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 (
    4109, 4032, 4033, 4034, 4035, 4036, 4164, 
    4161, 4162, 4175, 4176, 4177, 4178, 
    4179, 4180, 4181, 4182, 4183, 4184, 
    4185, 4186, 4187, 4188, 4192, 4193, 
    4194, 4195, 4199, 4200, 4201, 4202, 
    4367, 4020, 4021, 4022, 4023, 3934, 
    3932, 3970, 4024, 4014, 4065, 4113, 
    4086, 4089, 4092, 4093, 4097, 4018, 
    4028, 3929, 4052, 4010, 3955, 4150, 
    4151, 4050, 3930, 4189, 4037, 4038, 
    4039, 4040, 4025, 4119, 4126, 4127, 
    4072, 4145, 4146, 4147, 4060, 3974, 
    4041, 4103, 4148, 4102, 4366, 4064, 
    4062, 4101, 4063, 4074, 4075, 4076, 
    4077, 4078, 4079, 4080
  ) 
  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 0.02073

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 6449,
          "filtered": 37.89348602,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (4109,4032,4033,4034,4035,4036,4164,4161,4162,4175,4176,4177,4178,4179,4180,4181,4182,4183,4184,4185,4186,4187,4188,4192,4193,4194,4195,4199,4200,4201,4202,4367,4020,4021,4022,4023,3934,3932,3970,4024,4014,4065,4113,4086,4089,4092,4093,4097,4018,4028,3929,4052,4010,3955,4150,4151,4050,3930,4189,4037,4038,4039,4040,4025,4119,4126,4127,4072,4145,4146,4147,4060,3974,4041,4103,4148,4102,4366,4064,4062,4101,4063,4074,4075,4076,4077,4078,4079,4080) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}