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 (
    377, 379, 1296, 392, 2189, 2205, 414, 
    2696, 2409, 2858, 1552, 2206, 2144, 
    2559, 2666, 2774, 344, 2140, 1408
  ) 
  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 0.00094

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "13.76"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 20,
        "rows_produced_per_join": 3,
        "filtered": "19.88",
        "index_condition": "(`zdrowy_db`.`cscart_product_prices`.`product_id` in (377,379,1296,392,2189,2205,414,2696,2409,2858,1552,2206,2144,2559,2666,2774,344,2140,1408))",
        "cost_info": {
          "read_cost": "13.36",
          "eval_cost": "0.40",
          "prefix_cost": "13.76",
          "data_read_per_join": "95"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`zdrowy_db`.`cscart_product_prices`.`lower_limit` = 1) and (`zdrowy_db`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}