$ perl -MData::Dumper -e '
@arr = ("A[TCG]GG 3", "CTG[AA] 4");
@nar = map {  #get rid of trailing number 
              my $st = (split(" ",$_))[0];

              #replace bracket with S
              $st =~ s/\[[ATCG]+\]/S/g; } @arr; 
print Dumper \@nar
'