Conjugation of a Photosensitizer to an Oligoarginine-Based Cell-Penetrating Peptide Increases the Efficacy of Photodynamic Therapy

Enhancing navigation in biomedical databases by community voting and database-driven text classification

Background

The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ability to query such sources is still often suboptimal. Here, we introduce and apply community voting, database-driven text classification, and visual aids as a means to incorporate distributed expert knowledge, to automatically classify database entries and to efficiently retrieve them.

Results

Using a previously developed peptide database as an example, we compared several machine learning algorithms in their ability to classify abstracts of published literature results into categories relevant to peptide research, such as related or not related to cancer, angiogenesis, molecular imaging, etc. Ensembles of bagged decision trees met the requirements of our application best. No other algorithm consistently performed better in comparative testing. Moreover, we show that the algorithm produces meaningful class probability estimates, which can be used to visualize the confidence of automatic classification during the retrieval process. To allow viewing long lists of search results enriched by automatic classifications, we added a dynamic heat map to the web interface. We take advantage of community knowledge by enabling users to cast votes in Web 2.0 style in order to correct automated classification errors, which triggers reclassification of all entries. We used a novel framework in which the database "drives" the entire vote aggregation and reclassification process to increase speed while conserving computational resources and keeping the method scalable. In our experiments, we simulate community voting by adding various levels of noise to nearly perfectly labelled instances, and show that, under such conditions, classification can be improved significantly.

Conclusion

Using PepBank as a model database, we show how to build a classification-aided retrieval system that gathers training data from the community, is completely controlled by the database, scales well with concurrent change events, and can be adapted to add text classification capability to other biomedical databases.

The system can be accessed at .

High-yielding syntheses of hydrophilic conjugatable chlorins and bacteriochlorins

Next-generation photodynamic therapy agents based upon the conjugation of multiple photosensitizers to a targeting backbone will allow for more efficacious light-based therapies. To this end, we have developed glucose-modified chlorins and bacteriochlorins featuring a reactive carboxylic acid linker for conjugation to targeting moieties. The photosensitizers were synthesized in relatively high yields from meso-tetra(p-aminophenyl)porphyrin, and resulted in neutral, hydrophilic chromophores with superb absorption profiles in the far-red and near-infrared portions of the electromagnetic spectrum. In addition, conjugation of these photosensitizers to a model nanoscaffold (crosslinked dextran-coated nanoparticles) demonstrated that the inclusion of hydrophilic sugar moieties increased the number of dyes that can be loaded while maintaining suspension stability. The described compounds are expected to be particularly useful in the synthesis of a number of targeted nanotherapeutic systems.

Photosensitiser delivery for photodynamic therapy. Part 2: systemic carrier platforms

BACKGROUND

The treatment of solid tumours and angiogenic ocular diseases by photodynamic therapy (PDT) requires the injection of a photosensitiser (PS) to destroy target cells through a combination of visible light irradiation and molecular oxygen. There is currently great interest in the development of efficient and specific carrier delivery platforms for systemic PDT.

OBJECTIVE

This article aims to review recent developments in systemic carrier delivery platforms for PDT, with an emphasis on target specificity.

METHODS

Recent publications, spanning the last five years, concerning delivery carrier platforms for systemic PDT were reviewed, including PS conjugates, dendrimers, micelles, liposomes and nanoparticles.

RESULTS/CONCLUSION

PS conjugates and supramolecular delivery platforms can improve PDT selectivity by exploiting cellular and physiological specificities of the targeted tissue. Overexpression of receptors in cancer and angiogenic endothelial cells allows their targeting by affinity-based moieties for the selective uptake of PS conjugates and encapsulating delivery carriers, while the abnormal tumour neovascularisation induces a specific accumulation of heavy weighted PS carriers by enhanced permeability and retention (EPR) effect. In addition, polymeric prodrug delivery platforms triggered by the acidic nature of the tumour environment or the expression of proteases can be designed. Promising results obtained with recent systemic carrier platforms will, in due course, be translated into the clinic for highly efficient and selective PDT protocols.

Model Systems for Fluorescence and Singlet Oxygen Quenching by Metalloporphyrins

Next-generation photodynamic therapy agents will minimize extraneous phototoxicity by being active only at the target site. To this end, we have developed a model system to systematically investigate the excited-state quenching ability of a number of metalloporphyrins. Central metal ions that prefer four-coordinate, square planar orientations (Ag(II), Cu(II), Ni(II), Pd(II), and Zn(II)) were used. Porphyrin dimers based on 5-(4-aminophenyl)-10,15,20-triphenylporphyrin and comprising both a free base porphyrin and a metalloporphyrin covalently linked through a five-carbon alkyl chain were synthesized. The fluorescence and singlet oxygen quantum yields for the dimers were probed at 630 and 650 nm, respectively, resulting in the excitation of only the free base porphyrin and allowing a comparison of the quenching efficacy of each central metal ion. These results demonstrate that metalloporphyrins can serve as efficient quenchers, and may be useful in the design of novel light-activated therapeutic agents.