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 (
    406480, 437686, 423559, 424334, 460558, 
    456062, 432907, 404813, 447269, 409338, 
    403991, 456256, 420163, 453916, 414087, 
    424432, 428079, 401029, 456055, 445068, 
    418346, 407735, 436615, 428503
  ) 
  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 0.00137

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.099614043,
    "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": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (406480,437686,423559,424334,460558,456062,432907,404813,447269,409338,403991,456256,420163,453916,414087,424432,428079,401029,456055,445068,418346,407735,436615,428503) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}