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 (
    40744, 40745, 40758, 40759, 40761, 40768, 
    40769, 40770, 40776, 40788, 40789, 
    40790, 40791, 40792, 40793, 40794, 
    40795, 40796, 40809, 40821, 40827, 
    40828, 40829, 40830, 40831, 40832, 
    40833, 40834, 40835, 40836, 40837, 
    40839
  ) 
  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 0.00104

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "78.21"
    },
    "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": 33,
        "rows_produced_per_join": 6,
        "filtered": "19.99",
        "index_condition": "(`portal`.`q_product_prices`.`product_id` in (40744,40745,40758,40759,40761,40768,40769,40770,40776,40788,40789,40790,40791,40792,40793,40794,40795,40796,40809,40821,40827,40828,40829,40830,40831,40832,40833,40834,40835,40836,40837,40839))",
        "cost_info": {
          "read_cost": "76.89",
          "eval_cost": "1.32",
          "prefix_cost": "78.21",
          "data_read_per_join": "158"
        },
        "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)))"
      }
    }
  }
}