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 (
    33363, 4281, 38101, 33709, 41401, 5792, 
    35912, 40532, 1998, 45021, 764, 2454, 
    288, 40527, 49199, 44933, 5236, 37413, 
    41383, 36765, 36270, 4288, 32690, 27290, 
    37420, 6439, 6403, 33360, 44560, 3614, 
    4287, 3979
  ) 
  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 0.19236

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": 8.333330154,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (33363,4281,38101,33709,41401,5792,35912,40532,1998,45021,764,2454,288,40527,49199,44933,5236,37413,41383,36765,36270,4288,32690,27290,37420,6439,6403,33360,44560,3614,4287,3979) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}