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 (
    40437, 1896, 50216, 40451, 33725, 27361, 
    2320, 2319, 50194, 1893, 46822, 38074, 
    48846, 23152, 49873, 35279, 47084, 
    42255, 40350, 23158, 1057, 33723, 5715, 
    5716, 5717, 27359, 3517, 3516, 1103, 
    35782, 3518, 40445
  ) 
  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 0.00525

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "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": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (40437,1896,50216,40451,33725,27361,2320,2319,50194,1893,46822,38074,48846,23152,49873,35279,47084,42255,40350,23158,1057,33723,5715,5716,5717,27359,3517,3516,1103,35782,3518,40445)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}