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 (
    88194, 88192, 88190, 88189, 88188, 88186, 
    88185, 88137, 88136, 88135, 88054, 
    88053, 88052, 88051, 88050, 87782, 
    87781, 87697, 87696, 87695, 87694, 
    87581, 88552, 88551, 88550, 88549, 
    88548, 88547, 88080, 87985, 88796, 
    88795, 88083, 87879, 87704, 87693, 
    87690, 87587, 87586, 87669
  ) 
  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 0.00081

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