Here's an approach that seems to satisfy the OPer's (somewhat vaguely expressed, and with the inferred qualifications noted by others, and including a sentence ending with a period) requirements (needs Perl 5.10  \K regex enhancement):

>perl -wMstrict -le
"my @phrases = (
   'kinase i', 'hib', 'tor', 'tor SET6',
   'SET6', 'p16(INK4A)', 'cell',
   );
 my $delim = qr{ \. | \A \s* | \s+ | \s* \z }xms;
 my $phrase = join '|', reverse sort map quotemeta, @phrases;
 my $mark = qq{\x23};
 for my $s (@ARGV) {
   print '--------------';
   print $s;
   $s =~ s{ $delim \K ($phrase) (?= $delim) }
          {$mark$1$mark}xmsg;
   print $s;
   }
"
"cell kinase inhibitor SET6 activates p16(INK4A) in cell-wall tor SET6
+."
"kinase tor tor SET6"  "tor tor SET6 kinase"  "tor tor SET6"
"kinase tor tor SET6."  "tor tor SET6 kinase."  "tor tor SET6."
"kinase inhibitor"  "kinase inhibitor."
--------------
cell kinase inhibitor SET6 activates p16(INK4A) in cell-wall tor SET6.
#cell# kinase inhibitor #SET6# activates #p16(INK4A)# in cell-wall #to
+r SET6#.
--------------
kinase tor tor SET6
kinase #tor# #tor SET6#
--------------
tor tor SET6 kinase
#tor# #tor SET6# kinase
--------------
tor tor SET6
#tor# #tor SET6#
--------------
kinase tor tor SET6.
kinase #tor# #tor SET6#.
--------------
tor tor SET6 kinase.
#tor# #tor SET6# kinase.
--------------
tor tor SET6.
#tor# #tor SET6#.
--------------
kinase inhibitor
kinase inhibitor
--------------
kinase inhibitor.
kinase inhibitor.
[download]

(Note:  "\x23" is the  "#" character. Have to do this because of a peculiarity of my command line 'editor'.)

If Perl version 5.10 is not available, use
    s{ ($delim) ($phrase) (?= $delim) }{$1$mark$2$mark}xmsg;
as the substitution regex (tested).

Of course, a lot more testing is recommended!

The  reverse in the
    my $phrase = join '|',reverse sort map quotemeta, @phrases;
statement causes the ordered alternation to match the longest phrase substring.

See also Regexp::Assemble and related modules for other (and perhaps better) ways to compile the  $phrase regex.