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 (
    3141, 7318, 3142, 2643, 3143, 7760, 7761, 
    7762, 3144, 5414, 5411, 5413, 5412, 
    5415, 4321, 4320, 4323, 4322, 4324, 
    4325, 4337, 4338, 4340, 4339
  ) 
  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 0.00031

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "18.16"
    },
    "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": 27,
        "rows_produced_per_join": 5,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (3141,7318,3142,2643,3143,7760,7761,7762,3144,5414,5411,5413,5412,5415,4321,4320,4323,4322,4324,4325,4337,4338,4340,4339))",
        "cost_info": {
          "read_cost": "17.64",
          "eval_cost": "0.52",
          "prefix_cost": "18.16",
          "data_read_per_join": "123"
        },
        "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)))"
      }
    }
  }
}