Insert underscore in place of column

Try this:

awk '$1=$1' FS=\t OFS=_ file

try this one

awk -F'  +' 'BEGIN{OFS="_"}{$1=$1;print}' filename

output is

FHIT_Adenosine Monotungstate_Not Available CAD,HT,HT,T2D_Ado-P-Ch2-P-Ps-Ado_Not Available CAD,HT,HT,T2D
CS_Trifluoroacetonyl Coenzyme A_Not Available CAD,CAD,T1D_Alpha-Fluoro-Carboxymethyldethia Coenzyme a Complex_Not Available CAD,CAD,T1D_

In this case, the FS for awk be "t" and not the escape sequence.

Nope. I have a file with tabs in the first and the last column and spaces between a,b and c.

$ cat file
1       a  b  c 2
3               a  b  c 3
$
$ awk '$1=$1' FS=\t OFS=_ file
1_a  b  c_2
3__a  b  c_3
$
$echo 'DUMMY'|awk '{print FS}' FS=\t OFS=_|od -c
0000000    t  \n
0000002

$echo 'DUMMY'|awk '{print FS}' FS=\\t OFS=_|od -c
0000000   \t  \n
0000002