The language was developed by SOAS (School of Oriental and African Studies), University of London:
Dr. Anil Biltoo, one of the linguists who worked on the language, explains:
...the influence behind this language is Proto-Indo-European (PIE), a hypothesized spoken language that pre-dates (and is the ancestor of) ancient languages such as Sanskrit, Hittite and Greek.
It is not, however, an attempt to be academically rigorous and to reconstruct the language according to the most persuasive arguments from scholars working in this field.
The language of the engineers in Prometheus is not 'pure PIE' (whatever that's supposed to be, given that all reconstructions are hypothetical).
Any dialogue intended to be learned by actors has to be capable of being pronounced, which does not appear to be a quality discernible in reconstructions proposed thus far.
If the dialogue in Prometheus appears to contain words that have an immediate resonance with languages known to the viewer, that is all to the good since it is intended (The use of Proto-Afroasiatic would likely have yielded no such result).
The emphasis was less on authenticity with respect to what is generally agreed upon vis-a-vis PIE phonology and roots, and more on ease of articulation, sonorousness and the suggestion of a possible connection of 'Engineer' with terrestrial speech.