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 (
    339678, 220178, 431162, 431128, 339465, 
    339786, 339457, 431132, 339477, 431099, 
    431202, 339541, 339643, 265042, 339796, 
    391798, 392175, 339489, 430637, 430639, 
    431096, 339699, 339469, 339797, 392167, 
    339458, 339798, 339606, 339685, 339482, 
    431168, 431141, 339468, 339453, 431137, 
    431153, 431155, 431130, 431033, 339730, 
    430911, 339731, 430640, 381703, 431134, 
    339478, 431125, 431154, 431090, 339794, 
    431187, 431067, 431146, 339463, 431065, 
    339709, 431094, 431048, 339467, 430767, 
    430697, 431104, 339753, 431050, 339460, 
    381725, 430745, 431124, 431117, 339696, 
    339757, 339464, 339808, 339787, 339806, 
    339805, 392169, 431157, 431191, 339810, 
    431160, 339707, 339701, 339704, 430850, 
    430681, 430743, 431084, 431116, 430908, 
    431107, 392166, 339677, 430998, 339769, 
    339814, 339750, 339758, 430655, 430744
  ) 
  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 0.00123

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 (339678,220178,431162,431128,339465,339786,339457,431132,339477,431099,431202,339541,339643,265042,339796,391798,392175,339489,430637,430639,431096,339699,339469,339797,392167,339458,339798,339606,339685,339482,431168,431141,339468,339453,431137,431153,431155,431130,431033,339730,430911,339731,430640,381703,431134,339478,431125,431154,431090,339794,431187,431067,431146,339463,431065,339709,431094,431048,339467,430767,430697,431104,339753,431050,339460,381725,430745,431124,431117,339696,339757,339464,339808,339787,339806,339805,392169,431157,431191,339810,431160,339707,339701,339704,430850,430681,430743,431084,431116,430908,431107,392166,339677,430998,339769,339814,339750,339758,430655,430744)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}