SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    87227, 87226, 87225, 87224, 87223, 87222, 
    87221, 87220, 87219, 87218, 87217, 
    87216, 87000, 86999, 86998, 86997, 
    86996, 86995, 86994, 86993, 86506, 
    86447, 86446, 86445, 86444, 86384, 
    86383, 86382, 86381, 86380, 86379, 
    86378, 86377, 86376, 86375, 86374, 
    87116, 86470, 86469, 86468
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_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_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where