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 (
    4340, 2364, 13765, 13826, 13993, 2218, 
    2349, 2178, 2177, 11786, 2827, 2640, 
    2312, 2309, 2310, 2311, 3236, 4344, 
    3221, 3225, 3218, 3246, 3222, 4347, 
    3242, 12675, 11361, 12647, 12880, 12670
  ) 
  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 0.00798

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 6449,
          "filtered": 6.888854504,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (4340,2364,13765,13826,13993,2218,2349,2178,2177,11786,2827,2640,2312,2309,2310,2311,3236,4344,3221,3225,3218,3246,3222,4347,3242,12675,11361,12647,12880,12670) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}