Homology modeling of 5-lipoxygenase and hints for better inhibitor design

• Published in: Journal of computer-aided molecular design 2008-09, Vol.22 (9), p.611-619
• Main Authors: Aparoy, P., Reddy, R. N., Guruprasad, Lalitha, Reddy, M. R., Reddanna, P.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino acids; Animal Anatomy; Arachidonate 5-Lipoxygenase - chemistry; Binding Sites; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Design; Drug Design; Enzymes; Ethers; Fatty acids; Glycine max - enzymology; Histology; Lipoxygenase Inhibitors - chemistry; Lipoxygenase Inhibitors - pharmacology; Models, Molecular; Molecular biology; Molecular Sequence Data; Molecular Structure; Morphology; Oxygenation; Pharmacology; Physical Chemistry; Polyunsaturated fatty acids; Potatoes; Protein Conformation; Protein Folding; Proteins; Sequence Homology, Amino Acid; Solanum tuberosum - enzymology; Soybeans; Structure-Activity Relationship
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-008-9180-0

Lipoxygenases (LOXs) are a group of enzymes involved in the oxygenation of polyunsaturated fatty acids. Among these 5-lipoxygenase (5-LOX) is the key enzyme leading to the formation of pharmacologically important leukotrienes and lipoxins, the mediators of inflammatory and allergic disorders. In view of close functional similarity to mammalian lipoxygenase, potato 5-LOX is used extensively. In this study, the homology modeling technique has been used to construct the structure of potato 5-LOX. The amino acid sequence identity between the target protein and sequence of template protein 1NO3 (soybean LOX-3) searched from NCBI protein BLAST was 63%. Based on the template structure, the protein model was constructed by using the Homology program in InsightII. The protein model was briefly refined by energy minimization steps and validated using Profile-3D, ERRAT and PROCHECK. The results showed that 99.3% of the amino acids were in allowed regions of Ramachandran plot, suggesting that the model is accurate and its stereochemical quality good. Like all LOXs, 5-LOX also has a two-domain structure, the small N-terminal β-barrel domain and a larger catalytic domain containing a single atom of non-heme iron coordinating with His525, His530, His716 and Ile864. Asn720 is present in the fifth coordination position of iron. The sixth coordination position faces the open cavity occupied here by the ligands which are docked. Our model of the enzyme is further validated by examining the interactions of earlier reported inhibitors and by energy minimization studies which were carried out using molecular mechanics calculations. Four ligands, nordihydroguaiaretic acid (NDGA) having IC 50 of 1.5 μM and analogs of benzyl propargyl ethers having IC 50 values of 760 μM, 45 μM, and no inhibition respectively were selected for our docking and energy minimization studies. Our results correlated well with the experimental data reported earlier, which proved the quality of the model. This model generated can be further used for the design and development of more potent 5-LOX inhibitors.