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 (
    88461, 88412, 88396, 89357, 89198, 88514, 
    88484, 88483, 88482, 88463, 88462, 
    89197, 89196, 89013, 89012, 89011, 
    88992, 88991, 88990, 88989, 88988, 
    88987, 88986, 88985, 88984, 88983, 
    88982, 88952, 88951, 88950, 88949, 
    88948, 88947, 88946, 88841, 88840, 
    88831, 88830, 88829, 88828
  ) 
  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 0.00087

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