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 (
    10479, 10484, 10539, 10541, 10544, 10987, 
    11005, 11050, 11057, 11065, 11076, 
    11091, 11180, 11184, 11248, 11253, 
    11312, 7738, 7748, 7756, 8858, 8871, 
    8946, 10070, 10173, 10245, 10260, 10418, 
    10439, 10441, 10443, 10444, 10464, 
    10489, 10546, 10550, 10567, 10568, 
    10570, 10986
  ) 
  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 0.00116

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 (10479,10484,10539,10541,10544,10987,11005,11050,11057,11065,11076,11091,11180,11184,11248,11253,11312,7738,7748,7756,8858,8871,8946,10070,10173,10245,10260,10418,10439,10441,10443,10444,10464,10489,10546,10550,10567,10568,10570,10986)) 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"
        ]
      }
    }
  }
}