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 (
    41546, 41545, 41544, 41543, 41429, 41268, 
    41267, 41361, 41572, 41571, 41246, 
    41245, 41244, 41243, 41242, 41220, 
    41218, 41173, 41167, 41644, 41643, 
    41642, 41641, 41640, 41639, 41159, 
    41154, 41128, 41117, 41116, 41113, 
    41146, 41145, 41211, 41213, 41192, 
    41058, 41054, 41053, 41103, 41017, 
    40942, 40941, 40940, 40934, 40933, 
    40932, 40931, 40930, 40929, 40928, 
    40927, 40926, 40925, 40923, 40922, 
    40921, 40920, 40919, 40918, 40917, 
    40916, 40915, 40914, 40913, 40912, 
    40911, 40910, 40909, 40908, 40907, 
    40906, 40905, 40904, 40903, 40902, 
    40901, 40900, 40899, 41623
  ) 
  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 0.00109

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