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 (
    425013, 423301, 403335, 416458, 413195, 
    452439, 456232, 409981, 422412, 444874, 
    411736, 410485, 443778, 413186, 432494, 
    406992, 417005, 443366, 433693, 445954, 
    441514, 456101, 421337, 459209
  ) 
  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 0.00123

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.099597785,
    "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": 48,
          "cost": 0.08425304,
          "filtered": 49.99988556,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (425013,423301,403335,416458,413195,452439,456232,409981,422412,444874,411736,410485,443778,413186,432494,406992,417005,443366,433693,445954,441514,456101,421337,459209) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}