SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    46924, 46923, 46922, 46873, 46872, 46871, 
    46870, 46869, 46868, 46867, 46866, 
    46865, 46864, 46863, 46862, 46861, 
    46860, 46859, 46858, 46857, 46624, 
    46568, 46567, 46565, 46822, 46821, 
    46820, 46819, 46901, 46900, 46899, 
    46898, 46897, 46896, 46895, 46894, 
    46893, 46892, 46891, 46890, 46889, 
    46888, 46887, 46886, 46885, 46884, 
    46883, 46882, 46881, 46880, 46879, 
    46878, 46877, 46621, 46620, 46619, 
    46618, 46617, 46616, 46615, 46614, 
    46613, 46535, 46534, 46533, 46532, 
    46519, 46477, 46472, 46471, 46437, 
    46702, 46701, 46700, 46699, 46348, 
    46329, 46580, 46579, 46358
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00157

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 160 Using where

Result

product_id price
46329 1.69000000
46348 1.69000000
46358 1.69000000
46437 1.69000000
46471 1.69000000
46472 1.69000000
46477 1.69000000
46519 1.69000000
46532 1.69000000
46533 1.69000000
46534 1.69000000
46535 1.69000000
46565 1.69000000
46567 1.69000000
46568 1.69000000
46579 1.69000000
46580 1.69000000
46613 1.69000000
46614 1.69000000
46615 1.69000000
46616 1.69000000
46617 1.69000000
46618 1.69000000
46619 1.69000000
46620 1.69000000
46621 1.69000000
46624 1.69000000
46699 1.69000000
46700 1.69000000
46701 1.69000000
46702 1.69000000
46819 1.69000000
46820 1.69000000
46821 1.69000000
46822 1.69000000
46857 1.69000000
46858 1.69000000
46859 1.69000000
46860 1.69000000
46861 1.69000000
46862 1.69000000
46863 1.69000000
46864 1.69000000
46865 1.69000000
46866 1.69000000
46867 1.69000000
46868 1.69000000
46869 1.69000000
46870 1.69000000
46871 1.69000000
46872 1.69000000
46873 1.69000000
46877 1.69000000
46878 1.69000000
46879 1.69000000
46880 1.69000000
46881 1.69000000
46882 1.69000000
46883 1.69000000
46884 1.69000000
46885 1.69000000
46886 1.69000000
46887 1.69000000
46888 1.69000000
46889 1.69000000
46890 1.69000000
46891 1.69000000
46892 1.69000000
46893 1.69000000
46894 1.69000000
46895 1.69000000
46896 1.69000000
46897 1.69000000
46898 1.69000000
46899 1.69000000
46900 1.69000000
46901 1.69000000
46922 1.69000000
46923 1.69000000
46924 1.69000000