c:\@Work\Perl\monks>perl -wMstrict -le
"my $a = 'A_D1[1]';
 ;;
 my $str = '123 A_D1 XYZ A_D1[1] BLAH A_D1[1] BLAH';
 print qq{str = '$str'};
 ;;
 $str =~ s{ \b \Q$a\E [ ] }{-}xmsg;
 print qq{str = '$str'};
"
str = '123 A_D1 XYZ A_D1[1] BLAH A_D1[1] BLAH'
str = '123 A_D1 XYZ -BLAH -BLAH'
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(Note that I used a '-' (dash) as the replacement character just to make the example more clear.) (Update: See discussion of  \Q \E and friends in Quote and Quote-like Operators section of perlop. See also quotemeta.)