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 (
    12582, 12590, 12571, 12632, 12631, 15938, 
    12638, 12599, 12627, 12600, 12639, 
    15800, 12616, 12601, 12628, 12602, 
    12640, 12647, 12605, 12606, 12637, 
    12612, 12613, 12641, 12642, 12648, 
    12611, 12596, 12607, 12608, 12610, 
    12643
  ) 
  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 0.00097

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 32,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (12582,12590,12571,12632,12631,15938,12638,12599,12627,12600,12639,15800,12616,12601,12628,12602,12640,12647,12605,12606,12637,12612,12613,12641,12642,12648,12611,12596,12607,12608,12610,12643)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
12571 67629.15000000
12582 41728.72000000
12590 67629.15000000
12596 45140.72000000
12599 14092.68000000
12600 4597.28000000
12601 14092.68000000
12602 4597.28000000
12605 14092.68000000
12606 4597.28000000
12607 14092.68000000
12608 2296.27000000
12610 13507.47000000
12611 13507.47000000
12612 15852.84000000
12613 15852.84000000
12616 15852.84000000
12627 21943.06000000
12628 21943.06000000
12631 41728.72000000
12632 67629.15000000
12637 19650.51000000
12638 19593.76000000
12639 19593.76000000
12640 19593.76000000
12641 19593.76000000
12642 19593.76000000
12643 19593.76000000
12647 33378.35000000
12648 33378.35000000
15800 33378.35000000
15938 4889.00000000