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A method of and apparatus are disclosed for evolving successive populations of molecular structures and evaluating each evolved structure of each population with desired physical and/or theoretical properties. An initial population of molecules is provided in terms of representations of a number of member molecules. Evaluation is performed by a fitness function, which compares the initial population and evolved generations of member representations with the set of desired properties to provide a numerical measure or value of fitness for each structure. That numerical value indicates how closely the compared member representation corresponds with the set of desired properties. The next population is generated by changing the structure of selected molecules of a population dependent upon the numerical measure of fitness, and the process repeats. Subsequent populations evolve towards ever-better fitness. The process is terminated when an acceptable molecule evolves.

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Many approaches have been used to discover new chemicals, which are suitable for particular purposes. Although most of this methodology has been directed at drug discovery, there are examples in almost every chemical field: agrochemicals, engineering (materials), fuels, perfumes, cosmetics, photography, semiconductors, non-linearoptics, and others. The goal of chemical discovery is to find chemicals, which have specific reactivities, biological activities, chemical and/or physical properties. In general, none of the available methods are considered satisfactory.

Chemical discovery methods fall into two general categories: random screening and rational design. Random screening methods are based on the ability to screen a very large number of compounds quickly with the goal of finding one or more "lead" compounds for further testing and refinement (typically by rational design). Disadvantages of random screening are that it is extremely expensive and its probability of success is relatively low. Most companies engaged in chemical discovery use random screening because it has the best track record historically and, for many problems, it is the only feasible approach. Random screening experiments often have a minor "rational" component, e.g., chemicals screened are not truly random, but are picked to be representative of a larger set of compounds.

Rational design is based on the ability to rationalize the activity of various chemicals in terms of their molecular structure. Attempts to build a rigorous framework for this purpose date back to 1930's, e.g., see "History and Objectives of Quantitative Drug Design", by Michael S. Tute, Comprehensive Medicinal Chemistry, pub. Pergamon Press plc, ISBN 0-08-037060-8, 1990. The field developed rapidly in the early 1960's with the advent of the QSAR (Quantitative Structure-Activity Relationship) method developed by Corwin Hansch. With QSAR, the activity of a molecule is related statistically to the position and physical parameters of its functional groups. A great deal of further development has been done along these lines. Along with the ability to visualize three-dimensional (3-D) structures using computer graphics systems, this has led to the field known as "molecular modeling".

Comprehensive Medicinal Chemistry, Vol 4 Quantitative Drug Design, (1990) provides a good description of the current state of the art. Overall, the methods that have been developed are techniques for analysis rather than discovery. Much work has been done on predicting how a new molecule will behave. Refining lead structures has received a great amount of attention. There has been little work done on methods which suggest new molecules from an universe of all possible molecules. The reason that there are no methods for direct chemical discovery is that the problem has appeared to be intractable. Even for a very limited chemical classes, there is an enormous number of molecular structures possible.

Current successful approaches for computer assisted methods of designing molecules include the DOCK program, which is described in, "A geometric approach to macromolecule--ligand interactions", I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, T. E. Ferrin, J. Mol. Biol., 161, 269 (1982); the GROW PROGRAM, which is described in "Computer design of bioactive molecules: a method for receptor-based de novo ligand design", J. B. Moon and W. J. Howe, Proteins: Struct. Funct. Genet., 11, 314 (1991); and the LUDI program, which is described in "The computer program LUDI: A new method for the de novo drug design of enzyme inhibitors", H. J. Bohm, J. Comp.-Aided Mol. Design, 6, 61 (1992). DOCK selects from a database molecules, which are complementary in shape and electrostatics to a receptor or active site, and has successfully identified lead compounds in several different drug discovery projects. DOCK relies on a predetermined database of chemical structures and does not perform de novo design. LUDI uses a database of chemical fragments and heuristic rules about fragment-receptor complementarily and geometry to assemble molecules that fit a receptor or active site. GROW assembles peptides from a database of amino acid sidechains into a binding site and has successfully grown peptides that bind tightly to a few different enzymes. These three approaches are the most ambitious and successful to date, but still fall short of the goal of true de novo design of molecules with no or limited constraints, e.g., synthetic feasibility, that fit a specific receptor site optimally.