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 (
    12654, 12655, 12656, 12657, 12658, 12659, 
    12660, 12661, 12662, 12663, 12664, 
    12665, 12666, 12667, 12668, 12669, 
    12670, 12671, 12672, 12673, 12674, 
    12675, 12676, 12677, 12678, 12679, 
    12680, 12681, 12682, 12683
  ) 
  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 0.00098

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "42.01"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 60,
        "rows_produced_per_join": 60,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (12654,12655,12656,12657,12658,12659,12660,12661,12662,12663,12664,12665,12666,12667,12668,12669,12670,12671,12672,12673,12674,12675,12676,12677,12678,12679,12680,12681,12682,12683)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "36.01",
          "eval_cost": "6.00",
          "prefix_cost": "42.01",
          "data_read_per_join": "1K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}