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 (
    11021, 11035, 11215, 11302, 11514, 11134, 
    11555, 11264, 11294, 11353, 11374, 
    11590, 11214, 11259, 11295, 11224, 
    11298, 11392, 11408, 11083, 11344, 
    11465, 11473, 11601, 11369, 11372, 
    11130, 11234, 11138, 11209, 11296, 
    11026, 11144, 11268, 11377, 11090, 
    11524, 11235, 11410, 11305
  ) 
  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 0.00124

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.01"
    },
    "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": 80,
        "rows_produced_per_join": 80,
        "filtered": "100.00",
        "index_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (11021,11035,11215,11302,11514,11134,11555,11264,11294,11353,11374,11590,11214,11259,11295,11224,11298,11392,11408,11083,11344,11465,11473,11601,11369,11372,11130,11234,11138,11209,11296,11026,11144,11268,11377,11090,11524,11235,11410,11305)) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "48.01",
          "eval_cost": "8.00",
          "prefix_cost": "56.01",
          "data_read_per_join": "1K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}