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 (
    12520, 12497, 12528, 12512, 12511, 12527, 
    10580, 10579, 9936, 9931, 12521, 12504, 
    12502, 12505, 13099, 12514, 12513, 
    9759, 10496, 10560, 10561, 10581, 10102, 
    9940, 10578, 10143, 9947, 10567, 10568, 
    10565, 9933, 12499, 12500, 10200, 10201, 
    10566, 10545, 10227, 10552, 12506, 
    10693, 12508, 9953, 12522, 12507, 12498, 
    13101, 13100, 10699, 10695, 10195, 
    10576, 10696, 9760, 10583, 10701, 10582, 
    10139, 12503, 10575, 9932, 10075, 10135, 
    9952, 10074, 10573, 10577, 10651, 10642, 
    12529, 12515, 12525, 12532, 12523, 
    10198, 10557, 10202, 10556, 10101, 
    10558, 10142, 10134, 10141, 10053, 
    10138, 10130, 9934, 10563, 10569, 10572, 
    10602, 10603, 10137, 12517, 12531, 
    12526, 12509, 10226, 10551, 10550, 
    10193, 10659, 10664, 10666, 10661, 
    10663, 10190, 10657, 10658, 10194, 
    10692, 12530, 12516, 12496, 12519, 
    12510, 10087, 10100, 10698
  ) 
  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 0.00153

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": 119,
      "filtered": 99.23484039,
      "index_condition": "cscart_product_prices.product_id in (12520,12497,12528,12512,12511,12527,10580,10579,9936,9931,12521,12504,12502,12505,13099,12514,12513,9759,10496,10560,10561,10581,10102,9940,10578,10143,9947,10567,10568,10565,9933,12499,12500,10200,10201,10566,10545,10227,10552,12506,10693,12508,9953,12522,12507,12498,13101,13100,10699,10695,10195,10576,10696,9760,10583,10701,10582,10139,12503,10575,9932,10075,10135,9952,10074,10573,10577,10651,10642,12529,12515,12525,12532,12523,10198,10557,10202,10556,10101,10558,10142,10134,10141,10053,10138,10130,9934,10563,10569,10572,10602,10603,10137,12517,12531,12526,12509,10226,10551,10550,10193,10659,10664,10666,10661,10663,10190,10657,10658,10194,10692,12530,12516,12496,12519,12510,10087,10100,10698)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
9759 1955.00000000
9760 1754.00000000
9931 1331.00000000
9932 1563.00000000
9933 1563.00000000
9934 2039.00000000
9936 1331.00000000
9940 2142.00000000
9947 2022.00000000
9952 2041.00000000
9953 1960.00000000
10053 1955.00000000
10074 2369.00000000
10075 2369.00000000
10087 1635.00000000
10100 1635.00000000
10101 2405.00000000
10102 2142.00000000
10130 2121.00000000
10134 2121.00000000
10135 2041.00000000
10137 1924.00000000
10138 1955.00000000
10139 2338.00000000
10141 2153.00000000
10142 2121.00000000
10143 2205.00000000
10190 2257.00000000
10193 2325.00000000
10194 2257.00000000
10195 1815.00000000
10198 2405.00000000
10200 2234.00000000
10201 2234.00000000
10202 2405.00000000
10226 1524.00000000
10227 1997.00000000
10496 1955.00000000
10545 2143.00000000
10550 1995.00000000
10551 1995.00000000
10552 2143.00000000
10556 2658.00000000
10557 2658.00000000
10558 2658.00000000
10560 2098.00000000
10561 2098.00000000
10563 2039.00000000
10565 2691.00000000
10566 2089.00000000
10567 2691.00000000
10568 2691.00000000
10569 2325.00000000
10572 2325.00000000
10573 2369.00000000
10575 2210.00000000
10576 1815.00000000
10577 2041.00000000
10578 2205.00000000
10579 1791.00000000
10580 1791.00000000
10581 2142.00000000
10582 1754.00000000
10583 1754.00000000
10602 1885.00000000
10603 2517.00000000
10642 2369.00000000
10651 2041.00000000
10657 2671.00000000
10658 2671.00000000
10659 2686.00000000
10661 2262.00000000
10663 2262.00000000
10664 2325.00000000
10666 2325.00000000
10692 2671.00000000
10693 2089.00000000
10695 1848.00000000
10696 1840.00000000
10698 1635.00000000
10699 1551.00000000
10701 1840.00000000
12496 0.00000000
12497 0.00000000
12498 0.00000000
12499 0.00000000
12500 0.00000000
12502 0.00000000
12503 0.00000000
12504 0.00000000
12505 0.00000000
12506 0.00000000
12507 0.00000000
12508 0.00000000
12509 0.00000000
12510 0.00000000
12511 0.00000000
12512 0.00000000
12513 0.00000000
12514 0.00000000
12515 0.00000000
12516 0.00000000
12517 0.00000000
12519 0.00000000
12520 0.00000000
12521 0.00000000
12522 0.00000000
12523 0.00000000
12525 0.00000000
12526 0.00000000
12527 0.00000000
12528 0.00000000
12529 0.00000000
12530 0.00000000
12531 0.00000000
12532 0.00000000
13099 0.00000000
13100 0.00000000
13101 0.00000000