Gian Paolo Rizzardi

Isoaspartate-Glycine-Arginine: A New Tumor Vasculature–Targeting Motif

Asparagine deamidation in peptides or in fibronectin fragments containing the asparagine-glycine-arginine sequence generates isoaspartate-glycine-arginine (isoDGR), a new alphavbeta3 integrin-binding motif. Because alphavbeta3 is expressed in angiogenic vessels, we hypothesized that isoDGR-containing peptides could be exploited as ligands for targeted delivery of drugs to tumor neovasculature. We found that a cyclic CisoDGRC peptide coupled to fluorescent nanoparticles (quantum dots) could bind alphavbeta3 integrin and colocalize with anti-CD31, anti-alphavbeta3, and anti-alpha5beta1 antibodies in human renal cell carcinoma tissue sections, indicating that this peptide could efficiently recognize endothelial cells of angiogenic vessels. Using CisoDGRC fused to tumor necrosis factor alpha (TNF) we observed that ultralow doses (1-10 pg) of this product (called isoDGR-TNF), but not of TNF or CDGRC-TNF fusion protein, were sufficient to induce antitumor effects when administered alone or in combination with chemotherapy to tumor-bearing mice. The antitumor activity of isoDGR-TNF was efficiently inhibited by coadministration with an excess of free CisoDGRC, as expected for ligand-directed targeting mechanisms. These results suggest that isoDGR is a novel tumor vasculature-targeting motif. Peptides containing isoDGR could be exploited as ligands for targeted delivery of drugs, imaging agents, or other compounds to tumor vasculature.

Structural Basis for the Interaction of isoDGR with the RGD-binding Site of αvβ3 Integrin

Asparagine deamidation at the NGR sequence in the 5th type I repeat of fibronectin (FN-I5) generates isoDGR, an αvβ3 integrin-binding motif regulating endothelial cell adhesion and proliferation. By NMR and molecular dynamics studies, we analyzed the structure of CisoDGRC (isoDGR-2C), a cyclic β-peptide mimicking the FN-I5 site, and compared it with NGR, RGD, or DGR-containing cyclopeptides. Docking experiments show that isoDGR, exploiting an inverted orientation as compared with RGD, favorably interacts with the RGD-binding site of αvβ3, both recapitulating canonical RGD-αvβ3 contacts and establishing additional polar interactions. Conversely, NGR and DGR motifs lack the fundamental pharmacophoric requirements for high receptor affinity. Therefore, unlike NGR and DGR, isoDGR is a new natural recognition motif of the RGD-binding pocket of αvβ3. These findings contribute to explain the different functional properties of FN-I5 before and after deamidation, and provide support for the hypothesis that NGR → isoDGR transition can work as a molecular timer for activating latent integrin-binding sites in proteins, thus regulating protein function.

Critical Role of Flanking Residues in NGR-to-isoDGR Transition and CD13/Integrin Receptor Switching

Various NGR-containing peptides have been exploited for targeted delivery of drugs to CD13-positive tumor neovasculature. Recent studies have shown that compounds containing this motif can rapidly deamidate and generate isoaspartate-glycine-arginine (isoDGR), a ligand of αvβ3-integrin that can be also exploited for drug delivery to tumors. We have investigated the role of NGR and isoDGR peptide scaffolds on their biochemical and biological properties. Peptides containing the cyclic CNGRC sequence could bind CD13-positive endothelial cells more efficiently than those containing linear GNGRG. Peptide degradation studies showed that cyclic peptides mostly undergo NGR-to-isoDGR transition and CD13/integrin switching, whereas linear peptides mainly undergo degradation reactions involving the α-amino group, which generate non-functional six/seven-membered ring compounds, unable to bind αvβ3, and small amount of isoDGR. Structure-activity studies showed that cyclic isoDGR could bind αvβ3 with an affinity >100-fold higher than that of linear isoDGR and inhibited endothelial cell adhesion and tumor growth more efficiently. Cyclic isoDGR could also bind other integrins (αvβ5, αvβ6, αvβ8, and α5β1), although with 10–100-fold lower affinity. Peptide linearization caused loss of affinity for all integrins and loss of specificity, whereas α-amino group acetylation increased the affinity for all tested integrins, but caused loss of specificity. These results highlight the critical role of molecular scaffold on the biological properties of NGR/isoDGR peptides. These findings may have important implications for the design and development of anticancer drugs or tumor neovasculature-imaging compounds, and for the potential function of different NGR/isoDGR sites in natural proteins.

