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 (
    47014, 46993, 40434, 47016, 5779, 49306, 
    858, 857, 40452, 40454, 40453, 4894, 
    1892, 23162, 48770, 48843, 40492, 4266, 
    40455, 48071, 35195, 48844, 4269, 4270, 
    4263, 39612, 41390, 4262, 1056, 48850, 
    4271, 48849
  ) 
  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 0.09158

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": 9.595955849,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (47014,46993,40434,47016,5779,49306,858,857,40452,40454,40453,4894,1892,23162,48770,48843,40492,4266,40455,48071,35195,48844,4269,4270,4263,39612,41390,4262,1056,48850,4271,48849) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}