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 (
    5541, 5548, 5537, 5535, 5534, 5547, 5543, 
    5545, 5536, 5539, 5542, 5538, 5549, 
    5546, 5540, 5544, 6788, 6725, 6726, 
    6785, 6786, 6789, 6787
  ) 
  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 0.00034

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_ult_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_ult_product_prices",
          "access_type": "ALL",
          "possible_keys": [
            "usergroup",
            "product_id",
            "company_id",
            "lower_limit",
            "usergroup_id"
          ],
          "rows": 44,
          "filtered": 52.27272797,
          "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 (5541,5548,5537,5535,5534,5547,5543,5545,5536,5539,5542,5538,5549,5546,5540,5544,6788,6725,6726,6785,6786,6789,6787) and cscart_ult_product_prices.usergroup_id in (0,0,1)"
        }
      }
    }
  }
}