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 (
    2099, 2199, 2200, 1948, 2095, 2100, 2124, 
    2101, 2134, 2198, 2291, 2103, 2307, 
    2166, 2208, 2102, 2104, 2345, 2143, 
    2119, 2144, 2362, 2016, 2319, 1999, 
    2019, 2321, 2322, 2018, 1928, 2017, 
    1998, 2020, 2071, 2320, 2333, 2080, 
    2325, 2113, 2324
  ) 
  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 0.00045

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "28.46"
    },
    "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": 41,
        "rows_produced_per_join": 8,
        "filtered": "19.99",
        "index_condition": "(`cscartdevel`.`cscart_product_prices`.`product_id` in (2099,2199,2200,1948,2095,2100,2124,2101,2134,2198,2291,2103,2307,2166,2208,2102,2104,2345,2143,2119,2144,2362,2016,2319,1999,2019,2321,2322,2018,1928,2017,1998,2020,2071,2320,2333,2080,2325,2113,2324))",
        "cost_info": {
          "read_cost": "27.64",
          "eval_cost": "0.82",
          "prefix_cost": "28.46",
          "data_read_per_join": "196"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`cscartdevel`.`cscart_product_prices`.`lower_limit` = 1) and (`cscartdevel`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}