I would use split and regular expressions, too, but in a less complicated way:

#!/usr/bin/perl
use warnings;
use strict;

my $input = 'tar : ERGC [1] | ALX5 [2] | PT2 [3] | PRTD [4]  act:  Ago
+ [1] : Inhibit [2,3,4]';

my ($left, $right) = split /act:/, $input;

my %num2left;
while ($left =~ /(\S+) \[([0-9])\]/g) {
    $num2left{$2} = $1;
}

while ($right =~ /(\S+) \[([0-9,]+)\]/g) {
    my ($target, @indices) = ($1, split /,/, $2);
    for my $i (@indices) {
        print "$i $num2left{$i}\t$target\n";
    }
}
[download]

Output:

1 ERGC  Ago
2 ALX5  Inhibit
3 PT2   Inhibit
4 PRTD  Inhibit
[download]