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 (
    2241, 2238, 2164, 2283, 11114, 14589, 
    15137, 2743, 2742, 2687, 11797, 11796, 
    2688, 11899, 11898, 2756, 2755, 15156, 
    11810, 2189, 2328, 12694, 12696, 12695
  ) 
  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 0.02123

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": 4.757615089,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (2241,2238,2164,2283,11114,14589,15137,2743,2742,2687,11797,11796,2688,11899,11898,2756,2755,15156,11810,2189,2328,12694,12696,12695) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}