$string = '(1,(1,2,(1,(1,2,(1)),3)),3,(1,(1,2,((1,((1,(1,2,(1,2,3),4,5),3),2)),2)),((1,2,3),2,3),4,5),5)';

$result = $previous = [];

$current = $number = null;

$i = 0;

while ( isset($string[$i]) ) {

    $value = $string[$i];

    switch ($value) {

        case '(':

            if ( is_null($current) ) {

                $current = &$result;

            } else {

                $previous[] = &$current;

                $current[] = [];

                $current = &$current[count($current) - 1];

            }

            break;

        case ')':

            if ( !is_null($number) ) {

                $current[] = intval($number);

                $number = null;

            }

            $last = count($previous) - 1;

            $current = &$previous[$last];

            array_pop($previous);

            break;

        case ',':

            if ( !is_null($number) ) {

                $current[] = intval($number);

                $number = null;

            }

            break;

        default:

            $number .= $value;

            break;

    }

    $i++;

}

echo json_encode($result);