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 (
    3920, 3921, 3968, 3969, 3970, 3971, 3972, 
    3973, 3974, 4020, 4021, 4022, 4023, 
    4024, 4025, 4026, 4094, 4095, 4096, 
    4097, 4098, 4099, 4100, 4101, 4102, 
    4103, 4104, 4105, 4106, 4107, 4163, 
    4164, 4165, 4166, 4167, 4168, 4169, 
    4216, 4217, 4218, 4219, 4220, 4221, 
    4222, 196, 197, 198, 199
  ) 
  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 0.00093

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 (3920,3921,3968,3969,3970,3971,3972,3973,3974,4020,4021,4022,4023,4024,4025,4026,4094,4095,4096,4097,4098,4099,4100,4101,4102,4103,4104,4105,4106,4107,4163,4164,4165,4166,4167,4168,4169,4216,4217,4218,4219,4220,4221,4222,196,197,198,199))",
        "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)))"
      }
    }
  }
}