Seems like I could solve as following.

incoming_message     = request.form["Body"]

p = re.search('!(.*):', incoming_message)
# get extracted phone and replace + if available
whatsapp_to          = p.group(1)
whatsapp_to          = whatsapp_to.replace("%2B", "")
whatsapp_to          = re.sub("[+$@&%{}:=!]","",whatsapp_to)

m = re.search('%(.*)=', incoming_message)
# get extracted message and remove unwanted characters
extract_message      = m.group(1)
body_message         = re.sub("[+$@&%{}:=!]"," ",extract_message)
clean_message        = body_message.rstrip('%0A')
clean_message        = clean_message.replace(" 3A", ":")