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 (
    3354, 3834, 3308, 3306, 3841, 3212, 3226, 
    3350, 3218, 3392, 3301, 3751, 3828, 
    3520, 3529, 3809, 3518, 3918, 3215, 
    3213, 3597, 3752, 3552, 3836, 3232, 
    3589, 3556, 3845, 3822, 3370, 3843, 
    3840, 3882, 3377, 3373, 3593, 3551, 
    3831, 3519, 3919, 3356, 3404, 3366, 
    3222, 3522, 3401, 3358, 3537, 3291, 
    3225, 3844, 3876, 3559, 3917, 3528, 
    3819, 3922, 3534, 3531, 3812, 3372, 
    3374, 3309, 3590, 3351, 3532, 3546, 
    3827, 3548, 3521, 3355, 3398, 3357, 
    3369, 3807, 3525, 3408, 3746, 3393, 
    3744
  ) 
  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 0.00266

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.01"
    },
    "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": 80,
        "rows_produced_per_join": 15,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3354,3834,3308,3306,3841,3212,3226,3350,3218,3392,3301,3751,3828,3520,3529,3809,3518,3918,3215,3213,3597,3752,3552,3836,3232,3589,3556,3845,3822,3370,3843,3840,3882,3377,3373,3593,3551,3831,3519,3919,3356,3404,3366,3222,3522,3401,3358,3537,3291,3225,3844,3876,3559,3917,3528,3819,3922,3534,3531,3812,3372,3374,3309,3590,3351,3532,3546,3827,3548,3521,3355,3398,3357,3369,3807,3525,3408,3746,3393,3744))",
        "cost_info": {
          "read_cost": "54.41",
          "eval_cost": "1.60",
          "prefix_cost": "56.01",
          "data_read_per_join": "383"
        },
        "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
3212 4000.00000000
3213 6000.00000000
3215 12000.00000000
3218 12000.00000000
3222 13000.00000000
3225 14000.00000000
3226 15000.00000000
3232 15000.00000000
3291 17000.00000000
3301 21000.00000000
3306 21000.00000000
3308 21000.00000000
3309 22000.00000000
3350 25000.00000000
3351 25000.00000000
3354 28000.00000000
3355 29000.00000000
3356 31000.00000000
3357 33000.00000000
3358 37000.00000000
3366 42000.00000000
3369 44000.00000000
3370 46000.00000000
3372 47000.00000000
3373 55000.00000000
3374 56000.00000000
3377 65000.00000000
3392 67000.00000000
3393 71000.00000000
3398 89000.00000000
3401 102000.00000000
3404 107000.00000000
3408 107000.00000000
3518 7000.00000000
3519 11000.00000000
3520 12000.00000000
3521 12000.00000000
3522 13000.00000000
3525 14000.00000000
3528 15000.00000000
3529 15000.00000000
3531 16000.00000000
3532 17000.00000000
3534 18000.00000000
3537 22000.00000000
3546 29000.00000000
3548 29000.00000000
3551 31000.00000000
3552 28000.00000000
3556 44000.00000000
3559 47000.00000000
3589 47000.00000000
3590 49000.00000000
3593 55000.00000000
3597 61000.00000000
3744 75000.00000000
3746 89000.00000000
3751 205000.00000000
3752 261000.00000000
3807 11000.00000000
3809 12000.00000000
3812 17000.00000000
3819 17000.00000000
3822 17000.00000000
3827 22000.00000000
3828 23000.00000000
3831 25000.00000000
3834 25000.00000000
3836 27000.00000000
3840 28000.00000000
3841 28000.00000000
3843 28000.00000000
3844 29000.00000000
3845 31000.00000000
3876 40000.00000000
3882 84000.00000000
3917 89000.00000000
3918 89000.00000000
3919 92000.00000000
3922 273000.00000000