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 (
    406193, 451309, 446162, 438117, 439044, 
    406083, 415033, 460158, 422354, 409660, 
    453640, 424754, 410340, 417422, 422439, 
    422004, 421990, 446415, 436834, 440447, 
    410009, 439533, 411516, 442635
  ) 
  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 0.00151

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 (406193,451309,446162,438117,439044,406083,415033,460158,422354,409660,453640,424754,410340,417422,422439,422004,421990,446415,436834,440447,410009,439533,411516,442635) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}