Computer program PASS (Prediction of Activity Spectra for Substances) is described. Description of chemical structures, presetation of biological activity, mathematical method, training set, validation and applications are presented.
In: Predictive Toxicology. Ed. by Christoph Helma. Taylor & Francis, 2005, pp.459-478.

Computerized system PASS (Prediction of Activity Spectra for Substances) is described. PASS predcits more than 100 pharmacological effects, mechanisms of action and specific toxicities simultaneously. The average accuracy of prediction is about 80% both in leave-one-out cross-validation procedure for the total training set and by prediction for independent sample of 5000 biologically active compounds. The effectiveness of PASS used for heterogenic set of new drug-candidates possess different biological activities is 800% better than random guess-work and 300% better than estimation by skilled experts. PASS used in drug R&D might help to select compounds having structures dissimilar to well-known drugs and to estimate probable activity spectra for new compounds to optimize their synthesis abd testing.
Bioactive Compound Design: Possibilities for Industrial Use, BIOS Scientific Publishers, Oxford (UK), 1996, p.47-56.

PASS INet system for prediction of biological activity spectra via Internet is described.
Bioinformatics, 2000, 16 (8), 747-748.

The majority of biologically active compounds have both pharmacotherapeutic and side/toxic actions. To estimate general efficacy and safety of the molecules under study, their biological potential should be thoroughly evaluated. In an early stage of study, only information about structural formulae was available and was used as an input for computational prediction. Based on a structural formulae of compounds presented as SDF or MOL-files, computer program PASS predicts 900 pharmacological effects, mechanism of action, and specific toxicity. An average accuracy of prediction in leave-one-out cross-validation is about 85%. For evaluating new compounds, scientific community may use PASS via the Internet for free at URL: http://www.ibmh.msk.su/PASS. In the first 18 months of PASS Inet’s use, approximately 1000 researchers from 60 countries have obtained predicted biological activity spectra for about 23,000 different chemical compounds. More than 64 million PASS predictions for almost 250,000 compounds from Open NCI database are available on the web site http://cactus.nci.nih.gov/ncidb2/. These predictions are used for selecting compounds with desirable and without unwanted types of biological activities among the NCI samples available for screening.
SAR and QSAR in Environmental Research, 2003, 14 (5-6), 339-347.

The concept of Biological Activity Spectrum served as a basis for developing PASS (Prediction of Activity Spectra for Substances) software product. PASS predicts simultaneously more than 780 pharmacological effects and biochemical mechanisms based on the structural formula of a substance. It may be used for finding new targets (mechanisms) for known pharmaceuticals and for searching new biologically active substances. PASS prediction ability was evaluated by activity spectra prediction for 63 substances that are presented in the Molecule of the Month section of Prous Science (http://www.prous.com), belong to different chemical classes and reveal various types of biological activity. Mean accuracy of prediction turned out to be about 90%; therefore, it is reasonable to use PASS for finding and optimizing new lead compounds. A web-site with a new internet version of PASS is introduced into practice in December 2001 (http://www.ibmh.msk.su/PASS). On the site, one can find a detailed description of the PASS approach as well as some examples of its applications, and estimate the quality of prediction by submitting structures of substances with known activities.
Current Medicinal Chemistry, 2003, 10 (3), 225-233.

Due to the directed way of testing chemical compounds’ in drug research and development many projects fail because serious adverse effects and toxicity are discovered too late, and many existing prospective activities remain unstudied. Evaluation of the general biological potential of molecules is possible using a computer program PASS that predicts more than 780 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, etc. on the basis of structural formulae of compounds, with average accuracy ∼85%. PASS applications to both databases of available samples included hundreds of thousands compounds, and small collections of compounds synthesized by separate medicinal chemists are described. It is shown that 880 compounds from Prestwick chemical library represent a very diverse pharmacological space. New activities can be found in existing compounds by prediction. Therefore, on this basis, the selection of compounds with required and without unwanted properties is possible. Even when PASS cannot predict very new activities, it may recognize some unwanted actions at the early stage of R&D, providing the medicinal chemist with the means to increase the efficiency of projects.
Journal of Computer-Aided Molecular Design, 2002, 16 (11), 819-824.

Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of information contained in a training set. Suggestion that some relevant chemical information can be added to such training sets without disclosing chemical structures was generated at the recent ACS Symposium. We presented arguments that such safety exchange of relevant chemical information is impossible. Any relevant information about chemical structures can be used for search of either a particular compound itself or its close analogues. Risk of identifying such structures is enough to prevent pharma industry from relevant chemical information exchange.
Journal of Computer-Aided Molecular Design, 2005,19 (9-10), 705-713.

Toxicity of chemical compound is a complex phenomenon that may be caused by its interaction with different targets in the organism. Two distinct types of toxicity can be broadly pecified: the first one is caused by the strong compound’s interaction with a single target (e.g. AChE inhibition); while the second one is caused by the moderate compound’s interaction with many various targets. Computer program PASS predicts about 2500 kinds of biological activities based on the structural formula of chemical compounds. Prediction is based on the robust analysis of structure-activity relationships for about 60,000 biologically active compounds. Mean accuracy exceeds 90% in leave-one-out cross-validation. In addition to some kinds of adverse effects and specific toxicity (e.g. carcinogenicity, mutagenicity, etc.), PASS predicts
2000 kinds of biological activities at the molecular level, that providing an estimated profile of compound’s action in biological space. Such profiles can be used to recognize the most probable targets, interaction with which might be a reason of compound’s toxicity. Applications of PASS predictions for analysis of probable targets and mechanisms of toxicity are discussed.
SAR & QSAR in Environmental Research, 2007, 18 (1-2), 101-110.