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 (
    12731, 12725, 12727, 12724, 10923, 10920, 
    10922, 12730, 10918, 10916, 10919, 
    10833, 10837, 10835, 10836, 10834, 
    10819, 10827, 10829, 10830, 10832, 
    10828, 12726, 12732, 12598, 12599, 
    12601, 12603, 12600, 12602
  ) 
  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 0.00781

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": 4.305534363,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (12731,12725,12727,12724,10923,10920,10922,12730,10918,10916,10919,10833,10837,10835,10836,10834,10819,10827,10829,10830,10832,10828,12726,12732,12598,12599,12601,12603,12600,12602) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}