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 (
    8884, 10213, 10078, 8863, 10174, 395, 
    8873, 10163, 8894, 10212, 8885, 8893
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 2 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00050

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 24 Using index condition

Result

product_id price
395 2329.000000
8863 1248.000000
8873 2227.000000
8884 2832.000000
8885 2440.000000
8893 3493.000000
8894 3493.000000
10078 0.000000
10163 2629.000000
10174 3000.000000
10212 1613.000000
10213 2088.000000