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 (
    49614, 49613, 49612, 49611, 49610, 49609, 
    49608, 49607, 49606, 49605, 49604, 
    49603, 49602, 49601, 49556, 49906, 
    49561, 49552, 49551, 49500, 49330, 
    49329, 49499, 49498, 50076, 49497, 
    49459, 49435, 49291, 49290, 49726, 
    49450, 49454, 49453, 49238, 49237, 
    49236, 49407, 49281, 49243, 49242, 
    49241, 49224, 49223, 49348, 49347, 
    49346, 49207, 49190, 49189, 49188, 
    49183, 49182, 49181, 49180, 49179, 
    49178, 49177, 49176, 49175, 49174, 
    49173, 49172, 49171, 49170, 49169, 
    49343, 49304, 49303, 49302, 49282, 
    49165, 49141, 49140, 49139, 49138, 
    49153, 49152, 49151, 49150
  ) 
  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 0.00192

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
49138 1.69000000
49139 1.69000000
49140 1.69000000
49141 1.69000000
49150 1.69000000
49151 1.69000000
49152 1.69000000
49153 1.69000000
49165 1.69000000
49169 1.69000000
49170 1.69000000
49171 1.69000000
49172 1.69000000
49173 1.69000000
49174 1.69000000
49175 1.69000000
49176 1.69000000
49177 1.69000000
49178 1.69000000
49179 1.69000000
49180 1.69000000
49181 1.69000000
49182 1.69000000
49183 1.69000000
49188 1.69000000
49189 1.69000000
49190 1.69000000
49207 1.69000000
49223 1.69000000
49224 1.69000000
49236 1.69000000
49237 1.69000000
49238 1.69000000
49241 1.69000000
49242 1.69000000
49243 1.69000000
49281 1.69000000
49282 1.69000000
49290 1.69000000
49291 1.69000000
49302 1.69000000
49303 1.69000000
49304 1.69000000
49329 1.69000000
49330 1.69000000
49343 1.69000000
49346 1.69000000
49347 1.69000000
49348 1.69000000
49407 1.69000000
49435 1.69000000
49450 1.69000000
49453 1.69000000
49454 1.69000000
49459 1.69000000
49497 1.69000000
49498 1.69000000
49499 1.69000000
49500 1.69000000
49551 1.69000000
49552 1.69000000
49556 1.69000000
49561 1.69000000
49601 1.69000000
49602 1.69000000
49603 1.69000000
49604 1.69000000
49605 1.69000000
49606 1.69000000
49607 1.69000000
49608 1.69000000
49609 1.69000000
49610 1.69000000
49611 1.69000000
49612 1.69000000
49613 1.69000000
49614 1.69000000
49726 1.69000000
49906 1.69000000
50076 1.69000000