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, 41341, 41340, 47922, 47921, 41343, 
    47896, 47924, 47923, 41339, 31965, 
    1972, 36746, 2085, 2304, 5829, 41399, 
    15218, 3765, 3004, 2302, 22143, 18160, 
    4599, 2299, 47895, 3641, 2298, 3767, 
    5826, 4597, 2297
  ) 
  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 0.00259

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 (50216,41341,41340,47922,47921,41343,47896,47924,47923,41339,31965,1972,36746,2085,2304,5829,41399,15218,3765,3004,2302,22143,18160,4599,2299,47895,3641,2298,3767,5826,4597,2297)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}