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 (
    52499, 52498, 52497, 52496, 52495, 52494, 
    52493, 52492, 52491, 52490, 52489, 
    52488, 52487, 52486, 52485, 52484, 
    52483, 52482, 52481, 52480, 52479, 
    52478, 52477, 111379, 111375, 52473, 
    52472, 52471, 52470, 52469, 52468, 
    52467, 52466, 52626, 52458, 52457, 
    52456, 52455, 52454, 52453, 52451, 
    52450, 52449, 52448, 59351, 52580, 
    52579, 52447, 52446, 52431, 52426, 
    52423, 52416, 52411, 52683, 52399, 
    52398, 52394, 52393, 52392, 52391, 
    52390, 52389, 52388, 52387, 52386, 
    52385, 52384, 52383, 52382, 52381, 
    52380, 52379, 52378, 52377, 52376, 
    52375, 52374, 52373, 52372
  ) 
  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 0.00202

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
52372 1.69000000
52373 1.69000000
52374 1.69000000
52375 1.69000000
52376 1.69000000
52377 1.69000000
52378 1.69000000
52379 1.69000000
52380 1.69000000
52381 1.69000000
52382 1.69000000
52383 1.69000000
52384 1.69000000
52385 1.69000000
52386 1.69000000
52387 1.69000000
52388 1.69000000
52389 1.69000000
52390 1.69000000
52391 1.69000000
52392 1.69000000
52393 1.69000000
52394 1.69000000
52398 1.69000000
52399 1.69000000
52411 1.69000000
52416 1.69000000
52423 1.69000000
52426 1.69000000
52431 1.69000000
52446 1.69000000
52447 1.69000000
52448 1.69000000
52449 1.69000000
52450 1.69000000
52451 1.69000000
52453 1.69000000
52454 1.69000000
52455 1.69000000
52456 1.69000000
52457 1.69000000
52458 1.69000000
52466 1.69000000
52467 1.69000000
52468 1.69000000
52469 1.69000000
52470 1.69000000
52471 1.69000000
52472 1.69000000
52473 1.69000000
52477 1.69000000
52478 1.69000000
52479 1.69000000
52480 1.69000000
52481 1.69000000
52482 1.69000000
52483 1.69000000
52484 1.69000000
52485 1.69000000
52486 1.69000000
52487 1.69000000
52488 1.69000000
52489 1.69000000
52490 1.69000000
52491 1.69000000
52492 1.69000000
52493 1.69000000
52494 1.69000000
52495 1.69000000
52496 1.69000000
52497 1.69000000
52498 1.69000000
52499 1.69000000
52579 1.69000000
52580 1.69000000
52626 1.69000000
52683 1.69000000
59351 1.69000000
111375 1.69000000
111379 1.69000000