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 (
    2086, 2087, 2088, 2089, 2090, 2091, 2092, 
    2093, 2094, 2095, 2096, 2097, 2098, 
    2099, 2100, 2101, 5722, 5723, 5724, 
    5725, 5726, 5727, 5728, 5729, 5730, 
    5731, 5732, 5733, 5734, 5735, 5736, 
    5737, 5738, 5739, 5740, 5741, 5742, 
    5743, 5744, 5745, 5746, 5747, 5748, 
    5749, 5750, 5751, 5752, 5753
  ) 
  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 0.00087

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (2086,2087,2088,2089,2090,2091,2092,2093,2094,2095,2096,2097,2098,2099,2100,2101,5722,5723,5724,5725,5726,5727,5728,5729,5730,5731,5732,5733,5734,5735,5736,5737,5738,5739,5740,5741,5742,5743,5744,5745,5746,5747,5748,5749,5750,5751,5752,5753))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}