title: Optimization of antisense drug design against conservative local motif in simulant secondary structures of HER-2 mRNA and QSAR analysis.
abstract: OBJECTIVE
  To study the role of mRNA secondary structure stability in antisense drug design and obtain better antisense candidates against neu/HER-2/erbB-2 mRNA than previous report.
  
  
  METHODS
  Program RNAstructure was utilized to simulate the secondary structures of HER-2 mRNA. Then 21 antisense phosphorothioate oligodeoxynucleotides (S-ODN) targeting different parts of secondary structural motif were designed. HA4 was set as positive control. Mean 50 % inhibitory effects (IC(50)) of S-ODN on proliferations of SK-BR-3 breast cancer cells were evaluated. The expression of target mRNA was detected by RT-PCR. The multiple regression and quantitative structure-activity relationship (QSAR) analysis was preformed by SPSS software.
  
  
  RESULTS
  One optimal and two suboptimal secondary structures of target mRNA were obtained. Nine out of 11 S-ODN against completely conservative local motif (LM) (conservative among all simulant secondary structures) got lower or similar IC(50) values compared with HA4. On the other hand, 2 out of 3 S-ODN against relatively conservative LM (conservative between any two simulant secondary structures) got lower or similar IC(50) values compared with HA4. Only 2 out of 5 S-ODN targeting variable LM (variable among different predicted secondary structures) had acceptable activities. Average IC(50) of S-ODN against completely conservative LM was significantly lower than that of S-ODN against diverse LM. QSAR analysis suggested that stability, base number of bulge loops, and target free energies Delta GoT were statistically significant. In the multiple regression, R was 0.967, P=0.005.
  
  
  CONCLUSIONS
  Antisense drug design against conservative LM was helpful for improving the positive rate. Several S-ODN candidates better than positive control were screened.
authors.affiliation: Affiliated Hospital, Academy of Military Medical Sciences, Beijing 100850, China.
authors.forename: Shuan-Ping
authors.initials: SP
authors.lastname: Yang
authors.forename: San-Tai
authors.initials: ST
authors.lastname: Song
authors.forename: Zhong-Ming
authors.initials: ZM
authors.lastname: Tang
authors.forename: Hai-Feng
authors.initials: HF
authors.lastname: Song
mesh_terms: D000970:Antineoplastic Agents / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D001943:Breast Neoplasms / Q000473:pathology; D002455:Cell Division / Q000187:drug effects; D017076:Computer-Aided Design; D015195:Drug Design; D005260:Female; D018734:Genes, erbB-2; D006801:Humans; D020319:Oligodeoxyribonucleotides, Antisense / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D017433:Protein Structure, Secondary; D021281:Quantitative Structure-Activity Relationship; D012333:RNA, Messenger / Q000737:chemistry; D014407:Tumor Cells, Cultured; D015854:Up-Regulation
chemical_list: D000970:Antineoplastic Agents; D020319:Oligodeoxyribonucleotides, Antisense; D012333:RNA, Messenger