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 (
    4668, 4673, 4841, 4334, 4681, 4541, 4685, 
    4679, 3987, 4543, 4144, 4682, 4683, 
    4536, 4261, 4686, 4525, 4114, 4535, 
    3989, 4145, 4064, 3990, 4684, 4057, 
    4113, 4260, 4542, 4534, 4539, 4666, 
    4112, 4538, 4537, 4540
  ) 
  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 0.00144

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "24.51"
    },
    "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": 35,
        "rows_produced_per_join": 6,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (4668,4673,4841,4334,4681,4541,4685,4679,3987,4543,4144,4682,4683,4536,4261,4686,4525,4114,4535,3989,4145,4064,3990,4684,4057,4113,4260,4542,4534,4539,4666,4112,4538,4537,4540))",
        "cost_info": {
          "read_cost": "23.81",
          "eval_cost": "0.70",
          "prefix_cost": "24.51",
          "data_read_per_join": "167"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}