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 (
    428427, 427728, 430953, 401174, 410003, 
    414674, 454104, 409191, 447293, 430593, 
    420431, 401982, 404064, 412826, 455161, 
    400935, 449270, 402248, 406597, 433624, 
    446080, 455290, 427919, 433335, 418284, 
    431392, 437836, 439945, 404692, 455805, 
    438918, 427972, 404415, 421393, 416786, 
    457753, 430469, 450047, 448348, 413081, 
    440081, 460754, 410561, 424471, 455506, 
    456958, 425735, 457743
  ) 
  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 0.00160

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.198563002,
    "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": 96,
          "cost": 0.16771496,
          "filtered": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (428427,427728,430953,401174,410003,414674,454104,409191,447293,430593,420431,401982,404064,412826,455161,400935,449270,402248,406597,433624,446080,455290,427919,433335,418284,431392,437836,439945,404692,455805,438918,427972,404415,421393,416786,457753,430469,450047,448348,413081,440081,460754,410561,424471,455506,456958,425735,457743) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}