SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    4, 1, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 
    17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 
    27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 
    37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 
    47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 
    57, 58, 59, 60, 62, 63, 64, 65, 67, 68, 
    69, 70, 71, 72, 73, 74, 75, 76, 78, 79, 
    80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 
    90, 91, 92, 93, 94, 95, 96, 97, 100, 101, 
    102, 103, 104
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00120

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_ult_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_ult_product_prices",
              "access_type": "ALL",
              "possible_keys": [
                "usergroup",
                "product_id",
                "company_id",
                "lower_limit",
                "usergroup_id"
              ],
              "rows": 4,
              "filtered": 100,
              "attached_condition": "cscart_ult_product_prices.lower_limit = 1 and cscart_ult_product_prices.company_id = 1 and cscart_ult_product_prices.product_id in (4,1,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,62,63,64,65,67,68,69,70,71,72,73,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,100,101,102,103,104) and cscart_ult_product_prices.usergroup_id in (0,0,1)"
            }
          }
        ]
      }
    }
  }
}