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 (
    431225, 431483, 431058, 431207, 431430, 
    431475, 431496, 431086, 431479, 430986, 
    431036, 431282, 431351, 431391, 431450, 
    431223, 431059, 431227, 431437, 430716, 
    431294, 431492, 430996, 431278, 431296, 
    431396, 431435, 431460, 435511, 431413, 
    430777, 431367, 431221, 431261, 431323, 
    431331, 431485, 431276, 431258, 431307, 
    431312, 431348, 431471, 431382, 431448, 
    431095, 431477, 431499, 381714, 431214, 
    431310, 431375, 431449, 431266, 431299, 
    430728, 431491, 431347, 431366, 431436, 
    431441, 431075, 431418, 431489, 430709, 
    431228, 431265, 431321, 431400, 431363, 
    431486, 431189, 430670, 431206, 431370, 
    431374, 431388, 387053, 430774, 430779, 
    431209, 431232, 431256, 431257, 431379, 
    387048, 430710, 431179, 431404, 431445, 
    430668, 431293, 431277, 431286, 431462, 
    431317, 431473, 431476, 431320, 431390
  ) 
  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 0.00176

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (431225,431483,431058,431207,431430,431475,431496,431086,431479,430986,431036,431282,431351,431391,431450,431223,431059,431227,431437,430716,431294,431492,430996,431278,431296,431396,431435,431460,435511,431413,430777,431367,431221,431261,431323,431331,431485,431276,431258,431307,431312,431348,431471,431382,431448,431095,431477,431499,381714,431214,431310,431375,431449,431266,431299,430728,431491,431347,431366,431436,431441,431075,431418,431489,430709,431228,431265,431321,431400,431363,431486,431189,430670,431206,431370,431374,431388,387053,430774,430779,431209,431232,431256,431257,431379,387048,430710,431179,431404,431445,430668,431293,431277,431286,431462,431317,431473,431476,431320,431390)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}