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 (
    3927, 3928, 3976, 3977, 3978, 3979, 3980, 
    3981, 3982, 4028, 4029, 4030, 4031, 
    4032, 4033, 4034, 4035, 4036, 4037, 
    4038, 4039, 4040, 4041, 4117, 4118, 
    4119, 4120, 4121, 4122, 4123, 4171, 
    4172, 4173, 4174, 4175, 4176, 50, 51, 
    52, 53, 54, 55, 56, 97, 98, 99, 100, 101
  ) 
  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 0.00103

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 (3927,3928,3976,3977,3978,3979,3980,3981,3982,4028,4029,4030,4031,4032,4033,4034,4035,4036,4037,4038,4039,4040,4041,4117,4118,4119,4120,4121,4122,4123,4171,4172,4173,4174,4175,4176,50,51,52,53,54,55,56,97,98,99,100,101))",
        "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)))"
      }
    }
  }
}