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, 1930, 400, 424, 
    1931, 381, 1529, 401, 1465, 1932, 1933, 
    1935, 428, 415, 391, 406, 439, 390, 393, 
    394, 1929, 396, 397, 398, 399, 422, 434, 
    383, 412, 1927, 419, 430, 431, 432, 1928, 
    429, 384, 1934, 395, 420, 385, 405, 410, 
    413, 417, 1937, 414, 425, 407, 389, 402, 
    388, 426, 409, 404, 1936, 387, 386, 416, 
    441, 322
  ) 
  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 0.00135

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "163.01"
    },
    "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": 70,
        "rows_produced_per_join": 13,
        "filtered": "19.98",
        "index_condition": "(`eshopuga_upgr_4122`.`cscart_product_prices`.`product_id` in (421,427,408,382,418,1930,400,424,1931,381,1529,401,1465,1932,1933,1935,428,415,391,406,439,390,393,394,1929,396,397,398,399,422,434,383,412,1927,419,430,431,432,1928,429,384,1934,395,420,385,405,410,413,417,1937,414,425,407,389,402,388,426,409,404,1936,387,386,416,441,322))",
        "cost_info": {
          "read_cost": "160.21",
          "eval_cost": "2.80",
          "prefix_cost": "163.01",
          "data_read_per_join": "335"
        },
        "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)))"
      }
    }
  }
}