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 (
    426562, 446627, 409567, 403223, 456812, 
    416073, 444305, 414771, 405344, 428114, 
    460638, 435197, 412021, 450932, 405246, 
    430164, 444428, 428029, 441949, 460434, 
    433652, 426548, 416330, 447518, 427542, 
    408429, 447154, 419276, 421080, 437947, 
    413185, 419295, 403213, 403380, 408359, 
    409393, 430349, 453094, 411903, 422798, 
    422092, 433129, 424917, 459596, 425363, 
    441519, 434875, 460167
  ) 
  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 0.00225

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 (426562,446627,409567,403223,456812,416073,444305,414771,405344,428114,460638,435197,412021,450932,405246,430164,444428,428029,441949,460434,433652,426548,416330,447518,427542,408429,447154,419276,421080,437947,413185,419295,403213,403380,408359,409393,430349,453094,411903,422798,422092,433129,424917,459596,425363,441519,434875,460167) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}