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 (
    54, 5474, 345, 56, 59, 280, 73, 76, 82, 
    141, 92
  ) 
  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 0.00040

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": 22,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (54,5474,345,56,59,280,73,76,82,141,92) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
54 6.49000000
56 6.49000000
59 6.49000000
73 6.49000000
76 6.49000000
82 6.49000000
92 6.49000000
141 6.49000000
280 34.95000000
345 6.49000000
5474 6.49000000