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 (
    1356, 1357, 1358, 1359, 1360, 1361, 1362, 
    1363, 1364, 3688, 3689, 3690, 3691, 
    3692, 3693, 3694, 3695, 3696, 3697, 
    3709, 3710, 3711, 3712, 3713, 3714, 
    3715, 3716, 3717, 3718, 3708, 3152, 
    25, 1365, 3138, 3149, 6719, 3146, 3150, 
    1345, 1346, 1347, 1348, 1349, 1350, 
    1351, 1352, 1353, 1354
  ) 
  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 0.00129

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": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (1356,1357,1358,1359,1360,1361,1362,1363,1364,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3709,3710,3711,3712,3713,3714,3715,3716,3717,3718,3708,3152,25,1365,3138,3149,6719,3146,3150,1345,1346,1347,1348,1349,1350,1351,1352,1353,1354))",
        "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": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}