SELECT 
  product_prices.product_id, 
  MIN(
    IF(
      product_prices.percentage_discount = 0, 
      product_prices.price, 
      product_prices.price - (
        product_prices.price * product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  product_prices 
WHERE 
  product_prices.product_id IN (
    61531, 61355, 61660, 61673, 61532, 61671, 
    61688, 40769, 40774, 40778, 40785, 
    61699, 40810, 62983, 43856, 40771, 
    40789, 61704, 61690, 310237, 310332, 
    310242, 310266, 310338, 310236, 310335, 
    310329, 310330, 310336, 310241, 310328, 
    310334, 310331, 310333, 310238, 310239, 
    310240, 310337
  ) 
  AND product_prices.lower_limit = 1 
  AND product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  product_prices.product_id

Query time 0.00299

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "31.26"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "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": 38,
        "rows_produced_per_join": 3,
        "filtered": "10.00",
        "index_condition": "(`goimagine`.`product_prices`.`product_id` in (61531,61355,61660,61673,61532,61671,61688,40769,40774,40778,40785,61699,40810,62983,43856,40771,40789,61704,61690,310237,310332,310242,310266,310338,310236,310335,310329,310330,310336,310241,310328,310334,310331,310333,310238,310239,310240,310337))",
        "cost_info": {
          "read_cost": "30.89",
          "eval_cost": "0.38",
          "prefix_cost": "31.27",
          "data_read_per_join": "91"
        },
        "used_columns": [
          "id",
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`goimagine`.`product_prices`.`lower_limit` = 1) and (`goimagine`.`product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}