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 (
    427, 408, 1971, 382, 418, 1959, 1960, 
    1961, 381, 1529, 1465, 1962, 1933, 1958, 
    329, 439, 1969, 393, 394, 396, 1964, 
    383, 1927, 1965, 440, 1966, 1928, 1973, 
    1968, 1963, 327, 1934, 385, 405, 413, 
    1970, 1937, 414, 389, 1972
  ) 
  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 0.00333

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "110.01"
    },
    "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": 50,
        "rows_produced_per_join": 9,
        "filtered": "19.98",
        "index_condition": "(`eshopuga_upgr_4122`.`cscart_product_prices`.`product_id` in (427,408,1971,382,418,1959,1960,1961,381,1529,1465,1962,1933,1958,329,439,1969,393,394,396,1964,383,1927,1965,440,1966,1928,1973,1968,1963,327,1934,385,405,413,1970,1937,414,389,1972))",
        "cost_info": {
          "read_cost": "108.01",
          "eval_cost": "2.00",
          "prefix_cost": "110.01",
          "data_read_per_join": "239"
        },
        "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)))"
      }
    }
  }
}