SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    1128285, 1128289, 1129605, 1129852, 
    525901, 1128299, 1199097, 2055715, 
    1718556, 1128294, 1129606, 1444124, 
    1128290, 1199098, 1373431, 1722316, 
    1373435, 1373432, 1128108, 1199099, 
    1199095, 1129597, 1128097, 1129869, 
    1129863, 1128078, 1193387, 1198929, 
    1198866, 1129865, 1129867, 1198921, 
    1129873, 1129857, 1129861, 1129864, 
    2538988
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00099

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "1.20"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": false,
      "table": {
        "table_name": "cscart_ult_product_prices",
        "access_type": "ref",
        "possible_keys": [
          "usergroup",
          "product_id",
          "company_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "company_id",
        "used_key_parts": [
          "company_id"
        ],
        "key_length": "4",
        "ref": [
          "const"
        ],
        "rows_examined_per_scan": 7,
        "rows_produced_per_join": 1,
        "filtered": "27.00",
        "cost_info": {
          "read_cost": "0.50",
          "eval_cost": "0.19",
          "prefix_cost": "1.20",
          "data_read_per_join": "60"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "company_id",
          "usergroup_id"
        ],
        "attached_condition": "((`maniamall_cscart`.`cscart_ult_product_prices`.`lower_limit` = 1) and (`maniamall_cscart`.`cscart_ult_product_prices`.`product_id` in (1128285,1128289,1129605,1129852,525901,1128299,1199097,2055715,1718556,1128294,1129606,1444124,1128290,1199098,1373431,1722316,1373435,1373432,1128108,1199099,1199095,1129597,1128097,1129869,1129863,1128078,1193387,1198929,1198866,1129865,1129867,1198921,1129873,1129857,1129861,1129864,2538988)) and (`maniamall_cscart`.`cscart_ult_product_prices`.`usergroup_id` in (0,0,1)))"
      }
    }
  }
}