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 (
    45646, 45645, 45644, 45643, 45642, 45641, 
    45640, 45240, 45239, 45238, 45237, 
    45236, 45235, 45234, 45233, 45232, 
    45231, 45230, 45229, 45228
  ) 
  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 0.00072

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
45228 1.69000000
45229 1.69000000
45230 1.69000000
45231 1.69000000
45232 1.69000000
45233 1.69000000
45234 1.69000000
45235 1.69000000
45236 1.69000000
45237 1.69000000
45238 1.69000000
45239 1.69000000
45240 8.99000000
45640 1.69000000
45641 1.69000000
45642 1.69000000
45643 1.69000000
45644 1.69000000
45645 1.69000000
45646 1.69000000