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 (
    4539, 4359, 4035, 4324, 4657, 4360, 4548, 
    4662, 4062, 4677, 4505, 4046, 4076, 
    4242, 4829, 4068, 4095, 4469, 4112, 
    4509, 4702, 4665, 4050, 4259, 4330, 
    4506, 4266, 4409, 4691, 4697, 4338, 
    4408, 4521, 4692, 4407, 4381, 4523, 
    4241, 4274, 4507, 4520, 4361, 4676, 
    4061, 4413, 4237, 4538, 4512, 4537, 
    4658, 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 0.00121

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "35.71"
    },
    "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": 51,
        "rows_produced_per_join": 10,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (4539,4359,4035,4324,4657,4360,4548,4662,4062,4677,4505,4046,4076,4242,4829,4068,4095,4469,4112,4509,4702,4665,4050,4259,4330,4506,4266,4409,4691,4697,4338,4408,4521,4692,4407,4381,4523,4241,4274,4507,4520,4361,4676,4061,4413,4237,4538,4512,4537,4658,4540))",
        "cost_info": {
          "read_cost": "34.69",
          "eval_cost": "1.02",
          "prefix_cost": "35.71",
          "data_read_per_join": "244"
        },
        "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)))"
      }
    }
  }
}