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 (
    9743, 10015, 10017, 9721, 9748, 9906, 
    10018, 10331, 10019, 10338, 9761, 10001, 
    9752, 10362, 9722, 9745, 10337, 10000, 
    9746, 10002, 9720, 9998, 10003, 9755, 
    9995, 9999, 9763, 9912, 10342, 9911, 
    9992, 10014, 10306, 10334, 9900, 10330, 
    9910, 10301, 9759, 9905, 10300, 10304, 
    10307, 10308, 10332, 10340, 9750, 9867, 
    10302, 10333, 10336, 10341, 10343, 
    10363, 9757, 9902, 9908, 9984, 9990, 
    10016, 10305, 10329, 10335, 10339, 
    9873, 9891, 9889, 9893, 9987, 10303, 
    9896, 9899, 9986
  ) 
  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 0.00166

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "80.81"
    },
    "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": 139,
        "rows_produced_per_join": 27,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (9743,10015,10017,9721,9748,9906,10018,10331,10019,10338,9761,10001,9752,10362,9722,9745,10337,10000,9746,10002,9720,9998,10003,9755,9995,9999,9763,9912,10342,9911,9992,10014,10306,10334,9900,10330,9910,10301,9759,9905,10300,10304,10307,10308,10332,10340,9750,9867,10302,10333,10336,10341,10343,10363,9757,9902,9908,9984,9990,10016,10305,10329,10335,10339,9873,9891,9889,9893,9987,10303,9896,9899,9986))",
        "cost_info": {
          "read_cost": "78.03",
          "eval_cost": "2.78",
          "prefix_cost": "80.81",
          "data_read_per_join": "666"
        },
        "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)))"
      }
    }
  }
}