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 (
    4341, 4342, 6036, 4347, 6369, 4344, 4345, 
    5303, 6050, 7351, 5304, 4348, 4346, 
    6349, 6345, 4122, 2743, 3544, 3545, 
    3543, 3541, 3540, 4956, 5114, 2645, 
    7301, 7299, 7300, 2646, 2647, 2644, 
    1410, 5154, 5150, 5153, 2648, 5152, 
    5155, 5151, 2886, 6436, 2773, 6440, 
    7223, 7116, 7221, 7222, 7224
  ) 
  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 0.00130

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (4341,4342,6036,4347,6369,4344,4345,5303,6050,7351,5304,4348,4346,6349,6345,4122,2743,3544,3545,3543,3541,3540,4956,5114,2645,7301,7299,7300,2646,2647,2644,1410,5154,5150,5153,2648,5152,5155,5151,2886,6436,2773,6440,7223,7116,7221,7222,7224))",
        "cost_info": {
          "read_cost": "32.69",
          "eval_cost": "0.92",
          "prefix_cost": "33.61",
          "data_read_per_join": "220"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`dbggbern`.`cscart_product_prices`.`lower_limit` = 1) and (`dbggbern`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}