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 (
    25318, 49949, 49950, 49951, 49952, 49953, 
    49954, 49955, 49956, 49957, 49958, 
    49959, 49960, 49961, 49962, 49963, 
    49964, 49965, 49966, 49967, 49968, 
    49969, 49970, 49971, 49972, 49973, 
    49974, 49975, 49976, 49977, 49978, 
    49979, 49980, 49981, 49982, 49983, 
    49984, 49985, 49986, 49987, 49988, 
    49989, 49990, 49991, 49992, 49993, 
    49994, 49995, 49996, 49997, 49998, 
    49999, 50000, 50001, 50002, 50003, 
    50004, 50005, 50006, 50007, 50008, 
    50009, 50010, 50011, 50012, 50013, 
    50014, 50015, 50016, 50017, 50018, 
    50019, 50020, 50021, 50022, 50023, 
    50024, 50025, 50026, 50027, 50028, 
    50029, 50030, 50031, 50032, 50033, 
    50034, 50035, 50036, 50037
  ) 
  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 0.07463

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 25327,
              "filtered": 100,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (25318,49949,49950,49951,49952,49953,49954,49955,49956,49957,49958,49959,49960,49961,49962,49963,49964,49965,49966,49967,49968,49969,49970,49971,49972,49973,49974,49975,49976,49977,49978,49979,49980,49981,49982,49983,49984,49985,49986,49987,49988,49989,49990,49991,49992,49993,49994,49995,49996,49997,49998,49999,50000,50001,50002,50003,50004,50005,50006,50007,50008,50009,50010,50011,50012,50013,50014,50015,50016,50017,50018,50019,50020,50021,50022,50023,50024,50025,50026,50027,50028,50029,50030,50031,50032,50033,50034,50035,50036,50037) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}