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 (
    5095, 3147, 5094, 5097, 7732, 1522, 1683, 
    1685, 2447, 3554, 3552, 3553, 7603, 
    7604, 7605, 7606, 4059, 3865, 4054, 
    4058, 4052, 4056, 4053, 3870, 3872, 
    3871, 3873, 3862, 5512, 5513, 5511, 
    5514, 5359, 2958, 7024, 5863, 5862, 
    6860, 6859, 6856, 6761, 4591, 5781, 
    5714, 7427, 4969, 2626, 2627
  ) 
  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 0.00125

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 (5095,3147,5094,5097,7732,1522,1683,1685,2447,3554,3552,3553,7603,7604,7605,7606,4059,3865,4054,4058,4052,4056,4053,3870,3872,3871,3873,3862,5512,5513,5511,5514,5359,2958,7024,5863,5862,6860,6859,6856,6761,4591,5781,5714,7427,4969,2626,2627))",
        "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)))"
      }
    }
  }
}