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 (
    358341, 358580, 349830, 351247, 352470, 
    352592, 354508, 355725, 355735, 358488, 
    358587, 349696, 349745, 349793, 351351, 
    351461, 355932, 356531, 358738, 352521, 
    357444, 358729, 358885, 358938, 351397, 
    351399, 351531, 352355, 354978, 356486, 
    358942, 358993, 349953, 351340, 352731, 
    356310, 356671, 358386, 358895, 354431, 
    354616, 354875, 355018, 355681, 356569, 
    356699, 351392, 352707, 356390, 356404, 
    357799, 358782, 351438, 351530, 352761, 
    356212, 356593, 358543, 351407, 351805, 
    352232, 354507, 355974, 359019, 352306, 
    354395, 354795, 355655, 356243, 349754, 
    351457, 354388, 354497, 354865, 356242, 
    358460, 351318, 351334, 351398, 351424, 
    351447, 354405, 354838, 356661, 354415, 
    355850, 357493, 351576, 352583, 359028, 
    351286, 352445, 352554, 356046, 356363, 
    359046, 352393, 357522, 354767, 358637
  ) 
  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 0.00179

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 (358341,358580,349830,351247,352470,352592,354508,355725,355735,358488,358587,349696,349745,349793,351351,351461,355932,356531,358738,352521,357444,358729,358885,358938,351397,351399,351531,352355,354978,356486,358942,358993,349953,351340,352731,356310,356671,358386,358895,354431,354616,354875,355018,355681,356569,356699,351392,352707,356390,356404,357799,358782,351438,351530,352761,356212,356593,358543,351407,351805,352232,354507,355974,359019,352306,354395,354795,355655,356243,349754,351457,354388,354497,354865,356242,358460,351318,351334,351398,351424,351447,354405,354838,356661,354415,355850,357493,351576,352583,359028,351286,352445,352554,356046,356363,359046,352393,357522,354767,358637)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}