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 (
    846, 845, 844, 832, 829, 828, 822, 817, 
    816, 662, 814, 806, 805, 804, 803, 802, 
    801, 800, 799, 798, 797, 796, 795, 792, 
    787, 786, 782, 819, 781, 765, 764, 763, 
    762, 760, 758, 752, 751, 750, 749, 747, 
    744, 743, 742, 741, 732, 731, 727, 725
  ) 
  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 0.00099

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "38.56"
    },
    "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": 59,
        "rows_produced_per_join": 11,
        "filtered": "19.93",
        "index_condition": "(`betaatif_store`.`cscart_product_prices`.`product_id` in (846,845,844,832,829,828,822,817,816,662,814,806,805,804,803,802,801,800,799,798,797,796,795,792,787,786,782,819,781,765,764,763,762,760,758,752,751,750,749,747,744,743,742,741,732,731,727,725))",
        "cost_info": {
          "read_cost": "37.38",
          "eval_cost": "1.18",
          "prefix_cost": "38.56",
          "data_read_per_join": "282"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`betaatif_store`.`cscart_product_prices`.`lower_limit` = 1) and (`betaatif_store`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}