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 (
    44874, 44873, 44872, 44871, 44870, 44869, 
    44868, 44866, 44865, 44864, 44863, 
    44862, 44861, 44860, 44859, 44858, 
    44857, 44856, 44453, 44452
  ) 
  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 0.00065

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
44452 1.69000000
44453 8.99000000
44856 1.69000000
44857 1.69000000
44858 1.69000000
44859 1.69000000
44860 1.69000000
44861 1.69000000
44862 1.69000000
44863 1.69000000
44864 1.69000000
44865 1.69000000
44866 1.69000000
44868 1.69000000
44869 1.69000000
44870 1.69000000
44871 1.69000000
44872 1.69000000
44873 1.69000000
44874 1.69000000