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 (
    3826, 3660, 3649, 3733, 3740, 3743, 3944, 
    3741, 3811, 3441, 3653, 3946, 3768, 
    3734, 3821, 3747, 3641, 3952, 3738, 
    3435, 3798, 3443, 3730, 3737, 3638, 
    3655, 3729, 3658, 3851, 3668, 3942, 
    3732, 3448, 3702, 3728, 3852, 3850, 
    3731, 3769, 3642, 3745, 3943, 3623, 
    3670, 3684, 3645, 3437, 3637, 3682, 
    3767, 3950, 3644, 3659, 3766, 3864, 
    3940, 3436, 3739, 3444, 3785, 3442, 
    3787, 3945, 3438, 3770, 3865, 3447, 
    3793, 3450, 3772, 3795, 3788, 3439, 
    3446, 3687, 3860, 3794, 3858, 3869, 
    3948, 3449, 3941, 3871, 3786, 3853, 
    3857, 3863, 3867, 3951, 3862, 3854, 
    3949, 3727, 3699, 3881, 3855, 3859
  ) 
  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 0.00248

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.91"
    },
    "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": 97,
        "rows_produced_per_join": 19,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3826,3660,3649,3733,3740,3743,3944,3741,3811,3441,3653,3946,3768,3734,3821,3747,3641,3952,3738,3435,3798,3443,3730,3737,3638,3655,3729,3658,3851,3668,3942,3732,3448,3702,3728,3852,3850,3731,3769,3642,3745,3943,3623,3670,3684,3645,3437,3637,3682,3767,3950,3644,3659,3766,3864,3940,3436,3739,3444,3785,3442,3787,3945,3438,3770,3865,3447,3793,3450,3772,3795,3788,3439,3446,3687,3860,3794,3858,3869,3948,3449,3941,3871,3786,3853,3857,3863,3867,3951,3862,3854,3949,3727,3699,3881,3855,3859))",
        "cost_info": {
          "read_cost": "65.97",
          "eval_cost": "1.94",
          "prefix_cost": "67.91",
          "data_read_per_join": "465"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}

Result

product_id price
3435 25000.00000000
3436 25000.00000000
3437 36000.00000000
3438 36000.00000000
3439 9000.00000000
3441 9000.00000000
3442 9000.00000000
3443 9000.00000000
3444 9000.00000000
3446 9000.00000000
3447 9000.00000000
3448 12000.00000000
3449 7500.00000000
3450 7500.00000000
3623 12000.00000000
3637 12000.00000000
3638 12000.00000000
3641 9000.00000000
3642 9000.00000000
3644 9000.00000000
3645 9000.00000000
3649 10000.00000000
3653 60000.00000000
3655 7500.00000000
3658 7500.00000000
3659 7500.00000000
3660 7500.00000000
3668 18000.00000000
3670 20000.00000000
3682 10000.00000000
3684 10000.00000000
3687 6000.00000000
3699 5000.00000000
3702 8000.00000000
3727 5000.00000000
3728 7500.00000000
3729 7500.00000000
3730 7500.00000000
3731 7500.00000000
3732 7500.00000000
3733 7500.00000000
3734 7500.00000000
3737 6000.00000000
3738 6000.00000000
3739 6000.00000000
3740 6000.00000000
3741 6000.00000000
3743 6000.00000000
3745 4500.00000000
3747 4500.00000000
3766 4500.00000000
3767 4500.00000000
3768 4500.00000000
3769 4500.00000000
3770 4500.00000000
3772 4500.00000000
3785 4500.00000000
3786 4500.00000000
3787 4500.00000000
3788 4500.00000000
3793 4500.00000000
3794 4500.00000000
3795 4500.00000000
3798 5000.00000000
3811 8000.00000000
3821 18000.00000000
3826 8000.00000000
3850 6000.00000000
3851 6000.00000000
3852 6000.00000000
3853 8000.00000000
3854 18000.00000000
3855 20000.00000000
3857 8000.00000000
3858 18000.00000000
3859 20000.00000000
3860 8000.00000000
3862 14000.00000000
3863 20000.00000000
3864 4500.00000000
3865 4500.00000000
3867 10000.00000000
3869 10000.00000000
3871 12000.00000000
3881 12000.00000000
3940 10000.00000000
3941 10000.00000000
3942 18000.00000000
3943 18000.00000000
3944 60000.00000000
3945 67500.00000000
3946 60000.00000000
3948 25000.00000000
3949 25000.00000000
3950 25000.00000000
3951 25000.00000000
3952 10000.00000000