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 (
    51480, 51479, 51494, 51495, 132, 112, 
    3, 78, 2, 77, 87, 66, 22421, 22424, 22290, 
    50981, 50982, 133, 45, 143, 50983, 51416, 
    51043, 51421, 51471, 51413, 51057, 
    51472, 51547, 51470, 51500, 51412
  ) 
  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 0.00064

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "25.56"
    },
    "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": 39,
        "rows_produced_per_join": 7,
        "filtered": "19.96",
        "index_condition": "(`test_uchur_k`.`cscart_product_prices`.`product_id` in (51480,51479,51494,51495,132,112,3,78,2,77,87,66,22421,22424,22290,50981,50982,133,45,143,50983,51416,51043,51421,51471,51413,51057,51472,51547,51470,51500,51412))",
        "cost_info": {
          "read_cost": "24.78",
          "eval_cost": "0.78",
          "prefix_cost": "25.56",
          "data_read_per_join": "186"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test_uchur_k`.`cscart_product_prices`.`lower_limit` = 1) and (`test_uchur_k`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}