Computer-assisted identification of small-molecule Bcl-2 modulators.

Apoptosis, the programmed cell death, is a highly regulated process, necessary for normal development and homeostasis of the functions of organisms. The Bcl-2 inhibitors BH3I-1 and BH3I-2 were used as lead compounds to find possible Bcl-2 or Bcl-X(L) inhibitors by using computer-assisted screening with our in-house database, containing more than four million commercially available molecules. Identified compounds were further investigated regarding their possible application as a drug.

Cellular fingerprints: a novel approach using large-scale cancer cell line data for the identification of potential anticancer agents.

The cellular fingerprint, a novel in silico screening approach, was developed to identify new biologically active compounds in combination with structural fingerprints. To this end, high-throughput screening (HTS) data from the National Cancer Institute have been used. To validate this method, we have selected the proapoptotic, natural compound betulinic acid (BA). Because of its antiproliferative effect on a variety of cancer cell lines, the identification of novel BA analogs is of great interest. Novel analogs have been identified and validated in different apoptosis assays. In addition, the novel approach exhibited a strong correlation between structural similarity and biological activity, so that it offers enormous potential for the identification of novel biologically active compounds.

Inhibiting the inhibitors: retro-inverso Smac peptides.

Resistance against apoptosis-inducing anti-cancer drugs remains a severe problem in therapy. One reason is the overexpression of inhibitors of apoptosis proteins (IAPs), a group of proteins responsible for the prevention of apoptosis induction by inactivation of initiator caspases. The natural inhibitor of the IAPs is the protein Smac, which impedes the binding to the caspases. Although Smac is a potent inhibitor, Smac peptides are not very stable in vivo and thus not applicable in therapy. Bioinformatical methods were applied to design Smac-derived peptides to break the therapy resistance in IAP high-expressing tumor cells. The exchange of amino acids in the Smac peptides AVPI and AVPF against unnatural amino acids leads to an improvement of the apoptosis sensitivity. The variety of Smac peptides was filtered by computational docking. Moreover, Smac-derived peptides with sufficient binding to the IAPs were tested in IAP-expressing Hodgkin Lymphoma cell lines.

SuperToxic: a comprehensive database of toxic compounds.

Within our everyday life, we are confronted with a variety of toxic substances of natural or artificial origin. Toxins are already used, e.g. in medicine, but there is still an increasing number of toxic compounds, representing a tremendous potential to extract new substances. Since predictive toxicology gains in importance, the careful and extensive investigation of known toxins is the basis to assess the properties of unknown substances. In order to achieve this aim, we have collected toxic compounds from literature and web sources in the database SuperToxic. The current version of this database compiles about 60,000 compounds and their structures. These molecules are classified according to their toxicity, based on more than 2 million measurements. The SuperToxic database provides a variety of search options like name, CASRN, molecular weight and measured values of toxicity. With the aid of implemented similarity searches, information about possible biological interactions can be gained. Furthermore, connections to the Protein Data Bank, UniProt and the KEGG database are available, to allow the identification of targets and those pathways, the searched compounds are involved in. This database is available online at: http://bioinformatics.charite.de/supertoxic.

SuperScent--a database of flavors and scents.

Volatiles are efficient mediators of chemical communication acting universally as attractant, repellent or warning signal in all kingdoms of life. Beside this broad impact volatiles have in nature, scents are also widely used in pharmaceutical, food and cosmetic industries, so the identification of new scents is of great industrial interest. Despite this importance as well as the vast number and diversity of volatile compounds, there is currently no comprehensive public database providing information on structure and chemical classification of volatiles. Therefore, the database SuperScent was established to supply users with detailed information on the variety of odor components. The version of the database presented here comprises the 2D/3D structures of approximately 2100 volatiles and around 9200 synonyms as well as physicochemical properties, commercial availability and references. The volatiles are classified according to their origin, functionality and odorant groups. The information was extracted from the literature and web resources. SuperScent offers several search options, e.g. name, Pubchem ID number, species, functional groups, or molecular weight. SuperScent is available online at: http://bioinformatics.charite.de/superscent.

Toxicity versus potency: elucidation of toxicity properties discriminating between toxins, drugs, and natural compounds.

Within our everyday life we are confronted with a variety of toxic substances. A number of these compounds are already used as lead structures for the development of new drugs, but the amount of toxic substances is still a rich resource of new bioactive compounds. During the identification and development of new potential drugs, risk estimation of health hazards is an essential and topical subject in pharmaceutical industry. To face this challenge, an extensive investigation of known toxic compounds is going to be helpful to estimate the toxicity of potential drugs. "Toxicity properties" found during those investigations will also function as a guideline for the toxicological classification of other unknown substances. We have compiled a dataset of approximately 50,000 toxic compounds from literature and web sources. All compounds were classified according to their toxicity. During this study the collection of toxic compounds was investigated extensively regarding their chemical, functional, and structural properties and compared with a dataset of drugs and natural compounds. We were able to identify differences in properties within the toxic compounds as well as in comparison to drugs and natural compounds. These properties include molecular weight, hydrogen bond donors and acceptors, and functional groups which can be regarded as "toxicity properties", i.e. attributes defining toxicity.