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 (
    88127, 88126, 88125, 88124, 87662, 87418, 
    87417, 87416, 87415, 87414, 87413, 
    87412, 87411, 87410, 87409, 87363, 
    87362, 87158, 87157, 87659, 88123, 
    88122, 87708, 87707, 87676, 87675, 
    87475, 87169, 87083, 87082, 87081, 
    87067, 87024, 87854, 87853, 87852, 
    87713, 87712, 87711, 87710
  ) 
  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 0.00065

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