Phase II study of NGR-hTNF, a selective vascular targeting agent, in patients with metastatic colorectal cancer after failure of standard therapy

BACKGROUND NGR-hTNF consists of human tumour necrosis factor (hTNF) fused with the tumour-homing peptide Asp-Gly-Arg (NGR), which is able to selectively bind an aminopeptidase N overexpressed on tumour blood vessels. Preclinical antitumour activity was observed even at low doses. We evaluated the activity and safety of low-dose NGR-hTNF in colorectal cancer (CRC) patients failing standard therapies. PATIENTS AND METHODS Thirty-three patients with progressive disease at study entry received NGR-hTNF 0.8 μg/m(2) given intravenously every 3 weeks. The median number of prior treatment regimens was three (range, 2-5). One-quarter of patients had previously received four or more regimens and two-thirds targeted agents. Progression-free survival (PFS) was the primary study objective. RESULTS NGR-hTNF was well tolerated. No treatment-related grade 3 to 4 toxicities were detected, most common grade 1 to 2 adverse events being short-lived, infusion-time related chills (50.0%). One partial response and 12 stable diseases were observed, yielding a disease control rate of 39.4% (95% CI, 22.9-57.8%). Median PFS and overall survival were 2.5 months (95% CI, 2.1-2.8) and 13.1 months (95% CI, 8.9-17.3), respectively; whereas in patients who achieved disease control the median PFS and overall survival were 3.8 and 15.4 months, respectively. In an additional cohort of 13 patients treated at same dose with a weekly schedule, there was no increased toxicity and 2 patients experienced PFS longer than 10 months. CONCLUSION Based on tolerability and preliminary evidence of disease control in heavily pretreated CRC patients, NGR-hTNF deserves further evaluation in combination with standard chemotherapy.

Enhanced Expression of CD13 in Vessels of Inflammatory and Neoplastic Tissues

Aminopeptidase-N (CD13) is an important target of tumor vasculature-targeting drugs. The authors investigated its expression by immunohistochemistry with three anti-CD13 monoclonal antibodies (WM15, 3D8, and BF10) in normal and pathological human tissues, including 58 normal, 32 inflammatory, and 149 tumor tissue specimens. The three antibodies stained vessels in most neoplastic tissues, interestingly with different patterns. As a matter of fact, WM15 stained almost all intratumor and peritumor capillaries and only partially large vessels, whereas BF10 and 3D8 reacted with arteries and venules and to a lesser extent with capillaries. These antibodies also stained the stroma in about half of neoplastic tissues. In inflammatory lesions, the three antibodies stained vessels and stroma, whereas in normal tissues, they stained a small percentage of blood vessels. Finally, the three antibodies failed to stain endothelial cells of normal colon, whereas they reacted with activated human umbilical vein endothelial cells and with endothelial cells of colon adenocarcinoma vessels. Overall, WM15 was the most specific antibody for angiogenic tumor vessels, suggesting that it may be a good tool for detecting the CD13 form associated with the tumor vasculature. This finding may be relevant for CD13-mediated vascular targeting therapies.

Critical role of indoleamine 2,3-dioxygenase in tumor resistance to repeated treatments with targeted IFNγ

