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 (
    89, 1643, 1645, 1925, 1666, 1664, 1557, 
    1695, 1559, 1315, 1310, 1471, 1502, 
    86, 1504, 33, 1944, 1942, 1900, 1433, 
    1777, 1748, 1679, 1702
  ) 
  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 0.00119

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": 30,
      "filtered": 4.897957802,
      "index_condition": "cscart_product_prices.product_id in (89,1643,1645,1925,1666,1664,1557,1695,1559,1315,1310,1471,1502,86,1504,33,1944,1942,1900,1433,1777,1748,1679,1702)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}