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 (
    428274, 411586, 428067, 405254, 442920, 
    416803, 433221, 427872, 419871, 439094, 
    415819, 415673, 408268, 435233, 411645, 
    446751, 460445, 454691, 405290, 432307, 
    456571, 446699, 413014, 450688
  ) 
  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 0.00126

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 (428274,411586,428067,405254,442920,416803,433221,427872,419871,439094,415819,415673,408268,435233,411645,446751,460445,454691,405290,432307,456571,446699,413014,450688) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}