You are correct, the human body wasn't made to sit down for long periods of time. It is very unnatural, but with the information age, it is basically inevitable.
I work as a software developer and understand your pain. There are a few things you can do.
You can get a stand up desk, so that you limit straining your lower back and engraving an unnatural position for your spine. If this is not an option, try to get up and stretch every 20 minutes or so, go for a little walk, get a cup of tea, if your building has stairs, go up and down these stairs.
I don't really know your situation so I can't recommend any specific exercises but if none of these are an option, try to offset the time you spend sitting down by the time you spend standing up and moving. So if you work all day and sit down all day from 9-5, then when you get home, go to the gym, go for a long walk, go for a jog, go biking, play a sport, go gardening, anything that's movement will be beneficial. Just stay active :)