You could use additional parentheses:
subkeyword = (
Session.query(Subkeyword.subkeyword_id, Subkeyword.subkeyword_word)
.filter_by(subkeyword_company_id=self.e_company_id)
.filter_by(subkeyword_word=subkeyword_word)
.filter_by(subkeyword_active=True)
.one()
)