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 (
    55, 337, 5473, 345, 56, 336, 105, 280, 
    5556, 5477, 235, 92, 227
  ) 
  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 0.00050

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["product_id"],
      "key": "product_id",
      "key_length": "9",
      "used_key_parts": ["product_id", "lower_limit", "usergroup_id"],
      "rows": 26,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (55,337,5473,345,56,336,105,280,5556,5477,235,92,227) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
55 6.49000000
56 6.49000000
92 6.49000000
105 15.95000000
227 6.49000000
235 6.49000000
280 34.95000000
336 5.95000000
337 16.95000000
345 6.49000000
5473 12.95000000
5477 8.95000000
5556 12.95000000