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 (
    421, 427, 408, 382, 418, 400, 424, 381, 
    1529, 401, 1465, 1935, 428, 415, 391, 
    406, 439, 390, 393, 394, 396, 397, 398, 
    399
  ) 
  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 0.00093

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "59.01"
    },
    "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": 25,
        "rows_produced_per_join": 4,
        "filtered": "19.98",
        "index_condition": "(`eshopuga_upgr_4122`.`cscart_product_prices`.`product_id` in (421,427,408,382,418,400,424,381,1529,401,1465,1935,428,415,391,406,439,390,393,394,396,397,398,399))",
        "cost_info": {
          "read_cost": "58.01",
          "eval_cost": "1.00",
          "prefix_cost": "59.01",
          "data_read_per_join": "119"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`eshopuga_upgr_4122`.`cscart_product_prices`.`lower_limit` = 1) and (`eshopuga_upgr_4122`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}