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 (
    4013, 4067, 4219, 4215, 4170, 4172, 4166, 
    4482, 4085, 4198, 4173, 4869, 4222, 
    4483, 4217, 4480, 4174, 4872, 4878, 
    3988, 4084, 4481, 4474, 4089, 4866, 
    4877, 4871, 4875, 4083, 4168, 4201, 
    4162, 4868, 4477, 4223, 4090, 4860, 
    4078, 4202, 4547, 4216, 4221, 4876, 
    4011, 4545, 4171, 4551, 4169, 4175, 
    4220, 4858, 4859, 4199, 4484, 4550, 
    4873, 4546, 4549, 4874, 4867, 4082, 
    4479, 4865, 4200, 4864, 4214, 4863
  ) 
  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 0.00193

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "46.91"
    },
    "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": 67,
        "rows_produced_per_join": 13,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (4013,4067,4219,4215,4170,4172,4166,4482,4085,4198,4173,4869,4222,4483,4217,4480,4174,4872,4878,3988,4084,4481,4474,4089,4866,4877,4871,4875,4083,4168,4201,4162,4868,4477,4223,4090,4860,4078,4202,4547,4216,4221,4876,4011,4545,4171,4551,4169,4175,4220,4858,4859,4199,4484,4550,4873,4546,4549,4874,4867,4082,4479,4865,4200,4864,4214,4863))",
        "cost_info": {
          "read_cost": "45.57",
          "eval_cost": "1.34",
          "prefix_cost": "46.91",
          "data_read_per_join": "321"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}