The whole natural vs. synthetic debate is kind of meaningless. It actually grinds my gears a bit. Here's a thought experiment. One of these glucose molecules was made synthetically, with toxic lead and chromium reagents and chlorinated solvents. The other is a "natural" glucose molecule made by a, say, banana plant. Let's assume they are both purified by recrystallization to the point there's no other detectable impurities and the physical properties like melt point, refractive index, optical rotary power etc all match.
Can you tell the difference? I can't, because there isn't actually a meaningful one on a biochemical level. Your body really does not care where the chemicals come from, and any differences in isotopic composition don't change how the compounds behave in the body. Scientists can calculate the ratio of carbon 12 to carbon 13 atoms (not to be confused with carbon 14, which is used for radiometric carbon dating) which can then be used to determine if compounds were synthesized with carbon from "biological" sources in a C3 or C4 carbon fixation cycle or instead by some other means, because biochemical reactions incorporate a slightly different ratio of isotopes than traditional synthesis. The two different carbon fixation cycles actually produce reproducible ratios of C12/C13 that can be used as a useful fingerprint. In addition I believe it can be used to determine the origin of nitrogen that ends up in compounds, because nitrogen fixation in bacteria has a different prefertence for N14/N15 ratio than synthetic ammonia made for fertilizers. The important thing to remember is that even that sort of analysis is not 100% accurate and infallible, all it takes is using exclusively naturally produced starting materials rather than pertochemicals or Haber process ammonia.
Because of this, many of the man made drugs are what I would consider "mis-creations", things that should not be. It's not as simple as all natural drugs being good and all man made ones bad, thats not what I am saying. But it is very much my experience that by and large, the natural drugs are superior in effect and far less harmful than the man made ones.
I would say that's confirmation bias. More than ever in this day and age, partly because we have the ability to make and screen hundreds of thousands of candidates rapidly, and partly because of the litigous culture in the US, drugs have a higher and higher bar for what is considered to be safe and acceptable side effects. Because the age of 'heroic medicine' is basically over, the criteria for a drug to be judged 'safe' get stricter with every passing day. The number of natural drugs that are truly ideal as drugs in a pharamceutical sense of the word is a short list indeed.
Here's a neat article by a drug discovery blogger. He points out that a "natural" drug like aspirin (salicin if you're being very strict, I think aspirin is semi synthetic) would never be approved today. Nor would quite a few antibiotics. And if you think about it, lots of natural products suffer from problems that made people pursue syntheic analogues in the first place.
There are just as many drugs with nasty side effects as there are 'blockbuster' drugs. Often natural product drugs work well enough, but leave certain aspects lacking. Natural penicillin G has next to no oral bioavailibility, so semi-synthetic penicllin V or amoxicillin are more widely used today. Cocaine has a low oral bioavilibility is cardiotoxic and very short-acting, methylphenidate was developed to avoid both those issues. Morphine has a low oral bioavailibility and higher incidence of side effects than something like oxycodone. Local anesthetics like lidocaine are more controllable than something like cone snail venom. Non-depolarizing muscular paralyzing agents have a smoother induction period than "natural" curare alkaloids. If you've ever used ibuprofen or acetaminophen you've used painkillers with better efficacy and better tolerability than salicylic acid alone. If you've ever had a general anesthetic, it was with synthetic drugs with rapid elimination from the body and was probably not a morphine and atropine twilight coma where the doctor gambles every time. And so on, and so forth. In fact, I can't think of many natural drugs that actually are undeniably better than anything chemistry has come up with., with the notable exception of THC.
Even if you count all the natural drugs that *are* a good time, you almost always need to get chemistry involved at some stage, to extract and standardize the active principles. It is very rare for any biological to make products of high purity that are easily isolatable: even Cannabis took years of selective breeding to get high-THC, high-cannabinoid strains popular. It used to be, you needed to do a hash oil extraction, acid isomerization, then further purification to yield THC, nowadays people do it with a single butane wash. Other common problems inclusde, making penicillin in a huge fermenting tank and needing to get it out of the water and dead mould cells and into a sterile standardized dosage form. The coca plant doesn't produce pure cocaine. Nor is morphine the only active principle in opium. In addition, different plants of the same genetics can produce varying amounts of alkaloid in the different parts of the plant. Or even have significant variation between individual plants. Nature is tricky like that, synthesis was developed for a reaon.
I dunno. In the end, I think it's a more useful attitude to just treat all drugs as tools. They are just chemicals in the end, who made them and where they originated is demonstrably less important than what they actually are, in terms of purity and structure. There are comparatively harmless "synthetic" chemicals, and toxic "natural" ones, and I would say there are an equal fraction of toxic compounds in both camps. Nature is mean and doesn't prefer humans for a mysterious reason, we just like to find patterns and think we are special because of them. Chemists do actually have a lot of respect for natural products: it is almost always the case that plants are better at making some specific compounds, even on a large scale. e.g., nobody makes totally synthetic caffeine, and it would never be profitable, because it's a waste product from coffee decaffeination. The corollary holds that some rare and complex natural products with important usages as drugs have significant efforts to make them synthetically, rather than be beholden to a supply of plant or animal that could be endangered and can be inconsistent in availibility. The case of paclitaxel from Pacific Yew is one notable case, testosterone from bull testes, or vanillin from vanilla beans... they are all established extractions, but they take time, money, and effort which makes costs increase. Synthetic vanillin is about 1/10 the cost of natural vanillin because of the difficulty of growing, hand-pollinating, and ageing vanilla properly compared to using the waste product of paper pulping (availiable on a ton scale year-round - chemistry is big on re-use of "waste" streams as money makers) and there is no difference in flavor or odor if you have purified compounds.