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 (
    6959, 3425, 6958, 6960, 13124, 13125, 
    13126, 13098, 13105, 13112, 13118, 
    13064, 13071, 13078, 13085, 13091, 
    12956, 12958, 13014, 13028, 13040, 
    13052, 12960, 12974, 12988, 13000, 
    12926, 12942
  ) 
  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 0.00119

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "39.21"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 56,
        "rows_produced_per_join": 56,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (6959,3425,6958,6960,13124,13125,13126,13098,13105,13112,13118,13064,13071,13078,13085,13091,12956,12958,13014,13028,13040,13052,12960,12974,12988,13000,12926,12942)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "33.61",
          "eval_cost": "5.60",
          "prefix_cost": "39.21",
          "data_read_per_join": "1K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}