macOS Sierra 10.12.4 Update Problem (extremely slow)

I regularly update my MacBook Pro. I usually don't abuse my laptop. There is enough RAM and space. There is no overhead on the CPU. I've checked that in the activity monitor. Today I installed the following updates:

1- macOS Sierra 10.12.4 update.

2- Command Line Tools (macOS Sierra version 10.12) for Xcode.

After these updates, my laptop is a mess.

My laptop runs extremely slow. Every time I click on an icon or open an app, the spinning wheel starts and takes up to half minute. Restarting the laptop is a nightmare. I have to wait up to 6 minutes for the laptop to operates. I've done the following with no hope:

1- Repair the disk (i.e. First Aid).

2- Reset SMC & NVRAM.

3- Checked the CPU (i.e. no overhead).

4- Checked Memory (i.e. shows Green color).

5- Regularly clean junk files via Dr. Cleaner app plus the optimization.

6- In Display, reduce motion and increase contrast and Reduce transparency. (6- Note: I've noticed a better performance but still slow).

These are the info of my laptop

Model Name: MacBook Pro

Model Identifier: MacBookPro8,1

Processor Name: Intel Core i5

Processor Speed: 2.3 GHz

Number of Processors: 1

Total Number of Cores: 2

L2 Cache (per Core): 256 KB

L3 Cache: 3 MB

Memory: 4 GB

Boot ROM Version: MBP81.0047.B32

SMC Version (system): 1.68f99

Hardware UUID: 5BB19AD5-CDA2-51A3-8D39-DCD14C4427B1

Sudden Motion Sensor:

State: Enabled

CPU:

System: 6.79%

User: 5.19%

Idle: 91.88%

Threads: 863

Processes: 205

Memory:

Physical Used: 4.00GB

Memory Used: 2.83GB

Cached Fiels: 500MB

Swap Used: 500MB

Disk:

Reads in: 400,490

Writes out: 62,224

Reads in/sec: 9

Writes out/sec: 3

Thank you in advanced.