SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    88618, 88617, 88616, 88615, 88614, 88613, 
    88612, 88611, 88610, 88609, 88608, 
    88607, 88606, 88605, 88604, 88603, 
    88602, 88601, 88600, 88599, 88598, 
    88597, 88596, 88595, 88650, 88571, 
    88957, 88956, 88955, 88593, 88592, 
    88172, 88169, 88762, 88761, 88543, 
    88542, 88487, 88486, 88449
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00067

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where