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 (
    5346, 5387, 5309, 5386, 5370, 5369, 5371, 
    5392, 5390, 5372, 11255, 11277, 10956, 
    11280, 11456, 11118, 11131, 10954, 
    11074, 11222, 11102, 11112, 11069, 
    11099, 10955, 11119, 11120, 11311, 
    11057, 11058, 11076, 11091, 11253, 
    11312, 11059, 11098, 11113, 11262, 
    11283, 11314, 11329, 11010, 11012, 
    11060, 11062, 11115, 10961, 11079, 
    11092, 11116, 11285, 11002, 11061, 
    11063, 11066, 11078, 11095, 11097, 
    11114, 11221, 11286, 11379, 11103, 
    11290
  ) 
  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 0.00165

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "89.61"
    },
    "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": 128,
        "rows_produced_per_join": 128,
        "filtered": "100.00",
        "index_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5346,5387,5309,5386,5370,5369,5371,5392,5390,5372,11255,11277,10956,11280,11456,11118,11131,10954,11074,11222,11102,11112,11069,11099,10955,11119,11120,11311,11057,11058,11076,11091,11253,11312,11059,11098,11113,11262,11283,11314,11329,11010,11012,11060,11062,11115,10961,11079,11092,11116,11285,11002,11061,11063,11066,11078,11095,11097,11114,11221,11286,11379,11103,11290)) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "76.81",
          "eval_cost": "12.80",
          "prefix_cost": "89.61",
          "data_read_per_join": "3K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}