Method of inhibitor design and identification using a 3-D structure of human peptide deformylase
View Patent ↗The present invention provides the three-dimensional structure of human mitochondrial Homo sapiens peptide deformylase (HsPDF) protein, and HsPDF complexed to a binding compound, such as a PDF inhibitor. This crystallographic information will aid in the identification and development of novel binding compounds of HsPDF and other PDF family members which have anti-bacterial, anti-viral, anti-parasitical, anti-inflammatory, and/or anti-cancer activity.
1. A method for the design and identification of a potential binding compound for human peptide deformylase (HsPDF) comprising the steps of:
(a) generating, on a computer, a three-dimensional structure of HsPDF having the structural coordinates of Tables 1 and/or 2;
(b) identifying amino acid residues forming an HsPDF active site from the three-dimensional structure of HsPDF from step (a) in order to generate a three-dimensional model of the HsPDF active site, wherein the HsPDF active site comprises amino acids 50 CVGLSAPQ 57 (SEQ ID NO:10), 112 EGCES 116 (SEQ ID NO:12), and 156 HEMDHL 161 (SEQ ID NO:13), and 176 TNVYWMKVND 185 (SEQ ID NO:8) according to Table 1 and/or 2;
(c) designing and/or selecting a compound that potentially binds to the HsPDF active site using the three-dimensional model of the HsPDF active site; and
(d) synthesizing and/or choosing the potential binding compound.
2. The method according to claim 1 , the method further comprising the steps of:
(e) contacting the potential binding compound with HsPDF in the presence of a formylated substrate; and
(f) determining the percent inhibition of deformylase activity of HsPDF.
3. The method according to claim 1 , the method further comprising the steps of:
(e) contacting the potential binding compound with a cell, virus, bacterium, or parasite; and
(f) determining the cytotoxicity of the potential binding compound to the cell, virus, bacterium, or parasite.
4. The method of claim 1 , wherein the HsPDF active site comprises amino acid residues 50 CVGLSAPQ 57 (SEQ ID NO:11), 69 LPEALCRECPPRQRALRQMEPF 90 (SEQ ID NO:7), 104 DSRLVT 109 (SEQ ID NO:9), 112 EGCES 116 (SEQ ID NO:12), 117 VAG 119 , 149 WAARIIQ 155 (SEQ ID NO:10), 156 HEMDHL 161 (SEQ ID NO:13), and 176 TNVYWMKVND 185 (SEQ ID NO:8) according to Tables 1 and/or 2.
5. The method of claim 1 , wherein the HsPDF active site comprises amino acid residues 50 CVGLSAPQ 57 (SEQ ID NO:11), 104 DSRLVT 109 (SEQ ID NO:9), 112 EGCES 116 (SEQ ID NO:12), 117 VAG 119 , 149 WAARIIQ 155 (SEQ ID NO:10), and 156 HEMDHL 161 (SEQ ID NO:13), and 176 TNVYWMKVND 185 (SEQ ID NO:8) according to Tables 1 and/or 2.
6. A method for the design and identification of a potential binding compound for HsPDF comprising the steps of:
(a) generating, on a computer, a three-dimensional structure of HsPDF having the structural coordinates of Tables 1 andor 2;
(b) identifying amino acid residues and a Co 2+ cation forming an HsPDF active site from the three-dimensional structure of HsPDF from step (a) in order to generate a three-dimensional model of the HsPDF active site, wherein the HsPDF active site comprises amino acids 50 CVGLSAPQ 57 (SEQ ID NO:10), 112 EGCES 116 (SEQ ID NO:12), 156 HEMDHL 161 (SEQ ID NO:13) 176 TNVYWMKVND 185 (SEQ ID NO:8) , and the cation Co 2+ according to Tables 1 and/or 2;
(c) designing and/or selecting a compound that potentially binds to at least one amino acid in the active site of HsPDF using the three-dimensional model of the HsPDF active site from step (b); and
(d) synthesizing and/or choosing the potential binding compound.
7. The method according to claim 6 , the method further comprising the steps of:
(e) contacting the potential binding compound with HsPDF in the presence of a formylated substrate; and
(f) determining the percent inhibition of deformylase activity of HsPDF.
8. The method according to claim 6 , the method further comprising the steps of:
(e) contacting the potential binding compound with a cell, virus, bacterium, or parasite; and
(f) determining the cytotoxicity of the potential binding compound to the cell, virus, bacterium, or parasite.
9. The method of claim 6 , wherein the HsPDF active site comprises amino acid residues 50 CVGLSAPQ 57 (SEQ ID NO:11), 69 LPEALCRECPPRQRALRQMEPF 90 (SEQ ID NO:7), 104 DSRLVT 109 (SEQ ID NO:9), 112 EGCES 116 (SEQ ID NO:12), 117 VAG 119 , 149 WAARIIQ 155 (SEQ ID NO:10), 156 HEMDHL 161 (SEQ ID NO:13), and 176 TNVYWMKVND 185 (SEQ ID NO:8) and the cation Co 2+ according to Tables 1 and/or 2.
10. The method of claim 6 , wherein the HsPDF active site comprises amino acid residues 50 CVGLSAPQ 57 (SEQ ID NO:11), 104 DSRLVT 109 (SEQ ID NO:9), 112 EGCES 116 (SEQ ID NO:12), 117 VAG 119 , 149 WAARIIQ 155 (SEQ ID NO:10), and 156 HEMDHL 161 (SEQ ID NO:13), and 176 TNVYWMKVND 185 (SEQ ID NO:8) and the cation Co 2+ according to Tables 1 and/or 2.