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 (
    1431, 360, 1479, 1478, 414, 1866, 1427, 
    788, 1084, 1407, 1903, 1452, 1453, 538, 
    1864, 1863, 1461, 1199, 1943, 1901, 
    1200, 1212, 1939, 1211
  ) 
  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 0.00128

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": 28,
      "filtered": 4.897957802,
      "index_condition": "cscart_product_prices.product_id in (1431,360,1479,1478,414,1866,1427,788,1084,1407,1903,1452,1453,538,1864,1863,1461,1199,1943,1901,1200,1212,1939,1211)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}