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 (
    450261, 416995, 446789, 426059, 409013, 
    414886, 444321, 406390, 408586, 425085, 
    413163, 415231, 429505, 404254, 401286, 
    447216, 440066, 456947, 406411, 404724, 
    416102, 419585, 417300, 439809, 410868, 
    452526, 440855, 429487, 429075, 407708, 
    457100, 449639
  ) 
  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 0.00168

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.132572317,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 64,
          "cost": 0.11207368,
          "filtered": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (450261,416995,446789,426059,409013,414886,444321,406390,408586,425085,413163,415231,429505,404254,401286,447216,440066,456947,406411,404724,416102,419585,417300,439809,410868,452526,440855,429487,429075,407708,457100,449639) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}