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 (
    44431, 44430, 44429, 44428, 44072, 44071, 
    44070, 44069, 44068, 44067, 44066, 
    44065, 44064, 44063, 44062, 44061, 
    44060, 44059, 44058, 44057
  ) 
  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 0.00056

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
44057 1.69000000
44058 1.69000000
44059 1.69000000
44060 1.69000000
44061 1.69000000
44062 1.69000000
44063 1.69000000
44064 1.69000000
44065 1.69000000
44066 1.69000000
44067 1.69000000
44068 1.69000000
44069 1.69000000
44070 1.69000000
44071 1.69000000
44072 8.99000000
44428 1.69000000
44429 1.69000000
44430 1.69000000
44431 1.69000000