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 (
    109698, 109440, 109439, 109438, 109437, 
    109436, 109435, 109434, 109433, 109432, 
    109431, 109430, 109429, 109364, 109082, 
    109081, 109075, 109074, 109073, 109068
  ) 
  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 0.00084

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 usergroup 9 40 Using where

Result

product_id price
109068 1.69000000
109073 1.69000000
109074 1.69000000
109075 1.69000000
109081 1.69000000
109082 1.69000000
109364 1.69000000
109429 1.69000000
109430 1.69000000
109431 1.69000000
109432 1.69000000
109433 1.69000000
109434 1.69000000
109435 1.69000000
109436 1.69000000
109437 1.69000000
109438 1.69000000
109439 1.69000000
109440 1.69000000
109698 1.69000000