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
  ) 
  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 0.00094

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": 32,
      "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)",
      "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
12555 41728.72000000
12556 41728.72000000
12557 52280.84000000
12558 82018.56000000
12560 67629.15000000
12561 67629.15000000
12564 67629.15000000
12565 67629.15000000
12567 10552.12000000
12568 10552.12000000
12569 10552.12000000
12570 11031.68000000
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
12583 41728.72000000
12584 41160.00000000
12592 64680.00000000
12633 67629.15000000