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 (
    211, 
    210, 
    209, 
    67, 
    25, 
    116, 
    213, 
    215, 
    226, 
    200, 
    154, 
    53, 
    52, 
    111, 
    82, 
    84, 
    228, 
    85, 
    88, 
    287, 
    315, 
    26, 
    35, 
    47, 
    81, 
    107, 
    109, 
    91, 
    92, 
    161, 
    188, 
    202, 
    203, 
    34, 
    31, 
    38, 
    80, 
    165, 
    166, 
    86, 
    106, 
    105, 
    247, 
    101, 
    33, 
    32, 
    163, 
    244, 
    212, 
    155, 
    102, 
    55, 
    176, 
    69, 
    138, 
    110, 
    36, 
    206, 
    28, 
    184, 
    183, 
    133, 
    132, 
    125, 
    120, 
    223, 
    225, 
    224, 
    146, 
    147, 
    93, 
    117, 
    219, 
    222, 
    220, 
    221, 
    87, 
    113, 
    139, 
    118, 
    83, 
    157, 
    286, 
    123, 
    174, 
    171, 
    280, 
    282, 
    278, 
    331, 
    335, 
    339, 
    341, 
    355, 
    356, 
    357, 
    358, 
    359, 
    360, 
    361, 
    362, 
    363, 
    364, 
    365, 
    366, 
    367, 
    368, 
    369, 
    370, 
    379, 
    380, 
    381, 
    382, 
    383, 
    384, 
    385, 
    386, 
    387, 
    388, 
    389, 
    390, 
    391, 
    392, 
    393, 
    394, 
    395, 
    396, 
    397
  ) 
  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 0.00143

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "336.45"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "cost_info": {
        "sort_cost": "256.00"
      },
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "ALL",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "rows_examined_per_scan": 383,
        "rows_produced_per_join": 256,
        "filtered": "66.84",
        "cost_info": {
          "read_cost": "29.26",
          "eval_cost": "51.20",
          "prefix_cost": "80.46",
          "data_read_per_join": "6K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`pankajecarter_systemfour`.`cscart_product_prices`.`lower_limit` = 1) and (`pankajecarter_systemfour`.`cscart_product_prices`.`product_id` in (211,210,209,67,25,116,213,215,226,200,154,53,52,111,82,84,228,85,88,287,315,26,35,47,81,107,109,91,92,161,188,202,203,34,31,38,80,165,166,86,106,105,247,101,33,32,163,244,212,155,102,55,176,69,138,110,36,206,28,184,183,133,132,125,120,223,225,224,146,147,93,117,219,222,220,221,87,113,139,118,83,157,286,123,174,171,280,282,278,331,335,339,341,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397)) and (`pankajecarter_systemfour`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}

Result

product_id price
25 599.99000000
26 34.99000000
28 100.00000000
31 32.00000000
32 299.99000000
33 169.99000000
34 25.00000000
35 31.99000000
36 51.00000000
38 16.97000000
47 29.99000000
52 139.99000000
53 38.99000000
55 359.00000000
67 339.99000000
69 529.99000000
80 55.00000000
81 49.50000000
82 19.99000000
83 19.99000000
84 19.99000000
85 19.99000000
86 359.00000000
87 19.99000000
88 39.99000000
91 10700.00000000
92 3225.00000000
93 19.99000000
101 188.88000000
102 295.00000000
105 169.99000000
106 179.99000000
107 465.00000000
109 140.00000000
110 15.99000000
111 6.99000000
113 449.99000000
116 6.99000000
117 729.99000000
118 30.99000000
120 199.99000000
123 17.99000000
125 149.99000000
132 269.99000000
133 229.99000000
138 0.00000000
139 0.00000000
146 44.99000000
147 44.99000000
154 399.99000000
155 79.99000000
157 499.00000000
161 279.99000000
163 899.99000000
165 599.95000000
166 749.95000000
171 499.00000000
174 100.75000000
176 648.95000000
183 249.99000000
184 299.99000000
188 10.00000000
200 26.92000000
202 34.68000000
203 34.68000000
206 179.99000000
209 109.99000000
210 89.99000000
211 299.99000000
212 129.95000000
213 295.00000000
215 1095.00000000
219 529.99000000
220 1099.99000000
221 2049.00000000
222 529.99000000
223 499.99000000
224 479.99000000
225 199.99000000
226 269.99000000
228 349.99000000
244 729.99000000
247 329.49000000
278 75.00000000
280 50.00000000
282 75.00000000
286 12000.00000000
287 10000.00000000
315 10000.00000000
331 1200.00000000
335 1200.00000000
339 1200.00000000
341 1200.00000000
355 10200.00000000
356 10200.00000000
357 1200.00000000
358 1200.00000000
359 1200.00000000
360 1200.00000000
361 1200.00000000
362 1200.00000000
363 10200.00000000
364 10200.00000000
365 1200.00000000
366 1200.00000000
367 1200.00000000
368 1200.00000000
369 1200.00000000
370 1200.00000000
379 1200.00000000
380 1200.00000000
381 1200.00000000
382 1200.00000000
383 1200.00000000
384 1200.00000000
385 1200.00000000
386 1200.00000000
387 1200.00000000
388 1200.00000000
389 1200.00000000
390 1200.00000000
391 1200.00000000
392 1200.00000000
393 1200.00000000
394 1200.00000000
395 1200.00000000
396 1200.00000000
397 1200.00000000