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 (
    256, 253, 254, 425, 251, 252, 426, 599, 
    600, 601, 257, 258, 525, 255, 526, 602, 
    603, 604, 261, 262, 259, 260, 403, 404, 
    265, 266, 263, 264, 405, 406, 267, 268
  ) 
  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 0.00052

JSON explain

{
  "query_block": {
    "select_id": 1,
    "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": 66,
      "filtered": 96.96969604,
      "index_condition": "cscart_product_prices.product_id in (256,253,254,425,251,252,426,599,600,601,257,258,525,255,526,602,603,604,261,262,259,260,403,404,265,266,263,264,405,406,267,268)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}