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 (
    3715, 3716, 3717, 3718, 3708, 3152, 25, 
    1365, 3138, 3149, 6719, 3146, 3150, 
    1345, 1346, 1347, 1348, 1349, 1350, 
    1351, 1352, 1353, 1354, 3698, 3699, 
    3700, 3701, 3702, 3703, 3704, 3705, 
    3706, 3707, 6723, 6717, 6720, 3151, 
    3864, 3145, 6721, 3863, 3148, 6718, 
    6722, 3144, 3147, 3096, 339
  ) 
  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 0.00116

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 (3715,3716,3717,3718,3708,3152,25,1365,3138,3149,6719,3146,3150,1345,1346,1347,1348,1349,1350,1351,1352,1353,1354,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,6723,6717,6720,3151,3864,3145,6721,3863,3148,6718,6722,3144,3147,3096,339))",
        "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)))"
      }
    }
  }
}