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 (
    35279, 25318, 47597, 47084, 5787, 1767, 
    18608, 1057, 5790, 33723, 2803, 17265, 
    47655, 5789, 47922, 47921, 47896, 47924, 
    47923, 33312, 3287, 3286, 3872, 5300, 
    5297, 1579, 65, 1587, 47024, 1102, 41293, 
    17259
  ) 
  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 0.25936

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 25327,
              "filtered": 8.080804825,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (35279,25318,47597,47084,5787,1767,18608,1057,5790,33723,2803,17265,47655,5789,47922,47921,47896,47924,47923,33312,3287,3286,3872,5300,5297,1579,65,1587,47024,1102,41293,17259) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}