Targeted delivery of IFNγ to tumors has been achieved by fusing this cytokine with GCNGRC, a tumor neovasculature homing peptide. Although the therapeutic efficacy of this protein (called IFNγ-NGR) in animal models is greater than that of IFNγ, frequent administrations of IFNγ-NGR may result in lower efficacy and tumor resistance. We investigated the role of indoleamine 2,3-dioxygenase (IDO), an IFNγ-inducible enzyme that may down-regulate T cells by affecting local tryptophan catabolism in tumor resistance to repeated treatments with IFNγ-NGR. The study was carried out in immunocompetent mice and in nu/nu mice bearing RMA lymphoma, B16F melanoma, or WEHI-164 fibrosarcoma and in vitro using cultured tumor cells. IDO activity was increased in lymphoma homogenates after multiple treatments with IFNγ-NGR but not after a single treatment. Coadministration of 1-methyl-tryptophan, an inhibitor of IDO, increased tumor responses to multiple treatments in the lymphoma, melanoma, and fibrosarcoma models. No synergism between IFNγ-NGR and 1-methyl-tryptophan was observed in vitro in tumor cell proliferation assays or in nu/nu tumor-bearing mice, suggesting that the antitumor effect was host mediated. We conclude that IDO is critically involved in tumor resistance to repeated treatments with IFNγ-NGR, likely causing excessive stimulation of tryptophan catabolism and inhibiting antitumor immune mechanisms. Coadministration of IFNγ-NGR with IDO inhibitors could represent a new strategy for increasing its antitumor activity. [Mol Cancer Ther 2008;7(12):3859–66]

Use of Metadynamics in the Design of isoDGR‐Based αvβ3 Antagonists To Fine‐Tune the Conformational Ensemble

The integrin family of cell-adhesion receptors regulates cellular functions crucial to the initiation, progression, and metastasis of solid tumors. In particular, integrin avb3 plays a key role in endothelial cell survival and migration during tumor angiogenesis. It is therefore gaining increasing importance as a drug target in antiangiogenic cancer therapy. The sequence Arg-Gly-Asp (RGD), which is contained in natural avb3 interactors, such as vitronectin, fibronectin, fibrinogen, osteopontin, and tenascin, is by far the most prominent ligand to promote specific cell adhesion through stimulation. This sequence is therefore attractive as a lead for the development of different integrin antagonists. Recent biochemical studies showed that deamidation of the NGR sequence gives rise to isoDGR, a new avb3-binding motif. This sequence constitutes a novel class of peptidic integrin ligands and paves the way to drug-design studies with a focus on the synthesis and characterization of a new generation of isoDGR-based macrocycles. For the design of low-molecular-mass isoDGR-containing molecules, an accurate determination of their biologically active conformation is a prerequisite. The presence of the b bond induces high flexibility in isoDGR-containing macrocycles and thus augments the range of accessible interconverting conformations. However, the identification of relevant conformations that might affect binding affinity is challenging for standard spectroscopic and diffraction techniques. Atomistic simulations, such as molecular dynamics (MD), replica-exchange molecular dynamics (REMD), and Monte Carlo (MC) simulations, can complement experimental data. However, they often fail to generate reliable equilibrium conformations because of the rugged and complex nature of the free-energy surface (FES) that is accessible to the system. As a consequence, computational sampling is often relegated to some local, unrealistic minima, which compromise subsequent docking studies. As computational drug design becomes increasingly reliant on virtual screening and on high-throughput 3D modeling, the need for fast and accurate computational methods for sampling of the ensemble of energetically accessible conformations is warranted. In this context, several techniques, including the local-elevation method, taboo search, the Wang–Landau method, adaptive force bias, conformational flooding, umbrella sampling, weighted histogram techniques, transitionstate theory, and path sampling, have been developed to address the sampling problem, through either reconstruction of the free energy or the direct acceleration of events that might happen on a long timescale (“rare events”). Related to these methods, metadynamics (MetaD) has emerged as a powerful coarse-grained non-Markovian molecular-dynamics approach for the acceleration of rare events and the efficient and rapid computation of multidimensional free-energy surfaces as a function of a restricted number of degrees of freedom, named collective variables (CVs). If the CVs are appropriately chosen for the system under investigation, MetaD directly provides a good estimate of the free energy of the system projected into the CVs (see the Supporting Information for details). Notably, the free energy is not immediately deducible by other sampling methods, such as umbrella sampling, in which the free-energy profile is not obtained directly from the simulations and requires an additional computational step, such as the weighted histogram analysis method (WHAM). In this study, we developed a protocol based on the combination of MetaD and docking simulations to analyze the conformations and the avb3-binding properties of isoDGR-containing cyclopeptides and to predict the conformational effects of chemical modifications and discriminate binders from nonbinders in silico. To investigate the conformational equilibrium of RGD-, DGR-, and isoDGRcontaining cyclopeptides (cyclization mode involving cysteine side chains) and to exhaustively explore their FESs, we performed well-temperedMetaD simulations, for which we chose Gly f and y angles as CVs (Figure 1; for simulation details, see the Supporting Information). As it lacks a side chain, Gly has large conformational freedom around its backbone dihedral angles. Therefore, Gly can explore a considerably larger area in the Ramachandran energy diagram than any other amino acid, and occupies five [*] Dr. A. Spitaleri, Dr. M. Ghitti, Dr. S. Mari, Dr. G. Musco Dulbecco Telethon Institute, Biomolecular NMR Laboratory c/o Center of Genomic and Bioinformatics S. Raffaele Scientific Institute via Olgettina 58, 20132 Milan (Italy) Fax: (+39)02-2643-4153 E-mail: giovanna.musco@hsr.it

