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, 3308, 3397, 3841, 3212, 3928, 3660, 
    3828, 3518, 3918, 3400, 3232, 3740, 
    3743, 3741, 3440, 3441, 10078, 3768, 
    3747, 3406, 3827, 3738, 3403, 3443, 
    3737, 3655, 3658, 3769, 3745, 3767, 
    3950, 3659, 3766, 3739, 3444, 3785, 
    3442, 3787, 3770, 3447, 3793, 3450, 
    3772, 3795, 3788, 3439, 3446, 3794, 
    3948, 3449, 3871, 3786, 3867, 3951, 
    3949, 3881, 11629, 8597, 8280, 8443, 
    8596, 11632, 8405, 8584, 8588, 8437, 
    8515, 8542, 10446, 10492, 11623, 11624, 
    11625, 11626, 11627, 11628, 11631
  ) 
  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 0.00187

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "86.56"
    },
    "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": 149,
        "rows_produced_per_join": 29,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3354,3308,3397,3841,3212,3928,3660,3828,3518,3918,3400,3232,3740,3743,3741,3440,3441,10078,3768,3747,3406,3827,3738,3403,3443,3737,3655,3658,3769,3745,3767,3950,3659,3766,3739,3444,3785,3442,3787,3770,3447,3793,3450,3772,3795,3788,3439,3446,3794,3948,3449,3871,3786,3867,3951,3949,3881,11629,8597,8280,8443,8596,11632,8405,8584,8588,8437,8515,8542,10446,10492,11623,11624,11625,11626,11627,11628,11631))",
        "cost_info": {
          "read_cost": "83.58",
          "eval_cost": "2.98",
          "prefix_cost": "86.56",
          "data_read_per_join": "714"
        },
        "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)))"
      }
    }
  }
}