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 (
    61084, 61484, 61695, 62019, 59797, 61694, 
    58117, 59417, 64350, 63431, 59877, 
    59892, 59894, 62433, 59893, 64352, 
    62058, 64367, 64366, 62582, 62173, 
    62165, 59407, 63829
  ) 
  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 0.00124

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": 48,
        "selectivity_pct": 1.779095626
      },
      "rows": 48,
      "filtered": 100,
      "index_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (61084,61484,61695,62019,59797,61694,58117,59417,64350,63431,59877,59892,59894,62433,59893,64352,62058,64367,64366,62582,62173,62165,59407,63829) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result