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 (
    88272, 89076, 89032, 89031, 89027, 88842, 
    88839, 88838, 88837, 88836, 88835, 
    88834, 88833, 88832, 88319, 88318, 
    88317, 88316, 88315, 88314
  ) 
  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 0.00053

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
88272 1.69000000
88314 1.69000000
88315 1.69000000
88316 1.69000000
88317 1.69000000
88318 1.69000000
88319 1.69000000
88832 1.69000000
88833 1.69000000
88834 1.69000000
88835 1.69000000
88836 1.69000000
88837 1.69000000
88838 1.69000000
88839 1.69000000
88842 1.69000000
89027 1.69000000
89031 1.69000000
89032 1.69000000
89076 1.69000000