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 (
    15744, 12632, 12633, 10179, 10180, 10523, 
    10073, 10077, 10076, 10086, 10085, 
    10084, 10083, 10082, 10081, 10080, 
    10079, 10584, 10594, 12574, 10168, 
    10167, 12703, 15968, 15938, 10053, 
    10041, 9904, 9905, 15966, 15965, 9940
  ) 
  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 0.00489

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": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup_id",
          "key_length": "6",
          "used_key_parts": ["usergroup_id", "product_id"],
          "rows": 64,
          "filtered": 100,
          "index_condition": "cscart_product_prices.product_id in (15744,12632,12633,10179,10180,10523,10073,10077,10076,10086,10085,10084,10083,10082,10081,10080,10079,10584,10594,12574,10168,10167,12703,15968,15938,10053,10041,9904,9905,15966,15965,9940) and cscart_product_prices.usergroup_id in (0,1)",
          "attached_condition": "cscart_product_prices.lower_limit = 1"
        }
      }
    }
  }
}