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 (
    4159, 4160, 4161, 4162, 4209, 4210, 4211, 
    4212, 4213, 4214, 4215, 3102, 3110, 
    6670, 6685, 6698, 3095, 3101, 3108, 
    6683, 6697, 12594, 12609, 3099, 19, 
    20, 21, 3929, 3930, 3931, 12424, 12554, 
    12536, 12546, 6724, 3100, 3106, 3114, 
    3120, 3125, 3153, 3154, 6672, 6688, 
    6689, 6694, 6702, 6706
  ) 
  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 0.00207

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": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (4159,4160,4161,4162,4209,4210,4211,4212,4213,4214,4215,3102,3110,6670,6685,6698,3095,3101,3108,6683,6697,12594,12609,3099,19,20,21,3929,3930,3931,12424,12554,12536,12546,6724,3100,3106,3114,3120,3125,3153,3154,6672,6688,6689,6694,6702,6706))",
        "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": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}