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 (
    1335, 1338, 1233, 1324, 1323, 1081, 1326, 
    1325, 1333, 1082, 1321, 1330, 1331, 
    1329, 1334, 1337, 1339, 1340, 1343, 
    399, 1299, 1810, 1811, 2918, 1341, 1342, 
    1856, 2913, 1815, 1819, 2914, 1859, 
    1858, 1850, 1294, 1298, 1297, 1293, 
    1295, 1814, 1816, 1817, 1818, 1820, 
    1821, 1822, 1823, 1824
  ) 
  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 0.00107

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.102979907,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 96,
          "cost": 0.09071016,
          "filtered": 20,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (1335,1338,1233,1324,1323,1081,1326,1325,1333,1082,1321,1330,1331,1329,1334,1337,1339,1340,1343,399,1299,1810,1811,2918,1341,1342,1856,2913,1815,1819,2914,1859,1858,1850,1294,1298,1297,1293,1295,1814,1816,1817,1818,1820,1821,1822,1823,1824) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}