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 (
    36, 1046, 3332, 40, 1206, 1734, 5800, 
    5799, 7190, 7189, 5032, 5033, 6645, 
    6644, 4352, 5391, 5392, 6767, 6766, 
    4799, 4723, 4724, 7774, 7757, 3356, 
    5271, 5270, 5269, 5268, 4130, 4129, 
    4128, 4126, 4123, 4125, 4213, 4127, 
    4131, 4124, 1413, 1412, 1411, 1908, 
    1909, 4955, 4954, 4957, 4958
  ) 
  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 0.00140

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.06"
    },
    "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": 49,
        "rows_produced_per_join": 9,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (36,1046,3332,40,1206,1734,5800,5799,7190,7189,5032,5033,6645,6644,4352,5391,5392,6767,6766,4799,4723,4724,7774,7757,3356,5271,5270,5269,5268,4130,4129,4128,4126,4123,4125,4213,4127,4131,4124,1413,1412,1411,1908,1909,4955,4954,4957,4958))",
        "cost_info": {
          "read_cost": "33.12",
          "eval_cost": "0.94",
          "prefix_cost": "34.06",
          "data_read_per_join": "224"
        },
        "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)))"
      }
    }
  }
}