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 (
    49149, 49292, 49124, 49123, 49122, 49121, 
    49119, 49115, 49114, 49092, 49089, 
    49088, 49087, 49086, 49085, 49075, 
    49054, 49053, 48987, 48986, 48985, 
    48984, 48983, 109922, 109921, 109920, 
    109919, 49051, 49050, 49049, 49048, 
    49047, 49046, 49045, 49044, 49043, 
    49042, 49041, 49040, 48967, 48965, 
    48964, 48959, 48958, 48957, 48956, 
    48955, 48954, 48953, 48952, 48951, 
    48950, 49263, 49162, 48988, 49265, 
    48921, 48885, 48884, 48883, 48882, 
    49373, 49372, 49371, 49370, 49369, 
    49368, 49367, 49366, 49365, 49364, 
    49363, 49362, 49361, 49360, 49359, 
    49358, 49357, 49356, 49355
  ) 
  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 0.00152

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
48882 1.69000000
48883 1.69000000
48884 1.69000000
48885 1.69000000
48921 1.69000000
48950 1.69000000
48951 1.69000000
48952 1.69000000
48953 1.69000000
48954 1.69000000
48955 1.69000000
48956 1.69000000
48957 1.69000000
48958 1.69000000
48959 1.69000000
48964 1.69000000
48965 1.69000000
48967 1.69000000
48983 1.69000000
48984 1.69000000
48985 1.69000000
48986 1.69000000
48987 1.69000000
48988 1.69000000
49040 1.69000000
49041 1.69000000
49042 1.69000000
49043 1.69000000
49044 1.69000000
49045 1.69000000
49046 1.69000000
49047 1.69000000
49048 1.69000000
49049 1.69000000
49050 1.69000000
49051 1.69000000
49053 1.69000000
49054 1.69000000
49075 1.69000000
49085 1.69000000
49086 1.69000000
49087 1.69000000
49088 1.69000000
49089 1.69000000
49092 1.69000000
49114 1.69000000
49115 1.69000000
49119 1.69000000
49121 1.69000000
49122 1.69000000
49123 1.69000000
49124 1.69000000
49149 1.69000000
49162 1.69000000
49263 1.69000000
49265 1.69000000
49292 1.69000000
49355 1.69000000
49356 1.69000000
49357 1.69000000
49358 1.69000000
49359 1.69000000
49360 1.69000000
49361 1.69000000
49362 1.69000000
49363 1.69000000
49364 1.69000000
49365 1.69000000
49366 1.69000000
49367 1.69000000
49368 1.69000000
49369 1.69000000
49370 1.69000000
49371 1.69000000
49372 1.69000000
49373 1.69000000
109919 1.69000000
109920 1.69000000
109921 1.69000000
109922 1.69000000