Bother with fresh book about ancient city (7)
I believe the answer is:
perturb
'bother' is the definition.
(I've seen this before)
'fresh book about ancient city' is the wordplay.
'fresh' becomes 'pert' (I've seen this before).
'book' becomes 'b' (abbreviation for book).
'about' says to put letters next to each other.
'ancient city' becomes 'ur' (ancient Sumerian city state).
'b' put after 'ur' is 'urb'.
'pert'+'urb'='PERTURB'
'with' is the link.
(Other definitions for perturb that I've seen before include "upset" , "Disquiet, disturb" , "Discountenance" , "Bother" , "Make uneasy or cause to be worried" .)