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 (
    5022, 5006, 3927, 4781, 3335, 4961, 5009, 
    3336, 5208, 3954, 3509, 3934, 3961, 
    4006, 5467, 5554, 3958, 5013, 3933, 
    5370, 8789, 3484, 5566, 4824, 4989, 
    5377, 3477, 4821, 5369, 4660, 5188, 
    5567, 4238, 3468, 4005, 4010, 5477, 
    4292, 5866, 5374
  ) 
  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 0.00154

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": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5022,5006,3927,4781,3335,4961,5009,3336,5208,3954,3509,3934,3961,4006,5467,5554,3958,5013,3933,5370,8789,3484,5566,4824,4989,5377,3477,4821,5369,4660,5188,5567,4238,3468,4005,4010,5477,4292,5866,5374))",
        "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": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}