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 (
    87149, 87148, 87147, 87146, 87478, 87461, 
    87267, 87013, 87012, 86982, 87168, 
    87437, 87163, 87162, 87438, 87288, 
    87287, 87025, 87022, 86884, 88075, 
    88074, 88073, 88072, 87072, 87071, 
    87070, 86983, 86835, 86603, 86602, 
    86601, 87357, 86850, 86849, 86848, 
    86847, 86846, 86845, 86693
  ) 
  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 0.00051

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