$line =~ s/
    \*{2} ( [^\*]+ ) \*{2}
        \s
    ( kinase | isoform | protein | peptide | ligand )
        \s
    \${2} ( [^\$]+ ) \${2}
        \s
    [(,] \s
        \*{2} ( [^\*]+ ) \*{2}
    \s [),]
/**$1_$2_$3_($4)**/gx