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 (
    15943, 15951, 15952, 15956, 15958, 15959, 
    15944, 15960, 15961, 15962, 15966, 
    15957, 15965, 15945, 15968, 15946, 
    15947, 15949, 15950, 12520, 12497, 
    12528, 12512, 12511, 12527, 10580, 
    10579, 9936, 9931, 12521, 12504, 12502, 
    12505, 13099, 12514, 12513, 9759, 10496, 
    10560, 10561, 10581, 10102, 9940, 10578, 
    10143, 9947, 10567, 10568, 10565, 9933, 
    12499, 12500, 10200, 10201, 10566, 
    10545, 10227, 10552, 12506, 10693, 
    12508, 9953, 12522, 12507
  ) 
  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 0.00112

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": 128,
      "filtered": 100,
      "index_condition": "cscart_product_prices.product_id in (15943,15951,15952,15956,15958,15959,15944,15960,15961,15962,15966,15957,15965,15945,15968,15946,15947,15949,15950,12520,12497,12528,12512,12511,12527,10580,10579,9936,9931,12521,12504,12502,12505,13099,12514,12513,9759,10496,10560,10561,10581,10102,9940,10578,10143,9947,10567,10568,10565,9933,12499,12500,10200,10201,10566,10545,10227,10552,12506,10693,12508,9953,12522,12507)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9759 1955.00000000
9931 1331.00000000
9933 1563.00000000
9936 1331.00000000
9940 2142.00000000
9947 2022.00000000
9953 1960.00000000
10102 2142.00000000
10143 2205.00000000
10200 2234.00000000
10201 2234.00000000
10227 1997.00000000
10496 1955.00000000
10545 2143.00000000
10552 2143.00000000
10560 2098.00000000
10561 2098.00000000
10565 2691.00000000
10566 2089.00000000
10567 2691.00000000
10568 2691.00000000
10578 2205.00000000
10579 1791.00000000
10580 1791.00000000
10581 2142.00000000
10693 2089.00000000
12497 0.00000000
12499 0.00000000
12500 0.00000000
12502 0.00000000
12504 0.00000000
12505 0.00000000
12506 0.00000000
12507 0.00000000
12508 0.00000000
12511 0.00000000
12512 0.00000000
12513 0.00000000
12514 0.00000000
12520 0.00000000
12521 0.00000000
12522 0.00000000
12527 0.00000000
12528 0.00000000
13099 0.00000000
15943 6390.00000000
15944 6875.00000000
15945 6890.00000000
15946 6476.00000000
15947 6047.00000000
15949 4982.00000000
15950 4982.00000000
15951 7167.00000000
15952 3852.00000000
15956 6896.00000000
15957 4709.00000000
15958 5578.00000000
15959 6031.00000000
15960 6478.00000000
15961 6499.00000000
15962 6272.00000000
15965 6424.00000000
15966 5975.00000000
15968 4889.00000000