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 (
    3524, 9985, 10466, 9989, 10463, 10418, 
    10405, 10417, 10465, 10385, 10464, 
    10373
  ) 
  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 0.00044

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 13 Using index condition; Using where

Result

product_id price
3524 255.000000
9985 230.000000
9989 230.000000
10373 230.000000
10385 274.000000
10405 360.000000
10417 352.000000
10418 360.000000
10463 337.000000
10464 352.000000
10465 331.000000
10466 337.000000