SELECT 
  product_prices.product_id, 
  MIN(
    IF(
      product_prices.percentage_discount = 0, 
      product_prices.price, 
      product_prices.price - (
        product_prices.price * product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  product_prices 
WHERE 
  product_prices.product_id IN (
    408234, 408237, 408952, 408968, 408991, 
    408995, 408998, 409000, 409503, 409513, 
    409514, 409520
  ) 
  AND product_prices.lower_limit = 1 
  AND product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  product_prices.product_id

Query time 0.00096

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "10.08"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "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": 12,
        "rows_produced_per_join": 1,
        "filtered": "10.00",
        "index_condition": "(`goimagine`.`product_prices`.`product_id` in (408234,408237,408952,408968,408991,408995,408998,409000,409503,409513,409514,409520))",
        "cost_info": {
          "read_cost": "9.96",
          "eval_cost": "0.12",
          "prefix_cost": "10.08",
          "data_read_per_join": "28"
        },
        "used_columns": [
          "id",
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`goimagine`.`product_prices`.`lower_limit` = 1) and (`goimagine`.`product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}