Study On Computer-aided Design For Cyclooxygenase-2(COX-2) Inhibitors

Inflammation is the pathologic processe by which living tissues react to injury. Many mediators are involved in the inflammatory process. Among all of them, prostaglandins(PGs) take an inportment role in this process. Cyclooxygenases(COX) is the key enzyme which catalyze arachidonic acid(AA) to generate PGs. Two isoforms of COX , COX-1 and COX-2, have been identified at the beginning of 1990s. COX-1 distributes mainly in normal tissues and catalyze AA to generate PGs for maintaining physiological functions. COX-2 distributes mainly in inflammatory tissues. When it is activated by the inflammatory factors, PGs accumulated dramatically and promote the inflammatory reaction and the injury of the tissue. Nonsteroidal antiinflammatory drugs (NSAIDs) are conventional drugs in the treatment of inflammation. But long term usage of them often cause an undesirable gastrointestinal injury, for instance, bleeding, ulcer etc. Because NSAIDs inhibit simultaneously both of the COX isoforms, the inflammation is treated and PGs which maintain the phsiological function is inhibited at the same tune.Screening for the selective and effective COX-2 inhibitor becomes more and more importment.This studies were established on the platform of two molecule simulation softwares provided by Tripose Inc. ?Alchemy 2000 system and Sciprotein structure prediction system. Based on them, selective COX-2 inhibitor was designed and studied. All the data can be clues to screen selective and effective COX-2 inhibitor. The content of the research can be divided artificially into three steps.1. Structure analysis of COX-1 and COX-2 The primary structure of COX-1 and COX-2 was retrieved from SWISS-PROT database and the data of their X-ray diffraction crystallography was retrieved from PDB database. The three-dimensional structure of COX-1 and COX-2 was acquired after the data file had been inputted into the molecule modeling software桝lchemy 2000 system. Comparing the primary structure of COX-1 and COX-2 we found that there is crucial difference between the amino acid of them in the binding domain. The residue at 434 and 523 of COX-2 is valine, while that of COX-1 illecuine. The three-dimensional structure shows that the binding capacity of COX-2 is bigger than that of COX-1. Maybe it results from the fact that valine has one less methyl than isoleucine in chemical structure and then it is smaller than illeucine in spatial structure. According to these findings we can design a molecule which can bind completely with COX-2 while can not bind with COX-1 because it is relatively bigger than the space supplied by COX-1.2. Determination of Activity Conformation The compound crystallography structure of COX-2 and it's selective inhibitor SC-558 was retrieved from PDB database. The data file was inputted into Alchemy 2000 system, then put COX-2 selective inhibitor, SC-558, separately and calculate the molecular energy, stereochemistryproperty and physical chemistry property of SC-558 in isolation state and in low energy state. These data will facilitate the determination of activity Conformation of SC-558 when binding with COX-2. We found that the molecule potential energy difference between SC-558 in isolation state and in low energy state is only 12.8kcl/mol. Optimising the structure molecular dynamics of SC-558 and systematic conforming in the computer system, we found that the greater discrepency between various low energy conformations is only 5 kcl/mol. From these we conclude that the conformation of SC-558 in low energy state is the activity conformation when tri-loop chemicals bind with COX.3. Molecule design of selective COX-2 inhibitor Based on the result of X-ray crystallography, the selective COX-2 inhibitor SC-558 and the non-selective inhibitor indomethacin were docked into COX-1 and COX-2. We found that the free energy change of SC-558. was small (-60.3K.cal/mol) when docking into COX-1, it was big (-14.4 Kcal/mol) while docking into COX-1. The free energy changes of the non-selective inhibitor were almost the same (...