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 (
    64941, 62258, 60732, 60733, 60737, 64621, 
    61385, 64942, 60751, 60735, 64943, 
    64339, 63128, 60738, 62671, 64340, 
    61386, 64620, 64815, 65519, 65568, 
    65851, 65870, 65875, 65853, 65864, 
    65877, 65874, 65863, 65869, 65868, 
    65862, 65850, 65880, 65852, 65855, 
    65854, 65866, 65857, 65876, 65858, 
    65856, 65860, 65859, 65861
  ) 
  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 0.00316

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": "9",
      "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
      "rowid_filter": {
        "range": {
          "key": "lower_limit",
          "used_key_parts": ["lower_limit", "product_id", "usergroup_id"]
        },
        "rows": 90,
        "selectivity_pct": 3.335804299
      },
      "rows": 90,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (64941,62258,60732,60733,60737,64621,61385,64942,60751,60735,64943,64339,63128,60738,62671,64340,61386,64620,64815,65519,65568,65851,65870,65875,65853,65864,65877,65874,65863,65869,65868,65862,65850,65880,65852,65855,65854,65866,65857,65876,65858,65856,65860,65859,65861) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result