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 (
    259, 260, 261, 262, 263, 311, 312, 313, 
    314, 315, 316, 3539, 3540, 3541, 3542, 
    3543, 3544, 3545, 3954, 3955, 3956, 
    3957, 3958, 3959, 3960, 3999, 4000, 
    4001, 4002, 4003, 4004, 4005, 4059, 
    4060, 4061, 4062, 4063, 4064, 4065, 
    4142, 4143, 4144, 4145, 4146, 4147, 
    4148, 4195, 4196
  ) 
  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": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (259,260,261,262,263,311,312,313,314,315,316,3539,3540,3541,3542,3543,3544,3545,3954,3955,3956,3957,3958,3959,3960,3999,4000,4001,4002,4003,4004,4005,4059,4060,4061,4062,4063,4064,4065,4142,4143,4144,4145,4146,4147,4148,4195,4196))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}