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 (
    412939, 435593, 457221, 431380, 432643, 
    430955, 425786, 433168, 420963, 435716, 
    436514, 419288, 424427, 460521, 414020, 
    414696, 431630, 420330, 439312, 427057, 
    405641, 426607, 407640, 409611
  ) 
  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 0.00137

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.099614043,
    "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": 48,
          "cost": 0.08425304,
          "filtered": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (412939,435593,457221,431380,432643,430955,425786,433168,420963,435716,436514,419288,424427,460521,414020,414696,431630,420330,439312,427057,405641,426607,407640,409611) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}