RD2-MolPack-Chim3, a Packaging Cell Line for Stable Production of Lentiviral Vectors for Anti-HIV Gene Therapy

Over the last two decades, several attempts to generate packaging cells for lentiviral vectors (LV) have been made. Despite different technologies, no packaging clone is currently employed in clinical trials. We developed a new strategy for LV stable production based on the HEK-293T progenitor cells; the sequential insertion of the viral genes by integrating vectors; the constitutive expression of the viral components; and the RD114-TR envelope pseudotyping. We generated the intermediate clone PK-7 expressing constitutively gag/pol and rev genes and, by adding tat and rd114-tr genes, the stable packaging cell line RD2-MolPack, which can produce LV carrying any transfer vector (TV). Finally, we obtained the RD2-MolPack-Chim3 producer clone by transducing RD2-MolPack cells with the TV expressing the anti-HIV transgene Chim3. Remarkably, RD114-TR pseudovirions have much higher potency when produced by stable compared with transient technology. Most importantly, comparable transduction efficiency in hematopoietic stem cells (HSC) is obtained with 2-logs less physical particles respect to VSV-G pseudovirions produced by transient transfection. Altogether, RD2-MolPack technology should be considered a valid option for large-scale production of LV to be used in gene therapy protocols employing HSC, resulting in the possibility of downsizing the manufacturing scale by about 10-fold in respect to transient technology.

2D TR‐NOESY Experiments Interrogate and Rank Ligand–Receptor Interactions in Living Human Cancer Cells

Recent advances in cancer therapy include the design ofmolecules that interfer with tumor angiogenesis and moietiesthat recognize specific receptors expressed onto the tumorendothelium and/or onto tumor cells, thus allowing theligand-directed targeted delivery of various drugs and par-ticles to tumors. In this context, integrin avb3 and themembrane-spanning surface protein aminopeptidase N(CD13) play a pivotal role in tumor growth and metastaticspread, as they are important membrane-bound receptorshighly expressed during angiogenesis.

RD-MolPack technology for the constitutive production of self-inactivating lentiviral vectors pseudotyped with the nontoxic RD114-TR envelope

To date, gene therapy with transiently derived lentivectors has been very successful to cure rare infant genetic diseases. However, transient manufacturing is unfeasible to treat adult malignancies because large vector lots are required. By contrast, stable manufacturing is the best option for high-incidence diseases since it reduces the production cost, which is the major current limitation to scale up the transient methods. We have previously developed the proprietary RD2-MolPack technology for the stable production of second-generation lentivectors, based on the RD114-TR envelope. Of note, opposite to vesicular stomatitis virus glycoprotein (VSV-G) envelope, RD114-TR does not need inducible expression thanks to lack of toxicity. Here, we present the construction of RD2- and RD3-MolPack cells for the production of self-inactivating lentivectors expressing green fluorescent protein (GFP) as a proof-of-concept of the feasibility and safety of this technology before its later therapeutic exploitation. We report that human T lymphocytes transduced with self-inactivating lentivectors derived from RD3-MolPack cells or with self-inactivating VSV-G pseudotyped lentivectors derived from transient transfection show identical T-cell memory differentiation phenotype and comparable transduction efficiency in all T-cell subsets. RD-MolPack technology represents, therefore, a straightforward tool to simplify and standardize lentivector manufacturing to engineer T-cells for frontline immunotherapy applications.