SELECT 
  q_product_prices.product_id, 
  MIN(
    IF(
      q_product_prices.percentage_discount = 0, 
      q_product_prices.price, 
      q_product_prices.price - (
        q_product_prices.price * q_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  q_product_prices 
WHERE 
  q_product_prices.product_id IN (
    40981, 40982, 40983, 40984, 40985, 40986, 
    40987, 40988, 40989, 40990, 40991, 
    40992, 40993, 40994, 40995, 40996, 
    40997, 40998, 40999, 41000, 41001, 
    41002, 41003, 41004, 41005, 41006, 
    41007, 41008, 41009, 41010, 41011, 
    41012
  ) 
  AND q_product_prices.lower_limit = 1 
  AND q_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  q_product_prices.product_id

Query time 0.00084

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "81.01"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "q_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": 35,
        "rows_produced_per_join": 6,
        "filtered": "19.99",
        "index_condition": "(`portal`.`q_product_prices`.`product_id` in (40981,40982,40983,40984,40985,40986,40987,40988,40989,40990,40991,40992,40993,40994,40995,40996,40997,40998,40999,41000,41001,41002,41003,41004,41005,41006,41007,41008,41009,41010,41011,41012))",
        "cost_info": {
          "read_cost": "79.61",
          "eval_cost": "1.40",
          "prefix_cost": "81.01",
          "data_read_per_join": "167"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`portal`.`q_product_prices`.`lower_limit` = 1) and (`portal`.`q_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}