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 (
    90484, 89456, 89455, 91443, 90822, 91441, 
    91440, 91439, 91438, 91437, 91436, 
    91433, 91427, 91426, 89707, 91424, 
    91423, 91422, 91400, 91375
  ) 
  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
89455 1.69000000
89456 1.69000000
89707 1.69000000
90484 1.69000000
90822 1.69000000
91375 1.69000000
91400 1.69000000
91422 1.69000000
91423 1.69000000
91424 1.69000000
91426 1.69000000
91427 1.69000000
91433 1.69000000
91436 1.69000000
91437 1.69000000
91438 1.69000000
91439 1.69000000
91440 1.69000000
91441 1.69000000
91443 1.69000000