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 (
    50216, 47597, 18608, 27359, 3713, 37096, 
    27354, 27357, 27358, 27360, 27362, 
    36399, 19386, 27363, 3662, 36339, 3666, 
    637, 2553, 534, 25180, 3004, 47603, 
    37097, 47610, 43459, 43460, 41369, 
    43461, 40928, 43842, 43841
  ) 
  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 0.00250

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (50216,47597,18608,27359,3713,37096,27354,27357,27358,27360,27362,36399,19386,27363,3662,36339,3666,637,2553,534,25180,3004,47603,37097,47610,43459,43460,41369,43461,40928,43842,43841)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}