (␣5 and ␣8), and ␣IIb␤3 (24). RGD in its disulfidebonded cyclic form (CDCRGDCFC) binds more strongly to integrins than does its linear form (25). RGD has been extensively studied in targeting and killing tumor cells (26).…”

mentioning

confidence: 99%

Characteristics of Oncolytic Vesicular Stomatitis Virus Displaying Tumor-Targeting Ligands

Ammayappan

Peng

Russell

2013

J Virol

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bWe sought proof of principle that tumor-targeting ligands can be displayed on the surface of vesicular stomatitis virus (VSV) by engineering its glycoprotein. Here, we successfully rescued VSVs displaying tumor vasculature-targeting ligands. By using a rational approach, we investigated various feasible insertion sites on the G protein of VSV (VSV-G) for display of tumor vasculature-targeting ligands, cyclic RGD (cRGD) and echistatin. We found seven sites on VSV-G that tolerated insertion of the 9-residue cRGD peptide, two of which could tolerate insertion of the 49-amino acid echistatin domain. All of the ligand-displaying viruses replicated as well as the parental virus. In vitro studies demonstrated that the VSVechistatin viruses specifically bound to targeted integrins. Since the low-density lipoprotein receptor (LDLR) was recently identified as a major receptor for VSV, we investigated the entry of ligand-displaying viruses after masking LDLR. The experiment showed that the modified viruses can enter the cell independently of LDLR, whereas entry of unmodified virus is significantly blocked by a specific monoclonal antibody against LDLR. Both parental and ligand-displaying viruses displayed equal oncolytic efficacies in a syngeneic mouse myeloma model. We further demonstrated that single-chain antibody fragments against tumor-specific antigens can be inserted at the N terminus of the G protein and that corresponding replication-competent VSVs can be rescued efficiently. Overall, we demonstrated that functional tumor-targeting ligands can be displayed on replication-competent VSVs without perturbing viral growth and oncolytic efficacy. This study provides a rational foundation for the future development of fully retargeted oncolytic VSVs. V esicular stomatitis virus (VSV) is an enveloped, negativestrand RNA virus that belongs to the Vesiculovirus genus of the Rhabdoviridae family. VSV has the ability to infect and kill cancer cells while sparing normal cells (1-4). Exploitation of this oncolytic property provides a promising alternative approach for the treatment of cancer. For disseminated cancer, virotherapy should ideally be administered systemically (2, 5-7), but this route of delivery brings its own set of problems. The major concerns for VSV virotherapy are neurotoxicity, antibody neutralization, and sequestration in off-target organs, especially the liver and spleen. Many attempts have been made to address these drawbacks. To reduce the neurotoxicity, the matrix protein of VSV was mutated (8, 9), and microRNA targets (10) or picornaviral internal ribosome entry sites (11) were engineered into the VSV genome. Serum neutralization has been avoided by PEGylating the virus (12, 13) or loading onto antigen-specific T cells (14), which ultimately improved virotherapy outcomes.To circumvent all of the above hurdles in a single step, pseudotyping VSV with other viral envelope glycoproteins was considered a potentially feasible approach. Recent studies demonstrated that VSV neurotoxicity can be circumvented by...

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Solution Structures and Integrin Binding Activities of an RGD Peptide with Two Isomers

Cited by 136 publications

References 32 publications

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

Structure-Activity Relationships of Linear and Cyclic Peptides Containing the NGR Tumor-homing Motif

Characteristics of Oncolytic Vesicular Stomatitis Virus Displaying Tumor-Targeting Ligands

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