SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    10051, 10061, 10026, 10058, 10054, 10048, 
    10053, 10459, 10050, 10056, 10021, 
    10031
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00069

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id product_id 3 12 Using index condition; Using where

Result

product_id price
10021 98.400000
10026 78.050000
10031 45.100000
10048 63.900000
10050 63.900000
10051 105.840000
10053 105.840000
10054 105.840000
10056 45.510000
10058 50.450000
10061 125.690000
10459 126.000000