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
  ) 
  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 0.00186

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup_id",
          "key_length": "6",
          "used_key_parts": ["usergroup_id", "product_id"],
          "rows": 64,
          "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) and cscart_product_prices.usergroup_id in (0,1)",
          "attached_condition": "cscart_product_prices.lower_limit = 1"
        }
      }
    }
  }
}