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 (
    5378, 5383, 5379, 5381, 5380, 5382, 5384, 
    5385, 6371, 6356, 6277, 6393, 6394, 
    6332, 6362, 6392, 6354, 6331, 6337, 
    6395, 6423, 6364, 6359, 6330, 6355, 
    6396, 6372, 6398, 6358, 6365, 6361, 
    6397, 6360
  ) 
  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 0.00094

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "23.11"
    },
    "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": 33,
        "rows_produced_per_join": 6,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5378,5383,5379,5381,5380,5382,5384,5385,6371,6356,6277,6393,6394,6332,6362,6392,6354,6331,6337,6395,6423,6364,6359,6330,6355,6396,6372,6398,6358,6365,6361,6397,6360))",
        "cost_info": {
          "read_cost": "22.45",
          "eval_cost": "0.66",
          "prefix_cost": "23.11",
          "data_read_per_join": "158"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}