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 (
    88722, 88721, 88720, 88719, 88718, 88717, 
    88716, 88715, 88714, 88713, 88712, 
    88711, 88710, 88709, 88708, 88707, 
    88706, 89080, 89079, 89078, 88676, 
    88675, 88674, 88920, 88919, 88493, 
    89075, 88916, 88491, 89082, 89030, 
    89029, 89028, 88996, 88995, 88994, 
    88993, 88981, 88520, 88495
  ) 
  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