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 (
    1368, 1321, 1367, 1366, 1365, 1364, 1363, 
    1362, 1361, 1360, 1359, 1358, 1357, 
    1356, 1355, 1354, 1353, 1352, 1351, 
    1350, 1349, 1348, 1346, 1036, 1345, 
    1335, 1344, 1343, 1336, 1334, 1333, 
    1332, 1331, 1329, 1328, 1327, 1326, 
    1325, 1323, 1322, 1320, 1300, 1301, 
    1302, 1303, 1312, 1304, 1305
  ) 
  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 0.00174

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": 48,
      "filtered": 9.795915604,
      "index_condition": "cscart_product_prices.product_id in (1368,1321,1367,1366,1365,1364,1363,1362,1361,1360,1359,1358,1357,1356,1355,1354,1353,1352,1351,1350,1349,1348,1346,1036,1345,1335,1344,1343,1336,1334,1333,1332,1331,1329,1328,1327,1326,1325,1323,1322,1320,1300,1301,1302,1303,1312,1304,1305)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result

product_id price
1036 350000.00000000
1300 32000.00000000
1301 63000.00000000
1302 0.00000000
1303 0.00000000
1304 62000.00000000
1305 82000.00000000
1312 0.00000000
1320 22000.00000000
1321 20000.00000000
1322 52000.00000000
1323 110000.00000000
1325 130000.00000000
1326 12000.00000000
1327 12000.00000000
1328 12000.00000000
1329 9000.00000000
1331 68000.00000000
1332 138000.00000000
1333 138000.00000000
1334 138000.00000000
1335 230000.00000000
1336 60000.00000000
1343 116000.00000000
1344 35000.00000000
1345 300000.00000000
1346 0.00000000
1348 57000.00000000
1349 67000.00000000
1350 0.00000000
1351 0.00000000
1352 0.00000000
1353 0.00000000
1354 0.00000000
1355 0.00000000
1356 0.00000000
1357 0.00000000
1358 0.00000000
1359 0.00000000
1360 0.00000000
1361 0.00000000
1362 0.00000000
1363 0.00000000
1364 0.00000000
1365 0.00000000
1366 0.00000000
1367 0.00000000
1368 20000.00000000