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 (
    12664, 12667, 12666, 12751, 2641, 2642, 
    2635, 2636, 12691, 12690, 12692, 2199, 
    2200, 2237, 12678, 3238, 3237, 12656, 
    13107, 12672, 12671, 11136, 2772, 11808
  ) 
  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 0.00042

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": 34,
      "filtered": 100,
      "index_condition": "cscart_product_prices.product_id in (12664,12667,12666,12751,2641,2642,2635,2636,12691,12690,12692,2199,2200,2237,12678,3238,3237,12656,13107,12672,12671,11136,2772,11808)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}