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 (
    41027, 41026, 41025, 41024, 41023, 41022, 
    41021, 41020, 41019, 41018, 40998, 
    40954, 40896, 40895, 40894, 40888, 
    41357, 41356, 41355, 41354, 41353, 
    41352, 41351, 41350, 41349, 41348, 
    41347, 41346, 41345, 41344, 41343, 
    41342, 41341, 41340, 41338, 41337, 
    41336, 41335, 41334, 41333, 41332, 
    41331, 41330, 41329, 41328, 41327, 
    41326, 41325, 41324, 41140, 40854, 
    40853, 41004, 41003, 41002, 40946, 
    40842, 40841, 40837, 40836, 40835, 
    40834, 40833, 40872, 40866, 41147, 
    40784, 40783, 40777, 40776, 40798, 
    40797, 40686, 40671, 79898, 40781, 
    40780, 40642, 41150, 40634
  ) 
  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 0.00078

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