This paper describes a similarity-driven simple evolutionary approach to producing candidate molecules of new drugs. The aim of the method is to explore the candidates that are structurally similar to the reference molecule and yet somewhat different in not only peripheral chains but also their scaffolds. The method employs a known active molecule of our interest as a reference molecule which is used to navigate a huge chemical space. The reference molecule is also used to obtain seed fragments. An initial set of individual structures is prepared with the seed fragments and additional fragments using several connection rules. The fragment library is preferably prepared from a collection of known molecules related to the target of the reference molecule. Every fragment of the library can be used for fragment-based mutation. All the fragments are categorized into three classes; rings, linkers, and side chains. New individuals are produced by the crossover and the fragment-based mutation with the fragment library. Computer experiments with our own fragment library prepared from GPCR SARfari verified the feasibility of our approach to drug discovery.
Aiming at the prediction of pleiotropic effects of drugs, we have investigated the multilabel classification of drugs that have one or more of 100 different kinds of activity labels. Structural feature representation of each drug molecule was based on the topological fragment spectra method, which was proposed in our previous work. Support vector machine (SVM) was used for the classification and the prediction of their activity classes. Multilabel classification was carried out by a set of the SVM classifiers. The collective SVM classifiers were trained with a training set of 59,180 compounds and validated by another set (validation set) of 29,590 compounds. For a test set that consists of 9,864 compounds, the classifiers correctly classified 80.8% of the drugs into their own active classes. The SVM classifiers also successfully performed predictions of the activity spectra for multilabel compounds.
The (η -pentamethylcyclopentadienyl)cobalt(III) (Cp*Co )-catalyzed C-H bond functionalization of aromatic, heteroaromatic, and α,β-unsaturated Weinreb amides was explored. C-H allylation reactions with the use of allyl carbonate and a perfluoroalkene, oxidative alkenylation reactions with the use of ethyl acrylate, iodination reactions with the use of N-iodosuccinimide, and amidation reactions with the use of dioxazolones were catalyzed by Cp*Co(CO)I in the presence of a cationic Ag salt and AgOAc to afford various synthetically useful building blocks. Mechanistic studies of the C-H allylation disclosed that the C-H activation step was rate determining and virtually irreversible.
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