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 (
    61697, 60899, 61698, 61490, 61699, 62020, 
    62038, 64772, 61399, 62039, 64773, 
    62056, 62436, 64774, 64756, 62062, 
    64792, 64788, 64905, 64784, 64899, 
    65559, 65090, 64870
  ) 
  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 0.00172

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 (61697,60899,61698,61490,61699,62020,62038,64772,61399,62039,64773,62056,62436,64774,64756,62062,64792,64788,64905,64784,64899,65559,65090,64870) and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}

Result