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 (
    5531, 5528, 5525, 5521, 5526, 5515, 5501, 
    5529, 5503, 5512, 5514, 5511, 5523, 
    5513, 5516, 5524, 5518, 5527, 5519, 
    5532, 5530, 5517, 6766, 6730
  ) 
  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 0.00058

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": 24,
      "filtered": 93.46080017,
      "index_condition": "cscart_product_prices.product_id in (5531,5528,5525,5521,5526,5515,5501,5529,5503,5512,5514,5511,5523,5513,5516,5524,5518,5527,5519,5532,5530,5517,6766,6730)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}