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 (
    12546, 12633, 12573, 12548, 12580, 12576, 
    12565, 12567, 12549, 12581, 12557, 
    12558, 12570, 12578, 12568, 12547, 
    12569, 12584, 12592, 12575, 12574, 
    12550, 12544, 12564, 12577, 12579, 
    12555, 12560, 12556, 12561, 12572, 
    12583, 12591, 12582, 12590, 12571, 
    12632, 12559, 12631, 15938, 13091, 
    12551, 12638, 12634, 12636, 12635, 
    12599, 12627, 12600, 12639, 15800, 
    12595, 12587, 12593, 12620, 12623, 
    12619, 12585, 12616, 12601, 12628, 
    12602, 12640, 12647
  ) 
  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 0.00093

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 64,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (12546,12633,12573,12548,12580,12576,12565,12567,12549,12581,12557,12558,12570,12578,12568,12547,12569,12584,12592,12575,12574,12550,12544,12564,12577,12579,12555,12560,12556,12561,12572,12583,12591,12582,12590,12571,12632,12559,12631,15938,13091,12551,12638,12634,12636,12635,12599,12627,12600,12639,15800,12595,12587,12593,12620,12623,12619,12585,12616,12601,12628,12602,12640,12647)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
12544 41728.72000000
12546 67629.15000000
12547 67629.15000000
12548 52280.84000000
12549 43647.16000000
12550 47964.00000000
12551 15215.00000000
12555 41728.72000000
12556 41728.72000000
12557 52280.84000000
12558 82018.56000000
12559 48683.54000000
12560 67629.15000000
12561 67629.15000000
12564 67629.15000000
12565 67629.15000000
12567 10552.12000000
12568 10552.12000000
12569 10552.12000000
12570 11031.68000000
12571 67629.15000000
12572 42208.28000000
12573 68108.92000000
12574 78181.27000000
12575 47964.00000000
12576 41728.72000000
12577 42208.28000000
12578 36540.00000000
12579 10072.36000000
12580 11031.68000000
12581 70507.12000000
12582 41728.72000000
12583 41728.72000000
12584 41160.00000000
12585 209523.67000000
12587 209523.67000000
12590 67629.15000000
12591 67629.15000000
12592 64680.00000000
12593 349146.47000000
12595 131354.16000000
12599 14092.68000000
12600 4597.28000000
12601 14092.68000000
12602 4597.28000000
12616 15852.84000000
12619 131354.16000000
12620 131354.16000000
12623 209523.67000000
12627 21943.06000000
12628 21943.06000000
12631 41728.72000000
12632 67629.15000000
12633 67629.15000000
12634 25398.80000000
12635 25398.80000000
12636 46725.90000000
12638 19593.76000000
12639 19593.76000000
12640 19593.76000000
12647 33378.35000000
13091 6750.00000000
15800 33378.35000000
15938 4889.00000000