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 (
    12424, 12425, 12426, 12427, 12428, 12429, 
    12430, 12431, 12432, 12433, 12434, 
    12435, 12436, 12437, 12438, 12439, 
    12440, 12441, 12442, 12443, 12444, 
    12445, 12446, 12447, 12448, 12449, 
    12450, 12451, 12452, 12453, 12454, 
    12455, 12456, 12457, 12458, 12459, 
    12460, 12461, 12462, 12463
  ) 
  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 0.00097

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "28.01"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 40,
        "rows_produced_per_join": 7,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (12424,12425,12426,12427,12428,12429,12430,12431,12432,12433,12434,12435,12436,12437,12438,12439,12440,12441,12442,12443,12444,12445,12446,12447,12448,12449,12450,12451,12452,12453,12454,12455,12456,12457,12458,12459,12460,12461,12462,12463))",
        "cost_info": {
          "read_cost": "27.21",
          "eval_cost": "0.80",
          "prefix_cost": "28.01",
          "data_read_per_join": "191"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}