Yes, Muhammad Ali Jinnah explicitly referred to Afghanistan and Pakistan as "Brotherly Nations" . However, this expression of goodwill and friendship from Jinnah was unilaterally offered by Pakistan and one sided and was not reciprocated by the Afghan government at the time, which refused to even accept Pakistan.
Despite Jinnah's overtures, the official Afghan government's position was politically hostile, driven by its non-recognition of the Durand Line and its support for the "Pakhtunistan" demand. This overshadowed Jinnah's efforts and resulted in strained relations despite all his attempts, exemplified by Afghanistan's vote against Pakistan's entry into the UN in 1947.
The only thing this proves is that starting from Jinnah, we have been trying to be friends to them but they have been hostile to us form the get go.