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 (
    88095, 88094, 88093, 88092, 88091, 88090, 
    88089, 88088, 88087, 88086, 88082, 
    88081, 87851, 87731, 87730, 87729, 
    87728, 88625, 88624, 88623, 88039, 
    88532, 88531, 88530, 88406, 88405, 
    88404, 88403, 88402, 88401, 87762, 
    87678, 88629, 88628, 88627, 88626, 
    88575, 88574, 88573, 88149
  ) 
  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 0.00052

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