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 (
    40532, 49309, 36293, 44568, 44574, 4374, 
    45364, 36521, 44573, 4385, 45365, 40529, 
    44571, 40534, 36470, 47257, 25162, 
    47258, 47393, 44570, 24788, 40531, 
    2048, 49758
  ) 
  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 0.00808

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": 24,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (40532,49309,36293,44568,44574,4374,45364,36521,44573,4385,45365,40529,44571,40534,36470,47257,25162,47258,47393,44570,24788,40531,2048,49758)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}