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 (
    50522, 50521, 50520, 50519, 50518, 50517, 
    50516, 50515, 51281, 50485, 50484, 
    50462, 50461, 50103, 50447, 50408, 
    50465, 50464, 50463, 50393, 50389, 
    50388, 50387, 50072, 50267, 50234, 
    50233, 50232, 50231, 50230, 50229, 
    50228, 50227, 50226, 50225, 50224, 
    50223, 50067, 50066, 50065, 50064, 
    50275, 50274, 50269, 50265, 50039, 
    50001, 88490, 88489, 50040, 50034, 
    50033, 50025, 50152, 50151, 50124, 
    50123, 50122, 49944, 50110, 50107, 
    49954, 49953, 49952, 49951, 49950, 
    50219, 50218, 50217, 50216, 50215, 
    50214, 50213, 50212, 50211, 50210, 
    50209, 50208, 50207, 50206
  ) 
  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 0.00166

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
49944 1.69000000
49950 1.69000000
49951 1.69000000
49952 1.69000000
49953 1.69000000
49954 1.69000000
50001 1.69000000
50025 1.69000000
50033 1.69000000
50034 1.69000000
50039 1.69000000
50040 1.69000000
50064 1.69000000
50065 1.69000000
50066 1.69000000
50067 1.69000000
50072 1.69000000
50103 1.69000000
50107 1.69000000
50110 1.69000000
50122 1.69000000
50123 1.69000000
50124 1.69000000
50151 1.69000000
50152 1.69000000
50206 1.69000000
50207 1.69000000
50208 1.69000000
50209 1.69000000
50210 1.69000000
50211 1.69000000
50212 1.69000000
50213 1.69000000
50214 1.69000000
50215 1.69000000
50216 1.69000000
50217 1.69000000
50218 1.69000000
50219 1.69000000
50223 1.69000000
50224 1.69000000
50225 1.69000000
50226 1.69000000
50227 1.69000000
50228 1.69000000
50229 1.69000000
50230 1.69000000
50231 1.69000000
50232 1.69000000
50233 1.69000000
50234 1.69000000
50265 1.69000000
50267 1.69000000
50269 1.69000000
50274 1.69000000
50275 1.69000000
50387 1.69000000
50388 1.69000000
50389 1.69000000
50393 1.69000000
50408 1.69000000
50447 1.69000000
50461 1.69000000
50462 1.69000000
50463 1.69000000
50464 1.69000000
50465 1.69000000
50484 1.69000000
50485 1.69000000
50515 1.69000000
50516 1.69000000
50517 1.69000000
50518 1.69000000
50519 1.69000000
50520 1.69000000
50521 1.69000000
50522 1.69000000
51281 1.69000000
88489 1.69000000
88490 1.69000000