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 (
    316, 317, 320, 328, 330, 331, 5, 148, 180, 
    18, 16, 4
  ) 
  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 0.00037

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
4 699.99000000
5 899.99000000
16 349.99000000
18 299.99000000
148 166.00000000
180 199.99000000
316 450.00000000
317 450.00000000
320 250.00000000
328 800.00000000
330 8888.00000000
331 10000.00000000